Starting phenix.real_space_refine on Wed Jan 17 18:28:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fo9_29342/01_2024/8fo9_29342_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fo9_29342/01_2024/8fo9_29342.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fo9_29342/01_2024/8fo9_29342.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fo9_29342/01_2024/8fo9_29342.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fo9_29342/01_2024/8fo9_29342_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fo9_29342/01_2024/8fo9_29342_updated.pdb" } resolution = 3.48 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= 0.004 sd= 0.060 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: 5 Type Number sf(0) Gaussians P 20 5.49 5 S 326 5.16 5 C 34365 2.51 5 N 9253 2.21 5 O 9778 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 1566": "OE1" <-> "OE2" Residue "A PHE 2181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1650": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 2326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 1242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 1650": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 2326": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 53742 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 8781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1173, 8781 Classifications: {'peptide': 1173} Incomplete info: {'truncation_to_alanine': 158} Link IDs: {'PTRANS': 52, 'TRANS': 1120} Chain breaks: 4 Unresolved non-hydrogen bonds: 596 Unresolved non-hydrogen angles: 717 Unresolved non-hydrogen dihedrals: 492 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 16, 'ASP:plan': 18, 'PHE:plan': 4, 'GLU:plan': 29, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 370 Chain: "C" Number of atoms: 8772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1173, 8772 Classifications: {'peptide': 1173} Incomplete info: {'truncation_to_alanine': 160} Link IDs: {'PTRANS': 52, 'TRANS': 1120} Chain breaks: 4 Unresolved non-hydrogen bonds: 606 Unresolved non-hydrogen angles: 729 Unresolved non-hydrogen dihedrals: 503 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 17, 'ASP:plan': 17, 'PHE:plan': 4, 'GLU:plan': 29, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 377 Chain: "B" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1065 Classifications: {'peptide': 165} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 3, 'TRANS': 161} Chain breaks: 1 Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 333 Unresolved non-hydrogen dihedrals: 221 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 9, 'TYR:plan': 2, 'ASN:plan1': 7, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 8, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 183 Chain: "D" Number of atoms: 1046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1046 Classifications: {'peptide': 166} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PTRANS': 3, 'TRANS': 162} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 298 Unresolved non-hydrogen angles: 371 Unresolved non-hydrogen dihedrals: 247 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 9, 'TYR:plan': 2, 'ASN:plan1': 8, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 8, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 199 Chain: "E" Number of atoms: 16990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2287, 16990 Classifications: {'peptide': 2287} Incomplete info: {'truncation_to_alanine': 317} Link IDs: {'PCIS': 1, 'PTRANS': 85, 'TRANS': 2200} Chain breaks: 13 Unresolved non-hydrogen bonds: 1218 Unresolved non-hydrogen angles: 1501 Unresolved non-hydrogen dihedrals: 1019 Unresolved non-hydrogen chiralities: 61 Planarities with less than four sites: {'GLN:plan1': 23, 'HIS:plan': 13, 'TYR:plan': 6, 'ASN:plan1': 17, 'TRP:plan': 2, 'ASP:plan': 28, 'PHE:plan': 13, 'GLU:plan': 58, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 742 Chain: "F" Number of atoms: 16852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2289, 16852 Classifications: {'peptide': 2289} Incomplete info: {'truncation_to_alanine': 360} Link IDs: {'PCIS': 1, 'PTRANS': 85, 'TRANS': 2202} Chain breaks: 13 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1376 Unresolved non-hydrogen angles: 1690 Unresolved non-hydrogen dihedrals: 1142 Unresolved non-hydrogen chiralities: 70 Planarities with less than four sites: {'GLN:plan1': 27, 'HIS:plan': 12, 'TYR:plan': 6, 'ASN:plan1': 18, 'TRP:plan': 1, 'ASP:plan': 32, 'PHE:plan': 15, 'GLU:plan': 67, 'ARG:plan': 22} Unresolved non-hydrogen planarities: 837 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 20.67, per 1000 atoms: 0.38 Number of scatterers: 53742 At special positions: 0 Unit cell: (230.02, 266.06, 156.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 326 16.00 P 20 15.00 O 9778 8.00 N 9253 7.00 C 34365 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 16.68 Conformation dependent library (CDL) restraints added in 8.4 seconds 14338 Ramachandran restraints generated. 7169 Oldfield, 0 Emsley, 7169 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13806 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 269 helices and 66 sheets defined 36.3% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 14.76 Creating SS restraints... Processing helix chain 'A' and resid 1347 through 1355 Processing helix chain 'A' and resid 1399 through 1408 removed outlier: 4.564A pdb=" N SER A1403 " --> pdb=" O GLU A1400 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR A1404 " --> pdb=" O PHE A1401 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS A1405 " --> pdb=" O TYR A1402 " (cutoff:3.500A) Proline residue: A1406 - end of helix Processing helix chain 'A' and resid 1426 through 1430 Processing helix chain 'A' and resid 1432 through 1441 Processing helix chain 'A' and resid 1459 through 1475 Processing helix chain 'A' and resid 1495 through 1510 Processing helix chain 'A' and resid 1525 through 1540 Processing helix chain 'A' and resid 1550 through 1560 Processing helix chain 'A' and resid 1569 through 1579 Processing helix chain 'A' and resid 1600 through 1612 Processing helix chain 'A' and resid 1628 through 1634 Processing helix chain 'A' and resid 1641 through 1648 Processing helix chain 'A' and resid 1704 through 1713 removed outlier: 3.759A pdb=" N ILE A1709 " --> pdb=" O TRP A1705 " (cutoff:3.500A) Processing helix chain 'A' and resid 1771 through 1790 Processing helix chain 'A' and resid 1793 through 1796 Processing helix chain 'A' and resid 1827 through 1836 removed outlier: 4.375A pdb=" N LYS A1832 " --> pdb=" O ASP A1828 " (cutoff:3.500A) Processing helix chain 'A' and resid 1852 through 1855 No H-bonds generated for 'chain 'A' and resid 1852 through 1855' Processing helix chain 'A' and resid 1872 through 1874 No H-bonds generated for 'chain 'A' and resid 1872 through 1874' Processing helix chain 'A' and resid 1881 through 1883 No H-bonds generated for 'chain 'A' and resid 1881 through 1883' Processing helix chain 'A' and resid 1914 through 1924 removed outlier: 4.194A pdb=" N VAL A1923 " --> pdb=" O GLN A1919 " (cutoff:3.500A) Processing helix chain 'A' and resid 1955 through 1960 Processing helix chain 'A' and resid 1968 through 1987 Processing helix chain 'A' and resid 2041 through 2044 No H-bonds generated for 'chain 'A' and resid 2041 through 2044' Processing helix chain 'A' and resid 2052 through 2067 removed outlier: 3.759A pdb=" N TYR A2057 " --> pdb=" O ALA A2054 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER A2058 " --> pdb=" O ASP A2055 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE A2066 " --> pdb=" O LEU A2063 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU A2067 " --> pdb=" O TYR A2064 " (cutoff:3.500A) Processing helix chain 'A' and resid 2071 through 2078 removed outlier: 3.612A pdb=" N GLU A2075 " --> pdb=" O GLY A2071 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A2077 " --> pdb=" O ILE A2073 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LYS A2078 " --> pdb=" O VAL A2074 " (cutoff:3.500A) Processing helix chain 'A' and resid 2080 through 2089 Processing helix chain 'A' and resid 2095 through 2099 removed outlier: 3.668A pdb=" N TYR A2099 " --> pdb=" O PRO A2095 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2095 through 2099' Processing helix chain 'A' and resid 2105 through 2113 removed outlier: 3.500A pdb=" N LYS A2109 " --> pdb=" O PRO A2105 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LEU A2110 " --> pdb=" O MET A2106 " (cutoff:3.500A) Processing helix chain 'A' and resid 2125 through 2132 removed outlier: 3.520A pdb=" N PHE A2129 " --> pdb=" O SER A2125 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP A2130 " --> pdb=" O ALA A2126 " (cutoff:3.500A) Processing helix chain 'A' and resid 2209 through 2211 No H-bonds generated for 'chain 'A' and resid 2209 through 2211' Processing helix chain 'A' and resid 2277 through 2281 removed outlier: 4.283A pdb=" N LYS A2281 " --> pdb=" O LYS A2278 " (cutoff:3.500A) Processing helix chain 'A' and resid 2308 through 2310 No H-bonds generated for 'chain 'A' and resid 2308 through 2310' Processing helix chain 'A' and resid 2346 through 2348 No H-bonds generated for 'chain 'A' and resid 2346 through 2348' Processing helix chain 'A' and resid 2389 through 2397 removed outlier: 4.474A pdb=" N GLU A2395 " --> pdb=" O HIS A2391 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N VAL A2396 " --> pdb=" O PHE A2392 " (cutoff:3.500A) Processing helix chain 'A' and resid 2498 through 2526 Proline residue: A2501 - end of helix removed outlier: 4.029A pdb=" N VAL A2504 " --> pdb=" O PRO A2501 " (cutoff:3.500A) Processing helix chain 'C' and resid 1347 through 1355 Processing helix chain 'C' and resid 1399 through 1408 removed outlier: 4.569A pdb=" N SER C1403 " --> pdb=" O GLU C1400 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR C1404 " --> pdb=" O PHE C1401 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N HIS C1405 " --> pdb=" O TYR C1402 " (cutoff:3.500A) Proline residue: C1406 - end of helix Processing helix chain 'C' and resid 1426 through 1430 Processing helix chain 'C' and resid 1432 through 1441 Processing helix chain 'C' and resid 1454 through 1456 No H-bonds generated for 'chain 'C' and resid 1454 through 1456' Processing helix chain 'C' and resid 1459 through 1475 Processing helix chain 'C' and resid 1495 through 1510 Processing helix chain 'C' and resid 1525 through 1540 Processing helix chain 'C' and resid 1550 through 1560 Processing helix chain 'C' and resid 1569 through 1579 Processing helix chain 'C' and resid 1600 through 1612 Processing helix chain 'C' and resid 1628 through 1634 Processing helix chain 'C' and resid 1641 through 1648 Processing helix chain 'C' and resid 1704 through 1713 removed outlier: 3.795A pdb=" N ILE C1709 " --> pdb=" O TRP C1705 " (cutoff:3.500A) Processing helix chain 'C' and resid 1771 through 1790 Processing helix chain 'C' and resid 1827 through 1836 removed outlier: 4.369A pdb=" N LYS C1832 " --> pdb=" O ASP C1828 " (cutoff:3.500A) Processing helix chain 'C' and resid 1852 through 1855 No H-bonds generated for 'chain 'C' and resid 1852 through 1855' Processing helix chain 'C' and resid 1872 through 1874 No H-bonds generated for 'chain 'C' and resid 1872 through 1874' Processing helix chain 'C' and resid 1881 through 1883 No H-bonds generated for 'chain 'C' and resid 1881 through 1883' Processing helix chain 'C' and resid 1914 through 1924 removed outlier: 4.196A pdb=" N VAL C1923 " --> pdb=" O GLN C1919 " (cutoff:3.500A) Processing helix chain 'C' and resid 1955 through 1960 Processing helix chain 'C' and resid 1968 through 1987 Processing helix chain 'C' and resid 2041 through 2044 No H-bonds generated for 'chain 'C' and resid 2041 through 2044' Processing helix chain 'C' and resid 2052 through 2067 removed outlier: 3.774A pdb=" N TYR C2057 " --> pdb=" O ALA C2054 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER C2058 " --> pdb=" O ASP C2055 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE C2066 " --> pdb=" O LEU C2063 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU C2067 " --> pdb=" O TYR C2064 " (cutoff:3.500A) Processing helix chain 'C' and resid 2071 through 2078 removed outlier: 3.619A pdb=" N GLU C2075 " --> pdb=" O GLY C2071 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU C2077 " --> pdb=" O ILE C2073 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LYS C2078 " --> pdb=" O VAL C2074 " (cutoff:3.500A) Processing helix chain 'C' and resid 2080 through 2089 Processing helix chain 'C' and resid 2095 through 2099 removed outlier: 3.667A pdb=" N TYR C2099 " --> pdb=" O PRO C2095 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2095 through 2099' Processing helix chain 'C' and resid 2105 through 2113 removed outlier: 3.561A pdb=" N LYS C2109 " --> pdb=" O PRO C2105 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N LEU C2110 " --> pdb=" O MET C2106 " (cutoff:3.500A) Processing helix chain 'C' and resid 2125 through 2132 removed outlier: 3.520A pdb=" N PHE C2129 " --> pdb=" O SER C2125 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP C2130 " --> pdb=" O ALA C2126 " (cutoff:3.500A) Processing helix chain 'C' and resid 2209 through 2211 No H-bonds generated for 'chain 'C' and resid 2209 through 2211' Processing helix chain 'C' and resid 2277 through 2279 No H-bonds generated for 'chain 'C' and resid 2277 through 2279' Processing helix chain 'C' and resid 2308 through 2310 No H-bonds generated for 'chain 'C' and resid 2308 through 2310' Processing helix chain 'C' and resid 2346 through 2348 No H-bonds generated for 'chain 'C' and resid 2346 through 2348' Processing helix chain 'C' and resid 2389 through 2398 removed outlier: 4.576A pdb=" N GLU C2395 " --> pdb=" O HIS C2391 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N VAL C2396 " --> pdb=" O PHE C2392 " (cutoff:3.500A) Processing helix chain 'C' and resid 2498 through 2526 Proline residue: C2501 - end of helix removed outlier: 3.993A pdb=" N VAL C2504 " --> pdb=" O PRO C2501 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 27 removed outlier: 4.047A pdb=" N VAL B 24 " --> pdb=" O LYS B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 78 No H-bonds generated for 'chain 'B' and resid 75 through 78' Processing helix chain 'B' and resid 93 through 108 Processing helix chain 'B' and resid 136 through 145 removed outlier: 3.908A pdb=" N ARG B 141 " --> pdb=" O ASP B 137 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N PHE B 142 " --> pdb=" O GLN B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 175 Processing helix chain 'D' and resid 20 through 27 removed outlier: 4.063A pdb=" N VAL D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 78 No H-bonds generated for 'chain 'D' and resid 75 through 78' Processing helix chain 'D' and resid 93 through 108 Processing helix chain 'D' and resid 136 through 145 removed outlier: 3.889A pdb=" N ARG D 141 " --> pdb=" O ASP D 137 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N PHE D 142 " --> pdb=" O GLN D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 175 Processing helix chain 'E' and resid 13 through 23 Processing helix chain 'E' and resid 29 through 44 Processing helix chain 'E' and resid 58 through 60 No H-bonds generated for 'chain 'E' and resid 58 through 60' Processing helix chain 'E' and resid 62 through 70 Processing helix chain 'E' and resid 75 through 91 removed outlier: 4.839A pdb=" N TRP E 82 " --> pdb=" O GLN E 78 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N SER E 83 " --> pdb=" O GLN E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 99 Processing helix chain 'E' and resid 114 through 124 Processing helix chain 'E' and resid 129 through 143 removed outlier: 3.753A pdb=" N ILE E 134 " --> pdb=" O ASN E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 153 Processing helix chain 'E' and resid 159 through 166 Processing helix chain 'E' and resid 175 through 178 No H-bonds generated for 'chain 'E' and resid 175 through 178' Processing helix chain 'E' and resid 184 through 189 Processing helix chain 'E' and resid 193 through 216 Processing helix chain 'E' and resid 219 through 234 removed outlier: 3.662A pdb=" N ILE E 234 " --> pdb=" O HIS E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 242 removed outlier: 3.845A pdb=" N VAL E 239 " --> pdb=" O CYS E 236 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU E 240 " --> pdb=" O ASN E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 258 Processing helix chain 'E' and resid 264 through 276 Processing helix chain 'E' and resid 285 through 301 Processing helix chain 'E' and resid 306 through 323 removed outlier: 3.787A pdb=" N ILE E 310 " --> pdb=" O ALA E 306 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N SER E 311 " --> pdb=" O ALA E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 359 Processing helix chain 'E' and resid 364 through 380 Processing helix chain 'E' and resid 385 through 387 No H-bonds generated for 'chain 'E' and resid 385 through 387' Processing helix chain 'E' and resid 397 through 407 Processing helix chain 'E' and resid 412 through 428 Processing helix chain 'E' and resid 436 through 439 No H-bonds generated for 'chain 'E' and resid 436 through 439' Processing helix chain 'E' and resid 442 through 451 Processing helix chain 'E' and resid 456 through 469 Processing helix chain 'E' and resid 477 through 493 Proline residue: E 485 - end of helix Processing helix chain 'E' and resid 498 through 512 Processing helix chain 'E' and resid 526 through 539 Processing helix chain 'E' and resid 542 through 552 Processing helix chain 'E' and resid 557 through 571 Processing helix chain 'E' and resid 576 through 583 Processing helix chain 'E' and resid 585 through 595 Processing helix chain 'E' and resid 600 through 613 removed outlier: 4.066A pdb=" N GLY E 611 " --> pdb=" O LEU E 607 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TYR E 612 " --> pdb=" O SER E 608 " (cutoff:3.500A) Processing helix chain 'E' and resid 617 through 622 removed outlier: 7.356A pdb=" N ILE E 621 " --> pdb=" O ASN E 618 " (cutoff:3.500A) Processing helix chain 'E' and resid 625 through 637 Processing helix chain 'E' and resid 642 through 658 removed outlier: 3.648A pdb=" N LEU E 658 " --> pdb=" O ALA E 654 " (cutoff:3.500A) Processing helix chain 'E' and resid 660 through 668 Processing helix chain 'E' and resid 671 through 684 removed outlier: 3.839A pdb=" N ILE E 683 " --> pdb=" O MET E 679 " (cutoff:3.500A) Processing helix chain 'E' and resid 689 through 704 removed outlier: 3.634A pdb=" N MET E 704 " --> pdb=" O ALA E 700 " (cutoff:3.500A) Processing helix chain 'E' and resid 706 through 718 Processing helix chain 'E' and resid 722 through 731 removed outlier: 4.031A pdb=" N GLU E 726 " --> pdb=" O SER E 722 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N CYS E 727 " --> pdb=" O ILE E 723 " (cutoff:3.500A) Processing helix chain 'E' and resid 744 through 750 Processing helix chain 'E' and resid 755 through 763 Processing helix chain 'E' and resid 768 through 780 Processing helix chain 'E' and resid 784 through 794 removed outlier: 3.790A pdb=" N ARG E 793 " --> pdb=" O LEU E 789 " (cutoff:3.500A) Processing helix chain 'E' and resid 834 through 853 Processing helix chain 'E' and resid 998 through 1000 No H-bonds generated for 'chain 'E' and resid 998 through 1000' Processing helix chain 'E' and resid 1005 through 1009 removed outlier: 3.794A pdb=" N HIS E1009 " --> pdb=" O CYS E1005 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1005 through 1009' Processing helix chain 'E' and resid 1028 through 1033 Processing helix chain 'E' and resid 1054 through 1056 No H-bonds generated for 'chain 'E' and resid 1054 through 1056' Processing helix chain 'E' and resid 1102 through 1104 No H-bonds generated for 'chain 'E' and resid 1102 through 1104' Processing helix chain 'E' and resid 1190 through 1193 No H-bonds generated for 'chain 'E' and resid 1190 through 1193' Processing helix chain 'E' and resid 1241 through 1244 Processing helix chain 'E' and resid 1262 through 1266 Processing helix chain 'E' and resid 1287 through 1290 Processing helix chain 'E' and resid 1317 through 1327 Processing helix chain 'E' and resid 1350 through 1354 Processing helix chain 'E' and resid 1399 through 1401 No H-bonds generated for 'chain 'E' and resid 1399 through 1401' Processing helix chain 'E' and resid 1405 through 1408 Processing helix chain 'E' and resid 1421 through 1423 No H-bonds generated for 'chain 'E' and resid 1421 through 1423' Processing helix chain 'E' and resid 1427 through 1441 removed outlier: 3.920A pdb=" N LYS E1432 " --> pdb=" O VAL E1428 " (cutoff:3.500A) Proline residue: E1433 - end of helix Processing helix chain 'E' and resid 1464 through 1472 removed outlier: 4.088A pdb=" N SER E1467 " --> pdb=" O ALA E1464 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR E1470 " --> pdb=" O SER E1467 " (cutoff:3.500A) Processing helix chain 'E' and resid 1495 through 1509 Processing helix chain 'E' and resid 1518 through 1520 No H-bonds generated for 'chain 'E' and resid 1518 through 1520' Processing helix chain 'E' and resid 1525 through 1539 removed outlier: 4.469A pdb=" N LYS E1539 " --> pdb=" O LEU E1535 " (cutoff:3.500A) Processing helix chain 'E' and resid 1550 through 1559 Processing helix chain 'E' and resid 1566 through 1578 Proline residue: E1570 - end of helix removed outlier: 3.832A pdb=" N HIS E1574 " --> pdb=" O PRO E1570 " (cutoff:3.500A) Processing helix chain 'E' and resid 1600 through 1607 Processing helix chain 'E' and resid 1610 through 1612 No H-bonds generated for 'chain 'E' and resid 1610 through 1612' Processing helix chain 'E' and resid 1645 through 1655 removed outlier: 3.613A pdb=" N PHE E1650 " --> pdb=" O MET E1646 " (cutoff:3.500A) Processing helix chain 'E' and resid 1705 through 1708 No H-bonds generated for 'chain 'E' and resid 1705 through 1708' Processing helix chain 'E' and resid 1771 through 1791 removed outlier: 4.348A pdb=" N ILE E1775 " --> pdb=" O ARG E1771 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU E1776 " --> pdb=" O LYS E1772 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N HIS E1783 " --> pdb=" O GLN E1779 " (cutoff:3.500A) Processing helix chain 'E' and resid 1829 through 1834 Processing helix chain 'E' and resid 1852 through 1854 No H-bonds generated for 'chain 'E' and resid 1852 through 1854' Processing helix chain 'E' and resid 1866 through 1868 No H-bonds generated for 'chain 'E' and resid 1866 through 1868' Processing helix chain 'E' and resid 1872 through 1874 No H-bonds generated for 'chain 'E' and resid 1872 through 1874' Processing helix chain 'E' and resid 1883 through 1885 No H-bonds generated for 'chain 'E' and resid 1883 through 1885' Processing helix chain 'E' and resid 1914 through 1924 removed outlier: 3.937A pdb=" N VAL E1923 " --> pdb=" O GLN E1919 " (cutoff:3.500A) Processing helix chain 'E' and resid 1955 through 1961 Processing helix chain 'E' and resid 1970 through 1987 removed outlier: 3.746A pdb=" N ALA E1975 " --> pdb=" O GLN E1971 " (cutoff:3.500A) Processing helix chain 'E' and resid 1997 through 1999 No H-bonds generated for 'chain 'E' and resid 1997 through 1999' Processing helix chain 'E' and resid 2018 through 2025 Processing helix chain 'E' and resid 2041 through 2044 No H-bonds generated for 'chain 'E' and resid 2041 through 2044' Processing helix chain 'E' and resid 2052 through 2067 Processing helix chain 'E' and resid 2071 through 2076 Processing helix chain 'E' and resid 2080 through 2088 removed outlier: 4.735A pdb=" N GLU E2087 " --> pdb=" O PHE E2083 " (cutoff:3.500A) Processing helix chain 'E' and resid 2095 through 2098 No H-bonds generated for 'chain 'E' and resid 2095 through 2098' Processing helix chain 'E' and resid 2105 through 2114 Processing helix chain 'E' and resid 2125 through 2132 Processing helix chain 'E' and resid 2136 through 2139 No H-bonds generated for 'chain 'E' and resid 2136 through 2139' Processing helix chain 'E' and resid 2347 through 2350 No H-bonds generated for 'chain 'E' and resid 2347 through 2350' Processing helix chain 'E' and resid 2390 through 2395 removed outlier: 5.083A pdb=" N GLU E2395 " --> pdb=" O HIS E2391 " (cutoff:3.500A) Processing helix chain 'E' and resid 2498 through 2526 Proline residue: E2501 - end of helix Processing helix chain 'F' and resid 13 through 23 Processing helix chain 'F' and resid 29 through 44 Processing helix chain 'F' and resid 58 through 60 No H-bonds generated for 'chain 'F' and resid 58 through 60' Processing helix chain 'F' and resid 62 through 70 Processing helix chain 'F' and resid 75 through 91 removed outlier: 4.840A pdb=" N TRP F 82 " --> pdb=" O GLN F 78 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N SER F 83 " --> pdb=" O GLN F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 99 Processing helix chain 'F' and resid 114 through 124 Processing helix chain 'F' and resid 129 through 143 removed outlier: 3.753A pdb=" N ILE F 134 " --> pdb=" O ASN F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 149 through 153 Processing helix chain 'F' and resid 159 through 166 Processing helix chain 'F' and resid 175 through 188 Processing helix chain 'F' and resid 193 through 214 removed outlier: 3.800A pdb=" N GLU F 198 " --> pdb=" O GLU F 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 219 through 234 removed outlier: 3.665A pdb=" N ILE F 234 " --> pdb=" O HIS F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 236 through 242 removed outlier: 3.846A pdb=" N VAL F 239 " --> pdb=" O CYS F 236 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU F 240 " --> pdb=" O ASN F 237 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 258 Processing helix chain 'F' and resid 265 through 276 Processing helix chain 'F' and resid 285 through 301 Processing helix chain 'F' and resid 306 through 323 removed outlier: 3.782A pdb=" N ILE F 310 " --> pdb=" O ALA F 306 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N SER F 311 " --> pdb=" O ALA F 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 345 through 359 Processing helix chain 'F' and resid 364 through 380 Processing helix chain 'F' and resid 385 through 387 No H-bonds generated for 'chain 'F' and resid 385 through 387' Processing helix chain 'F' and resid 397 through 407 Processing helix chain 'F' and resid 412 through 428 Processing helix chain 'F' and resid 436 through 439 No H-bonds generated for 'chain 'F' and resid 436 through 439' Processing helix chain 'F' and resid 442 through 451 Processing helix chain 'F' and resid 456 through 469 Processing helix chain 'F' and resid 477 through 493 Proline residue: F 485 - end of helix Processing helix chain 'F' and resid 498 through 512 Processing helix chain 'F' and resid 526 through 539 Processing helix chain 'F' and resid 542 through 552 Processing helix chain 'F' and resid 557 through 571 Processing helix chain 'F' and resid 576 through 583 Processing helix chain 'F' and resid 585 through 595 Processing helix chain 'F' and resid 600 through 613 removed outlier: 4.052A pdb=" N GLY F 611 " --> pdb=" O LEU F 607 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR F 612 " --> pdb=" O SER F 608 " (cutoff:3.500A) Processing helix chain 'F' and resid 617 through 622 removed outlier: 7.356A pdb=" N ILE F 621 " --> pdb=" O ASN F 618 " (cutoff:3.500A) Processing helix chain 'F' and resid 625 through 637 Processing helix chain 'F' and resid 642 through 658 removed outlier: 3.648A pdb=" N LEU F 658 " --> pdb=" O ALA F 654 " (cutoff:3.500A) Processing helix chain 'F' and resid 660 through 668 Processing helix chain 'F' and resid 671 through 684 removed outlier: 3.841A pdb=" N ILE F 683 " --> pdb=" O MET F 679 " (cutoff:3.500A) Processing helix chain 'F' and resid 689 through 704 removed outlier: 3.642A pdb=" N MET F 704 " --> pdb=" O ALA F 700 " (cutoff:3.500A) Processing helix chain 'F' and resid 706 through 718 Processing helix chain 'F' and resid 722 through 731 removed outlier: 4.039A pdb=" N GLU F 726 " --> pdb=" O SER F 722 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N CYS F 727 " --> pdb=" O ILE F 723 " (cutoff:3.500A) Processing helix chain 'F' and resid 744 through 750 Processing helix chain 'F' and resid 755 through 763 Processing helix chain 'F' and resid 768 through 780 Processing helix chain 'F' and resid 784 through 794 removed outlier: 3.793A pdb=" N ARG F 793 " --> pdb=" O LEU F 789 " (cutoff:3.500A) Processing helix chain 'F' and resid 834 through 853 Processing helix chain 'F' and resid 998 through 1000 No H-bonds generated for 'chain 'F' and resid 998 through 1000' Processing helix chain 'F' and resid 1005 through 1009 removed outlier: 3.795A pdb=" N HIS F1009 " --> pdb=" O CYS F1005 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 1005 through 1009' Processing helix chain 'F' and resid 1028 through 1033 Processing helix chain 'F' and resid 1054 through 1056 No H-bonds generated for 'chain 'F' and resid 1054 through 1056' Processing helix chain 'F' and resid 1102 through 1104 No H-bonds generated for 'chain 'F' and resid 1102 through 1104' Processing helix chain 'F' and resid 1190 through 1193 No H-bonds generated for 'chain 'F' and resid 1190 through 1193' Processing helix chain 'F' and resid 1241 through 1244 Processing helix chain 'F' and resid 1262 through 1266 Processing helix chain 'F' and resid 1287 through 1290 Processing helix chain 'F' and resid 1317 through 1327 Processing helix chain 'F' and resid 1350 through 1354 Processing helix chain 'F' and resid 1399 through 1401 No H-bonds generated for 'chain 'F' and resid 1399 through 1401' Processing helix chain 'F' and resid 1405 through 1408 Processing helix chain 'F' and resid 1421 through 1423 No H-bonds generated for 'chain 'F' and resid 1421 through 1423' Processing helix chain 'F' and resid 1427 through 1441 removed outlier: 3.918A pdb=" N LYS F1432 " --> pdb=" O VAL F1428 " (cutoff:3.500A) Proline residue: F1433 - end of helix Processing helix chain 'F' and resid 1464 through 1472 removed outlier: 4.088A pdb=" N SER F1467 " --> pdb=" O ALA F1464 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR F1470 " --> pdb=" O SER F1467 " (cutoff:3.500A) Processing helix chain 'F' and resid 1495 through 1509 Processing helix chain 'F' and resid 1518 through 1520 No H-bonds generated for 'chain 'F' and resid 1518 through 1520' Processing helix chain 'F' and resid 1525 through 1539 removed outlier: 4.490A pdb=" N LYS F1539 " --> pdb=" O LEU F1535 " (cutoff:3.500A) Processing helix chain 'F' and resid 1550 through 1559 Processing helix chain 'F' and resid 1566 through 1578 Proline residue: F1570 - end of helix removed outlier: 3.831A pdb=" N HIS F1574 " --> pdb=" O PRO F1570 " (cutoff:3.500A) Processing helix chain 'F' and resid 1600 through 1607 Processing helix chain 'F' and resid 1610 through 1612 No H-bonds generated for 'chain 'F' and resid 1610 through 1612' Processing helix chain 'F' and resid 1645 through 1655 removed outlier: 3.609A pdb=" N PHE F1650 " --> pdb=" O MET F1646 " (cutoff:3.500A) Processing helix chain 'F' and resid 1705 through 1713 Processing helix chain 'F' and resid 1771 through 1791 removed outlier: 4.347A pdb=" N ILE F1775 " --> pdb=" O ARG F1771 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU F1776 " --> pdb=" O LYS F1772 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS F1783 " --> pdb=" O GLN F1779 " (cutoff:3.500A) Processing helix chain 'F' and resid 1829 through 1834 Processing helix chain 'F' and resid 1852 through 1854 No H-bonds generated for 'chain 'F' and resid 1852 through 1854' Processing helix chain 'F' and resid 1866 through 1868 No H-bonds generated for 'chain 'F' and resid 1866 through 1868' Processing helix chain 'F' and resid 1872 through 1874 No H-bonds generated for 'chain 'F' and resid 1872 through 1874' Processing helix chain 'F' and resid 1883 through 1885 No H-bonds generated for 'chain 'F' and resid 1883 through 1885' Processing helix chain 'F' and resid 1914 through 1924 removed outlier: 3.932A pdb=" N VAL F1923 " --> pdb=" O GLN F1919 " (cutoff:3.500A) Processing helix chain 'F' and resid 1955 through 1961 Processing helix chain 'F' and resid 1970 through 1987 removed outlier: 3.744A pdb=" N ALA F1975 " --> pdb=" O GLN F1971 " (cutoff:3.500A) Processing helix chain 'F' and resid 1997 through 1999 No H-bonds generated for 'chain 'F' and resid 1997 through 1999' Processing helix chain 'F' and resid 2018 through 2025 Processing helix chain 'F' and resid 2041 through 2044 No H-bonds generated for 'chain 'F' and resid 2041 through 2044' Processing helix chain 'F' and resid 2052 through 2067 Processing helix chain 'F' and resid 2071 through 2076 Processing helix chain 'F' and resid 2080 through 2088 removed outlier: 4.746A pdb=" N GLU F2087 " --> pdb=" O PHE F2083 " (cutoff:3.500A) Processing helix chain 'F' and resid 2095 through 2098 No H-bonds generated for 'chain 'F' and resid 2095 through 2098' Processing helix chain 'F' and resid 2105 through 2114 Processing helix chain 'F' and resid 2125 through 2132 Processing helix chain 'F' and resid 2136 through 2139 No H-bonds generated for 'chain 'F' and resid 2136 through 2139' Processing helix chain 'F' and resid 2347 through 2350 No H-bonds generated for 'chain 'F' and resid 2347 through 2350' Processing helix chain 'F' and resid 2390 through 2395 removed outlier: 5.081A pdb=" N GLU F2395 " --> pdb=" O HIS F2391 " (cutoff:3.500A) Processing helix chain 'F' and resid 2500 through 2526 Processing sheet with id= A, first strand: chain 'A' and resid 1413 through 1417 removed outlier: 8.900A pdb=" N LEU A1414 " --> pdb=" O ARG A1334 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LYS A1336 " --> pdb=" O LEU A1414 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N LEU A1416 " --> pdb=" O LYS A1336 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N MET A1338 " --> pdb=" O LEU A1416 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N VAL A1389 " --> pdb=" O MET A1335 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N LEU A1337 " --> pdb=" O VAL A1389 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ASN A1391 " --> pdb=" O LEU A1337 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ILE A1339 " --> pdb=" O ASN A1391 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N TRP A1393 " --> pdb=" O ILE A1339 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 1625 through 1627 Processing sheet with id= C, first strand: chain 'A' and resid 1823 through 1826 removed outlier: 4.645A pdb=" N ILE A1692 " --> pdb=" O LEU A1813 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N TYR A1747 " --> pdb=" O PRO A1768 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N CYS A1748 " --> pdb=" O ASN A1741 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N ASN A1741 " --> pdb=" O CYS A1748 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N VAL A1750 " --> pdb=" O TYR A1739 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N TYR A1739 " --> pdb=" O VAL A1750 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 1839 through 1841 Processing sheet with id= E, first strand: chain 'A' and resid 1875 through 1877 Processing sheet with id= F, first strand: chain 'A' and resid 2000 through 2002 Processing sheet with id= G, first strand: chain 'A' and resid 2188 through 2193 removed outlier: 4.123A pdb=" N GLN A2178 " --> pdb=" O CYS A2171 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER A2166 " --> pdb=" O THR A2158 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N CYS A2154 " --> pdb=" O GLY A2170 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 2226 through 2228 removed outlier: 3.658A pdb=" N CYS A2201 " --> pdb=" O GLY A2218 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 2250 through 2252 removed outlier: 3.809A pdb=" N LYS A2271 " --> pdb=" O THR A2267 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 2322 through 2325 removed outlier: 4.165A pdb=" N LYS A2334 " --> pdb=" O SER A2325 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 2354 through 2359 removed outlier: 7.049A pdb=" N ALA A2366 " --> pdb=" O ILE A2355 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N VAL A2357 " --> pdb=" O TYR A2364 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N TYR A2364 " --> pdb=" O VAL A2357 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N LYS A2367 " --> pdb=" O VAL A2372 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL A2372 " --> pdb=" O LYS A2367 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 2414 through 2419 removed outlier: 7.096A pdb=" N GLY A2428 " --> pdb=" O LYS A2415 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N LEU A2417 " --> pdb=" O TRP A2426 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N TRP A2426 " --> pdb=" O LEU A2417 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N LEU A2419 " --> pdb=" O ALA A2424 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N ALA A2424 " --> pdb=" O LEU A2419 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ASP A2438 " --> pdb=" O LEU A2444 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N LEU A2444 " --> pdb=" O ASP A2438 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 2140 through 2145 removed outlier: 6.793A pdb=" N VAL A2495 " --> pdb=" O THR A2141 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ARG A2143 " --> pdb=" O LEU A2493 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU A2493 " --> pdb=" O ARG A2143 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N LEU A2145 " --> pdb=" O SER A2491 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N SER A2491 " --> pdb=" O LEU A2145 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET A2470 " --> pdb=" O TRP A2496 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL A2469 " --> pdb=" O ALA A2461 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL A2457 " --> pdb=" O LEU A2473 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N TYR A2475 " --> pdb=" O VAL A2455 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N VAL A2455 " --> pdb=" O TYR A2475 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 1447 through 1451 removed outlier: 7.969A pdb=" N LEU A1449 " --> pdb=" O ARG A1483 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N TYR A1485 " --> pdb=" O LEU A1449 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N GLY A1451 " --> pdb=" O TYR A1485 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N PHE A1487 " --> pdb=" O GLY A1451 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'A' and resid 1884 through 1887 removed outlier: 7.184A pdb=" N VAL A1893 " --> pdb=" O LEU A1885 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 1413 through 1417 removed outlier: 8.853A pdb=" N LEU C1414 " --> pdb=" O ARG C1334 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LYS C1336 " --> pdb=" O LEU C1414 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N LEU C1416 " --> pdb=" O LYS C1336 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N MET C1338 " --> pdb=" O LEU C1416 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N VAL C1389 " --> pdb=" O MET C1335 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LEU C1337 " --> pdb=" O VAL C1389 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ASN C1391 " --> pdb=" O LEU C1337 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N ILE C1339 " --> pdb=" O ASN C1391 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N TRP C1393 " --> pdb=" O ILE C1339 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 1625 through 1627 Processing sheet with id= R, first strand: chain 'C' and resid 1823 through 1826 removed outlier: 4.650A pdb=" N ILE C1692 " --> pdb=" O LEU C1813 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N TYR C1747 " --> pdb=" O PRO C1768 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N CYS C1748 " --> pdb=" O ASN C1741 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ASN C1741 " --> pdb=" O CYS C1748 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N VAL C1750 " --> pdb=" O TYR C1739 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N TYR C1739 " --> pdb=" O VAL C1750 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 1839 through 1841 Processing sheet with id= T, first strand: chain 'C' and resid 1875 through 1877 Processing sheet with id= U, first strand: chain 'C' and resid 2000 through 2002 Processing sheet with id= V, first strand: chain 'C' and resid 2188 through 2193 removed outlier: 4.108A pdb=" N GLN C2178 " --> pdb=" O CYS C2171 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER C2166 " --> pdb=" O THR C2158 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N CYS C2154 " --> pdb=" O GLY C2170 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 2226 through 2228 removed outlier: 3.674A pdb=" N CYS C2201 " --> pdb=" O GLY C2218 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 2250 through 2252 removed outlier: 3.776A pdb=" N LYS C2271 " --> pdb=" O THR C2267 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'C' and resid 2322 through 2325 removed outlier: 4.099A pdb=" N LYS C2334 " --> pdb=" O SER C2325 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'C' and resid 2354 through 2359 removed outlier: 7.045A pdb=" N ALA C2366 " --> pdb=" O ILE C2355 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N VAL C2357 " --> pdb=" O TYR C2364 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N TYR C2364 " --> pdb=" O VAL C2357 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N LYS C2367 " --> pdb=" O VAL C2372 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL C2372 " --> pdb=" O LYS C2367 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'C' and resid 2414 through 2419 removed outlier: 7.091A pdb=" N GLY C2428 " --> pdb=" O LYS C2415 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N LEU C2417 " --> pdb=" O TRP C2426 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N TRP C2426 " --> pdb=" O LEU C2417 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N LEU C2419 " --> pdb=" O ALA C2424 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N ALA C2424 " --> pdb=" O LEU C2419 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ASP C2438 " --> pdb=" O LEU C2444 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N LEU C2444 " --> pdb=" O ASP C2438 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'C' and resid 2140 through 2145 removed outlier: 6.750A pdb=" N VAL C2495 " --> pdb=" O THR C2141 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ARG C2143 " --> pdb=" O LEU C2493 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU C2493 " --> pdb=" O ARG C2143 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N LEU C2145 " --> pdb=" O SER C2491 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N SER C2491 " --> pdb=" O LEU C2145 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N MET C2470 " --> pdb=" O TRP C2496 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL C2469 " --> pdb=" O ALA C2461 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL C2457 " --> pdb=" O LEU C2473 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N TYR C2475 " --> pdb=" O VAL C2455 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N VAL C2455 " --> pdb=" O TYR C2475 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'C' and resid 1447 through 1451 removed outlier: 7.947A pdb=" N LEU C1449 " --> pdb=" O ARG C1483 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N TYR C1485 " --> pdb=" O LEU C1449 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N GLY C1451 " --> pdb=" O TYR C1485 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N PHE C1487 " --> pdb=" O GLY C1451 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'C' and resid 1884 through 1887 removed outlier: 7.180A pdb=" N VAL C1893 " --> pdb=" O LEU C1885 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'B' and resid 150 through 153 removed outlier: 7.925A pdb=" N CYS B 84 " --> pdb=" O LEU B 121 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N LEU B 123 " --> pdb=" O CYS B 84 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ILE B 86 " --> pdb=" O LEU B 123 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ASN B 125 " --> pdb=" O ILE B 86 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N PHE B 88 " --> pdb=" O ASN B 125 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ASP B 43 " --> pdb=" O ASP B 63 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'D' and resid 150 through 153 removed outlier: 7.929A pdb=" N CYS D 84 " --> pdb=" O LEU D 121 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N LEU D 123 " --> pdb=" O CYS D 84 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILE D 86 " --> pdb=" O LEU D 123 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ASN D 125 " --> pdb=" O ILE D 86 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N PHE D 88 " --> pdb=" O ASN D 125 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ASP D 43 " --> pdb=" O ASP D 63 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'E' and resid 1087 through 1089 removed outlier: 6.706A pdb=" N GLN E1111 " --> pdb=" O PHE E1088 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ILE E1133 " --> pdb=" O LEU E1112 " (cutoff:3.500A) No H-bonds generated for sheet with id= AG Processing sheet with id= AH, first strand: chain 'E' and resid 1177 through 1179 removed outlier: 6.176A pdb=" N SER E1200 " --> pdb=" O LEU E1178 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N GLU E1224 " --> pdb=" O LEU E1201 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LYS E1249 " --> pdb=" O LEU E1225 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N SER E1272 " --> pdb=" O LEU E1250 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ASP E1296 " --> pdb=" O LEU E1273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AH Processing sheet with id= AI, first strand: chain 'E' and resid 1329 through 1332 removed outlier: 3.954A pdb=" N GLN E1521 " --> pdb=" O TYR E1332 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'E' and resid 1336 through 1339 removed outlier: 8.245A pdb=" N LEU E1337 " --> pdb=" O VAL E1389 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ASN E1391 " --> pdb=" O LEU E1337 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N ILE E1339 " --> pdb=" O ASN E1391 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N TRP E1393 " --> pdb=" O ILE E1339 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU E1390 " --> pdb=" O TRP E1376 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'E' and resid 1415 through 1418 removed outlier: 7.606A pdb=" N LEU E1449 " --> pdb=" O ARG E1483 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TYR E1485 " --> pdb=" O LEU E1449 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLY E1451 " --> pdb=" O TYR E1485 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N PHE E1487 " --> pdb=" O GLY E1451 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'E' and resid 1547 through 1549 Processing sheet with id= AM, first strand: chain 'E' and resid 1825 through 1828 removed outlier: 4.862A pdb=" N ILE E1692 " --> pdb=" O LEU E1813 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N TYR E1747 " --> pdb=" O PRO E1768 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N CYS E1748 " --> pdb=" O ASN E1741 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ASN E1741 " --> pdb=" O CYS E1748 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'E' and resid 1840 through 1842 Processing sheet with id= AO, first strand: chain 'E' and resid 1893 through 1898 removed outlier: 3.765A pdb=" N GLY E1939 " --> pdb=" O MET E1944 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA E1937 " --> pdb=" O VAL E1946 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N GLU E1948 " --> pdb=" O LEU E1935 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N LEU E1935 " --> pdb=" O GLU E1948 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'E' and resid 2000 through 2002 Processing sheet with id= AQ, first strand: chain 'E' and resid 2155 through 2157 Processing sheet with id= AR, first strand: chain 'E' and resid 2225 through 2227 removed outlier: 3.717A pdb=" N GLU E2212 " --> pdb=" O LEU E2207 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'E' and resid 2273 through 2276 removed outlier: 3.656A pdb=" N ALA E2273 " --> pdb=" O VAL E2265 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N CYS E2247 " --> pdb=" O GLY E2266 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'E' and resid 2315 through 2319 Processing sheet with id= AU, first strand: chain 'E' and resid 2354 through 2359 removed outlier: 7.196A pdb=" N ALA E2366 " --> pdb=" O ILE E2355 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N VAL E2357 " --> pdb=" O TYR E2364 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N TYR E2364 " --> pdb=" O VAL E2357 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N LYS E2367 " --> pdb=" O VAL E2372 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VAL E2372 " --> pdb=" O LYS E2367 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'E' and resid 2416 through 2419 removed outlier: 4.052A pdb=" N ARG E2446 " --> pdb=" O LEU E2436 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'E' and resid 2140 through 2145 removed outlier: 6.780A pdb=" N VAL E2495 " --> pdb=" O THR E2141 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ARG E2143 " --> pdb=" O LEU E2493 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LEU E2493 " --> pdb=" O ARG E2143 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N TYR E2475 " --> pdb=" O VAL E2455 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N VAL E2455 " --> pdb=" O TYR E2475 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'F' and resid 1087 through 1089 removed outlier: 6.702A pdb=" N GLN F1111 " --> pdb=" O PHE F1088 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ILE F1133 " --> pdb=" O LEU F1112 " (cutoff:3.500A) No H-bonds generated for sheet with id= AX Processing sheet with id= AY, first strand: chain 'F' and resid 1177 through 1179 removed outlier: 6.178A pdb=" N SER F1200 " --> pdb=" O LEU F1178 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N GLU F1224 " --> pdb=" O LEU F1201 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LYS F1249 " --> pdb=" O LEU F1225 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N SER F1272 " --> pdb=" O LEU F1250 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ASP F1296 " --> pdb=" O LEU F1273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AY Processing sheet with id= AZ, first strand: chain 'F' and resid 1329 through 1332 removed outlier: 3.957A pdb=" N GLN F1521 " --> pdb=" O TYR F1332 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'F' and resid 1336 through 1339 removed outlier: 8.244A pdb=" N LEU F1337 " --> pdb=" O VAL F1389 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ASN F1391 " --> pdb=" O LEU F1337 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N ILE F1339 " --> pdb=" O ASN F1391 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N TRP F1393 " --> pdb=" O ILE F1339 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU F1390 " --> pdb=" O TRP F1376 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'F' and resid 1415 through 1418 removed outlier: 7.607A pdb=" N LEU F1449 " --> pdb=" O ARG F1483 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N TYR F1485 " --> pdb=" O LEU F1449 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLY F1451 " --> pdb=" O TYR F1485 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N PHE F1487 " --> pdb=" O GLY F1451 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'F' and resid 1547 through 1549 Processing sheet with id= BD, first strand: chain 'F' and resid 1825 through 1828 removed outlier: 4.866A pdb=" N ILE F1692 " --> pdb=" O LEU F1813 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR F1766 " --> pdb=" O LEU F1749 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N TYR F1747 " --> pdb=" O PRO F1768 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N CYS F1748 " --> pdb=" O ASN F1741 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N ASN F1741 " --> pdb=" O CYS F1748 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N VAL F1750 " --> pdb=" O TYR F1739 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N TYR F1739 " --> pdb=" O VAL F1750 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY F1737 " --> pdb=" O TRP F1734 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'F' and resid 1840 through 1842 Processing sheet with id= BF, first strand: chain 'F' and resid 1893 through 1898 removed outlier: 3.766A pdb=" N GLY F1939 " --> pdb=" O MET F1944 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA F1937 " --> pdb=" O VAL F1946 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N GLU F1948 " --> pdb=" O LEU F1935 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N LEU F1935 " --> pdb=" O GLU F1948 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'F' and resid 2000 through 2002 Processing sheet with id= BH, first strand: chain 'F' and resid 2155 through 2157 Processing sheet with id= BI, first strand: chain 'F' and resid 2225 through 2227 removed outlier: 3.691A pdb=" N GLU F2212 " --> pdb=" O LEU F2207 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'F' and resid 2247 through 2250 removed outlier: 3.809A pdb=" N CYS F2247 " --> pdb=" O GLY F2266 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA F2273 " --> pdb=" O VAL F2265 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'F' and resid 2315 through 2319 Processing sheet with id= BL, first strand: chain 'F' and resid 2354 through 2359 removed outlier: 7.182A pdb=" N ALA F2366 " --> pdb=" O ILE F2355 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N VAL F2357 " --> pdb=" O TYR F2364 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N TYR F2364 " --> pdb=" O VAL F2357 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N LYS F2367 " --> pdb=" O VAL F2372 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL F2372 " --> pdb=" O LYS F2367 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'F' and resid 2416 through 2419 removed outlier: 4.066A pdb=" N ARG F2446 " --> pdb=" O LEU F2436 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'F' and resid 2140 through 2145 removed outlier: 6.804A pdb=" N VAL F2495 " --> pdb=" O THR F2141 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ARG F2143 " --> pdb=" O LEU F2493 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LEU F2493 " --> pdb=" O ARG F2143 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N TYR F2475 " --> pdb=" O VAL F2455 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N VAL F2455 " --> pdb=" O TYR F2475 " (cutoff:3.500A) 1978 hydrogen bonds defined for protein. 5364 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: 25.56 Time building geometry restraints manager: 17.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 8771 1.28 - 1.41: 12721 1.41 - 1.55: 32697 1.55 - 1.69: 66 1.69 - 1.82: 479 Bond restraints: 54734 Sorted by residual: bond pdb=" C THR E 213 " pdb=" O THR E 213 " ideal model delta sigma weight residual 1.236 1.391 -0.154 1.16e-02 7.43e+03 1.76e+02 bond pdb=" C LEU E 209 " pdb=" O LEU E 209 " ideal model delta sigma weight residual 1.236 1.361 -0.125 1.15e-02 7.56e+03 1.17e+02 bond pdb=" C TYR E 205 " pdb=" O TYR E 205 " ideal model delta sigma weight residual 1.236 1.358 -0.121 1.15e-02 7.56e+03 1.12e+02 bond pdb=" C LYS E 203 " pdb=" O LYS E 203 " ideal model delta sigma weight residual 1.237 1.141 0.096 1.19e-02 7.06e+03 6.45e+01 bond pdb=" C GLU E 201 " pdb=" O GLU E 201 " ideal model delta sigma weight residual 1.236 1.326 -0.089 1.15e-02 7.56e+03 6.04e+01 ... (remaining 54729 not shown) Histogram of bond angle deviations from ideal: 94.26 - 103.39: 596 103.39 - 112.52: 29765 112.52 - 121.65: 31133 121.65 - 130.78: 12816 130.78 - 139.91: 287 Bond angle restraints: 74597 Sorted by residual: angle pdb=" N LYS E 216 " pdb=" CA LYS E 216 " pdb=" C LYS E 216 " ideal model delta sigma weight residual 111.75 97.41 14.34 1.28e+00 6.10e-01 1.25e+02 angle pdb=" C LYS E 216 " pdb=" N ASP E 217 " pdb=" CA ASP E 217 " ideal model delta sigma weight residual 122.83 108.48 14.35 1.54e+00 4.22e-01 8.68e+01 angle pdb=" C LEU E 212 " pdb=" N THR E 213 " pdb=" CA THR E 213 " ideal model delta sigma weight residual 120.63 108.50 12.13 1.36e+00 5.41e-01 7.95e+01 angle pdb=" C PHE E 215 " pdb=" CA PHE E 215 " pdb=" CB PHE E 215 " ideal model delta sigma weight residual 109.29 124.84 -15.55 1.82e+00 3.02e-01 7.30e+01 angle pdb=" N LEU F 208 " pdb=" CA LEU F 208 " pdb=" C LEU F 208 " ideal model delta sigma weight residual 111.28 102.99 8.29 1.09e+00 8.42e-01 5.78e+01 ... (remaining 74592 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.13: 31109 22.13 - 44.26: 1655 44.26 - 66.38: 189 66.38 - 88.51: 56 88.51 - 110.64: 6 Dihedral angle restraints: 33015 sinusoidal: 11833 harmonic: 21182 Sorted by residual: dihedral pdb=" O2B GDP F2601 " pdb=" O3A GDP F2601 " pdb=" PB GDP F2601 " pdb=" PA GDP F2601 " ideal model delta sinusoidal sigma weight residual -180.00 -69.36 -110.64 1 2.00e+01 2.50e-03 3.25e+01 dihedral pdb=" O2B GDP E2601 " pdb=" O3A GDP E2601 " pdb=" PB GDP E2601 " pdb=" PA GDP E2601 " ideal model delta sinusoidal sigma weight residual -180.00 -69.42 -110.58 1 2.00e+01 2.50e-03 3.24e+01 dihedral pdb=" C PHE E 215 " pdb=" N PHE E 215 " pdb=" CA PHE E 215 " pdb=" CB PHE E 215 " ideal model delta harmonic sigma weight residual -122.60 -134.56 11.96 0 2.50e+00 1.60e-01 2.29e+01 ... (remaining 33012 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 8401 0.093 - 0.186: 610 0.186 - 0.279: 29 0.279 - 0.372: 3 0.372 - 0.465: 1 Chirality restraints: 9044 Sorted by residual: chirality pdb=" CB ILE F1709 " pdb=" CA ILE F1709 " pdb=" CG1 ILE F1709 " pdb=" CG2 ILE F1709 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.47 2.00e-01 2.50e+01 5.41e+00 chirality pdb=" CA VAL F 176 " pdb=" N VAL F 176 " pdb=" C VAL F 176 " pdb=" CB VAL F 176 " both_signs ideal model delta sigma weight residual False 2.44 2.79 -0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" CA LYS E 216 " pdb=" N LYS E 216 " pdb=" C LYS E 216 " pdb=" CB LYS E 216 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.22e+00 ... (remaining 9041 not shown) Planarity restraints: 9406 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA E 211 " 0.032 2.00e-02 2.50e+03 6.66e-02 4.44e+01 pdb=" C ALA E 211 " -0.115 2.00e-02 2.50e+03 pdb=" O ALA E 211 " 0.044 2.00e-02 2.50e+03 pdb=" N LEU E 212 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP E 204 " -0.030 2.00e-02 2.50e+03 6.06e-02 3.67e+01 pdb=" C ASP E 204 " 0.105 2.00e-02 2.50e+03 pdb=" O ASP E 204 " -0.039 2.00e-02 2.50e+03 pdb=" N TYR E 205 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU F 196 " -0.031 2.00e-02 2.50e+03 6.04e-02 3.65e+01 pdb=" C LEU F 196 " 0.105 2.00e-02 2.50e+03 pdb=" O LEU F 196 " -0.037 2.00e-02 2.50e+03 pdb=" N THR F 197 " -0.036 2.00e-02 2.50e+03 ... (remaining 9403 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 7535 2.76 - 3.30: 52625 3.30 - 3.83: 86455 3.83 - 4.37: 99666 4.37 - 4.90: 172547 Nonbonded interactions: 418828 Sorted by model distance: nonbonded pdb=" O SER E2213 " pdb=" OG1 THR E2229 " model vdw 2.227 2.440 nonbonded pdb=" OH TYR A1992 " pdb=" O ALA A2016 " model vdw 2.243 2.440 nonbonded pdb=" O SER F2213 " pdb=" OG1 THR F2229 " model vdw 2.244 2.440 nonbonded pdb=" O THR A2321 " pdb=" OG1 THR A2338 " model vdw 2.247 2.440 nonbonded pdb=" O SER E 990 " pdb=" ND2 ASN E1021 " model vdw 2.251 2.520 ... (remaining 418823 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' and (resid 1329 through 2005 or (resid 2006 and (name N or name CA or \ name C or name O or name CB )) or resid 2007 through 2147 or (resid 2148 and (n \ ame N or name CA or name C or name O or name CB )) or resid 2149 through 2184 or \ (resid 2185 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 186 through 2420 or (resid 2421 through 2422 and (name N or name CA or name C or \ name O or name CB )) or resid 2423 through 2491 or (resid 2492 and (name N or n \ ame CA or name C or name O or name CB )) or resid 2493 through 2527 or resid 260 \ 1 or resid 2602)) selection = (chain 'C' and (resid 1329 through 1866 or (resid 1867 and (name N or name CA or \ name C or name O or name CB )) or resid 1868 through 2183 or (resid 2184 throug \ h 2185 and (name N or name CA or name C or name O or name CB )) or resid 2186 th \ rough 2259 or (resid 2260 and (name N or name CA or name C or name O or name CB \ )) or resid 2261 through 2437 or (resid 2438 and (name N or name CA or name C or \ name O or name CB )) or resid 2439 through 2527 or resid 2601 or resid 2602)) } ncs_group { reference = (chain 'B' and (resid 5 through 9 or (resid 10 through 11 and (name N or name CA \ or name C or name O or name CB )) or resid 12 through 19 or (resid 20 and (name \ N or name CA or name C or name O or name CB )) or resid 21 through 24 or (resid \ 25 through 26 and (name N or name CA or name C or name O or name CB )) or resid \ 27 through 30 or (resid 31 through 37 and (name N or name CA or name C or name \ O or name CB )) or resid 38 through 63 or (resid 64 through 65 and (name N or na \ me CA or name C or name O or name CB )) or resid 66 through 112 or (resid 113 th \ rough 114 and (name N or name CA or name C or name O or name CB )) or resid 115 \ through 126 or resid 135 through 150 or (resid 151 and (name N or name CA or nam \ e C or name O or name CB )) or resid 152 through 162 or (resid 163 through 165 a \ nd (name N or name CA or name C or name O or name CB )) or resid 166 through 176 \ )) selection = (chain 'D' and (resid 5 through 86 or (resid 87 and (name N or name CA or name C \ or name O or name CB )) or resid 88 through 90 or (resid 91 through 94 and (nam \ e N or name CA or name C or name O or name CB )) or resid 95 through 126 or resi \ d 135 through 176)) } ncs_group { reference = (chain 'E' and (resid 12 through 60 or (resid 61 through 62 and (name N or name \ CA or name C or name O or name CB )) or resid 63 through 178 or (resid 179 and ( \ name N or name CA or name C or name O or name CB )) or resid 180 through 187 or \ (resid 188 through 191 and (name N or name CA or name C or name O or name CB )) \ or resid 192 through 207 or (resid 208 through 209 and (name N or name CA or nam \ e C or name O or name CB )) or resid 210 through 601 or (resid 602 and (name N o \ r name CA or name C or name O or name CB )) or resid 603 through 642 or (resid 6 \ 43 and (name N or name CA or name C or name O or name CB )) or resid 644 through \ 829 or (resid 830 through 832 and (name N or name CA or name C or name O or nam \ e CB )) or resid 833 through 844 or (resid 845 and (name N or name CA or name C \ or name O or name CB )) or resid 846 through 1619 or (resid 1620 and (name N or \ name CA or name C or name O or name CB )) or resid 1621 through 1695 or (resid 1 \ 696 and (name N or name CA or name C or name O or name CB )) or resid 1697 throu \ gh 1713 or (resid 1714 and (name N or name CA or name C or name O or name CB )) \ or resid 1715 through 1717 or (resid 1718 and (name N or name CA or name C or na \ me O or name CB )) or resid 1719 through 1727 or (resid 1728 and (name N or name \ CA or name C or name O or name CB )) or resid 1729 or (resid 1730 and (name N o \ r name CA or name C or name O or name CB )) or resid 1731 through 1752 or (resid \ 1753 and (name N or name CA or name C or name O or name CB )) or resid 1754 thr \ ough 1756 or (resid 1757 and (name N or name CA or name C or name O or name CB ) \ ) or resid 1758 through 1759 or (resid 1760 and (name N or name CA or name C or \ name O or name CB )) or resid 1761 through 2074 or (resid 2075 and (name N or na \ me CA or name C or name O or name CB )) or resid 2076 through 2135 or (resid 213 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 2137 through \ 2174 or (resid 2175 through 2176 and (name N or name CA or name C or name O or \ name CB )) or resid 2177 through 2186 or (resid 2187 and (name N or name CA or n \ ame C or name O or name CB )) or resid 2188 through 2192 or (resid 2193 and (nam \ e N or name CA or name C or name O or name CB )) or resid 2194 through 2195 or ( \ resid 2196 and (name N or name CA or name C or name O or name CB )) or resid 219 \ 7 or (resid 2198 and (name N or name CA or name C or name O or name CB )) or res \ id 2199 or (resid 2200 through 2201 and (name N or name CA or name C or name O o \ r name CB )) or resid 2202 through 2208 or (resid 2209 through 2211 and (name N \ or name CA or name C or name O or name CB )) or resid 2212 through 2219 or (resi \ d 2220 through 2221 and (name N or name CA or name C or name O or name CB )) or \ resid 2222 through 2239 or (resid 2240 and (name N or name CA or name C or name \ O or name CB )) or resid 2241 or (resid 2242 through 2244 and (name N or name CA \ or name C or name O or name CB )) or resid 2245 through 2270 or (resid 2271 and \ (name N or name CA or name C or name O or name CB )) or resid 2272 through 2280 \ or (resid 2281 through 2283 and (name N or name CA or name C or name O or name \ CB )) or resid 2284 through 2288 or (resid 2289 through 2293 and (name N or name \ CA or name C or name O or name CB )) or resid 2294 or (resid 2299 and (name N o \ r name CA or name C or name O or name CB )) or resid 2300 through 2310 or (resid \ 2311 through 2312 and (name N or name CA or name C or name O or name CB )) or r \ esid 2313 through 2328 or (resid 2329 through 2331 and (name N or name CA or nam \ e C or name O or name CB )) or resid 2332 or (resid 2333 through 2335 and (name \ N or name CA or name C or name O or name CB )) or resid 2336 through 2343 or (re \ sid 2344 and (name N or name CA or name C or name O or name CB )) or resid 2345 \ through 2380 or (resid 2381 through 2383 and (name N or name CA or name C or nam \ e O or name CB )) or resid 2384 through 2497 or (resid 2498 and (name N or name \ CA or name C or name O or name CB )) or resid 2499 through 2527 or resid 2601 or \ resid 2602)) selection = (chain 'F' and (resid 12 through 135 or (resid 136 through 137 and (name N or na \ me CA or name C or name O or name CB )) or resid 138 through 197 or (resid 198 a \ nd (name N or name CA or name C or name O or name CB )) or resid 199 through 410 \ or (resid 411 through 413 and (name N or name CA or name C or name O or name CB \ )) or resid 414 through 738 or (resid 739 and (name N or name CA or name C or n \ ame O or name CB )) or resid 740 through 828 or (resid 829 through 832 and (name \ N or name CA or name C or name O or name CB )) or resid 833 through 2080 or (re \ sid 2081 and (name N or name CA or name C or name O or name CB )) or resid 2082 \ through 2084 or (resid 2085 and (name N or name CA or name C or name O or name C \ B )) or resid 2086 through 2158 or (resid 2159 through 2160 and (name N or name \ CA or name C or name O or name CB )) or resid 2161 through 2213 or (resid 2214 a \ nd (name N or name CA or name C or name O or name CB )) or resid 2215 through 22 \ 48 or (resid 2249 and (name N or name CA or name C or name O or name CB )) or re \ sid 2250 through 2253 or resid 2260 through 2450 or (resid 2451 and (name N or n \ ame CA or name C or name O or name CB )) or resid 2452 through 2527 or resid 260 \ 1 or resid 2602)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 3.830 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: 22.490 Check model and map are aligned: 0.600 Set scattering table: 0.370 Process input model: 115.300 Find NCS groups from input model: 3.320 Set up NCS constraints: 0.290 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:2.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 148.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 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 : 0.004 0.154 54734 Z= 0.273 Angle : 0.814 15.548 74597 Z= 0.448 Chirality : 0.050 0.465 9044 Planarity : 0.006 0.092 9406 Dihedral : 13.642 110.641 19209 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.09 % Favored : 92.87 % Rotamer: Outliers : 0.22 % Allowed : 1.02 % Favored : 98.75 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.96 (0.10), residues: 7169 helix: 0.78 (0.11), residues: 2663 sheet: -1.16 (0.15), residues: 1184 loop : -1.62 (0.11), residues: 3322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP F1734 HIS 0.009 0.001 HIS C1621 PHE 0.017 0.002 PHE A2181 TYR 0.023 0.001 TYR E1992 ARG 0.011 0.001 ARG A1728 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14338 Ramachandran restraints generated. 7169 Oldfield, 0 Emsley, 7169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14338 Ramachandran restraints generated. 7169 Oldfield, 0 Emsley, 7169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 6514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 407 time to evaluate : 4.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2489 ILE cc_start: 0.8421 (mt) cc_final: 0.8201 (mt) REVERT: C 1646 MET cc_start: 0.7787 (ttp) cc_final: 0.7535 (tmm) REVERT: C 2489 ILE cc_start: 0.8422 (mt) cc_final: 0.8208 (mt) REVERT: E 2364 TYR cc_start: 0.4950 (m-10) cc_final: 0.4654 (m-10) REVERT: F 2364 TYR cc_start: 0.5109 (m-10) cc_final: 0.4750 (m-10) outliers start: 12 outliers final: 2 residues processed: 417 average time/residue: 0.4902 time to fit residues: 352.0587 Evaluate side-chains 265 residues out of total 6514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 263 time to evaluate : 4.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1730 ASN Chi-restraints excluded: chain F residue 200 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 722 random chunks: chunk 609 optimal weight: 10.0000 chunk 547 optimal weight: 9.9990 chunk 303 optimal weight: 0.9980 chunk 186 optimal weight: 0.9980 chunk 369 optimal weight: 20.0000 chunk 292 optimal weight: 4.9990 chunk 565 optimal weight: 5.9990 chunk 218 optimal weight: 0.9980 chunk 344 optimal weight: 10.0000 chunk 421 optimal weight: 3.9990 chunk 655 optimal weight: 9.9990 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1405 HIS ** C1560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 444 ASN ** E 992 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1140 HIS ** E1278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1324 GLN E1783 HIS E1961 GLN ** F 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 992 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1140 HIS ** F1278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1324 GLN F1961 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 54734 Z= 0.292 Angle : 0.615 10.720 74597 Z= 0.311 Chirality : 0.043 0.159 9044 Planarity : 0.005 0.059 9406 Dihedral : 6.482 87.206 7805 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.53 % Favored : 93.44 % Rotamer: Outliers : 0.37 % Allowed : 7.46 % Favored : 92.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.00 (0.10), residues: 7169 helix: 0.76 (0.10), residues: 2696 sheet: -1.25 (0.15), residues: 1225 loop : -1.64 (0.11), residues: 3248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP F1734 HIS 0.007 0.001 HIS A1783 PHE 0.021 0.002 PHE E1650 TYR 0.021 0.002 TYR A1645 ARG 0.006 0.000 ARG C1847 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14338 Ramachandran restraints generated. 7169 Oldfield, 0 Emsley, 7169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14338 Ramachandran restraints generated. 7169 Oldfield, 0 Emsley, 7169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 6514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 259 time to evaluate : 4.660 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2489 ILE cc_start: 0.8409 (mt) cc_final: 0.8195 (mt) REVERT: C 1338 MET cc_start: 0.8466 (mmt) cc_final: 0.7919 (mmt) REVERT: C 2489 ILE cc_start: 0.8458 (mt) cc_final: 0.8256 (mt) REVERT: E 1431 MET cc_start: 0.7153 (mmp) cc_final: 0.6877 (tpp) REVERT: E 1765 ILE cc_start: 0.8819 (OUTLIER) cc_final: 0.8534 (mt) REVERT: E 2315 MET cc_start: -0.0267 (mtm) cc_final: -0.1331 (mmm) REVERT: E 2459 MET cc_start: 0.7027 (pmm) cc_final: 0.6715 (pmm) REVERT: E 2499 ASN cc_start: 0.8266 (m-40) cc_final: 0.7865 (p0) REVERT: F 100 MET cc_start: 0.2263 (mmp) cc_final: -0.0457 (ppp) REVERT: F 704 MET cc_start: 0.7753 (OUTLIER) cc_final: 0.7535 (tpp) REVERT: F 1431 MET cc_start: 0.7201 (mmp) cc_final: 0.6915 (tpp) REVERT: F 2364 TYR cc_start: 0.4970 (m-80) cc_final: 0.4694 (m-10) REVERT: F 2459 MET cc_start: 0.7753 (ppp) cc_final: 0.7545 (ppp) outliers start: 20 outliers final: 11 residues processed: 273 average time/residue: 0.4754 time to fit residues: 230.6045 Evaluate side-chains 253 residues out of total 6514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 240 time to evaluate : 4.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2200 LEU Chi-restraints excluded: chain A residue 2492 CYS Chi-restraints excluded: chain C residue 1418 VAL Chi-restraints excluded: chain C residue 2200 LEU Chi-restraints excluded: chain E residue 704 MET Chi-restraints excluded: chain E residue 1414 LEU Chi-restraints excluded: chain E residue 1712 LEU Chi-restraints excluded: chain E residue 1765 ILE Chi-restraints excluded: chain E residue 1947 MET Chi-restraints excluded: chain E residue 2018 TYR Chi-restraints excluded: chain F residue 704 MET Chi-restraints excluded: chain F residue 1414 LEU Chi-restraints excluded: chain F residue 1719 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 722 random chunks: chunk 364 optimal weight: 0.9990 chunk 203 optimal weight: 5.9990 chunk 545 optimal weight: 0.9980 chunk 446 optimal weight: 0.0010 chunk 180 optimal weight: 0.5980 chunk 656 optimal weight: 6.9990 chunk 709 optimal weight: 10.0000 chunk 584 optimal weight: 20.0000 chunk 651 optimal weight: 1.9990 chunk 223 optimal weight: 3.9990 chunk 526 optimal weight: 5.9990 overall best weight: 0.9190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 309 GLN ** E 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 992 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 309 GLN ** F 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 992 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1710 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 54734 Z= 0.155 Angle : 0.529 7.448 74597 Z= 0.267 Chirality : 0.041 0.153 9044 Planarity : 0.004 0.055 9406 Dihedral : 6.164 79.875 7802 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 0.60 % Allowed : 9.84 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.88 (0.10), residues: 7169 helix: 0.80 (0.10), residues: 2712 sheet: -1.13 (0.15), residues: 1233 loop : -1.55 (0.11), residues: 3224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F1734 HIS 0.004 0.001 HIS E1407 PHE 0.019 0.001 PHE E1650 TYR 0.013 0.001 TYR F1992 ARG 0.004 0.000 ARG C1847 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14338 Ramachandran restraints generated. 7169 Oldfield, 0 Emsley, 7169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14338 Ramachandran restraints generated. 7169 Oldfield, 0 Emsley, 7169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 6514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 249 time to evaluate : 4.714 Fit side-chains REVERT: A 1335 MET cc_start: 0.8027 (tpp) cc_final: 0.7626 (tpp) REVERT: A 1338 MET cc_start: 0.8222 (mmt) cc_final: 0.7785 (mmt) REVERT: A 1562 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7475 (mm) REVERT: A 1714 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7294 (pm20) REVERT: A 2489 ILE cc_start: 0.8425 (mt) cc_final: 0.8215 (mt) REVERT: C 1702 MET cc_start: 0.8321 (mtm) cc_final: 0.8103 (mtm) REVERT: C 2489 ILE cc_start: 0.8446 (mt) cc_final: 0.8239 (mt) REVERT: D 87 MET cc_start: 0.0939 (tmm) cc_final: 0.0644 (tmm) REVERT: E 100 MET cc_start: 0.2618 (mmm) cc_final: 0.2365 (mmp) REVERT: E 1431 MET cc_start: 0.7302 (OUTLIER) cc_final: 0.6954 (tpp) REVERT: E 2315 MET cc_start: -0.0382 (mtm) cc_final: -0.1397 (mmm) REVERT: E 2459 MET cc_start: 0.7059 (pmm) cc_final: 0.6364 (pmm) REVERT: E 2499 ASN cc_start: 0.8151 (m-40) cc_final: 0.7718 (p0) REVERT: F 100 MET cc_start: 0.2707 (mmp) cc_final: 0.1805 (mpp) REVERT: F 1431 MET cc_start: 0.7353 (OUTLIER) cc_final: 0.6968 (tpp) REVERT: F 1765 ILE cc_start: 0.8844 (OUTLIER) cc_final: 0.8467 (mt) REVERT: F 2364 TYR cc_start: 0.4844 (m-80) cc_final: 0.4518 (m-10) REVERT: F 2499 ASN cc_start: 0.7979 (m-40) cc_final: 0.7597 (p0) outliers start: 32 outliers final: 8 residues processed: 274 average time/residue: 0.5087 time to fit residues: 252.1865 Evaluate side-chains 252 residues out of total 6514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 239 time to evaluate : 4.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1562 LEU Chi-restraints excluded: chain A residue 1714 GLU Chi-restraints excluded: chain A residue 2492 CYS Chi-restraints excluded: chain C residue 1418 VAL Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 704 MET Chi-restraints excluded: chain E residue 1431 MET Chi-restraints excluded: chain E residue 1712 LEU Chi-restraints excluded: chain F residue 704 MET Chi-restraints excluded: chain F residue 1431 MET Chi-restraints excluded: chain F residue 1719 MET Chi-restraints excluded: chain F residue 1733 TYR Chi-restraints excluded: chain F residue 1765 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 722 random chunks: chunk 648 optimal weight: 6.9990 chunk 493 optimal weight: 5.9990 chunk 340 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 chunk 313 optimal weight: 6.9990 chunk 441 optimal weight: 10.0000 chunk 659 optimal weight: 8.9990 chunk 697 optimal weight: 40.0000 chunk 344 optimal weight: 3.9990 chunk 624 optimal weight: 10.0000 chunk 188 optimal weight: 0.8980 overall best weight: 2.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1437 ASN ** C1560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 719 GLN ** F 992 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 54734 Z= 0.300 Angle : 0.603 9.318 74597 Z= 0.304 Chirality : 0.043 0.166 9044 Planarity : 0.004 0.053 9406 Dihedral : 6.270 78.150 7802 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.01 % Allowed : 6.40 % Favored : 93.58 % Rotamer: Outliers : 1.12 % Allowed : 11.82 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.91 (0.10), residues: 7169 helix: 0.77 (0.10), residues: 2694 sheet: -1.04 (0.15), residues: 1212 loop : -1.60 (0.11), residues: 3263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F1734 HIS 0.009 0.001 HIS A1783 PHE 0.020 0.002 PHE E1650 TYR 0.030 0.002 TYR A1649 ARG 0.005 0.000 ARG E 845 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14338 Ramachandran restraints generated. 7169 Oldfield, 0 Emsley, 7169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14338 Ramachandran restraints generated. 7169 Oldfield, 0 Emsley, 7169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 6514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 239 time to evaluate : 4.753 Fit side-chains REVERT: A 1714 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7607 (pm20) REVERT: A 2115 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.8894 (mp) REVERT: A 2321 THR cc_start: 0.9195 (OUTLIER) cc_final: 0.8912 (m) REVERT: C 1714 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7327 (pm20) REVERT: C 2115 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.8912 (mp) REVERT: C 2321 THR cc_start: 0.9215 (OUTLIER) cc_final: 0.8948 (m) REVERT: B 166 MET cc_start: 0.7265 (mmt) cc_final: 0.7006 (mmm) REVERT: D 87 MET cc_start: 0.1087 (tmm) cc_final: 0.0834 (tmm) REVERT: E 1431 MET cc_start: 0.7407 (mmp) cc_final: 0.6990 (tpp) REVERT: E 1765 ILE cc_start: 0.8960 (OUTLIER) cc_final: 0.8455 (mt) REVERT: E 1869 MET cc_start: 0.7457 (tmm) cc_final: 0.7203 (tmm) REVERT: E 2315 MET cc_start: -0.0171 (mtm) cc_final: -0.2446 (ttt) REVERT: E 2458 MET cc_start: 0.5620 (OUTLIER) cc_final: 0.5147 (ptt) REVERT: E 2459 MET cc_start: 0.7213 (pmm) cc_final: 0.6752 (pmm) REVERT: E 2499 ASN cc_start: 0.8083 (m-40) cc_final: 0.7774 (p0) REVERT: F 100 MET cc_start: 0.2627 (mmp) cc_final: 0.1230 (mpp) REVERT: F 1168 MET cc_start: 0.2882 (mmm) cc_final: 0.2642 (mmp) REVERT: F 1175 MET cc_start: 0.3748 (tpp) cc_final: 0.3445 (tmm) REVERT: F 1431 MET cc_start: 0.7339 (OUTLIER) cc_final: 0.6912 (tpp) REVERT: F 1765 ILE cc_start: 0.8928 (OUTLIER) cc_final: 0.8522 (mt) REVERT: F 1869 MET cc_start: 0.7426 (tmm) cc_final: 0.7142 (tmm) REVERT: F 2315 MET cc_start: -0.0103 (mtm) cc_final: -0.2566 (ttt) REVERT: F 2364 TYR cc_start: 0.5183 (m-80) cc_final: 0.4717 (m-10) outliers start: 60 outliers final: 30 residues processed: 284 average time/residue: 0.5159 time to fit residues: 263.4626 Evaluate side-chains 271 residues out of total 6514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 231 time to evaluate : 4.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1368 THR Chi-restraints excluded: chain A residue 1562 LEU Chi-restraints excluded: chain A residue 1697 MET Chi-restraints excluded: chain A residue 1714 GLU Chi-restraints excluded: chain A residue 1733 TYR Chi-restraints excluded: chain A residue 1940 ILE Chi-restraints excluded: chain A residue 2115 LEU Chi-restraints excluded: chain A residue 2138 VAL Chi-restraints excluded: chain A residue 2224 LEU Chi-restraints excluded: chain A residue 2321 THR Chi-restraints excluded: chain A residue 2492 CYS Chi-restraints excluded: chain C residue 1368 THR Chi-restraints excluded: chain C residue 1418 VAL Chi-restraints excluded: chain C residue 1714 GLU Chi-restraints excluded: chain C residue 1733 TYR Chi-restraints excluded: chain C residue 1756 ASP Chi-restraints excluded: chain C residue 1940 ILE Chi-restraints excluded: chain C residue 2115 LEU Chi-restraints excluded: chain C residue 2224 LEU Chi-restraints excluded: chain C residue 2321 THR Chi-restraints excluded: chain E residue 458 VAL Chi-restraints excluded: chain E residue 704 MET Chi-restraints excluded: chain E residue 1414 LEU Chi-restraints excluded: chain E residue 1598 VAL Chi-restraints excluded: chain E residue 1712 LEU Chi-restraints excluded: chain E residue 1733 TYR Chi-restraints excluded: chain E residue 1765 ILE Chi-restraints excluded: chain E residue 1947 MET Chi-restraints excluded: chain E residue 2161 ASN Chi-restraints excluded: chain E residue 2458 MET Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 458 VAL Chi-restraints excluded: chain F residue 704 MET Chi-restraints excluded: chain F residue 1414 LEU Chi-restraints excluded: chain F residue 1431 MET Chi-restraints excluded: chain F residue 1719 MET Chi-restraints excluded: chain F residue 1733 TYR Chi-restraints excluded: chain F residue 1765 ILE Chi-restraints excluded: chain F residue 1947 MET Chi-restraints excluded: chain F residue 2159 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 722 random chunks: chunk 581 optimal weight: 0.7980 chunk 396 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 519 optimal weight: 0.8980 chunk 287 optimal weight: 20.0000 chunk 595 optimal weight: 7.9990 chunk 482 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 356 optimal weight: 6.9990 chunk 626 optimal weight: 2.9990 chunk 176 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1405 HIS ** E 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F2053 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 54734 Z= 0.215 Angle : 0.537 9.362 74597 Z= 0.272 Chirality : 0.041 0.149 9044 Planarity : 0.004 0.052 9406 Dihedral : 6.089 74.039 7802 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.86 % Favored : 94.13 % Rotamer: Outliers : 1.14 % Allowed : 13.04 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.80 (0.10), residues: 7169 helix: 0.86 (0.10), residues: 2674 sheet: -1.01 (0.15), residues: 1220 loop : -1.50 (0.11), residues: 3275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F1734 HIS 0.005 0.001 HIS C1783 PHE 0.018 0.001 PHE F1650 TYR 0.018 0.001 TYR C1733 ARG 0.009 0.000 ARG A1847 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14338 Ramachandran restraints generated. 7169 Oldfield, 0 Emsley, 7169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14338 Ramachandran restraints generated. 7169 Oldfield, 0 Emsley, 7169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 6514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 241 time to evaluate : 4.773 Fit side-chains REVERT: A 1338 MET cc_start: 0.8247 (mmt) cc_final: 0.7810 (mmt) REVERT: A 2115 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.8892 (mp) REVERT: A 2301 MET cc_start: 0.7802 (pmm) cc_final: 0.7268 (pmm) REVERT: A 2321 THR cc_start: 0.9178 (OUTLIER) cc_final: 0.8926 (m) REVERT: C 2115 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.8935 (mp) REVERT: C 2275 PHE cc_start: 0.7321 (m-80) cc_final: 0.7026 (m-10) REVERT: C 2301 MET cc_start: 0.7744 (pmm) cc_final: 0.7537 (pmm) REVERT: C 2321 THR cc_start: 0.9181 (OUTLIER) cc_final: 0.8921 (m) REVERT: D 87 MET cc_start: 0.1249 (tmm) cc_final: 0.1029 (tmm) REVERT: E 1175 MET cc_start: 0.4539 (tmm) cc_final: 0.3410 (tpp) REVERT: E 1335 MET cc_start: 0.6862 (mmm) cc_final: 0.6299 (ttt) REVERT: E 1431 MET cc_start: 0.7272 (mmp) cc_final: 0.6916 (tpp) REVERT: E 1697 MET cc_start: 0.7127 (ptt) cc_final: 0.6737 (ptt) REVERT: E 1765 ILE cc_start: 0.8946 (OUTLIER) cc_final: 0.8560 (mt) REVERT: E 2315 MET cc_start: -0.0286 (mtm) cc_final: -0.2502 (ttt) REVERT: E 2459 MET cc_start: 0.7244 (pmm) cc_final: 0.6813 (pmm) REVERT: E 2499 ASN cc_start: 0.8130 (m-40) cc_final: 0.7810 (p0) REVERT: F 100 MET cc_start: 0.2705 (mmp) cc_final: 0.1615 (mpp) REVERT: F 1335 MET cc_start: 0.6846 (mmm) cc_final: 0.6289 (ttt) REVERT: F 1431 MET cc_start: 0.7287 (OUTLIER) cc_final: 0.6816 (tpp) REVERT: F 1765 ILE cc_start: 0.8898 (OUTLIER) cc_final: 0.8499 (mt) REVERT: F 2301 MET cc_start: 0.3072 (ptp) cc_final: 0.2659 (pmm) REVERT: F 2315 MET cc_start: 0.0165 (mtm) cc_final: -0.2577 (ttt) REVERT: F 2364 TYR cc_start: 0.5257 (m-80) cc_final: 0.4790 (m-10) REVERT: F 2458 MET cc_start: 0.5113 (ptt) cc_final: 0.4692 (ptt) outliers start: 61 outliers final: 29 residues processed: 288 average time/residue: 0.4672 time to fit residues: 242.5380 Evaluate side-chains 268 residues out of total 6514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 232 time to evaluate : 4.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1429 ASP Chi-restraints excluded: chain A residue 1697 MET Chi-restraints excluded: chain A residue 1733 TYR Chi-restraints excluded: chain A residue 2020 ILE Chi-restraints excluded: chain A residue 2115 LEU Chi-restraints excluded: chain A residue 2136 GLU Chi-restraints excluded: chain A residue 2224 LEU Chi-restraints excluded: chain A residue 2264 LEU Chi-restraints excluded: chain A residue 2275 PHE Chi-restraints excluded: chain A residue 2321 THR Chi-restraints excluded: chain A residue 2492 CYS Chi-restraints excluded: chain C residue 1418 VAL Chi-restraints excluded: chain C residue 1649 TYR Chi-restraints excluded: chain C residue 1733 TYR Chi-restraints excluded: chain C residue 2020 ILE Chi-restraints excluded: chain C residue 2115 LEU Chi-restraints excluded: chain C residue 2321 THR Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 458 VAL Chi-restraints excluded: chain E residue 704 MET Chi-restraints excluded: chain E residue 985 THR Chi-restraints excluded: chain E residue 1598 VAL Chi-restraints excluded: chain E residue 1712 LEU Chi-restraints excluded: chain E residue 1733 TYR Chi-restraints excluded: chain E residue 1765 ILE Chi-restraints excluded: chain E residue 1893 VAL Chi-restraints excluded: chain E residue 1947 MET Chi-restraints excluded: chain F residue 704 MET Chi-restraints excluded: chain F residue 985 THR Chi-restraints excluded: chain F residue 1431 MET Chi-restraints excluded: chain F residue 1719 MET Chi-restraints excluded: chain F residue 1733 TYR Chi-restraints excluded: chain F residue 1765 ILE Chi-restraints excluded: chain F residue 1947 MET Chi-restraints excluded: chain F residue 2159 HIS Chi-restraints excluded: chain F residue 2161 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 722 random chunks: chunk 234 optimal weight: 0.7980 chunk 628 optimal weight: 9.9990 chunk 137 optimal weight: 8.9990 chunk 409 optimal weight: 8.9990 chunk 172 optimal weight: 0.9990 chunk 698 optimal weight: 9.9990 chunk 579 optimal weight: 9.9990 chunk 323 optimal weight: 7.9990 chunk 58 optimal weight: 0.9980 chunk 231 optimal weight: 1.9990 chunk 366 optimal weight: 10.0000 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1560 ASN C1684 HIS C2333 GLN ** E 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1093 ASN ** E1278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2053 GLN ** F 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 721 ASN ** F1021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1093 ASN ** F1278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 54734 Z= 0.301 Angle : 0.596 9.307 74597 Z= 0.301 Chirality : 0.043 0.218 9044 Planarity : 0.004 0.051 9406 Dihedral : 6.198 77.182 7802 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.01 % Allowed : 6.96 % Favored : 93.03 % Rotamer: Outliers : 1.71 % Allowed : 13.66 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.86 (0.10), residues: 7169 helix: 0.79 (0.10), residues: 2651 sheet: -1.07 (0.15), residues: 1236 loop : -1.49 (0.11), residues: 3282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F1734 HIS 0.007 0.001 HIS C1783 PHE 0.026 0.002 PHE E1148 TYR 0.019 0.002 TYR E1695 ARG 0.006 0.000 ARG A1847 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14338 Ramachandran restraints generated. 7169 Oldfield, 0 Emsley, 7169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14338 Ramachandran restraints generated. 7169 Oldfield, 0 Emsley, 7169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 6514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 233 time to evaluate : 4.758 Fit side-chains revert: symmetry clash REVERT: A 1338 MET cc_start: 0.8297 (mmt) cc_final: 0.7867 (mmt) REVERT: A 2115 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.8912 (mp) REVERT: A 2321 THR cc_start: 0.9258 (OUTLIER) cc_final: 0.8986 (m) REVERT: C 1763 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8846 (tt) REVERT: C 2115 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.8916 (mp) REVERT: C 2321 THR cc_start: 0.9250 (OUTLIER) cc_final: 0.8973 (m) REVERT: D 87 MET cc_start: 0.1609 (tmm) cc_final: 0.1347 (tmm) REVERT: D 174 MET cc_start: 0.6418 (OUTLIER) cc_final: 0.6037 (tpt) REVERT: E 1175 MET cc_start: 0.4849 (tmm) cc_final: 0.3941 (tpp) REVERT: E 1335 MET cc_start: 0.6784 (mmm) cc_final: 0.6327 (ttt) REVERT: E 1431 MET cc_start: 0.7227 (mmp) cc_final: 0.6852 (tpp) REVERT: E 1697 MET cc_start: 0.7264 (ptt) cc_final: 0.6899 (ptt) REVERT: E 1765 ILE cc_start: 0.9010 (OUTLIER) cc_final: 0.8501 (mt) REVERT: E 2315 MET cc_start: -0.0085 (mtm) cc_final: -0.2499 (ttt) REVERT: E 2459 MET cc_start: 0.7193 (pmm) cc_final: 0.6791 (pmm) REVERT: E 2499 ASN cc_start: 0.8174 (m-40) cc_final: 0.7909 (p0) REVERT: F 100 MET cc_start: 0.3059 (mmp) cc_final: 0.2099 (mpp) REVERT: F 1168 MET cc_start: 0.2586 (mmm) cc_final: 0.2247 (mmp) REVERT: F 1335 MET cc_start: 0.6843 (mmm) cc_final: 0.6287 (ttt) REVERT: F 1431 MET cc_start: 0.7281 (mmp) cc_final: 0.6823 (tpp) REVERT: F 1765 ILE cc_start: 0.8938 (OUTLIER) cc_final: 0.8524 (mt) REVERT: F 2315 MET cc_start: -0.0113 (mtm) cc_final: -0.2640 (ttt) REVERT: F 2458 MET cc_start: 0.5504 (ptt) cc_final: 0.4639 (ptt) outliers start: 92 outliers final: 49 residues processed: 306 average time/residue: 0.4698 time to fit residues: 259.5806 Evaluate side-chains 289 residues out of total 6514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 232 time to evaluate : 4.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1368 THR Chi-restraints excluded: chain A residue 1429 ASP Chi-restraints excluded: chain A residue 1549 ASP Chi-restraints excluded: chain A residue 1562 LEU Chi-restraints excluded: chain A residue 1610 ILE Chi-restraints excluded: chain A residue 1649 TYR Chi-restraints excluded: chain A residue 1697 MET Chi-restraints excluded: chain A residue 1716 SER Chi-restraints excluded: chain A residue 1733 TYR Chi-restraints excluded: chain A residue 1940 ILE Chi-restraints excluded: chain A residue 2020 ILE Chi-restraints excluded: chain A residue 2115 LEU Chi-restraints excluded: chain A residue 2224 LEU Chi-restraints excluded: chain A residue 2264 LEU Chi-restraints excluded: chain A residue 2275 PHE Chi-restraints excluded: chain A residue 2321 THR Chi-restraints excluded: chain A residue 2492 CYS Chi-restraints excluded: chain C residue 1368 THR Chi-restraints excluded: chain C residue 1418 VAL Chi-restraints excluded: chain C residue 1549 ASP Chi-restraints excluded: chain C residue 1610 ILE Chi-restraints excluded: chain C residue 1649 TYR Chi-restraints excluded: chain C residue 1716 SER Chi-restraints excluded: chain C residue 1733 TYR Chi-restraints excluded: chain C residue 1763 LEU Chi-restraints excluded: chain C residue 1940 ILE Chi-restraints excluded: chain C residue 2020 ILE Chi-restraints excluded: chain C residue 2115 LEU Chi-restraints excluded: chain C residue 2138 VAL Chi-restraints excluded: chain C residue 2224 LEU Chi-restraints excluded: chain C residue 2321 THR Chi-restraints excluded: chain C residue 2393 LEU Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 458 VAL Chi-restraints excluded: chain E residue 704 MET Chi-restraints excluded: chain E residue 985 THR Chi-restraints excluded: chain E residue 1054 LEU Chi-restraints excluded: chain E residue 1598 VAL Chi-restraints excluded: chain E residue 1712 LEU Chi-restraints excluded: chain E residue 1733 TYR Chi-restraints excluded: chain E residue 1765 ILE Chi-restraints excluded: chain E residue 1893 VAL Chi-restraints excluded: chain E residue 1947 MET Chi-restraints excluded: chain E residue 2161 ASN Chi-restraints excluded: chain F residue 458 VAL Chi-restraints excluded: chain F residue 704 MET Chi-restraints excluded: chain F residue 985 THR Chi-restraints excluded: chain F residue 1054 LEU Chi-restraints excluded: chain F residue 1719 MET Chi-restraints excluded: chain F residue 1733 TYR Chi-restraints excluded: chain F residue 1765 ILE Chi-restraints excluded: chain F residue 1893 VAL Chi-restraints excluded: chain F residue 1947 MET Chi-restraints excluded: chain F residue 2159 HIS Chi-restraints excluded: chain F residue 2161 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 722 random chunks: chunk 673 optimal weight: 0.8980 chunk 78 optimal weight: 0.6980 chunk 398 optimal weight: 0.4980 chunk 510 optimal weight: 5.9990 chunk 395 optimal weight: 0.0060 chunk 588 optimal weight: 2.9990 chunk 390 optimal weight: 20.0000 chunk 695 optimal weight: 6.9990 chunk 435 optimal weight: 0.9990 chunk 424 optimal weight: 2.9990 chunk 321 optimal weight: 1.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2476 ASN C1560 ASN C2333 GLN C2476 ASN ** E 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 721 ASN ** E1021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 721 ASN ** F1021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 54734 Z= 0.139 Angle : 0.522 9.118 74597 Z= 0.261 Chirality : 0.041 0.228 9044 Planarity : 0.004 0.055 9406 Dihedral : 5.821 67.554 7802 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.20 % Favored : 94.78 % Rotamer: Outliers : 1.14 % Allowed : 14.92 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.67 (0.10), residues: 7169 helix: 0.94 (0.11), residues: 2669 sheet: -0.93 (0.16), residues: 1207 loop : -1.40 (0.11), residues: 3293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E1434 HIS 0.004 0.001 HIS F 230 PHE 0.017 0.001 PHE F1650 TYR 0.019 0.001 TYR C1733 ARG 0.005 0.000 ARG E1334 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14338 Ramachandran restraints generated. 7169 Oldfield, 0 Emsley, 7169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14338 Ramachandran restraints generated. 7169 Oldfield, 0 Emsley, 7169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 6514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 238 time to evaluate : 4.684 Fit side-chains revert: symmetry clash REVERT: A 1646 MET cc_start: 0.8049 (tmm) cc_final: 0.7707 (tmm) REVERT: A 1763 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8802 (tt) REVERT: A 2115 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.8871 (mp) REVERT: A 2301 MET cc_start: 0.7775 (pmm) cc_final: 0.7142 (pmm) REVERT: A 2321 THR cc_start: 0.9164 (OUTLIER) cc_final: 0.8944 (m) REVERT: C 1763 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8778 (tt) REVERT: C 2321 THR cc_start: 0.9166 (OUTLIER) cc_final: 0.8938 (m) REVERT: D 87 MET cc_start: 0.1584 (tmm) cc_final: 0.1350 (tmm) REVERT: E 1175 MET cc_start: 0.4833 (tmm) cc_final: 0.3935 (tpp) REVERT: E 1335 MET cc_start: 0.6630 (mmm) cc_final: 0.6422 (ttm) REVERT: E 1431 MET cc_start: 0.7107 (mmp) cc_final: 0.6849 (tpp) REVERT: E 1765 ILE cc_start: 0.8828 (OUTLIER) cc_final: 0.8529 (mt) REVERT: E 2089 GLN cc_start: 0.5007 (OUTLIER) cc_final: 0.4794 (pt0) REVERT: E 2315 MET cc_start: -0.0162 (mtm) cc_final: -0.2481 (ttt) REVERT: E 2459 MET cc_start: 0.7094 (pmm) cc_final: 0.6644 (pmm) REVERT: E 2499 ASN cc_start: 0.8137 (m-40) cc_final: 0.7875 (p0) REVERT: F 100 MET cc_start: 0.2978 (mmp) cc_final: 0.2103 (mpp) REVERT: F 1175 MET cc_start: 0.4772 (tmm) cc_final: 0.4150 (tpp) REVERT: F 1335 MET cc_start: 0.6670 (mmm) cc_final: 0.6454 (ttm) REVERT: F 1431 MET cc_start: 0.7161 (mmp) cc_final: 0.6679 (tpp) REVERT: F 1765 ILE cc_start: 0.8779 (OUTLIER) cc_final: 0.8438 (mt) REVERT: F 1869 MET cc_start: 0.7339 (tmm) cc_final: 0.6770 (tmm) REVERT: F 2315 MET cc_start: -0.0413 (mtm) cc_final: -0.2625 (ttt) REVERT: F 2458 MET cc_start: 0.5061 (ptt) cc_final: 0.4629 (ptt) outliers start: 61 outliers final: 36 residues processed: 285 average time/residue: 0.4688 time to fit residues: 239.7202 Evaluate side-chains 278 residues out of total 6514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 234 time to evaluate : 4.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1429 ASP Chi-restraints excluded: chain A residue 1562 LEU Chi-restraints excluded: chain A residue 1649 TYR Chi-restraints excluded: chain A residue 1697 MET Chi-restraints excluded: chain A residue 1733 TYR Chi-restraints excluded: chain A residue 1754 VAL Chi-restraints excluded: chain A residue 1763 LEU Chi-restraints excluded: chain A residue 2020 ILE Chi-restraints excluded: chain A residue 2115 LEU Chi-restraints excluded: chain A residue 2303 LEU Chi-restraints excluded: chain A residue 2321 THR Chi-restraints excluded: chain A residue 2492 CYS Chi-restraints excluded: chain C residue 1418 VAL Chi-restraints excluded: chain C residue 1485 TYR Chi-restraints excluded: chain C residue 1560 ASN Chi-restraints excluded: chain C residue 1562 LEU Chi-restraints excluded: chain C residue 1649 TYR Chi-restraints excluded: chain C residue 1733 TYR Chi-restraints excluded: chain C residue 1763 LEU Chi-restraints excluded: chain C residue 2020 ILE Chi-restraints excluded: chain C residue 2321 THR Chi-restraints excluded: chain C residue 2393 LEU Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 704 MET Chi-restraints excluded: chain E residue 985 THR Chi-restraints excluded: chain E residue 1054 LEU Chi-restraints excluded: chain E residue 1598 VAL Chi-restraints excluded: chain E residue 1712 LEU Chi-restraints excluded: chain E residue 1765 ILE Chi-restraints excluded: chain E residue 1893 VAL Chi-restraints excluded: chain E residue 2067 LEU Chi-restraints excluded: chain E residue 2089 GLN Chi-restraints excluded: chain E residue 2161 ASN Chi-restraints excluded: chain F residue 704 MET Chi-restraints excluded: chain F residue 985 THR Chi-restraints excluded: chain F residue 1054 LEU Chi-restraints excluded: chain F residue 1719 MET Chi-restraints excluded: chain F residue 1733 TYR Chi-restraints excluded: chain F residue 1765 ILE Chi-restraints excluded: chain F residue 1893 VAL Chi-restraints excluded: chain F residue 1947 MET Chi-restraints excluded: chain F residue 2067 LEU Chi-restraints excluded: chain F residue 2161 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 722 random chunks: chunk 430 optimal weight: 0.3980 chunk 277 optimal weight: 30.0000 chunk 415 optimal weight: 0.7980 chunk 209 optimal weight: 5.9990 chunk 136 optimal weight: 9.9990 chunk 134 optimal weight: 5.9990 chunk 442 optimal weight: 7.9990 chunk 474 optimal weight: 20.0000 chunk 344 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 546 optimal weight: 5.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2476 ASN ** C1560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2333 GLN C2476 ASN ** E 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 721 ASN ** E1021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1911 HIS ** F 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 625 HIS ** F 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 721 ASN ** F1021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 54734 Z= 0.331 Angle : 0.598 9.883 74597 Z= 0.302 Chirality : 0.043 0.260 9044 Planarity : 0.004 0.051 9406 Dihedral : 6.035 73.918 7802 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.01 % Allowed : 6.83 % Favored : 93.15 % Rotamer: Outliers : 1.38 % Allowed : 15.07 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.80 (0.10), residues: 7169 helix: 0.82 (0.10), residues: 2674 sheet: -0.99 (0.15), residues: 1224 loop : -1.47 (0.11), residues: 3271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F1734 HIS 0.007 0.001 HIS A1783 PHE 0.027 0.002 PHE F1148 TYR 0.026 0.002 TYR D 27 ARG 0.005 0.000 ARG A1847 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14338 Ramachandran restraints generated. 7169 Oldfield, 0 Emsley, 7169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14338 Ramachandran restraints generated. 7169 Oldfield, 0 Emsley, 7169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 6514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 235 time to evaluate : 4.736 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2115 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.8964 (mp) REVERT: A 2321 THR cc_start: 0.9261 (OUTLIER) cc_final: 0.8993 (m) REVERT: C 1338 MET cc_start: 0.8484 (mmt) cc_final: 0.8009 (mmt) REVERT: C 1763 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8829 (tt) REVERT: C 2115 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.8963 (mp) REVERT: C 2301 MET cc_start: 0.7778 (pmm) cc_final: 0.7551 (pmm) REVERT: C 2321 THR cc_start: 0.9243 (OUTLIER) cc_final: 0.8987 (m) REVERT: E 1175 MET cc_start: 0.4922 (tmm) cc_final: 0.4641 (tpp) REVERT: E 1335 MET cc_start: 0.6666 (mmm) cc_final: 0.6464 (ttm) REVERT: E 1431 MET cc_start: 0.7287 (mmp) cc_final: 0.6979 (tpp) REVERT: E 1765 ILE cc_start: 0.8997 (OUTLIER) cc_final: 0.8519 (mt) REVERT: E 2089 GLN cc_start: 0.5058 (OUTLIER) cc_final: 0.4795 (pt0) REVERT: E 2315 MET cc_start: -0.0185 (mtm) cc_final: -0.2637 (ttt) REVERT: E 2499 ASN cc_start: 0.8370 (m-40) cc_final: 0.7932 (p0) REVERT: F 100 MET cc_start: 0.3355 (mmp) cc_final: 0.2475 (mpp) REVERT: F 1175 MET cc_start: 0.4416 (tmm) cc_final: 0.3804 (tpp) REVERT: F 1431 MET cc_start: 0.7196 (mmp) cc_final: 0.6807 (tpp) REVERT: F 1765 ILE cc_start: 0.8944 (OUTLIER) cc_final: 0.8510 (mt) REVERT: F 2315 MET cc_start: -0.0475 (mtm) cc_final: -0.2882 (ttt) REVERT: F 2458 MET cc_start: 0.5484 (ptt) cc_final: 0.5018 (ptt) outliers start: 74 outliers final: 47 residues processed: 295 average time/residue: 0.4748 time to fit residues: 251.9632 Evaluate side-chains 286 residues out of total 6514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 231 time to evaluate : 4.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1429 ASP Chi-restraints excluded: chain A residue 1519 VAL Chi-restraints excluded: chain A residue 1549 ASP Chi-restraints excluded: chain A residue 1562 LEU Chi-restraints excluded: chain A residue 1649 TYR Chi-restraints excluded: chain A residue 1697 MET Chi-restraints excluded: chain A residue 1733 TYR Chi-restraints excluded: chain A residue 1754 VAL Chi-restraints excluded: chain A residue 2020 ILE Chi-restraints excluded: chain A residue 2115 LEU Chi-restraints excluded: chain A residue 2138 VAL Chi-restraints excluded: chain A residue 2303 LEU Chi-restraints excluded: chain A residue 2321 THR Chi-restraints excluded: chain C residue 1368 THR Chi-restraints excluded: chain C residue 1418 VAL Chi-restraints excluded: chain C residue 1429 ASP Chi-restraints excluded: chain C residue 1519 VAL Chi-restraints excluded: chain C residue 1549 ASP Chi-restraints excluded: chain C residue 1562 LEU Chi-restraints excluded: chain C residue 1649 TYR Chi-restraints excluded: chain C residue 1716 SER Chi-restraints excluded: chain C residue 1733 TYR Chi-restraints excluded: chain C residue 1763 LEU Chi-restraints excluded: chain C residue 2020 ILE Chi-restraints excluded: chain C residue 2115 LEU Chi-restraints excluded: chain C residue 2138 VAL Chi-restraints excluded: chain C residue 2303 LEU Chi-restraints excluded: chain C residue 2321 THR Chi-restraints excluded: chain C residue 2393 LEU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 704 MET Chi-restraints excluded: chain E residue 985 THR Chi-restraints excluded: chain E residue 1054 LEU Chi-restraints excluded: chain E residue 1194 ASN Chi-restraints excluded: chain E residue 1452 THR Chi-restraints excluded: chain E residue 1598 VAL Chi-restraints excluded: chain E residue 1712 LEU Chi-restraints excluded: chain E residue 1733 TYR Chi-restraints excluded: chain E residue 1765 ILE Chi-restraints excluded: chain E residue 1893 VAL Chi-restraints excluded: chain E residue 1947 MET Chi-restraints excluded: chain E residue 2089 GLN Chi-restraints excluded: chain E residue 2161 ASN Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 704 MET Chi-restraints excluded: chain F residue 985 THR Chi-restraints excluded: chain F residue 1054 LEU Chi-restraints excluded: chain F residue 1719 MET Chi-restraints excluded: chain F residue 1733 TYR Chi-restraints excluded: chain F residue 1765 ILE Chi-restraints excluded: chain F residue 1893 VAL Chi-restraints excluded: chain F residue 1947 MET Chi-restraints excluded: chain F residue 2161 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 722 random chunks: chunk 633 optimal weight: 3.9990 chunk 666 optimal weight: 7.9990 chunk 608 optimal weight: 7.9990 chunk 648 optimal weight: 6.9990 chunk 390 optimal weight: 9.9990 chunk 282 optimal weight: 40.0000 chunk 509 optimal weight: 7.9990 chunk 199 optimal weight: 1.9990 chunk 585 optimal weight: 7.9990 chunk 613 optimal weight: 8.9990 chunk 646 optimal weight: 0.8980 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1437 ASN A1684 HIS ** A1730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2053 GLN C1560 ASN C2053 GLN ** E 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1779 GLN ** E1999 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1741 ASN ** F1999 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.3908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 54734 Z= 0.464 Angle : 0.705 13.453 74597 Z= 0.357 Chirality : 0.046 0.269 9044 Planarity : 0.005 0.053 9406 Dihedral : 6.573 79.527 7802 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.01 % Allowed : 7.95 % Favored : 92.04 % Rotamer: Outliers : 1.43 % Allowed : 15.11 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.20 (0.10), residues: 7169 helix: 0.46 (0.10), residues: 2658 sheet: -1.16 (0.16), residues: 1202 loop : -1.68 (0.11), residues: 3309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C2376 HIS 0.009 0.001 HIS C1783 PHE 0.023 0.002 PHE A2083 TYR 0.026 0.002 TYR F1695 ARG 0.011 0.001 ARG F1957 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14338 Ramachandran restraints generated. 7169 Oldfield, 0 Emsley, 7169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14338 Ramachandran restraints generated. 7169 Oldfield, 0 Emsley, 7169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 6514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 234 time to evaluate : 4.733 Fit side-chains REVERT: A 2115 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.8979 (mp) REVERT: A 2301 MET cc_start: 0.7815 (pmm) cc_final: 0.7194 (pmm) REVERT: A 2321 THR cc_start: 0.9376 (OUTLIER) cc_final: 0.9109 (m) REVERT: C 1338 MET cc_start: 0.8461 (mmt) cc_final: 0.7942 (mmt) REVERT: C 2115 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.8982 (mp) REVERT: C 2321 THR cc_start: 0.9364 (OUTLIER) cc_final: 0.9091 (m) REVERT: E 100 MET cc_start: 0.4326 (mmm) cc_final: 0.3803 (mmp) REVERT: E 1175 MET cc_start: 0.5196 (tmm) cc_final: 0.4867 (tmm) REVERT: E 1335 MET cc_start: 0.6863 (mmm) cc_final: 0.6404 (ttt) REVERT: E 1431 MET cc_start: 0.7354 (mmp) cc_final: 0.7055 (tpp) REVERT: E 1702 MET cc_start: 0.8408 (tpp) cc_final: 0.8062 (tpp) REVERT: E 1765 ILE cc_start: 0.9006 (OUTLIER) cc_final: 0.8560 (mt) REVERT: E 2089 GLN cc_start: 0.5002 (OUTLIER) cc_final: 0.4478 (pt0) REVERT: E 2315 MET cc_start: 0.0193 (mtm) cc_final: -0.2425 (ttt) REVERT: E 2459 MET cc_start: 0.7386 (pmm) cc_final: 0.6670 (pmm) REVERT: F 1175 MET cc_start: 0.4591 (tmm) cc_final: 0.4270 (mmm) REVERT: F 1431 MET cc_start: 0.7239 (mmp) cc_final: 0.6882 (tpp) REVERT: F 1765 ILE cc_start: 0.9046 (OUTLIER) cc_final: 0.8580 (mt) REVERT: F 2301 MET cc_start: 0.3895 (ptp) cc_final: 0.3321 (pmm) REVERT: F 2315 MET cc_start: -0.0294 (mtm) cc_final: -0.2767 (ttt) REVERT: F 2458 MET cc_start: 0.5637 (ptt) cc_final: 0.4754 (ptt) outliers start: 77 outliers final: 59 residues processed: 292 average time/residue: 0.4843 time to fit residues: 254.0439 Evaluate side-chains 297 residues out of total 6514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 231 time to evaluate : 4.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1368 THR Chi-restraints excluded: chain A residue 1429 ASP Chi-restraints excluded: chain A residue 1431 MET Chi-restraints excluded: chain A residue 1519 VAL Chi-restraints excluded: chain A residue 1549 ASP Chi-restraints excluded: chain A residue 1562 LEU Chi-restraints excluded: chain A residue 1610 ILE Chi-restraints excluded: chain A residue 1649 TYR Chi-restraints excluded: chain A residue 1697 MET Chi-restraints excluded: chain A residue 1733 TYR Chi-restraints excluded: chain A residue 2020 ILE Chi-restraints excluded: chain A residue 2053 GLN Chi-restraints excluded: chain A residue 2115 LEU Chi-restraints excluded: chain A residue 2138 VAL Chi-restraints excluded: chain A residue 2303 LEU Chi-restraints excluded: chain A residue 2321 THR Chi-restraints excluded: chain C residue 1368 THR Chi-restraints excluded: chain C residue 1418 VAL Chi-restraints excluded: chain C residue 1429 ASP Chi-restraints excluded: chain C residue 1519 VAL Chi-restraints excluded: chain C residue 1549 ASP Chi-restraints excluded: chain C residue 1560 ASN Chi-restraints excluded: chain C residue 1562 LEU Chi-restraints excluded: chain C residue 1610 ILE Chi-restraints excluded: chain C residue 1649 TYR Chi-restraints excluded: chain C residue 1716 SER Chi-restraints excluded: chain C residue 1733 TYR Chi-restraints excluded: chain C residue 1754 VAL Chi-restraints excluded: chain C residue 2020 ILE Chi-restraints excluded: chain C residue 2053 GLN Chi-restraints excluded: chain C residue 2115 LEU Chi-restraints excluded: chain C residue 2138 VAL Chi-restraints excluded: chain C residue 2224 LEU Chi-restraints excluded: chain C residue 2303 LEU Chi-restraints excluded: chain C residue 2321 THR Chi-restraints excluded: chain C residue 2393 LEU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 704 MET Chi-restraints excluded: chain E residue 810 ILE Chi-restraints excluded: chain E residue 985 THR Chi-restraints excluded: chain E residue 1054 LEU Chi-restraints excluded: chain E residue 1194 ASN Chi-restraints excluded: chain E residue 1452 THR Chi-restraints excluded: chain E residue 1598 VAL Chi-restraints excluded: chain E residue 1712 LEU Chi-restraints excluded: chain E residue 1733 TYR Chi-restraints excluded: chain E residue 1765 ILE Chi-restraints excluded: chain E residue 1893 VAL Chi-restraints excluded: chain E residue 1947 MET Chi-restraints excluded: chain E residue 2089 GLN Chi-restraints excluded: chain E residue 2161 ASN Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 704 MET Chi-restraints excluded: chain F residue 810 ILE Chi-restraints excluded: chain F residue 985 THR Chi-restraints excluded: chain F residue 1054 LEU Chi-restraints excluded: chain F residue 1194 ASN Chi-restraints excluded: chain F residue 1719 MET Chi-restraints excluded: chain F residue 1733 TYR Chi-restraints excluded: chain F residue 1765 ILE Chi-restraints excluded: chain F residue 1893 VAL Chi-restraints excluded: chain F residue 1947 MET Chi-restraints excluded: chain F residue 2161 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 722 random chunks: chunk 425 optimal weight: 7.9990 chunk 685 optimal weight: 7.9990 chunk 418 optimal weight: 3.9990 chunk 325 optimal weight: 0.7980 chunk 476 optimal weight: 4.9990 chunk 719 optimal weight: 3.9990 chunk 662 optimal weight: 10.0000 chunk 572 optimal weight: 0.3980 chunk 59 optimal weight: 1.9990 chunk 442 optimal weight: 8.9990 chunk 351 optimal weight: 0.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2053 GLN C1560 ASN C2053 GLN B 25 GLN ** E 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 721 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1999 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1999 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 54734 Z= 0.215 Angle : 0.580 20.122 74597 Z= 0.289 Chirality : 0.042 0.253 9044 Planarity : 0.004 0.051 9406 Dihedral : 6.200 72.745 7802 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.01 % Allowed : 6.32 % Favored : 93.67 % Rotamer: Outliers : 1.19 % Allowed : 15.26 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.92 (0.10), residues: 7169 helix: 0.72 (0.10), residues: 2671 sheet: -1.08 (0.16), residues: 1201 loop : -1.54 (0.11), residues: 3297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C1811 HIS 0.005 0.001 HIS A1453 PHE 0.017 0.001 PHE F1650 TYR 0.025 0.001 TYR C1645 ARG 0.005 0.000 ARG A1847 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14338 Ramachandran restraints generated. 7169 Oldfield, 0 Emsley, 7169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14338 Ramachandran restraints generated. 7169 Oldfield, 0 Emsley, 7169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 6514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 228 time to evaluate : 4.755 Fit side-chains REVERT: A 1763 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8804 (tt) REVERT: A 2115 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.8950 (mp) REVERT: A 2301 MET cc_start: 0.7765 (pmm) cc_final: 0.7129 (pmm) REVERT: A 2321 THR cc_start: 0.9277 (OUTLIER) cc_final: 0.9032 (m) REVERT: C 1338 MET cc_start: 0.8446 (mmt) cc_final: 0.7954 (mmt) REVERT: C 1646 MET cc_start: 0.8063 (ttp) cc_final: 0.7806 (tmm) REVERT: C 2115 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.8965 (mp) REVERT: C 2321 THR cc_start: 0.9271 (OUTLIER) cc_final: 0.9026 (m) REVERT: E 72 MET cc_start: 0.6841 (pmm) cc_final: 0.6583 (mmt) REVERT: E 100 MET cc_start: 0.3842 (mmm) cc_final: 0.3320 (mmp) REVERT: E 1175 MET cc_start: 0.5138 (tmm) cc_final: 0.4730 (tpp) REVERT: E 1335 MET cc_start: 0.6700 (mmm) cc_final: 0.6237 (ttt) REVERT: E 1431 MET cc_start: 0.7242 (mmp) cc_final: 0.6907 (tpp) REVERT: E 1702 MET cc_start: 0.8388 (tpp) cc_final: 0.8108 (tpp) REVERT: E 1765 ILE cc_start: 0.8918 (OUTLIER) cc_final: 0.8627 (mt) REVERT: E 2089 GLN cc_start: 0.4768 (OUTLIER) cc_final: 0.4374 (pt0) REVERT: E 2315 MET cc_start: -0.0031 (mtm) cc_final: -0.2539 (ttt) REVERT: E 2459 MET cc_start: 0.7289 (pmm) cc_final: 0.6551 (pmm) REVERT: F 1175 MET cc_start: 0.4557 (tmm) cc_final: 0.4052 (mmm) REVERT: F 1431 MET cc_start: 0.7156 (mmp) cc_final: 0.6784 (tpp) REVERT: F 1697 MET cc_start: 0.8064 (ppp) cc_final: 0.7220 (ptt) REVERT: F 1765 ILE cc_start: 0.8891 (OUTLIER) cc_final: 0.8527 (mt) REVERT: F 2301 MET cc_start: 0.3940 (ptp) cc_final: 0.3470 (pmm) REVERT: F 2315 MET cc_start: -0.0789 (mtm) cc_final: -0.2943 (ttt) REVERT: F 2458 MET cc_start: 0.5373 (ptt) cc_final: 0.4414 (ptt) outliers start: 64 outliers final: 52 residues processed: 279 average time/residue: 0.4771 time to fit residues: 241.1334 Evaluate side-chains 286 residues out of total 6514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 226 time to evaluate : 4.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1429 ASP Chi-restraints excluded: chain A residue 1549 ASP Chi-restraints excluded: chain A residue 1562 LEU Chi-restraints excluded: chain A residue 1610 ILE Chi-restraints excluded: chain A residue 1649 TYR Chi-restraints excluded: chain A residue 1697 MET Chi-restraints excluded: chain A residue 1733 TYR Chi-restraints excluded: chain A residue 1754 VAL Chi-restraints excluded: chain A residue 1763 LEU Chi-restraints excluded: chain A residue 2020 ILE Chi-restraints excluded: chain A residue 2053 GLN Chi-restraints excluded: chain A residue 2115 LEU Chi-restraints excluded: chain A residue 2303 LEU Chi-restraints excluded: chain A residue 2321 THR Chi-restraints excluded: chain C residue 1418 VAL Chi-restraints excluded: chain C residue 1429 ASP Chi-restraints excluded: chain C residue 1549 ASP Chi-restraints excluded: chain C residue 1560 ASN Chi-restraints excluded: chain C residue 1562 LEU Chi-restraints excluded: chain C residue 1610 ILE Chi-restraints excluded: chain C residue 1649 TYR Chi-restraints excluded: chain C residue 1733 TYR Chi-restraints excluded: chain C residue 1754 VAL Chi-restraints excluded: chain C residue 2020 ILE Chi-restraints excluded: chain C residue 2053 GLN Chi-restraints excluded: chain C residue 2115 LEU Chi-restraints excluded: chain C residue 2224 LEU Chi-restraints excluded: chain C residue 2303 LEU Chi-restraints excluded: chain C residue 2321 THR Chi-restraints excluded: chain C residue 2393 LEU Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 704 MET Chi-restraints excluded: chain E residue 985 THR Chi-restraints excluded: chain E residue 1054 LEU Chi-restraints excluded: chain E residue 1131 LEU Chi-restraints excluded: chain E residue 1194 ASN Chi-restraints excluded: chain E residue 1598 VAL Chi-restraints excluded: chain E residue 1712 LEU Chi-restraints excluded: chain E residue 1733 TYR Chi-restraints excluded: chain E residue 1765 ILE Chi-restraints excluded: chain E residue 1893 VAL Chi-restraints excluded: chain E residue 1947 MET Chi-restraints excluded: chain E residue 2089 GLN Chi-restraints excluded: chain E residue 2161 ASN Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 704 MET Chi-restraints excluded: chain F residue 810 ILE Chi-restraints excluded: chain F residue 985 THR Chi-restraints excluded: chain F residue 1054 LEU Chi-restraints excluded: chain F residue 1131 LEU Chi-restraints excluded: chain F residue 1194 ASN Chi-restraints excluded: chain F residue 1719 MET Chi-restraints excluded: chain F residue 1733 TYR Chi-restraints excluded: chain F residue 1765 ILE Chi-restraints excluded: chain F residue 1893 VAL Chi-restraints excluded: chain F residue 1947 MET Chi-restraints excluded: chain F residue 2017 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 722 random chunks: chunk 454 optimal weight: 9.9990 chunk 610 optimal weight: 9.9990 chunk 175 optimal weight: 0.6980 chunk 528 optimal weight: 0.0470 chunk 84 optimal weight: 3.9990 chunk 159 optimal weight: 1.9990 chunk 573 optimal weight: 2.9990 chunk 240 optimal weight: 50.0000 chunk 589 optimal weight: 8.9990 chunk 72 optimal weight: 0.0970 chunk 105 optimal weight: 6.9990 overall best weight: 1.1680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2053 GLN ** C1560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2053 GLN ** E 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1999 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1999 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.097196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.065836 restraints weight = 211746.983| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 4.55 r_work: 0.3135 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 54734 Z= 0.177 Angle : 0.554 15.682 74597 Z= 0.276 Chirality : 0.041 0.254 9044 Planarity : 0.004 0.055 9406 Dihedral : 5.975 69.373 7802 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.01 % Allowed : 6.49 % Favored : 93.50 % Rotamer: Outliers : 1.21 % Allowed : 15.43 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.75 (0.10), residues: 7169 helix: 0.85 (0.10), residues: 2683 sheet: -1.00 (0.16), residues: 1199 loop : -1.44 (0.11), residues: 3287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F1734 HIS 0.005 0.001 HIS F 543 PHE 0.017 0.001 PHE E1650 TYR 0.017 0.001 TYR A1645 ARG 0.005 0.000 ARG A1847 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8641.75 seconds wall clock time: 154 minutes 54.85 seconds (9294.85 seconds total)