Starting phenix.real_space_refine on Wed Feb 21 00:47:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s6x_10108/02_2024/6s6x_10108_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s6x_10108/02_2024/6s6x_10108.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s6x_10108/02_2024/6s6x_10108.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s6x_10108/02_2024/6s6x_10108.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s6x_10108/02_2024/6s6x_10108_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s6x_10108/02_2024/6s6x_10108_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.020 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: 6 Type Number sf(0) Gaussians Fe 66 7.16 5 P 18 5.49 5 S 534 5.16 5 C 56418 2.51 5 N 16254 2.21 5 O 17052 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 19": "OE1" <-> "OE2" Residue "A GLU 23": "OE1" <-> "OE2" Residue "A GLU 127": "OE1" <-> "OE2" Residue "A ARG 154": "NH1" <-> "NH2" Residue "A GLU 198": "OE1" <-> "OE2" Residue "A GLU 233": "OE1" <-> "OE2" Residue "A GLU 516": "OE1" <-> "OE2" Residue "A ARG 556": "NH1" <-> "NH2" Residue "A GLU 673": "OE1" <-> "OE2" Residue "A GLU 677": "OE1" <-> "OE2" Residue "A GLU 760": "OE1" <-> "OE2" Residue "A GLU 769": "OE1" <-> "OE2" Residue "A ARG 782": "NH1" <-> "NH2" Residue "A GLU 842": "OE1" <-> "OE2" Residue "A ARG 893": "NH1" <-> "NH2" Residue "A GLU 1148": "OE1" <-> "OE2" Residue "A ARG 1156": "NH1" <-> "NH2" Residue "A ARG 1173": "NH1" <-> "NH2" Residue "A GLU 1176": "OE1" <-> "OE2" Residue "A ARG 1186": "NH1" <-> "NH2" Residue "A GLU 1194": "OE1" <-> "OE2" Residue "A ARG 1214": "NH1" <-> "NH2" Residue "A GLU 1224": "OE1" <-> "OE2" Residue "A ARG 1252": "NH1" <-> "NH2" Residue "A GLU 1316": "OE1" <-> "OE2" Residue "A ARG 1345": "NH1" <-> "NH2" Residue "A ARG 1449": "NH1" <-> "NH2" Residue "A GLU 1461": "OE1" <-> "OE2" Residue "A ARG 1465": "NH1" <-> "NH2" Residue "B GLU 23": "OE1" <-> "OE2" Residue "B GLU 127": "OE1" <-> "OE2" Residue "B ASP 147": "OD1" <-> "OD2" Residue "B ARG 154": "NH1" <-> "NH2" Residue "B GLU 162": "OE1" <-> "OE2" Residue "B GLU 198": "OE1" <-> "OE2" Residue "B GLU 233": "OE1" <-> "OE2" Residue "B GLU 474": "OE1" <-> "OE2" Residue "B GLU 516": "OE1" <-> "OE2" Residue "B GLU 554": "OE1" <-> "OE2" Residue "B ARG 556": "NH1" <-> "NH2" Residue "B GLU 673": "OE1" <-> "OE2" Residue "B GLU 677": "OE1" <-> "OE2" Residue "B GLU 726": "OE1" <-> "OE2" Residue "B ARG 782": "NH1" <-> "NH2" Residue "B GLU 842": "OE1" <-> "OE2" Residue "B GLU 844": "OE1" <-> "OE2" Residue "B ARG 893": "NH1" <-> "NH2" Residue "B GLU 929": "OE1" <-> "OE2" Residue "B ARG 1156": "NH1" <-> "NH2" Residue "B ARG 1173": "NH1" <-> "NH2" Residue "B ARG 1186": "NH1" <-> "NH2" Residue "B GLU 1194": "OE1" <-> "OE2" Residue "B ARG 1214": "NH1" <-> "NH2" Residue "B GLU 1224": "OE1" <-> "OE2" Residue "B ARG 1252": "NH1" <-> "NH2" Residue "B GLU 1316": "OE1" <-> "OE2" Residue "B ARG 1345": "NH1" <-> "NH2" Residue "B GLU 1408": "OE1" <-> "OE2" Residue "B GLU 1434": "OE1" <-> "OE2" Residue "B ARG 1449": "NH1" <-> "NH2" Residue "B ARG 1465": "NH1" <-> "NH2" Residue "C GLU 19": "OE1" <-> "OE2" Residue "C GLU 23": "OE1" <-> "OE2" Residue "C GLU 119": "OE1" <-> "OE2" Residue "C GLU 127": "OE1" <-> "OE2" Residue "C ARG 154": "NH1" <-> "NH2" Residue "C GLU 162": "OE1" <-> "OE2" Residue "C GLU 198": "OE1" <-> "OE2" Residue "C GLU 252": "OE1" <-> "OE2" Residue "C GLU 438": "OE1" <-> "OE2" Residue "C GLU 470": "OE1" <-> "OE2" Residue "C GLU 554": "OE1" <-> "OE2" Residue "C ARG 556": "NH1" <-> "NH2" Residue "C ASP 564": "OD1" <-> "OD2" Residue "C GLU 673": "OE1" <-> "OE2" Residue "C GLU 677": "OE1" <-> "OE2" Residue "C ARG 782": "NH1" <-> "NH2" Residue "C GLU 842": "OE1" <-> "OE2" Residue "C GLU 844": "OE1" <-> "OE2" Residue "C ARG 893": "NH1" <-> "NH2" Residue "C GLU 929": "OE1" <-> "OE2" Residue "C ARG 1156": "NH1" <-> "NH2" Residue "C ARG 1173": "NH1" <-> "NH2" Residue "C ARG 1186": "NH1" <-> "NH2" Residue "C ARG 1214": "NH1" <-> "NH2" Residue "C GLU 1224": "OE1" <-> "OE2" Residue "C ARG 1252": "NH1" <-> "NH2" Residue "C GLU 1316": "OE1" <-> "OE2" Residue "C ARG 1345": "NH1" <-> "NH2" Residue "C GLU 1408": "OE1" <-> "OE2" Residue "C ARG 1449": "NH1" <-> "NH2" Residue "C GLU 1461": "OE1" <-> "OE2" Residue "C ARG 1465": "NH1" <-> "NH2" Residue "D GLU 19": "OE1" <-> "OE2" Residue "D GLU 23": "OE1" <-> "OE2" Residue "D GLU 127": "OE1" <-> "OE2" Residue "D ARG 154": "NH1" <-> "NH2" Residue "D GLU 198": "OE1" <-> "OE2" Residue "D GLU 233": "OE1" <-> "OE2" Residue "D GLU 516": "OE1" <-> "OE2" Residue "D ARG 556": "NH1" <-> "NH2" Residue "D GLU 673": "OE1" <-> "OE2" Residue "D GLU 677": "OE1" <-> "OE2" Residue "D GLU 760": "OE1" <-> "OE2" Residue "D GLU 769": "OE1" <-> "OE2" Residue "D ARG 782": "NH1" <-> "NH2" Residue "D GLU 842": "OE1" <-> "OE2" Residue "D ARG 893": "NH1" <-> "NH2" Residue "D GLU 1148": "OE1" <-> "OE2" Residue "D ARG 1156": "NH1" <-> "NH2" Residue "D ARG 1173": "NH1" <-> "NH2" Residue "D GLU 1176": "OE1" <-> "OE2" Residue "D ARG 1186": "NH1" <-> "NH2" Residue "D GLU 1194": "OE1" <-> "OE2" Residue "D ARG 1214": "NH1" <-> "NH2" Residue "D GLU 1224": "OE1" <-> "OE2" Residue "D ARG 1252": "NH1" <-> "NH2" Residue "D GLU 1316": "OE1" <-> "OE2" Residue "D ARG 1345": "NH1" <-> "NH2" Residue "D ARG 1449": "NH1" <-> "NH2" Residue "D GLU 1461": "OE1" <-> "OE2" Residue "D ARG 1465": "NH1" <-> "NH2" Residue "E GLU 23": "OE1" <-> "OE2" Residue "E GLU 127": "OE1" <-> "OE2" Residue "E ASP 147": "OD1" <-> "OD2" Residue "E ARG 154": "NH1" <-> "NH2" Residue "E GLU 162": "OE1" <-> "OE2" Residue "E GLU 198": "OE1" <-> "OE2" Residue "E GLU 233": "OE1" <-> "OE2" Residue "E GLU 474": "OE1" <-> "OE2" Residue "E GLU 516": "OE1" <-> "OE2" Residue "E GLU 554": "OE1" <-> "OE2" Residue "E ARG 556": "NH1" <-> "NH2" Residue "E GLU 673": "OE1" <-> "OE2" Residue "E GLU 677": "OE1" <-> "OE2" Residue "E GLU 726": "OE1" <-> "OE2" Residue "E ARG 782": "NH1" <-> "NH2" Residue "E GLU 842": "OE1" <-> "OE2" Residue "E GLU 844": "OE1" <-> "OE2" Residue "E ARG 893": "NH1" <-> "NH2" Residue "E GLU 929": "OE1" <-> "OE2" Residue "E ARG 1156": "NH1" <-> "NH2" Residue "E ARG 1173": "NH1" <-> "NH2" Residue "E ARG 1186": "NH1" <-> "NH2" Residue "E GLU 1194": "OE1" <-> "OE2" Residue "E ARG 1214": "NH1" <-> "NH2" Residue "E GLU 1224": "OE1" <-> "OE2" Residue "E ARG 1252": "NH1" <-> "NH2" Residue "E GLU 1316": "OE1" <-> "OE2" Residue "E ARG 1345": "NH1" <-> "NH2" Residue "E GLU 1408": "OE1" <-> "OE2" Residue "E GLU 1434": "OE1" <-> "OE2" Residue "E ARG 1449": "NH1" <-> "NH2" Residue "E ARG 1465": "NH1" <-> "NH2" Residue "F GLU 19": "OE1" <-> "OE2" Residue "F GLU 23": "OE1" <-> "OE2" Residue "F GLU 119": "OE1" <-> "OE2" Residue "F GLU 127": "OE1" <-> "OE2" Residue "F ARG 154": "NH1" <-> "NH2" Residue "F GLU 162": "OE1" <-> "OE2" Residue "F GLU 198": "OE1" <-> "OE2" Residue "F GLU 252": "OE1" <-> "OE2" Residue "F GLU 438": "OE1" <-> "OE2" Residue "F GLU 470": "OE1" <-> "OE2" Residue "F GLU 554": "OE1" <-> "OE2" Residue "F ARG 556": "NH1" <-> "NH2" Residue "F ASP 564": "OD1" <-> "OD2" Residue "F GLU 673": "OE1" <-> "OE2" Residue "F GLU 677": "OE1" <-> "OE2" Residue "F ARG 782": "NH1" <-> "NH2" Residue "F GLU 842": "OE1" <-> "OE2" Residue "F GLU 844": "OE1" <-> "OE2" Residue "F ARG 893": "NH1" <-> "NH2" Residue "F GLU 929": "OE1" <-> "OE2" Residue "F ARG 1156": "NH1" <-> "NH2" Residue "F ARG 1173": "NH1" <-> "NH2" Residue "F ARG 1186": "NH1" <-> "NH2" Residue "F ARG 1214": "NH1" <-> "NH2" Residue "F GLU 1224": "OE1" <-> "OE2" Residue "F ARG 1252": "NH1" <-> "NH2" Residue "F GLU 1316": "OE1" <-> "OE2" Residue "F ARG 1345": "NH1" <-> "NH2" Residue "F GLU 1408": "OE1" <-> "OE2" Residue "F ARG 1449": "NH1" <-> "NH2" Residue "F GLU 1461": "OE1" <-> "OE2" Residue "F ARG 1465": "NH1" <-> "NH2" Residue "G ARG 5": "NH1" <-> "NH2" Residue "G ARG 47": "NH1" <-> "NH2" Residue "G ARG 77": "NH1" <-> "NH2" Residue "G GLU 80": "OE1" <-> "OE2" Residue "G GLU 83": "OE1" <-> "OE2" Residue "G ARG 103": "NH1" <-> "NH2" Residue "G GLU 165": "OE1" <-> "OE2" Residue "G ARG 179": "NH1" <-> "NH2" Residue "G ARG 204": "NH1" <-> "NH2" Residue "G ARG 223": "NH1" <-> "NH2" Residue "G ARG 232": "NH1" <-> "NH2" Residue "G ARG 247": "NH1" <-> "NH2" Residue "G GLU 282": "OE1" <-> "OE2" Residue "G ARG 311": "NH1" <-> "NH2" Residue "G ARG 325": "NH1" <-> "NH2" Residue "G ARG 333": "NH1" <-> "NH2" Residue "G GLU 344": "OE1" <-> "OE2" Residue "G ARG 364": "NH1" <-> "NH2" Residue "G ARG 367": "NH1" <-> "NH2" Residue "G GLU 385": "OE1" <-> "OE2" Residue "G GLU 413": "OE1" <-> "OE2" Residue "G ARG 420": "NH1" <-> "NH2" Residue "G ARG 429": "NH1" <-> "NH2" Residue "G GLU 463": "OE1" <-> "OE2" Residue "H ARG 5": "NH1" <-> "NH2" Residue "H ARG 47": "NH1" <-> "NH2" Residue "H ARG 77": "NH1" <-> "NH2" Residue "H GLU 80": "OE1" <-> "OE2" Residue "H GLU 83": "OE1" <-> "OE2" Residue "H ARG 103": "NH1" <-> "NH2" Residue "H ARG 179": "NH1" <-> "NH2" Residue "H ARG 204": "NH1" <-> "NH2" Residue "H ARG 223": "NH1" <-> "NH2" Residue "H ARG 232": "NH1" <-> "NH2" Residue "H ARG 247": "NH1" <-> "NH2" Residue "H GLU 282": "OE1" <-> "OE2" Residue "H ARG 311": "NH1" <-> "NH2" Residue "H ARG 325": "NH1" <-> "NH2" Residue "H ARG 333": "NH1" <-> "NH2" Residue "H ARG 364": "NH1" <-> "NH2" Residue "H ARG 367": "NH1" <-> "NH2" Residue "H ARG 420": "NH1" <-> "NH2" Residue "H ARG 429": "NH1" <-> "NH2" Residue "I ARG 5": "NH1" <-> "NH2" Residue "I ARG 47": "NH1" <-> "NH2" Residue "I ARG 77": "NH1" <-> "NH2" Residue "I GLU 80": "OE1" <-> "OE2" Residue "I GLU 83": "OE1" <-> "OE2" Residue "I ARG 103": "NH1" <-> "NH2" Residue "I ARG 179": "NH1" <-> "NH2" Residue "I ARG 204": "NH1" <-> "NH2" Residue "I ARG 223": "NH1" <-> "NH2" Residue "I ARG 232": "NH1" <-> "NH2" Residue "I ARG 247": "NH1" <-> "NH2" Residue "I GLU 282": "OE1" <-> "OE2" Residue "I ARG 311": "NH1" <-> "NH2" Residue "I ARG 325": "NH1" <-> "NH2" Residue "I ARG 333": "NH1" <-> "NH2" Residue "I GLU 334": "OE1" <-> "OE2" Residue "I ARG 364": "NH1" <-> "NH2" Residue "I ARG 367": "NH1" <-> "NH2" Residue "I ARG 420": "NH1" <-> "NH2" Residue "I ARG 429": "NH1" <-> "NH2" Residue "J ARG 5": "NH1" <-> "NH2" Residue "J ARG 47": "NH1" <-> "NH2" Residue "J ARG 77": "NH1" <-> "NH2" Residue "J GLU 80": "OE1" <-> "OE2" Residue "J GLU 83": "OE1" <-> "OE2" Residue "J ARG 103": "NH1" <-> "NH2" Residue "J GLU 165": "OE1" <-> "OE2" Residue "J ARG 179": "NH1" <-> "NH2" Residue "J ARG 204": "NH1" <-> "NH2" Residue "J ARG 223": "NH1" <-> "NH2" Residue "J ARG 232": "NH1" <-> "NH2" Residue "J ARG 247": "NH1" <-> "NH2" Residue "J GLU 282": "OE1" <-> "OE2" Residue "J ARG 311": "NH1" <-> "NH2" Residue "J ARG 325": "NH1" <-> "NH2" Residue "J ARG 333": "NH1" <-> "NH2" Residue "J GLU 344": "OE1" <-> "OE2" Residue "J ARG 364": "NH1" <-> "NH2" Residue "J ARG 367": "NH1" <-> "NH2" Residue "J GLU 385": "OE1" <-> "OE2" Residue "J GLU 413": "OE1" <-> "OE2" Residue "J ARG 420": "NH1" <-> "NH2" Residue "J ARG 429": "NH1" <-> "NH2" Residue "J GLU 463": "OE1" <-> "OE2" Residue "K ARG 5": "NH1" <-> "NH2" Residue "K ARG 47": "NH1" <-> "NH2" Residue "K ARG 77": "NH1" <-> "NH2" Residue "K GLU 80": "OE1" <-> "OE2" Residue "K GLU 83": "OE1" <-> "OE2" Residue "K ARG 103": "NH1" <-> "NH2" Residue "K ARG 179": "NH1" <-> "NH2" Residue "K ARG 204": "NH1" <-> "NH2" Residue "K ARG 223": "NH1" <-> "NH2" Residue "K ARG 232": "NH1" <-> "NH2" Residue "K ARG 247": "NH1" <-> "NH2" Residue "K GLU 282": "OE1" <-> "OE2" Residue "K ARG 311": "NH1" <-> "NH2" Residue "K ARG 325": "NH1" <-> "NH2" Residue "K ARG 333": "NH1" <-> "NH2" Residue "K ARG 364": "NH1" <-> "NH2" Residue "K ARG 367": "NH1" <-> "NH2" Residue "K ARG 420": "NH1" <-> "NH2" Residue "K ARG 429": "NH1" <-> "NH2" Residue "L ARG 5": "NH1" <-> "NH2" Residue "L ARG 47": "NH1" <-> "NH2" Residue "L ARG 77": "NH1" <-> "NH2" Residue "L GLU 80": "OE1" <-> "OE2" Residue "L GLU 83": "OE1" <-> "OE2" Residue "L ARG 103": "NH1" <-> "NH2" Residue "L ARG 179": "NH1" <-> "NH2" Residue "L ARG 204": "NH1" <-> "NH2" Residue "L ARG 223": "NH1" <-> "NH2" Residue "L ARG 232": "NH1" <-> "NH2" Residue "L ARG 247": "NH1" <-> "NH2" Residue "L GLU 282": "OE1" <-> "OE2" Residue "L ARG 311": "NH1" <-> "NH2" Residue "L ARG 325": "NH1" <-> "NH2" Residue "L ARG 333": "NH1" <-> "NH2" Residue "L ARG 364": "NH1" <-> "NH2" Residue "L ARG 367": "NH1" <-> "NH2" Residue "L ARG 420": "NH1" <-> "NH2" Residue "L ARG 429": "NH1" <-> "NH2" Time to flip residues: 0.20s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 90342 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 11337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1472, 11337 Classifications: {'peptide': 1472} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1409} Chain: "B" Number of atoms: 11337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1472, 11337 Classifications: {'peptide': 1472} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1409} Chain: "C" Number of atoms: 11337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1472, 11337 Classifications: {'peptide': 1472} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1409} Chain: "D" Number of atoms: 11337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1472, 11337 Classifications: {'peptide': 1472} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1409} Chain: "E" Number of atoms: 11337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1472, 11337 Classifications: {'peptide': 1472} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1409} Chain: "F" Number of atoms: 11337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1472, 11337 Classifications: {'peptide': 1472} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1409} Chain: "G" Number of atoms: 3613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3613 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 20, 'TRANS': 451} Chain: "H" Number of atoms: 3613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3613 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 20, 'TRANS': 451} Chain: "I" Number of atoms: 3613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3613 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 20, 'TRANS': 451} Chain: "J" Number of atoms: 3613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3613 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 20, 'TRANS': 451} Chain: "K" Number of atoms: 3613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3613 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 20, 'TRANS': 451} Chain: "L" Number of atoms: 3613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3613 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 20, 'TRANS': 451} Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {'F3S': 1, 'FMN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {'F3S': 1, 'FMN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {'F3S': 1, 'FMN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {'F3S': 1, 'FMN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {'F3S': 1, 'FMN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {'F3S': 1, 'FMN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 69 Unusual residues: {'FAD': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 69 Unusual residues: {'FAD': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 69 Unusual residues: {'FAD': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 69 Unusual residues: {'FAD': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 69 Unusual residues: {'FAD': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 69 Unusual residues: {'FAD': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 8585 SG CYS A1113 65.064 146.067 60.709 1.00 36.27 S ATOM 8499 SG CYS A1102 68.385 140.568 61.135 1.00 32.94 S ATOM 8548 SG CYS A1108 70.598 145.919 58.233 1.00 37.19 S ATOM 19922 SG CYS B1113 60.839 138.950 140.318 1.00 78.78 S ATOM 19836 SG CYS B1102 66.172 135.657 141.944 1.00 75.44 S ATOM 19885 SG CYS B1108 61.662 133.152 138.183 1.00 73.48 S ATOM 31259 SG CYS C1113 109.451 199.775 99.706 1.00 51.30 S ATOM 31173 SG CYS C1102 114.441 196.154 97.637 1.00 46.52 S ATOM 31222 SG CYS C1108 113.434 197.704 103.844 1.00 53.12 S ATOM 42596 SG CYS D1113 177.413 107.750 60.663 1.00 36.22 S ATOM 42510 SG CYS D1102 174.088 113.248 61.078 1.00 32.91 S ATOM 42559 SG CYS D1108 171.883 107.892 58.178 1.00 37.81 S ATOM 53933 SG CYS E1113 132.882 53.925 99.568 1.00 49.82 S ATOM 53847 SG CYS E1102 127.883 57.603 97.718 1.00 45.61 S ATOM 53896 SG CYS E1108 128.791 55.944 103.816 1.00 50.96 S ATOM 65270 SG CYS F1113 181.614 115.023 140.397 1.00 78.45 S ATOM 65184 SG CYS F1102 176.217 118.186 142.174 1.00 75.19 S ATOM 65233 SG CYS F1108 180.733 120.670 138.251 1.00 73.55 S ATOM 68418 SG CYS G 51 60.840 140.363 52.527 1.00 34.96 S ATOM 68453 SG CYS G 56 57.035 137.420 49.809 1.00 36.56 S ATOM 68397 SG CYS G 48 57.299 143.311 48.563 1.00 41.84 S ATOM 68868 SG CYS G 109 54.650 141.027 53.921 1.00 38.90 S ATOM 68841 SG CYS G 105 49.134 134.523 50.234 1.00 45.21 S ATOM 68485 SG CYS G 60 52.044 130.627 46.912 1.00 38.65 S ATOM 68792 SG CYS G 99 45.850 130.598 48.806 1.00 54.34 S ATOM 72031 SG CYS H 51 58.399 134.820 149.967 1.00 88.53 S ATOM 72066 SG CYS H 56 57.284 134.733 156.050 1.00 93.34 S ATOM 72010 SG CYS H 48 52.717 135.298 152.017 1.00 96.12 S ATOM 72481 SG CYS H 109 56.614 140.388 153.010 1.00100.96 S ATOM 72454 SG CYS H 105 56.509 139.972 162.646 1.00111.12 S ATOM 72098 SG CYS H 60 58.287 134.844 164.733 1.00102.26 S ATOM 72405 SG CYS H 99 56.992 140.266 167.725 1.00129.21 S ATOM 75644 SG CYS I 51 116.790 207.373 96.694 1.00 53.12 S ATOM 75679 SG CYS I 56 119.264 211.378 93.087 1.00 51.75 S ATOM 75623 SG CYS I 48 115.785 213.029 97.692 1.00 58.53 S ATOM 76094 SG CYS I 109 112.919 210.504 92.384 1.00 56.91 S ATOM 76067 SG CYS I 105 117.569 215.753 86.024 1.00 64.12 S ATOM 75711 SG CYS I 60 123.408 215.294 86.364 1.00 54.95 S ATOM 76018 SG CYS I 99 119.895 218.089 81.913 1.00 74.60 S ATOM 79257 SG CYS J 51 181.475 113.703 52.430 1.00 35.03 S ATOM 79292 SG CYS J 56 185.298 116.641 49.732 1.00 36.41 S ATOM 79236 SG CYS J 48 185.036 110.749 48.489 1.00 41.99 S ATOM 79707 SG CYS J 109 187.656 113.035 53.860 1.00 37.14 S ATOM 79680 SG CYS J 105 193.199 119.532 50.202 1.00 44.09 S ATOM 79324 SG CYS J 60 190.311 123.428 46.860 1.00 38.86 S ATOM 79631 SG CYS J 99 196.494 123.453 48.790 1.00 52.75 S ATOM 82870 SG CYS K 51 125.688 46.532 96.711 1.00 52.53 S ATOM 82905 SG CYS K 56 123.157 42.306 92.971 1.00 52.25 S ATOM 82849 SG CYS K 48 126.723 40.636 97.655 1.00 58.24 S ATOM 83320 SG CYS K 109 129.515 43.289 92.434 1.00 57.15 S ATOM 83293 SG CYS K 105 124.814 37.997 85.882 1.00 63.37 S ATOM 82937 SG CYS K 60 119.031 38.452 86.298 1.00 55.16 S ATOM 83244 SG CYS K 99 122.623 35.652 81.906 1.00 73.91 S ATOM 86483 SG CYS L 51 184.175 118.949 150.126 1.00 89.89 S ATOM 86518 SG CYS L 56 185.170 119.078 155.972 1.00 95.24 S ATOM 86462 SG CYS L 48 189.673 118.578 152.033 1.00 96.31 S ATOM 86933 SG CYS L 109 185.904 113.346 153.122 1.00102.92 S ATOM 86906 SG CYS L 105 186.053 113.833 162.575 1.00111.49 S ATOM 86550 SG CYS L 60 184.175 118.956 164.730 1.00103.20 S ATOM 86857 SG CYS L 99 185.454 113.583 167.804 1.00129.36 S Time building chain proxies: 34.39, per 1000 atoms: 0.38 Number of scatterers: 90342 At special positions: 0 Unit cell: (242.42, 255.254, 211.048, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 66 26.01 S 534 16.00 P 18 15.00 O 17052 8.00 N 16254 7.00 C 56418 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: 25.33 Conformation dependent library (CDL) restraints added in 12.1 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" F3S A1502 " pdb="FE4 F3S A1502 " - pdb=" SG CYS A1108 " pdb="FE1 F3S A1502 " - pdb=" SG CYS A1113 " pdb="FE3 F3S A1502 " - pdb=" SG CYS A1102 " pdb=" F3S B1502 " pdb="FE4 F3S B1502 " - pdb=" SG CYS B1108 " pdb="FE1 F3S B1502 " - pdb=" SG CYS B1113 " pdb="FE3 F3S B1502 " - pdb=" SG CYS B1102 " pdb=" F3S C1502 " pdb="FE4 F3S C1502 " - pdb=" SG CYS C1108 " pdb="FE1 F3S C1502 " - pdb=" SG CYS C1113 " pdb="FE3 F3S C1502 " - pdb=" SG CYS C1102 " pdb=" F3S D1502 " pdb="FE4 F3S D1502 " - pdb=" SG CYS D1108 " pdb="FE1 F3S D1502 " - pdb=" SG CYS D1113 " pdb="FE3 F3S D1502 " - pdb=" SG CYS D1102 " pdb=" F3S E1502 " pdb="FE4 F3S E1502 " - pdb=" SG CYS E1108 " pdb="FE1 F3S E1502 " - pdb=" SG CYS E1113 " pdb="FE3 F3S E1502 " - pdb=" SG CYS E1102 " pdb=" F3S F1502 " pdb="FE4 F3S F1502 " - pdb=" SG CYS F1108 " pdb="FE1 F3S F1502 " - pdb=" SG CYS F1113 " pdb="FE3 F3S F1502 " - pdb=" SG CYS F1102 " pdb=" SF4 G 501 " pdb="FE4 SF4 G 501 " - pdb=" SG CYS G 109 " pdb="FE2 SF4 G 501 " - pdb=" SG CYS G 56 " pdb="FE3 SF4 G 501 " - pdb=" SG CYS G 48 " pdb="FE1 SF4 G 501 " - pdb=" SG CYS G 51 " pdb=" SF4 G 502 " pdb="FE1 SF4 G 502 " - pdb=" SG CYS G 105 " pdb="FE2 SF4 G 502 " - pdb=" SG CYS G 60 " pdb="FE4 SF4 G 502 " - pdb=" SG CYS G 99 " pdb=" SF4 H 501 " pdb="FE2 SF4 H 501 " - pdb=" SG CYS H 56 " pdb="FE4 SF4 H 501 " - pdb=" SG CYS H 109 " pdb="FE3 SF4 H 501 " - pdb=" SG CYS H 48 " pdb="FE1 SF4 H 501 " - pdb=" SG CYS H 51 " pdb=" SF4 H 502 " pdb="FE1 SF4 H 502 " - pdb=" SG CYS H 105 " pdb="FE2 SF4 H 502 " - pdb=" SG CYS H 60 " pdb="FE4 SF4 H 502 " - pdb=" SG CYS H 99 " pdb=" SF4 I 501 " pdb="FE2 SF4 I 501 " - pdb=" SG CYS I 56 " pdb="FE3 SF4 I 501 " - pdb=" SG CYS I 48 " pdb="FE4 SF4 I 501 " - pdb=" SG CYS I 109 " pdb="FE1 SF4 I 501 " - pdb=" SG CYS I 51 " pdb=" SF4 I 502 " pdb="FE1 SF4 I 502 " - pdb=" SG CYS I 105 " pdb="FE2 SF4 I 502 " - pdb=" SG CYS I 60 " pdb="FE4 SF4 I 502 " - pdb=" SG CYS I 99 " pdb=" SF4 J 501 " pdb="FE4 SF4 J 501 " - pdb=" SG CYS J 109 " pdb="FE2 SF4 J 501 " - pdb=" SG CYS J 56 " pdb="FE3 SF4 J 501 " - pdb=" SG CYS J 48 " pdb="FE1 SF4 J 501 " - pdb=" SG CYS J 51 " pdb=" SF4 J 502 " pdb="FE1 SF4 J 502 " - pdb=" SG CYS J 105 " pdb="FE2 SF4 J 502 " - pdb=" SG CYS J 60 " pdb="FE4 SF4 J 502 " - pdb=" SG CYS J 99 " pdb=" SF4 K 501 " pdb="FE2 SF4 K 501 " - pdb=" SG CYS K 56 " pdb="FE4 SF4 K 501 " - pdb=" SG CYS K 109 " pdb="FE3 SF4 K 501 " - pdb=" SG CYS K 48 " pdb="FE1 SF4 K 501 " - pdb=" SG CYS K 51 " pdb=" SF4 K 502 " pdb="FE1 SF4 K 502 " - pdb=" SG CYS K 105 " pdb="FE2 SF4 K 502 " - pdb=" SG CYS K 60 " pdb="FE4 SF4 K 502 " - pdb=" SG CYS K 99 " pdb=" SF4 L 501 " pdb="FE2 SF4 L 501 " - pdb=" SG CYS L 56 " pdb="FE3 SF4 L 501 " - pdb=" SG CYS L 48 " pdb="FE4 SF4 L 501 " - pdb=" SG CYS L 109 " pdb="FE1 SF4 L 501 " - pdb=" SG CYS L 51 " pdb=" SF4 L 502 " pdb="FE1 SF4 L 502 " - pdb=" SG CYS L 105 " pdb="FE2 SF4 L 502 " - pdb=" SG CYS L 60 " pdb="FE4 SF4 L 502 " - pdb=" SG CYS L 99 " Number of angles added : 180 23280 Ramachandran restraints generated. 11640 Oldfield, 0 Emsley, 11640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 21036 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 462 helices and 82 sheets defined 35.1% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 20.83 Creating SS restraints... Processing helix chain 'A' and resid 15 through 27 removed outlier: 3.887A pdb=" N ALA A 27 " --> pdb=" O GLU A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 85 through 97 Processing helix chain 'A' and resid 141 through 161 Processing helix chain 'A' and resid 188 through 191 No H-bonds generated for 'chain 'A' and resid 188 through 191' Processing helix chain 'A' and resid 193 through 196 Processing helix chain 'A' and resid 219 through 221 No H-bonds generated for 'chain 'A' and resid 219 through 221' Processing helix chain 'A' and resid 240 through 250 removed outlier: 3.651A pdb=" N ALA A 246 " --> pdb=" O ASN A 242 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N THR A 249 " --> pdb=" O LYS A 245 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ARG A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 263 Processing helix chain 'A' and resid 273 through 287 removed outlier: 3.639A pdb=" N ASP A 278 " --> pdb=" O SER A 274 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ALA A 287 " --> pdb=" O VAL A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 298 Processing helix chain 'A' and resid 311 through 323 Processing helix chain 'A' and resid 403 through 412 removed outlier: 4.148A pdb=" N THR A 412 " --> pdb=" O ASP A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.981A pdb=" N GLN A 421 " --> pdb=" O ASP A 417 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N ASN A 422 " --> pdb=" O LYS A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 432 Processing helix chain 'A' and resid 444 through 452 Processing helix chain 'A' and resid 459 through 462 No H-bonds generated for 'chain 'A' and resid 459 through 462' Processing helix chain 'A' and resid 466 through 470 Processing helix chain 'A' and resid 495 through 497 No H-bonds generated for 'chain 'A' and resid 495 through 497' Processing helix chain 'A' and resid 517 through 519 No H-bonds generated for 'chain 'A' and resid 517 through 519' Processing helix chain 'A' and resid 537 through 540 Processing helix chain 'A' and resid 552 through 562 Processing helix chain 'A' and resid 581 through 597 removed outlier: 3.872A pdb=" N GLU A 594 " --> pdb=" O ARG A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 633 Processing helix chain 'A' and resid 652 through 661 Processing helix chain 'A' and resid 669 through 680 Processing helix chain 'A' and resid 689 through 710 Processing helix chain 'A' and resid 732 through 738 Processing helix chain 'A' and resid 752 through 767 Processing helix chain 'A' and resid 792 through 804 Processing helix chain 'A' and resid 807 through 818 Processing helix chain 'A' and resid 825 through 827 No H-bonds generated for 'chain 'A' and resid 825 through 827' Processing helix chain 'A' and resid 840 through 842 No H-bonds generated for 'chain 'A' and resid 840 through 842' Processing helix chain 'A' and resid 846 through 852 removed outlier: 4.623A pdb=" N ARG A 852 " --> pdb=" O ALA A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 878 removed outlier: 3.564A pdb=" N ARG A 877 " --> pdb=" O VAL A 873 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ILE A 878 " --> pdb=" O ALA A 874 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 893 No H-bonds generated for 'chain 'A' and resid 891 through 893' Processing helix chain 'A' and resid 951 through 957 Processing helix chain 'A' and resid 977 through 990 Processing helix chain 'A' and resid 1006 through 1016 removed outlier: 3.674A pdb=" N LYS A1015 " --> pdb=" O ALA A1011 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA A1016 " --> pdb=" O GLY A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1035 through 1039 Processing helix chain 'A' and resid 1045 through 1058 removed outlier: 3.583A pdb=" N SER A1050 " --> pdb=" O GLU A1046 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN A1054 " --> pdb=" O SER A1050 " (cutoff:3.500A) Processing helix chain 'A' and resid 1062 through 1064 No H-bonds generated for 'chain 'A' and resid 1062 through 1064' Processing helix chain 'A' and resid 1076 through 1085 Processing helix chain 'A' and resid 1093 through 1100 Processing helix chain 'A' and resid 1122 through 1127 removed outlier: 4.515A pdb=" N LYS A1127 " --> pdb=" O LYS A1123 " (cutoff:3.500A) Processing helix chain 'A' and resid 1132 through 1153 Processing helix chain 'A' and resid 1158 through 1160 No H-bonds generated for 'chain 'A' and resid 1158 through 1160' Processing helix chain 'A' and resid 1165 through 1167 No H-bonds generated for 'chain 'A' and resid 1165 through 1167' Processing helix chain 'A' and resid 1183 through 1187 Processing helix chain 'A' and resid 1211 through 1218 Processing helix chain 'A' and resid 1220 through 1224 Processing helix chain 'A' and resid 1245 through 1253 Processing helix chain 'A' and resid 1317 through 1319 No H-bonds generated for 'chain 'A' and resid 1317 through 1319' Processing helix chain 'A' and resid 1401 through 1404 No H-bonds generated for 'chain 'A' and resid 1401 through 1404' Processing helix chain 'A' and resid 1418 through 1435 removed outlier: 3.585A pdb=" N GLN A1423 " --> pdb=" O HIS A1419 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A1424 " --> pdb=" O TYR A1420 " (cutoff:3.500A) Processing helix chain 'A' and resid 1439 through 1445 Processing helix chain 'A' and resid 1447 through 1453 removed outlier: 4.848A pdb=" N THR A1452 " --> pdb=" O ALA A1448 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N LYS A1453 " --> pdb=" O ARG A1449 " (cutoff:3.500A) Processing helix chain 'A' and resid 1461 through 1463 No H-bonds generated for 'chain 'A' and resid 1461 through 1463' Processing helix chain 'B' and resid 15 through 27 removed outlier: 3.844A pdb=" N ALA B 27 " --> pdb=" O GLU B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 62 Processing helix chain 'B' and resid 84 through 97 Processing helix chain 'B' and resid 141 through 161 Processing helix chain 'B' and resid 188 through 191 No H-bonds generated for 'chain 'B' and resid 188 through 191' Processing helix chain 'B' and resid 193 through 196 Processing helix chain 'B' and resid 219 through 221 No H-bonds generated for 'chain 'B' and resid 219 through 221' Processing helix chain 'B' and resid 240 through 249 removed outlier: 3.547A pdb=" N ALA B 246 " --> pdb=" O ASN B 242 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N THR B 249 " --> pdb=" O LYS B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 263 Processing helix chain 'B' and resid 273 through 287 removed outlier: 3.549A pdb=" N ASP B 278 " --> pdb=" O SER B 274 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA B 287 " --> pdb=" O VAL B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 298 Processing helix chain 'B' and resid 311 through 323 Processing helix chain 'B' and resid 376 through 378 No H-bonds generated for 'chain 'B' and resid 376 through 378' Processing helix chain 'B' and resid 403 through 410 Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.711A pdb=" N GLN B 421 " --> pdb=" O ASP B 417 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N ASN B 422 " --> pdb=" O LYS B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 432 Processing helix chain 'B' and resid 444 through 454 removed outlier: 3.777A pdb=" N PHE B 454 " --> pdb=" O ARG B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 462 removed outlier: 4.001A pdb=" N GLU B 462 " --> pdb=" O GLU B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 471 Processing helix chain 'B' and resid 495 through 497 No H-bonds generated for 'chain 'B' and resid 495 through 497' Processing helix chain 'B' and resid 537 through 540 Processing helix chain 'B' and resid 552 through 565 removed outlier: 5.774A pdb=" N ASP B 564 " --> pdb=" O ASP B 560 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N THR B 565 " --> pdb=" O TYR B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 599 removed outlier: 3.796A pdb=" N GLU B 594 " --> pdb=" O ARG B 590 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY B 599 " --> pdb=" O ASP B 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 633 Processing helix chain 'B' and resid 652 through 661 removed outlier: 3.626A pdb=" N ALA B 656 " --> pdb=" O THR B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 680 Processing helix chain 'B' and resid 689 through 710 Processing helix chain 'B' and resid 732 through 738 Processing helix chain 'B' and resid 751 through 766 Processing helix chain 'B' and resid 792 through 804 Processing helix chain 'B' and resid 807 through 819 removed outlier: 3.749A pdb=" N LYS B 819 " --> pdb=" O GLU B 815 " (cutoff:3.500A) Processing helix chain 'B' and resid 825 through 827 No H-bonds generated for 'chain 'B' and resid 825 through 827' Processing helix chain 'B' and resid 840 through 842 No H-bonds generated for 'chain 'B' and resid 840 through 842' Processing helix chain 'B' and resid 846 through 852 removed outlier: 4.518A pdb=" N ARG B 852 " --> pdb=" O ALA B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 865 through 877 Processing helix chain 'B' and resid 891 through 893 No H-bonds generated for 'chain 'B' and resid 891 through 893' Processing helix chain 'B' and resid 919 through 922 No H-bonds generated for 'chain 'B' and resid 919 through 922' Processing helix chain 'B' and resid 951 through 957 Processing helix chain 'B' and resid 977 through 990 Processing helix chain 'B' and resid 1006 through 1016 removed outlier: 3.776A pdb=" N LYS B1015 " --> pdb=" O ALA B1011 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA B1016 " --> pdb=" O GLY B1012 " (cutoff:3.500A) Processing helix chain 'B' and resid 1035 through 1039 Processing helix chain 'B' and resid 1045 through 1058 removed outlier: 3.724A pdb=" N SER B1050 " --> pdb=" O GLU B1046 " (cutoff:3.500A) Processing helix chain 'B' and resid 1062 through 1064 No H-bonds generated for 'chain 'B' and resid 1062 through 1064' Processing helix chain 'B' and resid 1076 through 1085 Processing helix chain 'B' and resid 1093 through 1100 Processing helix chain 'B' and resid 1125 through 1127 No H-bonds generated for 'chain 'B' and resid 1125 through 1127' Processing helix chain 'B' and resid 1132 through 1153 Processing helix chain 'B' and resid 1158 through 1160 No H-bonds generated for 'chain 'B' and resid 1158 through 1160' Processing helix chain 'B' and resid 1165 through 1167 No H-bonds generated for 'chain 'B' and resid 1165 through 1167' Processing helix chain 'B' and resid 1184 through 1187 No H-bonds generated for 'chain 'B' and resid 1184 through 1187' Processing helix chain 'B' and resid 1211 through 1218 Processing helix chain 'B' and resid 1220 through 1224 Processing helix chain 'B' and resid 1245 through 1253 Processing helix chain 'B' and resid 1418 through 1435 removed outlier: 3.588A pdb=" N GLN B1423 " --> pdb=" O HIS B1419 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU B1424 " --> pdb=" O TYR B1420 " (cutoff:3.500A) Processing helix chain 'B' and resid 1439 through 1445 Processing helix chain 'B' and resid 1451 through 1453 No H-bonds generated for 'chain 'B' and resid 1451 through 1453' Processing helix chain 'C' and resid 15 through 27 removed outlier: 3.748A pdb=" N ALA C 27 " --> pdb=" O GLU C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 62 Processing helix chain 'C' and resid 84 through 97 Processing helix chain 'C' and resid 141 through 162 removed outlier: 3.768A pdb=" N GLU C 162 " --> pdb=" O ALA C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 191 No H-bonds generated for 'chain 'C' and resid 188 through 191' Processing helix chain 'C' and resid 193 through 196 Processing helix chain 'C' and resid 219 through 221 No H-bonds generated for 'chain 'C' and resid 219 through 221' Processing helix chain 'C' and resid 240 through 249 removed outlier: 3.500A pdb=" N ALA C 246 " --> pdb=" O ASN C 242 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N THR C 249 " --> pdb=" O LYS C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 263 Processing helix chain 'C' and resid 273 through 287 removed outlier: 3.558A pdb=" N ASP C 278 " --> pdb=" O SER C 274 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA C 287 " --> pdb=" O VAL C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 298 Processing helix chain 'C' and resid 311 through 323 Processing helix chain 'C' and resid 376 through 378 No H-bonds generated for 'chain 'C' and resid 376 through 378' Processing helix chain 'C' and resid 403 through 410 Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.723A pdb=" N GLN C 421 " --> pdb=" O ASP C 417 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ASN C 422 " --> pdb=" O LYS C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 432 Processing helix chain 'C' and resid 444 through 454 removed outlier: 3.814A pdb=" N PHE C 454 " --> pdb=" O ARG C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 462 removed outlier: 3.949A pdb=" N GLU C 462 " --> pdb=" O GLU C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 471 Processing helix chain 'C' and resid 495 through 497 No H-bonds generated for 'chain 'C' and resid 495 through 497' Processing helix chain 'C' and resid 517 through 519 No H-bonds generated for 'chain 'C' and resid 517 through 519' Processing helix chain 'C' and resid 537 through 540 Processing helix chain 'C' and resid 552 through 562 Processing helix chain 'C' and resid 581 through 599 removed outlier: 3.870A pdb=" N GLU C 594 " --> pdb=" O ARG C 590 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY C 599 " --> pdb=" O ASP C 595 " (cutoff:3.500A) Processing helix chain 'C' and resid 620 through 633 Processing helix chain 'C' and resid 652 through 661 removed outlier: 3.720A pdb=" N ALA C 656 " --> pdb=" O THR C 652 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 680 Processing helix chain 'C' and resid 689 through 710 Processing helix chain 'C' and resid 732 through 738 Processing helix chain 'C' and resid 751 through 767 Processing helix chain 'C' and resid 792 through 804 Processing helix chain 'C' and resid 807 through 819 removed outlier: 3.804A pdb=" N LYS C 819 " --> pdb=" O GLU C 815 " (cutoff:3.500A) Processing helix chain 'C' and resid 825 through 827 No H-bonds generated for 'chain 'C' and resid 825 through 827' Processing helix chain 'C' and resid 840 through 842 No H-bonds generated for 'chain 'C' and resid 840 through 842' Processing helix chain 'C' and resid 846 through 852 removed outlier: 4.296A pdb=" N ARG C 852 " --> pdb=" O ALA C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 865 through 877 Processing helix chain 'C' and resid 891 through 893 No H-bonds generated for 'chain 'C' and resid 891 through 893' Processing helix chain 'C' and resid 919 through 922 No H-bonds generated for 'chain 'C' and resid 919 through 922' Processing helix chain 'C' and resid 951 through 957 Processing helix chain 'C' and resid 977 through 990 Processing helix chain 'C' and resid 1006 through 1016 removed outlier: 3.759A pdb=" N LYS C1015 " --> pdb=" O ALA C1011 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA C1016 " --> pdb=" O GLY C1012 " (cutoff:3.500A) Processing helix chain 'C' and resid 1035 through 1039 Processing helix chain 'C' and resid 1045 through 1058 removed outlier: 3.708A pdb=" N SER C1050 " --> pdb=" O GLU C1046 " (cutoff:3.500A) Processing helix chain 'C' and resid 1062 through 1064 No H-bonds generated for 'chain 'C' and resid 1062 through 1064' Processing helix chain 'C' and resid 1076 through 1085 Processing helix chain 'C' and resid 1093 through 1100 Processing helix chain 'C' and resid 1108 through 1110 No H-bonds generated for 'chain 'C' and resid 1108 through 1110' Processing helix chain 'C' and resid 1125 through 1127 No H-bonds generated for 'chain 'C' and resid 1125 through 1127' Processing helix chain 'C' and resid 1132 through 1153 Processing helix chain 'C' and resid 1158 through 1160 No H-bonds generated for 'chain 'C' and resid 1158 through 1160' Processing helix chain 'C' and resid 1165 through 1167 No H-bonds generated for 'chain 'C' and resid 1165 through 1167' Processing helix chain 'C' and resid 1183 through 1187 Processing helix chain 'C' and resid 1211 through 1218 Processing helix chain 'C' and resid 1220 through 1224 Processing helix chain 'C' and resid 1245 through 1253 Processing helix chain 'C' and resid 1418 through 1435 removed outlier: 3.510A pdb=" N GLN C1423 " --> pdb=" O HIS C1419 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU C1424 " --> pdb=" O TYR C1420 " (cutoff:3.500A) Processing helix chain 'C' and resid 1439 through 1445 Processing helix chain 'C' and resid 1451 through 1453 No H-bonds generated for 'chain 'C' and resid 1451 through 1453' Processing helix chain 'D' and resid 15 through 27 removed outlier: 3.888A pdb=" N ALA D 27 " --> pdb=" O GLU D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 62 Processing helix chain 'D' and resid 85 through 97 Processing helix chain 'D' and resid 141 through 161 Processing helix chain 'D' and resid 188 through 191 No H-bonds generated for 'chain 'D' and resid 188 through 191' Processing helix chain 'D' and resid 193 through 196 Processing helix chain 'D' and resid 219 through 221 No H-bonds generated for 'chain 'D' and resid 219 through 221' Processing helix chain 'D' and resid 240 through 250 removed outlier: 3.651A pdb=" N ALA D 246 " --> pdb=" O ASN D 242 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N THR D 249 " --> pdb=" O LYS D 245 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ARG D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 263 Processing helix chain 'D' and resid 273 through 287 removed outlier: 3.640A pdb=" N ASP D 278 " --> pdb=" O SER D 274 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ALA D 287 " --> pdb=" O VAL D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 298 Processing helix chain 'D' and resid 311 through 323 Processing helix chain 'D' and resid 403 through 412 removed outlier: 4.148A pdb=" N THR D 412 " --> pdb=" O ASP D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 422 removed outlier: 3.981A pdb=" N GLN D 421 " --> pdb=" O ASP D 417 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ASN D 422 " --> pdb=" O LYS D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 427 through 432 Processing helix chain 'D' and resid 444 through 452 Processing helix chain 'D' and resid 459 through 462 No H-bonds generated for 'chain 'D' and resid 459 through 462' Processing helix chain 'D' and resid 466 through 470 Processing helix chain 'D' and resid 495 through 497 No H-bonds generated for 'chain 'D' and resid 495 through 497' Processing helix chain 'D' and resid 517 through 519 No H-bonds generated for 'chain 'D' and resid 517 through 519' Processing helix chain 'D' and resid 537 through 540 Processing helix chain 'D' and resid 552 through 562 Processing helix chain 'D' and resid 581 through 597 removed outlier: 3.872A pdb=" N GLU D 594 " --> pdb=" O ARG D 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 620 through 633 Processing helix chain 'D' and resid 652 through 661 Processing helix chain 'D' and resid 669 through 680 Processing helix chain 'D' and resid 689 through 710 Processing helix chain 'D' and resid 732 through 738 Processing helix chain 'D' and resid 752 through 767 Processing helix chain 'D' and resid 792 through 804 Processing helix chain 'D' and resid 807 through 818 Processing helix chain 'D' and resid 825 through 827 No H-bonds generated for 'chain 'D' and resid 825 through 827' Processing helix chain 'D' and resid 840 through 842 No H-bonds generated for 'chain 'D' and resid 840 through 842' Processing helix chain 'D' and resid 846 through 852 removed outlier: 4.623A pdb=" N ARG D 852 " --> pdb=" O ALA D 848 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 878 removed outlier: 3.565A pdb=" N ARG D 877 " --> pdb=" O VAL D 873 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ILE D 878 " --> pdb=" O ALA D 874 " (cutoff:3.500A) Processing helix chain 'D' and resid 891 through 893 No H-bonds generated for 'chain 'D' and resid 891 through 893' Processing helix chain 'D' and resid 951 through 957 Processing helix chain 'D' and resid 977 through 990 Processing helix chain 'D' and resid 1006 through 1016 removed outlier: 3.674A pdb=" N LYS D1015 " --> pdb=" O ALA D1011 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA D1016 " --> pdb=" O GLY D1012 " (cutoff:3.500A) Processing helix chain 'D' and resid 1035 through 1039 Processing helix chain 'D' and resid 1045 through 1058 removed outlier: 3.584A pdb=" N SER D1050 " --> pdb=" O GLU D1046 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN D1054 " --> pdb=" O SER D1050 " (cutoff:3.500A) Processing helix chain 'D' and resid 1062 through 1064 No H-bonds generated for 'chain 'D' and resid 1062 through 1064' Processing helix chain 'D' and resid 1076 through 1085 Processing helix chain 'D' and resid 1093 through 1100 Processing helix chain 'D' and resid 1122 through 1127 removed outlier: 4.515A pdb=" N LYS D1127 " --> pdb=" O LYS D1123 " (cutoff:3.500A) Processing helix chain 'D' and resid 1132 through 1153 Processing helix chain 'D' and resid 1158 through 1160 No H-bonds generated for 'chain 'D' and resid 1158 through 1160' Processing helix chain 'D' and resid 1165 through 1167 No H-bonds generated for 'chain 'D' and resid 1165 through 1167' Processing helix chain 'D' and resid 1183 through 1187 Processing helix chain 'D' and resid 1211 through 1218 Processing helix chain 'D' and resid 1220 through 1224 Processing helix chain 'D' and resid 1245 through 1253 Processing helix chain 'D' and resid 1317 through 1319 No H-bonds generated for 'chain 'D' and resid 1317 through 1319' Processing helix chain 'D' and resid 1401 through 1404 No H-bonds generated for 'chain 'D' and resid 1401 through 1404' Processing helix chain 'D' and resid 1418 through 1435 removed outlier: 3.585A pdb=" N GLN D1423 " --> pdb=" O HIS D1419 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU D1424 " --> pdb=" O TYR D1420 " (cutoff:3.500A) Processing helix chain 'D' and resid 1439 through 1445 Processing helix chain 'D' and resid 1447 through 1453 removed outlier: 4.848A pdb=" N THR D1452 " --> pdb=" O ALA D1448 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N LYS D1453 " --> pdb=" O ARG D1449 " (cutoff:3.500A) Processing helix chain 'D' and resid 1461 through 1463 No H-bonds generated for 'chain 'D' and resid 1461 through 1463' Processing helix chain 'E' and resid 15 through 27 removed outlier: 3.844A pdb=" N ALA E 27 " --> pdb=" O GLU E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 62 Processing helix chain 'E' and resid 84 through 97 Processing helix chain 'E' and resid 141 through 161 Processing helix chain 'E' and resid 188 through 191 No H-bonds generated for 'chain 'E' and resid 188 through 191' Processing helix chain 'E' and resid 193 through 196 Processing helix chain 'E' and resid 219 through 221 No H-bonds generated for 'chain 'E' and resid 219 through 221' Processing helix chain 'E' and resid 240 through 249 removed outlier: 3.547A pdb=" N ALA E 246 " --> pdb=" O ASN E 242 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N THR E 249 " --> pdb=" O LYS E 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 263 Processing helix chain 'E' and resid 273 through 287 removed outlier: 3.549A pdb=" N ASP E 278 " --> pdb=" O SER E 274 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA E 287 " --> pdb=" O VAL E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 298 Processing helix chain 'E' and resid 311 through 323 Processing helix chain 'E' and resid 376 through 378 No H-bonds generated for 'chain 'E' and resid 376 through 378' Processing helix chain 'E' and resid 403 through 410 Processing helix chain 'E' and resid 416 through 422 removed outlier: 3.710A pdb=" N GLN E 421 " --> pdb=" O ASP E 417 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N ASN E 422 " --> pdb=" O LYS E 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 427 through 432 Processing helix chain 'E' and resid 444 through 454 removed outlier: 3.777A pdb=" N PHE E 454 " --> pdb=" O ARG E 450 " (cutoff:3.500A) Processing helix chain 'E' and resid 458 through 462 removed outlier: 4.001A pdb=" N GLU E 462 " --> pdb=" O GLU E 459 " (cutoff:3.500A) Processing helix chain 'E' and resid 466 through 471 Processing helix chain 'E' and resid 495 through 497 No H-bonds generated for 'chain 'E' and resid 495 through 497' Processing helix chain 'E' and resid 537 through 540 Processing helix chain 'E' and resid 552 through 565 removed outlier: 5.774A pdb=" N ASP E 564 " --> pdb=" O ASP E 560 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N THR E 565 " --> pdb=" O TYR E 561 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 599 removed outlier: 3.796A pdb=" N GLU E 594 " --> pdb=" O ARG E 590 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY E 599 " --> pdb=" O ASP E 595 " (cutoff:3.500A) Processing helix chain 'E' and resid 620 through 633 Processing helix chain 'E' and resid 652 through 661 removed outlier: 3.626A pdb=" N ALA E 656 " --> pdb=" O THR E 652 " (cutoff:3.500A) Processing helix chain 'E' and resid 669 through 680 Processing helix chain 'E' and resid 689 through 710 Processing helix chain 'E' and resid 732 through 738 Processing helix chain 'E' and resid 751 through 766 Processing helix chain 'E' and resid 792 through 804 Processing helix chain 'E' and resid 807 through 819 removed outlier: 3.749A pdb=" N LYS E 819 " --> pdb=" O GLU E 815 " (cutoff:3.500A) Processing helix chain 'E' and resid 825 through 827 No H-bonds generated for 'chain 'E' and resid 825 through 827' Processing helix chain 'E' and resid 840 through 842 No H-bonds generated for 'chain 'E' and resid 840 through 842' Processing helix chain 'E' and resid 846 through 852 removed outlier: 4.518A pdb=" N ARG E 852 " --> pdb=" O ALA E 848 " (cutoff:3.500A) Processing helix chain 'E' and resid 865 through 877 Processing helix chain 'E' and resid 891 through 893 No H-bonds generated for 'chain 'E' and resid 891 through 893' Processing helix chain 'E' and resid 919 through 922 No H-bonds generated for 'chain 'E' and resid 919 through 922' Processing helix chain 'E' and resid 951 through 957 Processing helix chain 'E' and resid 977 through 990 Processing helix chain 'E' and resid 1006 through 1016 removed outlier: 3.776A pdb=" N LYS E1015 " --> pdb=" O ALA E1011 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA E1016 " --> pdb=" O GLY E1012 " (cutoff:3.500A) Processing helix chain 'E' and resid 1035 through 1039 Processing helix chain 'E' and resid 1045 through 1058 removed outlier: 3.725A pdb=" N SER E1050 " --> pdb=" O GLU E1046 " (cutoff:3.500A) Processing helix chain 'E' and resid 1062 through 1064 No H-bonds generated for 'chain 'E' and resid 1062 through 1064' Processing helix chain 'E' and resid 1076 through 1085 Processing helix chain 'E' and resid 1093 through 1100 Processing helix chain 'E' and resid 1125 through 1127 No H-bonds generated for 'chain 'E' and resid 1125 through 1127' Processing helix chain 'E' and resid 1132 through 1153 Processing helix chain 'E' and resid 1158 through 1160 No H-bonds generated for 'chain 'E' and resid 1158 through 1160' Processing helix chain 'E' and resid 1165 through 1167 No H-bonds generated for 'chain 'E' and resid 1165 through 1167' Processing helix chain 'E' and resid 1184 through 1187 No H-bonds generated for 'chain 'E' and resid 1184 through 1187' Processing helix chain 'E' and resid 1211 through 1218 Processing helix chain 'E' and resid 1220 through 1224 Processing helix chain 'E' and resid 1245 through 1253 Processing helix chain 'E' and resid 1418 through 1435 removed outlier: 3.587A pdb=" N GLN E1423 " --> pdb=" O HIS E1419 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU E1424 " --> pdb=" O TYR E1420 " (cutoff:3.500A) Processing helix chain 'E' and resid 1439 through 1445 Processing helix chain 'E' and resid 1451 through 1453 No H-bonds generated for 'chain 'E' and resid 1451 through 1453' Processing helix chain 'F' and resid 15 through 27 removed outlier: 3.746A pdb=" N ALA F 27 " --> pdb=" O GLU F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 62 Processing helix chain 'F' and resid 84 through 97 Processing helix chain 'F' and resid 141 through 162 removed outlier: 3.767A pdb=" N GLU F 162 " --> pdb=" O ALA F 158 " (cutoff:3.500A) Processing helix chain 'F' and resid 188 through 191 No H-bonds generated for 'chain 'F' and resid 188 through 191' Processing helix chain 'F' and resid 193 through 196 Processing helix chain 'F' and resid 219 through 221 No H-bonds generated for 'chain 'F' and resid 219 through 221' Processing helix chain 'F' and resid 240 through 249 removed outlier: 4.742A pdb=" N THR F 249 " --> pdb=" O LYS F 245 " (cutoff:3.500A) Processing helix chain 'F' and resid 257 through 263 Processing helix chain 'F' and resid 273 through 287 removed outlier: 3.559A pdb=" N ASP F 278 " --> pdb=" O SER F 274 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA F 287 " --> pdb=" O VAL F 283 " (cutoff:3.500A) Processing helix chain 'F' and resid 291 through 298 Processing helix chain 'F' and resid 311 through 323 Processing helix chain 'F' and resid 376 through 378 No H-bonds generated for 'chain 'F' and resid 376 through 378' Processing helix chain 'F' and resid 403 through 410 Processing helix chain 'F' and resid 416 through 422 removed outlier: 3.721A pdb=" N GLN F 421 " --> pdb=" O ASP F 417 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ASN F 422 " --> pdb=" O LYS F 418 " (cutoff:3.500A) Processing helix chain 'F' and resid 427 through 432 Processing helix chain 'F' and resid 444 through 454 removed outlier: 3.813A pdb=" N PHE F 454 " --> pdb=" O ARG F 450 " (cutoff:3.500A) Processing helix chain 'F' and resid 458 through 462 removed outlier: 3.949A pdb=" N GLU F 462 " --> pdb=" O GLU F 459 " (cutoff:3.500A) Processing helix chain 'F' and resid 466 through 471 Processing helix chain 'F' and resid 495 through 497 No H-bonds generated for 'chain 'F' and resid 495 through 497' Processing helix chain 'F' and resid 517 through 519 No H-bonds generated for 'chain 'F' and resid 517 through 519' Processing helix chain 'F' and resid 537 through 540 Processing helix chain 'F' and resid 552 through 562 Processing helix chain 'F' and resid 581 through 599 removed outlier: 3.870A pdb=" N GLU F 594 " --> pdb=" O ARG F 590 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY F 599 " --> pdb=" O ASP F 595 " (cutoff:3.500A) Processing helix chain 'F' and resid 620 through 633 Processing helix chain 'F' and resid 652 through 661 removed outlier: 3.722A pdb=" N ALA F 656 " --> pdb=" O THR F 652 " (cutoff:3.500A) Processing helix chain 'F' and resid 669 through 680 Processing helix chain 'F' and resid 689 through 710 Processing helix chain 'F' and resid 732 through 738 Processing helix chain 'F' and resid 751 through 767 Processing helix chain 'F' and resid 792 through 804 Processing helix chain 'F' and resid 807 through 819 removed outlier: 3.804A pdb=" N LYS F 819 " --> pdb=" O GLU F 815 " (cutoff:3.500A) Processing helix chain 'F' and resid 825 through 827 No H-bonds generated for 'chain 'F' and resid 825 through 827' Processing helix chain 'F' and resid 840 through 842 No H-bonds generated for 'chain 'F' and resid 840 through 842' Processing helix chain 'F' and resid 846 through 852 removed outlier: 4.295A pdb=" N ARG F 852 " --> pdb=" O ALA F 848 " (cutoff:3.500A) Processing helix chain 'F' and resid 865 through 877 Processing helix chain 'F' and resid 891 through 893 No H-bonds generated for 'chain 'F' and resid 891 through 893' Processing helix chain 'F' and resid 919 through 922 No H-bonds generated for 'chain 'F' and resid 919 through 922' Processing helix chain 'F' and resid 951 through 957 Processing helix chain 'F' and resid 977 through 990 Processing helix chain 'F' and resid 1006 through 1016 removed outlier: 3.758A pdb=" N LYS F1015 " --> pdb=" O ALA F1011 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA F1016 " --> pdb=" O GLY F1012 " (cutoff:3.500A) Processing helix chain 'F' and resid 1035 through 1039 Processing helix chain 'F' and resid 1045 through 1058 removed outlier: 3.708A pdb=" N SER F1050 " --> pdb=" O GLU F1046 " (cutoff:3.500A) Processing helix chain 'F' and resid 1062 through 1064 No H-bonds generated for 'chain 'F' and resid 1062 through 1064' Processing helix chain 'F' and resid 1076 through 1085 Processing helix chain 'F' and resid 1093 through 1100 Processing helix chain 'F' and resid 1108 through 1110 No H-bonds generated for 'chain 'F' and resid 1108 through 1110' Processing helix chain 'F' and resid 1125 through 1127 No H-bonds generated for 'chain 'F' and resid 1125 through 1127' Processing helix chain 'F' and resid 1132 through 1153 Processing helix chain 'F' and resid 1158 through 1160 No H-bonds generated for 'chain 'F' and resid 1158 through 1160' Processing helix chain 'F' and resid 1165 through 1167 No H-bonds generated for 'chain 'F' and resid 1165 through 1167' Processing helix chain 'F' and resid 1183 through 1187 Processing helix chain 'F' and resid 1211 through 1218 Processing helix chain 'F' and resid 1220 through 1224 Processing helix chain 'F' and resid 1245 through 1253 Processing helix chain 'F' and resid 1418 through 1435 removed outlier: 3.509A pdb=" N GLN F1423 " --> pdb=" O HIS F1419 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU F1424 " --> pdb=" O TYR F1420 " (cutoff:3.500A) Processing helix chain 'F' and resid 1439 through 1445 Processing helix chain 'F' and resid 1451 through 1453 No H-bonds generated for 'chain 'F' and resid 1451 through 1453' Processing helix chain 'G' and resid 22 through 25 No H-bonds generated for 'chain 'G' and resid 22 through 25' Processing helix chain 'G' and resid 38 through 46 removed outlier: 4.156A pdb=" N ASN G 46 " --> pdb=" O ASN G 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 58 No H-bonds generated for 'chain 'G' and resid 55 through 58' Processing helix chain 'G' and resid 66 through 73 Processing helix chain 'G' and resid 78 through 88 removed outlier: 4.314A pdb=" N THR G 88 " --> pdb=" O VAL G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 98 Processing helix chain 'G' and resid 110 through 113 No H-bonds generated for 'chain 'G' and resid 110 through 113' Processing helix chain 'G' and resid 121 through 130 Processing helix chain 'G' and resid 158 through 170 Processing helix chain 'G' and resid 185 through 189 removed outlier: 3.686A pdb=" N TYR G 189 " --> pdb=" O LEU G 186 " (cutoff:3.500A) Processing helix chain 'G' and resid 198 through 211 removed outlier: 3.786A pdb=" N GLU G 202 " --> pdb=" O LYS G 198 " (cutoff:3.500A) Processing helix chain 'G' and resid 221 through 224 No H-bonds generated for 'chain 'G' and resid 221 through 224' Processing helix chain 'G' and resid 227 through 233 Processing helix chain 'G' and resid 262 through 274 Processing helix chain 'G' and resid 279 through 281 No H-bonds generated for 'chain 'G' and resid 279 through 281' Processing helix chain 'G' and resid 300 through 311 Processing helix chain 'G' and resid 333 through 341 Processing helix chain 'G' and resid 451 through 474 Processing helix chain 'H' and resid 22 through 25 No H-bonds generated for 'chain 'H' and resid 22 through 25' Processing helix chain 'H' and resid 38 through 46 removed outlier: 3.777A pdb=" N GLU H 43 " --> pdb=" O GLU H 39 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ASN H 46 " --> pdb=" O ASN H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 58 No H-bonds generated for 'chain 'H' and resid 55 through 58' Processing helix chain 'H' and resid 66 through 75 removed outlier: 3.735A pdb=" N GLU H 75 " --> pdb=" O LYS H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 88 removed outlier: 4.130A pdb=" N THR H 88 " --> pdb=" O VAL H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 92 through 98 Processing helix chain 'H' and resid 101 through 104 No H-bonds generated for 'chain 'H' and resid 101 through 104' Processing helix chain 'H' and resid 110 through 113 No H-bonds generated for 'chain 'H' and resid 110 through 113' Processing helix chain 'H' and resid 121 through 134 removed outlier: 4.040A pdb=" N ALA H 132 " --> pdb=" O ILE H 128 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N TRP H 133 " --> pdb=" O ASN H 129 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP H 134 " --> pdb=" O ASP H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 158 through 170 Processing helix chain 'H' and resid 185 through 189 removed outlier: 3.734A pdb=" N TYR H 189 " --> pdb=" O LEU H 186 " (cutoff:3.500A) Processing helix chain 'H' and resid 198 through 211 removed outlier: 3.580A pdb=" N GLU H 202 " --> pdb=" O LYS H 198 " (cutoff:3.500A) Processing helix chain 'H' and resid 227 through 233 Processing helix chain 'H' and resid 262 through 274 Processing helix chain 'H' and resid 279 through 282 No H-bonds generated for 'chain 'H' and resid 279 through 282' Processing helix chain 'H' and resid 300 through 311 Processing helix chain 'H' and resid 333 through 341 Processing helix chain 'H' and resid 407 through 410 No H-bonds generated for 'chain 'H' and resid 407 through 410' Processing helix chain 'H' and resid 443 through 446 No H-bonds generated for 'chain 'H' and resid 443 through 446' Processing helix chain 'H' and resid 451 through 474 Processing helix chain 'I' and resid 8 through 10 No H-bonds generated for 'chain 'I' and resid 8 through 10' Processing helix chain 'I' and resid 22 through 25 No H-bonds generated for 'chain 'I' and resid 22 through 25' Processing helix chain 'I' and resid 38 through 46 removed outlier: 3.796A pdb=" N GLU I 43 " --> pdb=" O GLU I 39 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ASN I 46 " --> pdb=" O ASN I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 58 No H-bonds generated for 'chain 'I' and resid 55 through 58' Processing helix chain 'I' and resid 66 through 75 removed outlier: 3.616A pdb=" N GLU I 75 " --> pdb=" O LYS I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 78 through 88 removed outlier: 4.188A pdb=" N THR I 88 " --> pdb=" O VAL I 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 92 through 98 Processing helix chain 'I' and resid 101 through 104 No H-bonds generated for 'chain 'I' and resid 101 through 104' Processing helix chain 'I' and resid 110 through 113 No H-bonds generated for 'chain 'I' and resid 110 through 113' Processing helix chain 'I' and resid 121 through 134 removed outlier: 4.029A pdb=" N ALA I 132 " --> pdb=" O ILE I 128 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N TRP I 133 " --> pdb=" O ASN I 129 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASP I 134 " --> pdb=" O ASP I 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 158 through 170 Processing helix chain 'I' and resid 185 through 189 removed outlier: 3.756A pdb=" N TYR I 189 " --> pdb=" O LEU I 186 " (cutoff:3.500A) Processing helix chain 'I' and resid 198 through 211 removed outlier: 3.566A pdb=" N GLU I 202 " --> pdb=" O LYS I 198 " (cutoff:3.500A) Processing helix chain 'I' and resid 227 through 233 Processing helix chain 'I' and resid 262 through 274 Processing helix chain 'I' and resid 279 through 282 No H-bonds generated for 'chain 'I' and resid 279 through 282' Processing helix chain 'I' and resid 300 through 311 Processing helix chain 'I' and resid 325 through 327 No H-bonds generated for 'chain 'I' and resid 325 through 327' Processing helix chain 'I' and resid 333 through 341 Processing helix chain 'I' and resid 407 through 410 No H-bonds generated for 'chain 'I' and resid 407 through 410' Processing helix chain 'I' and resid 451 through 474 Processing helix chain 'J' and resid 22 through 25 No H-bonds generated for 'chain 'J' and resid 22 through 25' Processing helix chain 'J' and resid 38 through 46 removed outlier: 4.155A pdb=" N ASN J 46 " --> pdb=" O ASN J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 58 No H-bonds generated for 'chain 'J' and resid 55 through 58' Processing helix chain 'J' and resid 66 through 73 Processing helix chain 'J' and resid 78 through 88 removed outlier: 4.313A pdb=" N THR J 88 " --> pdb=" O VAL J 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 92 through 98 Processing helix chain 'J' and resid 110 through 113 No H-bonds generated for 'chain 'J' and resid 110 through 113' Processing helix chain 'J' and resid 121 through 130 Processing helix chain 'J' and resid 158 through 170 Processing helix chain 'J' and resid 185 through 189 removed outlier: 3.686A pdb=" N TYR J 189 " --> pdb=" O LEU J 186 " (cutoff:3.500A) Processing helix chain 'J' and resid 198 through 211 removed outlier: 3.785A pdb=" N GLU J 202 " --> pdb=" O LYS J 198 " (cutoff:3.500A) Processing helix chain 'J' and resid 221 through 224 No H-bonds generated for 'chain 'J' and resid 221 through 224' Processing helix chain 'J' and resid 227 through 233 Processing helix chain 'J' and resid 262 through 274 Processing helix chain 'J' and resid 279 through 281 No H-bonds generated for 'chain 'J' and resid 279 through 281' Processing helix chain 'J' and resid 300 through 311 Processing helix chain 'J' and resid 333 through 341 Processing helix chain 'J' and resid 451 through 474 Processing helix chain 'K' and resid 22 through 25 No H-bonds generated for 'chain 'K' and resid 22 through 25' Processing helix chain 'K' and resid 38 through 46 removed outlier: 3.776A pdb=" N GLU K 43 " --> pdb=" O GLU K 39 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASN K 46 " --> pdb=" O ASN K 42 " (cutoff:3.500A) Processing helix chain 'K' and resid 55 through 58 No H-bonds generated for 'chain 'K' and resid 55 through 58' Processing helix chain 'K' and resid 66 through 75 removed outlier: 3.735A pdb=" N GLU K 75 " --> pdb=" O LYS K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 78 through 88 removed outlier: 4.130A pdb=" N THR K 88 " --> pdb=" O VAL K 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 92 through 98 Processing helix chain 'K' and resid 101 through 104 No H-bonds generated for 'chain 'K' and resid 101 through 104' Processing helix chain 'K' and resid 110 through 113 No H-bonds generated for 'chain 'K' and resid 110 through 113' Processing helix chain 'K' and resid 121 through 134 removed outlier: 4.040A pdb=" N ALA K 132 " --> pdb=" O ILE K 128 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N TRP K 133 " --> pdb=" O ASN K 129 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASP K 134 " --> pdb=" O ASP K 130 " (cutoff:3.500A) Processing helix chain 'K' and resid 158 through 170 Processing helix chain 'K' and resid 185 through 189 removed outlier: 3.734A pdb=" N TYR K 189 " --> pdb=" O LEU K 186 " (cutoff:3.500A) Processing helix chain 'K' and resid 198 through 211 removed outlier: 3.579A pdb=" N GLU K 202 " --> pdb=" O LYS K 198 " (cutoff:3.500A) Processing helix chain 'K' and resid 227 through 233 Processing helix chain 'K' and resid 262 through 274 Processing helix chain 'K' and resid 279 through 282 No H-bonds generated for 'chain 'K' and resid 279 through 282' Processing helix chain 'K' and resid 300 through 311 Processing helix chain 'K' and resid 333 through 341 Processing helix chain 'K' and resid 407 through 410 No H-bonds generated for 'chain 'K' and resid 407 through 410' Processing helix chain 'K' and resid 443 through 446 No H-bonds generated for 'chain 'K' and resid 443 through 446' Processing helix chain 'K' and resid 451 through 474 Processing helix chain 'L' and resid 8 through 10 No H-bonds generated for 'chain 'L' and resid 8 through 10' Processing helix chain 'L' and resid 22 through 25 No H-bonds generated for 'chain 'L' and resid 22 through 25' Processing helix chain 'L' and resid 38 through 46 removed outlier: 3.796A pdb=" N GLU L 43 " --> pdb=" O GLU L 39 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ASN L 46 " --> pdb=" O ASN L 42 " (cutoff:3.500A) Processing helix chain 'L' and resid 55 through 58 No H-bonds generated for 'chain 'L' and resid 55 through 58' Processing helix chain 'L' and resid 66 through 75 removed outlier: 3.616A pdb=" N GLU L 75 " --> pdb=" O LYS L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 88 removed outlier: 4.189A pdb=" N THR L 88 " --> pdb=" O VAL L 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 92 through 98 Processing helix chain 'L' and resid 101 through 104 No H-bonds generated for 'chain 'L' and resid 101 through 104' Processing helix chain 'L' and resid 110 through 113 No H-bonds generated for 'chain 'L' and resid 110 through 113' Processing helix chain 'L' and resid 121 through 134 removed outlier: 4.028A pdb=" N ALA L 132 " --> pdb=" O ILE L 128 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N TRP L 133 " --> pdb=" O ASN L 129 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASP L 134 " --> pdb=" O ASP L 130 " (cutoff:3.500A) Processing helix chain 'L' and resid 158 through 170 Processing helix chain 'L' and resid 185 through 189 removed outlier: 3.756A pdb=" N TYR L 189 " --> pdb=" O LEU L 186 " (cutoff:3.500A) Processing helix chain 'L' and resid 198 through 211 removed outlier: 3.566A pdb=" N GLU L 202 " --> pdb=" O LYS L 198 " (cutoff:3.500A) Processing helix chain 'L' and resid 227 through 233 Processing helix chain 'L' and resid 262 through 274 Processing helix chain 'L' and resid 279 through 282 No H-bonds generated for 'chain 'L' and resid 279 through 282' Processing helix chain 'L' and resid 300 through 311 Processing helix chain 'L' and resid 325 through 327 No H-bonds generated for 'chain 'L' and resid 325 through 327' Processing helix chain 'L' and resid 333 through 341 Processing helix chain 'L' and resid 407 through 410 No H-bonds generated for 'chain 'L' and resid 407 through 410' Processing helix chain 'L' and resid 451 through 474 Processing sheet with id= A, first strand: chain 'A' and resid 379 through 384 removed outlier: 6.951A pdb=" N ILE A 357 " --> pdb=" O ILE A 380 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N LYS A 382 " --> pdb=" O TYR A 355 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N TYR A 355 " --> pdb=" O LYS A 382 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU A 362 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N PHE A 204 " --> pdb=" O ALA A 49 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ALA A 49 " --> pdb=" O PHE A 204 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 168 through 173 removed outlier: 6.566A pdb=" N GLN A 75 " --> pdb=" O CYS A 170 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LEU A 172 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL A 73 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY A 106 " --> pdb=" O ILE A 132 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLY A 134 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N ILE A 104 " --> pdb=" O GLY A 134 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 230 through 232 Processing sheet with id= D, first strand: chain 'A' and resid 524 through 526 Processing sheet with id= E, first strand: chain 'A' and resid 566 through 569 removed outlier: 6.666A pdb=" N HIS A 603 " --> pdb=" O ALA A 567 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N ILE A 569 " --> pdb=" O HIS A 603 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE A 605 " --> pdb=" O ILE A 569 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 572 through 574 Processing sheet with id= G, first strand: chain 'A' and resid 643 through 646 removed outlier: 6.675A pdb=" N THR A 665 " --> pdb=" O VAL A 644 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N THR A 646 " --> pdb=" O THR A 665 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ASN A 667 " --> pdb=" O THR A 646 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'A' and resid 829 through 831 Processing sheet with id= I, first strand: chain 'A' and resid 907 through 910 removed outlier: 6.754A pdb=" N GLU A 927 " --> pdb=" O LYS A 908 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N VAL A 910 " --> pdb=" O GLU A 927 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N GLU A 929 " --> pdb=" O VAL A 910 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N LYS A 995 " --> pdb=" O LEU A 928 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N ILE A 930 " --> pdb=" O LYS A 995 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N THR A 997 " --> pdb=" O ILE A 930 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE A1020 " --> pdb=" O VAL A 998 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N LEU A1000 " --> pdb=" O ILE A1020 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU A1022 " --> pdb=" O LEU A1000 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ARG A1066 " --> pdb=" O ILE A1021 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N ILE A1023 " --> pdb=" O ARG A1066 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ARG A1068 " --> pdb=" O ILE A1023 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLU A1089 " --> pdb=" O THR A1069 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'A' and resid 1229 through 1233 removed outlier: 3.875A pdb=" N THR A1265 " --> pdb=" O MET A1229 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG A1269 " --> pdb=" O TYR A1233 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR A1304 " --> pdb=" O LEU A1286 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N VAL A1288 " --> pdb=" O THR A1304 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL A1306 " --> pdb=" O VAL A1288 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LYS A1335 " --> pdb=" O ILE A1305 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N VAL A1307 " --> pdb=" O LYS A1335 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N PHE A1337 " --> pdb=" O VAL A1307 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N THR A1354 " --> pdb=" O LEU A1336 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N ALA A1338 " --> pdb=" O THR A1354 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N VAL A1356 " --> pdb=" O ALA A1338 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N THR A1372 " --> pdb=" O VAL A1355 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N VAL A1357 " --> pdb=" O THR A1372 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N VAL A1374 " --> pdb=" O VAL A1357 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N MET A1391 " --> pdb=" O ALA A1373 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N ILE A1375 " --> pdb=" O MET A1391 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N TYR A1393 " --> pdb=" O ILE A1375 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 379 through 384 removed outlier: 6.900A pdb=" N ILE B 357 " --> pdb=" O ILE B 380 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N LYS B 382 " --> pdb=" O TYR B 355 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N TYR B 355 " --> pdb=" O LYS B 382 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU B 362 " --> pdb=" O THR B 358 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N PHE B 204 " --> pdb=" O ALA B 49 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ALA B 49 " --> pdb=" O PHE B 204 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 168 through 173 removed outlier: 6.375A pdb=" N GLN B 75 " --> pdb=" O CYS B 170 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N LEU B 172 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N VAL B 73 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY B 106 " --> pdb=" O ILE B 132 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLY B 134 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N ILE B 104 " --> pdb=" O GLY B 134 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 230 through 234 Processing sheet with id= N, first strand: chain 'B' and resid 524 through 526 Processing sheet with id= O, first strand: chain 'B' and resid 566 through 570 removed outlier: 6.327A pdb=" N HIS B 603 " --> pdb=" O ALA B 567 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ILE B 569 " --> pdb=" O HIS B 603 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE B 605 " --> pdb=" O ILE B 569 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N SER B 641 " --> pdb=" O VAL B 604 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N LEU B 606 " --> pdb=" O SER B 641 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ASN B 643 " --> pdb=" O LEU B 606 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N THR B 665 " --> pdb=" O VAL B 644 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N THR B 646 " --> pdb=" O THR B 665 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ASN B 667 " --> pdb=" O THR B 646 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'B' and resid 572 through 574 Processing sheet with id= Q, first strand: chain 'B' and resid 829 through 831 Processing sheet with id= R, first strand: chain 'B' and resid 907 through 910 removed outlier: 7.040A pdb=" N GLU B 927 " --> pdb=" O LYS B 908 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N VAL B 910 " --> pdb=" O GLU B 927 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N GLU B 929 " --> pdb=" O VAL B 910 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'B' and resid 997 through 1001 removed outlier: 6.653A pdb=" N ILE B1020 " --> pdb=" O VAL B 998 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N LEU B1000 " --> pdb=" O ILE B1020 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU B1022 " --> pdb=" O LEU B1000 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ARG B1066 " --> pdb=" O ILE B1021 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N ILE B1023 " --> pdb=" O ARG B1066 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ARG B1068 " --> pdb=" O ILE B1023 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'B' and resid 1229 through 1234 removed outlier: 3.739A pdb=" N THR B1265 " --> pdb=" O MET B1229 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N THR B1304 " --> pdb=" O LEU B1286 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N VAL B1288 " --> pdb=" O THR B1304 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL B1306 " --> pdb=" O VAL B1288 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LYS B1335 " --> pdb=" O ILE B1305 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N VAL B1307 " --> pdb=" O LYS B1335 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N PHE B1337 " --> pdb=" O VAL B1307 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N THR B1354 " --> pdb=" O LEU B1336 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N ALA B1338 " --> pdb=" O THR B1354 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VAL B1356 " --> pdb=" O ALA B1338 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N THR B1372 " --> pdb=" O VAL B1355 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N VAL B1357 " --> pdb=" O THR B1372 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N VAL B1374 " --> pdb=" O VAL B1357 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N MET B1391 " --> pdb=" O ALA B1373 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N ILE B1375 " --> pdb=" O MET B1391 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N TYR B1393 " --> pdb=" O ILE B1375 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 379 through 384 removed outlier: 6.882A pdb=" N ILE C 357 " --> pdb=" O ILE C 380 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N LYS C 382 " --> pdb=" O TYR C 355 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N TYR C 355 " --> pdb=" O LYS C 382 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU C 362 " --> pdb=" O THR C 358 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N PHE C 204 " --> pdb=" O ALA C 49 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ALA C 49 " --> pdb=" O PHE C 204 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 168 through 173 removed outlier: 6.386A pdb=" N GLN C 75 " --> pdb=" O CYS C 170 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N LEU C 172 " --> pdb=" O VAL C 73 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL C 73 " --> pdb=" O LEU C 172 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY C 106 " --> pdb=" O ILE C 132 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N GLY C 134 " --> pdb=" O ILE C 104 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N ILE C 104 " --> pdb=" O GLY C 134 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 230 through 234 Processing sheet with id= X, first strand: chain 'C' and resid 524 through 526 Processing sheet with id= Y, first strand: chain 'C' and resid 566 through 570 removed outlier: 6.353A pdb=" N HIS C 603 " --> pdb=" O ALA C 567 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ILE C 569 " --> pdb=" O HIS C 603 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ILE C 605 " --> pdb=" O ILE C 569 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N SER C 641 " --> pdb=" O VAL C 604 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N LEU C 606 " --> pdb=" O SER C 641 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ASN C 643 " --> pdb=" O LEU C 606 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N THR C 665 " --> pdb=" O VAL C 644 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N THR C 646 " --> pdb=" O THR C 665 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ASN C 667 " --> pdb=" O THR C 646 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'C' and resid 572 through 574 Processing sheet with id= AA, first strand: chain 'C' and resid 829 through 831 Processing sheet with id= AB, first strand: chain 'C' and resid 907 through 910 removed outlier: 6.954A pdb=" N GLU C 927 " --> pdb=" O LYS C 908 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N VAL C 910 " --> pdb=" O GLU C 927 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N GLU C 929 " --> pdb=" O VAL C 910 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N LYS C 995 " --> pdb=" O LEU C 928 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ILE C 930 " --> pdb=" O LYS C 995 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N THR C 997 " --> pdb=" O ILE C 930 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE C1020 " --> pdb=" O VAL C 998 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N LEU C1000 " --> pdb=" O ILE C1020 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU C1022 " --> pdb=" O LEU C1000 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ARG C1066 " --> pdb=" O ILE C1021 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ILE C1023 " --> pdb=" O ARG C1066 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ARG C1068 " --> pdb=" O ILE C1023 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'C' and resid 1229 through 1235 removed outlier: 3.788A pdb=" N THR C1265 " --> pdb=" O MET C1229 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N THR C1271 " --> pdb=" O ALA C1235 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP C1291 " --> pdb=" O GLY C1270 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N THR C1304 " --> pdb=" O LEU C1286 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N VAL C1288 " --> pdb=" O THR C1304 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL C1306 " --> pdb=" O VAL C1288 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N GLY C1290 " --> pdb=" O VAL C1306 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N ARG C1308 " --> pdb=" O GLY C1290 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LYS C1335 " --> pdb=" O ILE C1305 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N VAL C1307 " --> pdb=" O LYS C1335 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N PHE C1337 " --> pdb=" O VAL C1307 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N THR C1354 " --> pdb=" O LEU C1336 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ALA C1338 " --> pdb=" O THR C1354 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL C1356 " --> pdb=" O ALA C1338 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N THR C1372 " --> pdb=" O VAL C1355 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N VAL C1357 " --> pdb=" O THR C1372 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N VAL C1374 " --> pdb=" O VAL C1357 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N MET C1391 " --> pdb=" O ALA C1373 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N ILE C1375 " --> pdb=" O MET C1391 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TYR C1393 " --> pdb=" O ILE C1375 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'D' and resid 379 through 384 removed outlier: 6.951A pdb=" N ILE D 357 " --> pdb=" O ILE D 380 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N LYS D 382 " --> pdb=" O TYR D 355 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N TYR D 355 " --> pdb=" O LYS D 382 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU D 362 " --> pdb=" O THR D 358 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N PHE D 204 " --> pdb=" O ALA D 49 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ALA D 49 " --> pdb=" O PHE D 204 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'D' and resid 168 through 173 removed outlier: 6.565A pdb=" N GLN D 75 " --> pdb=" O CYS D 170 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N LEU D 172 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL D 73 " --> pdb=" O LEU D 172 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY D 106 " --> pdb=" O ILE D 132 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLY D 134 " --> pdb=" O ILE D 104 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N ILE D 104 " --> pdb=" O GLY D 134 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'D' and resid 230 through 232 Processing sheet with id= AG, first strand: chain 'D' and resid 524 through 526 Processing sheet with id= AH, first strand: chain 'D' and resid 566 through 569 removed outlier: 6.666A pdb=" N HIS D 603 " --> pdb=" O ALA D 567 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N ILE D 569 " --> pdb=" O HIS D 603 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE D 605 " --> pdb=" O ILE D 569 " (cutoff:3.500A) No H-bonds generated for sheet with id= AH Processing sheet with id= AI, first strand: chain 'D' and resid 572 through 574 Processing sheet with id= AJ, first strand: chain 'D' and resid 643 through 646 removed outlier: 6.674A pdb=" N THR D 665 " --> pdb=" O VAL D 644 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N THR D 646 " --> pdb=" O THR D 665 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ASN D 667 " --> pdb=" O THR D 646 " (cutoff:3.500A) No H-bonds generated for sheet with id= AJ Processing sheet with id= AK, first strand: chain 'D' and resid 829 through 831 Processing sheet with id= AL, first strand: chain 'D' and resid 907 through 910 removed outlier: 6.754A pdb=" N GLU D 927 " --> pdb=" O LYS D 908 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N VAL D 910 " --> pdb=" O GLU D 927 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N GLU D 929 " --> pdb=" O VAL D 910 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N LYS D 995 " --> pdb=" O LEU D 928 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N ILE D 930 " --> pdb=" O LYS D 995 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N THR D 997 " --> pdb=" O ILE D 930 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE D1020 " --> pdb=" O VAL D 998 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N LEU D1000 " --> pdb=" O ILE D1020 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU D1022 " --> pdb=" O LEU D1000 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ARG D1066 " --> pdb=" O ILE D1021 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N ILE D1023 " --> pdb=" O ARG D1066 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ARG D1068 " --> pdb=" O ILE D1023 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLU D1089 " --> pdb=" O THR D1069 " (cutoff:3.500A) No H-bonds generated for sheet with id= AL Processing sheet with id= AM, first strand: chain 'D' and resid 1229 through 1233 removed outlier: 3.874A pdb=" N THR D1265 " --> pdb=" O MET D1229 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG D1269 " --> pdb=" O TYR D1233 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR D1304 " --> pdb=" O LEU D1286 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N VAL D1288 " --> pdb=" O THR D1304 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL D1306 " --> pdb=" O VAL D1288 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LYS D1335 " --> pdb=" O ILE D1305 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N VAL D1307 " --> pdb=" O LYS D1335 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N PHE D1337 " --> pdb=" O VAL D1307 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N THR D1354 " --> pdb=" O LEU D1336 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N ALA D1338 " --> pdb=" O THR D1354 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N VAL D1356 " --> pdb=" O ALA D1338 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR D1372 " --> pdb=" O VAL D1355 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N VAL D1357 " --> pdb=" O THR D1372 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N VAL D1374 " --> pdb=" O VAL D1357 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N MET D1391 " --> pdb=" O ALA D1373 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N ILE D1375 " --> pdb=" O MET D1391 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N TYR D1393 " --> pdb=" O ILE D1375 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'E' and resid 379 through 384 removed outlier: 6.901A pdb=" N ILE E 357 " --> pdb=" O ILE E 380 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N LYS E 382 " --> pdb=" O TYR E 355 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N TYR E 355 " --> pdb=" O LYS E 382 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU E 362 " --> pdb=" O THR E 358 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N PHE E 204 " --> pdb=" O ALA E 49 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ALA E 49 " --> pdb=" O PHE E 204 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'E' and resid 168 through 173 removed outlier: 6.375A pdb=" N GLN E 75 " --> pdb=" O CYS E 170 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N LEU E 172 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N VAL E 73 " --> pdb=" O LEU E 172 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY E 106 " --> pdb=" O ILE E 132 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLY E 134 " --> pdb=" O ILE E 104 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ILE E 104 " --> pdb=" O GLY E 134 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'E' and resid 230 through 234 Processing sheet with id= AQ, first strand: chain 'E' and resid 524 through 526 Processing sheet with id= AR, first strand: chain 'E' and resid 566 through 570 removed outlier: 6.327A pdb=" N HIS E 603 " --> pdb=" O ALA E 567 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ILE E 569 " --> pdb=" O HIS E 603 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE E 605 " --> pdb=" O ILE E 569 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N SER E 641 " --> pdb=" O VAL E 604 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N LEU E 606 " --> pdb=" O SER E 641 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ASN E 643 " --> pdb=" O LEU E 606 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N THR E 665 " --> pdb=" O VAL E 644 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N THR E 646 " --> pdb=" O THR E 665 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ASN E 667 " --> pdb=" O THR E 646 " (cutoff:3.500A) No H-bonds generated for sheet with id= AR Processing sheet with id= AS, first strand: chain 'E' and resid 572 through 574 Processing sheet with id= AT, first strand: chain 'E' and resid 829 through 831 Processing sheet with id= AU, first strand: chain 'E' and resid 907 through 910 removed outlier: 7.041A pdb=" N GLU E 927 " --> pdb=" O LYS E 908 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N VAL E 910 " --> pdb=" O GLU E 927 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N GLU E 929 " --> pdb=" O VAL E 910 " (cutoff:3.500A) No H-bonds generated for sheet with id= AU Processing sheet with id= AV, first strand: chain 'E' and resid 997 through 1001 removed outlier: 6.653A pdb=" N ILE E1020 " --> pdb=" O VAL E 998 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N LEU E1000 " --> pdb=" O ILE E1020 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU E1022 " --> pdb=" O LEU E1000 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ARG E1066 " --> pdb=" O ILE E1021 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N ILE E1023 " --> pdb=" O ARG E1066 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ARG E1068 " --> pdb=" O ILE E1023 " (cutoff:3.500A) No H-bonds generated for sheet with id= AV Processing sheet with id= AW, first strand: chain 'E' and resid 1229 through 1234 removed outlier: 3.738A pdb=" N THR E1265 " --> pdb=" O MET E1229 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N THR E1304 " --> pdb=" O LEU E1286 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N VAL E1288 " --> pdb=" O THR E1304 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL E1306 " --> pdb=" O VAL E1288 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LYS E1335 " --> pdb=" O ILE E1305 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N VAL E1307 " --> pdb=" O LYS E1335 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N PHE E1337 " --> pdb=" O VAL E1307 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N THR E1354 " --> pdb=" O LEU E1336 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N ALA E1338 " --> pdb=" O THR E1354 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VAL E1356 " --> pdb=" O ALA E1338 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N THR E1372 " --> pdb=" O VAL E1355 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N VAL E1357 " --> pdb=" O THR E1372 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N VAL E1374 " --> pdb=" O VAL E1357 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N MET E1391 " --> pdb=" O ALA E1373 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N ILE E1375 " --> pdb=" O MET E1391 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N TYR E1393 " --> pdb=" O ILE E1375 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'F' and resid 379 through 384 removed outlier: 6.883A pdb=" N ILE F 357 " --> pdb=" O ILE F 380 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N LYS F 382 " --> pdb=" O TYR F 355 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N TYR F 355 " --> pdb=" O LYS F 382 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU F 362 " --> pdb=" O THR F 358 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N PHE F 204 " --> pdb=" O ALA F 49 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ALA F 49 " --> pdb=" O PHE F 204 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'F' and resid 168 through 173 removed outlier: 6.389A pdb=" N GLN F 75 " --> pdb=" O CYS F 170 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N LEU F 172 " --> pdb=" O VAL F 73 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL F 73 " --> pdb=" O LEU F 172 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY F 106 " --> pdb=" O ILE F 132 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLY F 134 " --> pdb=" O ILE F 104 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ILE F 104 " --> pdb=" O GLY F 134 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'F' and resid 230 through 234 Processing sheet with id= BA, first strand: chain 'F' and resid 524 through 526 Processing sheet with id= BB, first strand: chain 'F' and resid 566 through 570 removed outlier: 6.354A pdb=" N HIS F 603 " --> pdb=" O ALA F 567 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N ILE F 569 " --> pdb=" O HIS F 603 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ILE F 605 " --> pdb=" O ILE F 569 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N SER F 641 " --> pdb=" O VAL F 604 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N LEU F 606 " --> pdb=" O SER F 641 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ASN F 643 " --> pdb=" O LEU F 606 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N THR F 665 " --> pdb=" O VAL F 644 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N THR F 646 " --> pdb=" O THR F 665 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ASN F 667 " --> pdb=" O THR F 646 " (cutoff:3.500A) No H-bonds generated for sheet with id= BB Processing sheet with id= BC, first strand: chain 'F' and resid 572 through 574 Processing sheet with id= BD, first strand: chain 'F' and resid 829 through 831 Processing sheet with id= BE, first strand: chain 'F' and resid 907 through 910 removed outlier: 6.955A pdb=" N GLU F 927 " --> pdb=" O LYS F 908 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N VAL F 910 " --> pdb=" O GLU F 927 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N GLU F 929 " --> pdb=" O VAL F 910 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N LYS F 995 " --> pdb=" O LEU F 928 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ILE F 930 " --> pdb=" O LYS F 995 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N THR F 997 " --> pdb=" O ILE F 930 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE F1020 " --> pdb=" O VAL F 998 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N LEU F1000 " --> pdb=" O ILE F1020 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU F1022 " --> pdb=" O LEU F1000 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ARG F1066 " --> pdb=" O ILE F1021 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N ILE F1023 " --> pdb=" O ARG F1066 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ARG F1068 " --> pdb=" O ILE F1023 " (cutoff:3.500A) No H-bonds generated for sheet with id= BE Processing sheet with id= BF, first strand: chain 'F' and resid 1229 through 1235 removed outlier: 3.790A pdb=" N THR F1265 " --> pdb=" O MET F1229 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N THR F1271 " --> pdb=" O ALA F1235 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP F1291 " --> pdb=" O GLY F1270 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N THR F1304 " --> pdb=" O LEU F1286 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N VAL F1288 " --> pdb=" O THR F1304 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL F1306 " --> pdb=" O VAL F1288 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N GLY F1290 " --> pdb=" O VAL F1306 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N ARG F1308 " --> pdb=" O GLY F1290 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LYS F1335 " --> pdb=" O ILE F1305 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N VAL F1307 " --> pdb=" O LYS F1335 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N PHE F1337 " --> pdb=" O VAL F1307 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N THR F1354 " --> pdb=" O LEU F1336 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N ALA F1338 " --> pdb=" O THR F1354 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL F1356 " --> pdb=" O ALA F1338 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N THR F1372 " --> pdb=" O VAL F1355 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N VAL F1357 " --> pdb=" O THR F1372 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N VAL F1374 " --> pdb=" O VAL F1357 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N MET F1391 " --> pdb=" O ALA F1373 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N ILE F1375 " --> pdb=" O MET F1391 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N TYR F1393 " --> pdb=" O ILE F1375 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'G' and resid 173 through 177 removed outlier: 6.067A pdb=" N ALA G 236 " --> pdb=" O GLY G 152 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N ILE G 154 " --> pdb=" O ALA G 236 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LEU G 238 " --> pdb=" O ILE G 154 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'G' and resid 259 through 261 removed outlier: 6.675A pdb=" N VAL G 396 " --> pdb=" O VAL G 260 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N SER G 316 " --> pdb=" O VAL G 293 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N VAL G 295 " --> pdb=" O SER G 316 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LYS G 318 " --> pdb=" O VAL G 295 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N GLU G 344 " --> pdb=" O CYS G 319 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'G' and resid 388 through 392 removed outlier: 5.657A pdb=" N VAL G 366 " --> pdb=" O PRO G 351 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'G' and resid 368 through 370 Processing sheet with id= BK, first strand: chain 'H' and resid 173 through 177 removed outlier: 6.195A pdb=" N ALA H 236 " --> pdb=" O GLY H 152 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N ILE H 154 " --> pdb=" O ALA H 236 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LEU H 238 " --> pdb=" O ILE H 154 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'H' and resid 259 through 261 removed outlier: 6.499A pdb=" N VAL H 396 " --> pdb=" O VAL H 260 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N SER H 316 " --> pdb=" O VAL H 293 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N VAL H 295 " --> pdb=" O SER H 316 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N LYS H 318 " --> pdb=" O VAL H 295 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'H' and resid 388 through 392 removed outlier: 6.012A pdb=" N VAL H 366 " --> pdb=" O PRO H 351 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'H' and resid 368 through 370 Processing sheet with id= BO, first strand: chain 'I' and resid 173 through 177 removed outlier: 6.196A pdb=" N ALA I 236 " --> pdb=" O GLY I 152 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE I 154 " --> pdb=" O ALA I 236 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU I 238 " --> pdb=" O ILE I 154 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'I' and resid 259 through 261 removed outlier: 6.522A pdb=" N VAL I 396 " --> pdb=" O VAL I 260 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N SER I 316 " --> pdb=" O VAL I 293 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N VAL I 295 " --> pdb=" O SER I 316 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LYS I 318 " --> pdb=" O VAL I 295 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N GLU I 344 " --> pdb=" O CYS I 319 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'I' and resid 388 through 392 removed outlier: 5.992A pdb=" N VAL I 366 " --> pdb=" O PRO I 351 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain 'I' and resid 368 through 370 Processing sheet with id= BS, first strand: chain 'J' and resid 173 through 177 removed outlier: 6.067A pdb=" N ALA J 236 " --> pdb=" O GLY J 152 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N ILE J 154 " --> pdb=" O ALA J 236 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU J 238 " --> pdb=" O ILE J 154 " (cutoff:3.500A) Processing sheet with id= BT, first strand: chain 'J' and resid 259 through 261 removed outlier: 6.676A pdb=" N VAL J 396 " --> pdb=" O VAL J 260 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N SER J 316 " --> pdb=" O VAL J 293 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N VAL J 295 " --> pdb=" O SER J 316 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LYS J 318 " --> pdb=" O VAL J 295 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N GLU J 344 " --> pdb=" O CYS J 319 " (cutoff:3.500A) Processing sheet with id= BU, first strand: chain 'J' and resid 388 through 392 removed outlier: 5.657A pdb=" N VAL J 366 " --> pdb=" O PRO J 351 " (cutoff:3.500A) Processing sheet with id= BV, first strand: chain 'J' and resid 368 through 370 Processing sheet with id= BW, first strand: chain 'K' and resid 173 through 177 removed outlier: 6.196A pdb=" N ALA K 236 " --> pdb=" O GLY K 152 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N ILE K 154 " --> pdb=" O ALA K 236 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LEU K 238 " --> pdb=" O ILE K 154 " (cutoff:3.500A) Processing sheet with id= BX, first strand: chain 'K' and resid 259 through 261 removed outlier: 6.499A pdb=" N VAL K 396 " --> pdb=" O VAL K 260 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N SER K 316 " --> pdb=" O VAL K 293 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N VAL K 295 " --> pdb=" O SER K 316 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LYS K 318 " --> pdb=" O VAL K 295 " (cutoff:3.500A) Processing sheet with id= BY, first strand: chain 'K' and resid 388 through 392 removed outlier: 6.011A pdb=" N VAL K 366 " --> pdb=" O PRO K 351 " (cutoff:3.500A) Processing sheet with id= BZ, first strand: chain 'K' and resid 368 through 370 Processing sheet with id= CA, first strand: chain 'L' and resid 173 through 177 removed outlier: 6.196A pdb=" N ALA L 236 " --> pdb=" O GLY L 152 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE L 154 " --> pdb=" O ALA L 236 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU L 238 " --> pdb=" O ILE L 154 " (cutoff:3.500A) Processing sheet with id= CB, first strand: chain 'L' and resid 259 through 261 removed outlier: 6.522A pdb=" N VAL L 396 " --> pdb=" O VAL L 260 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N SER L 316 " --> pdb=" O VAL L 293 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N VAL L 295 " --> pdb=" O SER L 316 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LYS L 318 " --> pdb=" O VAL L 295 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N GLU L 344 " --> pdb=" O CYS L 319 " (cutoff:3.500A) Processing sheet with id= CC, first strand: chain 'L' and resid 388 through 392 removed outlier: 5.991A pdb=" N VAL L 366 " --> pdb=" O PRO L 351 " (cutoff:3.500A) Processing sheet with id= CD, first strand: chain 'L' and resid 368 through 370 2795 hydrogen bonds defined for protein. 7857 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: 49.34 Time building geometry restraints manager: 28.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.76: 91116 1.76 - 2.31: 960 2.31 - 2.86: 6 2.86 - 3.41: 0 3.41 - 3.96: 18 Bond restraints: 92100 Sorted by residual: bond pdb=" S4 F3S A1502 " pdb="FE1 F3S A1502 " ideal model delta sigma weight residual 2.233 3.925 -1.692 2.00e-02 2.50e+03 7.16e+03 bond pdb=" S4 F3S D1502 " pdb="FE1 F3S D1502 " ideal model delta sigma weight residual 2.233 3.924 -1.691 2.00e-02 2.50e+03 7.15e+03 bond pdb=" S4 F3S B1502 " pdb="FE1 F3S B1502 " ideal model delta sigma weight residual 2.233 3.920 -1.687 2.00e-02 2.50e+03 7.11e+03 bond pdb=" S4 F3S E1502 " pdb="FE1 F3S E1502 " ideal model delta sigma weight residual 2.233 3.920 -1.687 2.00e-02 2.50e+03 7.11e+03 bond pdb=" S4 F3S F1502 " pdb="FE1 F3S F1502 " ideal model delta sigma weight residual 2.233 3.915 -1.682 2.00e-02 2.50e+03 7.07e+03 ... (remaining 92095 not shown) Histogram of bond angle deviations from ideal: 41.07 - 59.67: 24 59.67 - 78.26: 192 78.26 - 96.85: 0 96.85 - 115.45: 59581 115.45 - 134.04: 65021 Bond angle restraints: 124818 Sorted by residual: angle pdb=" S1 F3S C1502 " pdb="FE4 F3S C1502 " pdb=" S3 F3S C1502 " ideal model delta sigma weight residual 114.75 64.56 50.19 3.00e+00 1.11e-01 2.80e+02 angle pdb=" S1 F3S F1502 " pdb="FE4 F3S F1502 " pdb=" S3 F3S F1502 " ideal model delta sigma weight residual 114.75 64.58 50.17 3.00e+00 1.11e-01 2.80e+02 angle pdb=" S1 F3S E1502 " pdb="FE4 F3S E1502 " pdb=" S3 F3S E1502 " ideal model delta sigma weight residual 114.75 64.62 50.13 3.00e+00 1.11e-01 2.79e+02 angle pdb=" S1 F3S B1502 " pdb="FE4 F3S B1502 " pdb=" S3 F3S B1502 " ideal model delta sigma weight residual 114.75 64.63 50.12 3.00e+00 1.11e-01 2.79e+02 angle pdb=" S1 F3S A1502 " pdb="FE4 F3S A1502 " pdb=" S3 F3S A1502 " ideal model delta sigma weight residual 114.75 64.76 49.99 3.00e+00 1.11e-01 2.78e+02 ... (remaining 124813 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.78: 53624 29.78 - 59.56: 1573 59.56 - 89.34: 156 89.34 - 119.12: 17 119.12 - 148.90: 4 Dihedral angle restraints: 55374 sinusoidal: 22404 harmonic: 32970 Sorted by residual: dihedral pdb=" CA LYS F 898 " pdb=" C LYS F 898 " pdb=" N ASN F 899 " pdb=" CA ASN F 899 " ideal model delta harmonic sigma weight residual 180.00 153.76 26.24 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" CA LYS C 898 " pdb=" C LYS C 898 " pdb=" N ASN C 899 " pdb=" CA ASN C 899 " ideal model delta harmonic sigma weight residual 180.00 153.77 26.23 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" O5' FAD G 503 " pdb=" O3P FAD G 503 " pdb=" P FAD G 503 " pdb=" PA FAD G 503 " ideal model delta sinusoidal sigma weight residual -61.77 87.13 -148.90 1 3.00e+01 1.11e-03 1.98e+01 ... (remaining 55371 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.009: 13879 1.009 - 2.019: 0 2.019 - 3.028: 0 3.028 - 4.037: 6 4.037 - 5.047: 5 Chirality restraints: 13890 Sorted by residual: chirality pdb=" C4' FAD L 503 " pdb=" C3' FAD L 503 " pdb=" C5' FAD L 503 " pdb=" O4' FAD L 503 " both_signs ideal model delta sigma weight residual False -2.48 2.57 -5.05 2.00e-01 2.50e+01 6.37e+02 chirality pdb=" C4' FAD I 503 " pdb=" C3' FAD I 503 " pdb=" C5' FAD I 503 " pdb=" O4' FAD I 503 " both_signs ideal model delta sigma weight residual False -2.48 2.48 -4.96 2.00e-01 2.50e+01 6.14e+02 chirality pdb=" C3' FAD I 503 " pdb=" C2' FAD I 503 " pdb=" C4' FAD I 503 " pdb=" O3' FAD I 503 " both_signs ideal model delta sigma weight residual False -2.55 2.36 -4.91 2.00e-01 2.50e+01 6.03e+02 ... (remaining 13887 not shown) Planarity restraints: 16326 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN H 4 " -0.026 2.00e-02 2.50e+03 5.29e-02 2.80e+01 pdb=" CD GLN H 4 " 0.091 2.00e-02 2.50e+03 pdb=" OE1 GLN H 4 " -0.035 2.00e-02 2.50e+03 pdb=" NE2 GLN H 4 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN K 4 " -0.026 2.00e-02 2.50e+03 5.26e-02 2.76e+01 pdb=" CD GLN K 4 " 0.091 2.00e-02 2.50e+03 pdb=" OE1 GLN K 4 " -0.035 2.00e-02 2.50e+03 pdb=" NE2 GLN K 4 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP C1218 " -0.013 2.00e-02 2.50e+03 2.69e-02 7.26e+00 pdb=" CG ASP C1218 " 0.047 2.00e-02 2.50e+03 pdb=" OD1 ASP C1218 " -0.017 2.00e-02 2.50e+03 pdb=" OD2 ASP C1218 " -0.017 2.00e-02 2.50e+03 ... (remaining 16323 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 1460 2.67 - 3.23: 84147 3.23 - 3.78: 127661 3.78 - 4.34: 182513 4.34 - 4.90: 306247 Nonbonded interactions: 702028 Sorted by model distance: nonbonded pdb=" O2' FAD L 503 " pdb=" O4' FAD L 503 " model vdw 2.111 2.440 nonbonded pdb=" OD2 ASP E 512 " pdb=" NH1 ARG E 515 " model vdw 2.113 2.520 nonbonded pdb=" OE1 GLU I 125 " pdb="FE3 SF4 I 502 " model vdw 2.116 3.000 nonbonded pdb=" OE1 GLU L 125 " pdb="FE3 SF4 L 502 " model vdw 2.117 3.000 nonbonded pdb=" OE1 GLU K 125 " pdb="FE3 SF4 K 502 " model vdw 2.125 3.000 ... (remaining 702023 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.090 Extract box with map and model: 10.070 Check model and map are aligned: 1.020 Set scattering table: 0.640 Process input model: 206.080 Find NCS groups from input model: 4.980 Set up NCS constraints: 0.670 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: 0.020 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 227.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 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 : 0.023 1.692 92100 Z= 1.501 Angle : 0.994 50.187 124818 Z= 0.434 Chirality : 0.127 5.047 13890 Planarity : 0.004 0.053 16326 Dihedral : 14.214 148.903 34338 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.04 % Allowed : 5.54 % Favored : 94.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % 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: -2.91 (0.07), residues: 11640 helix: -0.97 (0.07), residues: 4188 sheet: -2.00 (0.11), residues: 1890 loop : -2.68 (0.07), residues: 5562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP L 69 HIS 0.011 0.001 HIS F 971 PHE 0.021 0.001 PHE F 781 TYR 0.014 0.001 TYR C 807 ARG 0.006 0.000 ARG H 429 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23280 Ramachandran restraints generated. 11640 Oldfield, 0 Emsley, 11640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23280 Ramachandran restraints generated. 11640 Oldfield, 0 Emsley, 11640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1572 residues out of total 9444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1568 time to evaluate : 7.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 MET cc_start: 0.8619 (tpp) cc_final: 0.8284 (tpp) REVERT: A 296 MET cc_start: 0.8951 (tpp) cc_final: 0.8495 (tpp) REVERT: A 442 MET cc_start: 0.8496 (mtm) cc_final: 0.6940 (mtm) REVERT: A 460 ASP cc_start: 0.8182 (m-30) cc_final: 0.7847 (m-30) REVERT: A 473 LYS cc_start: 0.8528 (ptpt) cc_final: 0.8315 (pptt) REVERT: A 819 LYS cc_start: 0.8421 (mmtm) cc_final: 0.8051 (mmmt) REVERT: A 1176 GLU cc_start: 0.7818 (pm20) cc_final: 0.7563 (pm20) REVERT: A 1177 HIS cc_start: 0.7727 (m-70) cc_final: 0.7476 (m-70) REVERT: A 1229 MET cc_start: 0.8974 (mmm) cc_final: 0.8749 (mmt) REVERT: A 1368 MET cc_start: 0.8659 (ttt) cc_final: 0.8378 (ttm) REVERT: A 1391 MET cc_start: 0.8609 (ttm) cc_final: 0.8345 (ttm) REVERT: A 1462 MET cc_start: 0.8151 (mtp) cc_final: 0.7915 (mtt) REVERT: B 235 ASN cc_start: 0.7756 (m-40) cc_final: 0.7475 (m-40) REVERT: B 375 ASP cc_start: 0.7018 (p0) cc_final: 0.6580 (p0) REVERT: B 708 MET cc_start: 0.8423 (ttp) cc_final: 0.8173 (ttp) REVERT: B 818 ASN cc_start: 0.7066 (m-40) cc_final: 0.6753 (m110) REVERT: B 881 LYS cc_start: 0.8186 (mtmm) cc_final: 0.7954 (mtmm) REVERT: B 1092 ILE cc_start: 0.7010 (mt) cc_final: 0.6776 (mm) REVERT: B 1100 MET cc_start: 0.7995 (mtm) cc_final: 0.7679 (mtm) REVERT: B 1269 ARG cc_start: 0.8359 (mtp-110) cc_final: 0.8102 (ttm110) REVERT: C 165 ASN cc_start: 0.8489 (m110) cc_final: 0.8235 (m110) REVERT: C 260 MET cc_start: 0.8492 (tpp) cc_final: 0.8252 (tpt) REVERT: C 391 ILE cc_start: 0.8845 (tt) cc_final: 0.8631 (tp) REVERT: C 458 MET cc_start: 0.7140 (ptm) cc_final: 0.6316 (ptm) REVERT: C 473 LYS cc_start: 0.7972 (ptpt) cc_final: 0.7618 (pttt) REVERT: C 518 ARG cc_start: 0.8381 (ptt-90) cc_final: 0.8085 (ttp80) REVERT: C 687 MET cc_start: 0.7006 (ptp) cc_final: 0.6734 (ptp) REVERT: C 725 PHE cc_start: 0.8313 (m-80) cc_final: 0.7916 (m-80) REVERT: C 747 SER cc_start: 0.8948 (m) cc_final: 0.8644 (p) REVERT: C 1047 MET cc_start: 0.8006 (mtt) cc_final: 0.7233 (mtt) REVERT: C 1242 ILE cc_start: 0.8988 (mt) cc_final: 0.8724 (tp) REVERT: D 296 MET cc_start: 0.8835 (tpp) cc_final: 0.8592 (tpp) REVERT: D 353 MET cc_start: 0.8820 (mmm) cc_final: 0.8526 (mmm) REVERT: D 442 MET cc_start: 0.8395 (mtm) cc_final: 0.7116 (mtm) REVERT: D 460 ASP cc_start: 0.8194 (m-30) cc_final: 0.7800 (m-30) REVERT: D 473 LYS cc_start: 0.8450 (ptpt) cc_final: 0.8228 (mttm) REVERT: D 819 LYS cc_start: 0.8274 (mmtm) cc_final: 0.7870 (mmmt) REVERT: D 1229 MET cc_start: 0.9116 (mmm) cc_final: 0.8905 (mmt) REVERT: D 1368 MET cc_start: 0.8672 (ttt) cc_final: 0.8301 (ttm) REVERT: D 1391 MET cc_start: 0.8543 (ttm) cc_final: 0.8289 (ttm) REVERT: E 116 ILE cc_start: 0.8395 (pt) cc_final: 0.7940 (mm) REVERT: E 166 ASP cc_start: 0.7647 (m-30) cc_final: 0.7183 (t70) REVERT: E 458 MET cc_start: 0.7629 (ptm) cc_final: 0.6916 (ptt) REVERT: E 460 ASP cc_start: 0.7782 (m-30) cc_final: 0.7488 (m-30) REVERT: E 558 MET cc_start: 0.8019 (ttp) cc_final: 0.7711 (ttp) REVERT: E 562 MET cc_start: 0.8416 (mtm) cc_final: 0.8177 (mtm) REVERT: E 745 ARG cc_start: 0.7614 (mtp180) cc_final: 0.7145 (mtt90) REVERT: E 780 ARG cc_start: 0.8035 (mtm180) cc_final: 0.7482 (ptp-170) REVERT: E 805 ASP cc_start: 0.8196 (t0) cc_final: 0.7614 (t0) REVERT: E 819 LYS cc_start: 0.8580 (mmtm) cc_final: 0.8264 (mmtt) REVERT: E 1060 ARG cc_start: 0.8214 (mmp80) cc_final: 0.7964 (mmm-85) REVERT: E 1229 MET cc_start: 0.7602 (mmm) cc_final: 0.6798 (mmm) REVERT: E 1256 MET cc_start: 0.8888 (mtp) cc_final: 0.8628 (mtm) REVERT: F 1256 MET cc_start: 0.8391 (mtp) cc_final: 0.8093 (mtp) REVERT: G 6 MET cc_start: 0.8557 (ptm) cc_final: 0.7798 (ptm) REVERT: H 149 LEU cc_start: 0.7251 (mt) cc_final: 0.7000 (mt) REVERT: H 204 ARG cc_start: 0.7378 (tpp-160) cc_final: 0.7127 (mtt-85) REVERT: H 218 ASN cc_start: 0.7809 (m110) cc_final: 0.7554 (m110) REVERT: H 303 MET cc_start: 0.5955 (mmp) cc_final: 0.5448 (mmm) REVERT: H 324 ASP cc_start: 0.4772 (t0) cc_final: 0.4571 (p0) REVERT: H 415 GLU cc_start: 0.7403 (mt-10) cc_final: 0.6780 (tt0) REVERT: H 429 ARG cc_start: 0.7461 (mmm160) cc_final: 0.7047 (tpt90) REVERT: J 406 ASP cc_start: 0.7427 (t0) cc_final: 0.7112 (t0) REVERT: K 432 MET cc_start: 0.8521 (ttp) cc_final: 0.8310 (ttp) REVERT: L 149 LEU cc_start: 0.7960 (mt) cc_final: 0.7738 (mt) REVERT: L 204 ARG cc_start: 0.7681 (tpp-160) cc_final: 0.7413 (mtt-85) REVERT: L 218 ASN cc_start: 0.7783 (m110) cc_final: 0.7534 (m110) REVERT: L 303 MET cc_start: 0.5885 (mmp) cc_final: 0.5247 (mmm) REVERT: L 415 GLU cc_start: 0.7612 (mt-10) cc_final: 0.6942 (tt0) outliers start: 4 outliers final: 1 residues processed: 1569 average time/residue: 0.9367 time to fit residues: 2410.7082 Evaluate side-chains 800 residues out of total 9444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 799 time to evaluate : 7.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 324 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1164 random chunks: chunk 982 optimal weight: 0.0770 chunk 882 optimal weight: 0.0980 chunk 489 optimal weight: 5.9990 chunk 301 optimal weight: 6.9990 chunk 595 optimal weight: 8.9990 chunk 471 optimal weight: 6.9990 chunk 912 optimal weight: 0.8980 chunk 353 optimal weight: 8.9990 chunk 554 optimal weight: 0.9990 chunk 679 optimal weight: 9.9990 chunk 1057 optimal weight: 1.9990 overall best weight: 0.8142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS A 52 GLN A 165 ASN A 240 ASN A 497 HIS A 635 ASN A 643 ASN A 762 HIS A 824 GLN A 872 ASN ** A 876 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1159 ASN A1177 HIS A1205 ASN A1325 ASN A1363 ASN A1406 ASN A1419 HIS A1423 GLN B 30 HIS B 52 GLN B 143 GLN B 165 ASN B 259 HIS B 497 HIS ** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 643 ASN B 653 HIS B 738 HIS B 762 HIS B 799 GLN ** B1120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1177 HIS B1195 ASN B1205 ASN B1325 ASN B1363 ASN C 30 HIS C 52 GLN C 143 GLN C 165 ASN C 240 ASN C 497 HIS C 539 GLN C 653 HIS C 738 HIS C 762 HIS C 824 GLN ** C 876 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 971 HIS C1177 HIS C1205 ASN C1230 GLN C1325 ASN C1363 ASN C1456 GLN D 30 HIS D 52 GLN D 165 ASN D 240 ASN D 378 GLN D 497 HIS D 635 ASN D 643 ASN D 653 HIS D 762 HIS D 824 GLN D 872 ASN ** D 876 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1159 ASN D1177 HIS D1205 ASN D1325 ASN D1363 ASN D1406 ASN D1419 HIS D1423 GLN E 30 HIS E 52 GLN E 163 GLN E 259 HIS E 313 HIS E 378 GLN E 421 GLN E 497 HIS ** E 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 643 ASN E 653 HIS E 738 HIS E 762 HIS E 799 GLN E 824 GLN ** E1063 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1169 HIS E1177 HIS ** E1195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1205 ASN E1230 GLN E1325 ASN F 30 HIS F 52 GLN F 143 GLN F 240 ASN F 497 HIS F 539 GLN F 643 ASN F 653 HIS F 738 HIS F 762 HIS F 818 ASN ** F 876 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 971 HIS F1177 HIS F1205 ASN F1325 ASN F1363 ASN G 4 GLN G 11 HIS G 64 ASN ** G 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 129 ASN G 218 ASN G 234 HIS G 270 ASN H 11 HIS H 50 GLN H 86 GLN H 129 ASN H 218 ASN H 234 HIS H 327 ASN I 11 HIS I 50 GLN I 86 GLN I 129 ASN I 216 HIS I 218 ASN I 234 HIS J 4 GLN J 11 HIS J 64 ASN ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 129 ASN J 218 ASN J 234 HIS J 270 ASN K 11 HIS K 50 GLN K 64 ASN K 86 GLN K 129 ASN K 216 HIS K 218 ASN K 234 HIS L 11 HIS L 50 GLN L 86 GLN L 218 ASN L 234 HIS L 327 ASN ** L 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 149 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.137 92100 Z= 0.165 Angle : 0.806 82.824 124818 Z= 0.330 Chirality : 0.055 2.002 13890 Planarity : 0.004 0.049 16326 Dihedral : 6.167 152.372 13070 Min Nonbonded Distance : 1.608 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.25 % Allowed : 9.37 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % 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: -1.84 (0.07), residues: 11640 helix: 0.07 (0.08), residues: 4194 sheet: -1.48 (0.11), residues: 1920 loop : -2.16 (0.07), residues: 5526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP I 69 HIS 0.006 0.001 HIS F 603 PHE 0.014 0.001 PHE J 36 TYR 0.016 0.001 TYR F 813 ARG 0.007 0.000 ARG B 832 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23280 Ramachandran restraints generated. 11640 Oldfield, 0 Emsley, 11640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23280 Ramachandran restraints generated. 11640 Oldfield, 0 Emsley, 11640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1002 residues out of total 9444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 884 time to evaluate : 7.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 MET cc_start: 0.8760 (tpp) cc_final: 0.8485 (tpp) REVERT: A 296 MET cc_start: 0.8924 (tpp) cc_final: 0.8331 (tpp) REVERT: A 473 LYS cc_start: 0.8553 (ptpt) cc_final: 0.8286 (mttm) REVERT: A 693 MET cc_start: 0.8792 (mmm) cc_final: 0.8204 (mmm) REVERT: A 1176 GLU cc_start: 0.7782 (pm20) cc_final: 0.7547 (pm20) REVERT: A 1229 MET cc_start: 0.9058 (mmm) cc_final: 0.8808 (mmt) REVERT: A 1368 MET cc_start: 0.8720 (ttt) cc_final: 0.8418 (ttm) REVERT: A 1391 MET cc_start: 0.8568 (ttm) cc_final: 0.8316 (ttm) REVERT: B 84 ASP cc_start: 0.7738 (OUTLIER) cc_final: 0.7268 (t70) REVERT: B 235 ASN cc_start: 0.7708 (m-40) cc_final: 0.7396 (m-40) REVERT: B 375 ASP cc_start: 0.7012 (p0) cc_final: 0.6641 (p0) REVERT: B 818 ASN cc_start: 0.7023 (m-40) cc_final: 0.6660 (m110) REVERT: B 823 MET cc_start: 0.6558 (mtp) cc_final: 0.5811 (mtp) REVERT: B 846 ILE cc_start: 0.8400 (mm) cc_final: 0.8099 (mm) REVERT: B 1092 ILE cc_start: 0.6899 (mt) cc_final: 0.6672 (mm) REVERT: C 165 ASN cc_start: 0.8558 (m-40) cc_final: 0.8263 (m110) REVERT: C 263 LEU cc_start: 0.8651 (mt) cc_final: 0.8410 (mp) REVERT: C 389 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7799 (mp0) REVERT: C 391 ILE cc_start: 0.8838 (tt) cc_final: 0.8637 (tp) REVERT: C 687 MET cc_start: 0.6912 (ptp) cc_final: 0.6650 (ptp) REVERT: C 747 SER cc_start: 0.8888 (m) cc_final: 0.8564 (p) REVERT: C 964 MET cc_start: 0.7748 (tpp) cc_final: 0.7313 (tpp) REVERT: C 1242 ILE cc_start: 0.8949 (mt) cc_final: 0.8692 (tp) REVERT: D 244 MET cc_start: 0.8608 (tpp) cc_final: 0.8074 (tpt) REVERT: D 353 MET cc_start: 0.8801 (mmm) cc_final: 0.8506 (mmm) REVERT: D 460 ASP cc_start: 0.8191 (m-30) cc_final: 0.7978 (m-30) REVERT: D 473 LYS cc_start: 0.8424 (ptpt) cc_final: 0.8184 (mttm) REVERT: D 819 LYS cc_start: 0.8309 (mmtm) cc_final: 0.7909 (mmmt) REVERT: D 1229 MET cc_start: 0.9144 (mmm) cc_final: 0.8861 (mmt) REVERT: D 1368 MET cc_start: 0.8600 (ttt) cc_final: 0.8313 (ttm) REVERT: D 1391 MET cc_start: 0.8491 (ttm) cc_final: 0.8245 (ttm) REVERT: E 116 ILE cc_start: 0.8277 (pt) cc_final: 0.8029 (mm) REVERT: E 233 GLU cc_start: 0.7153 (tm-30) cc_final: 0.6812 (tm-30) REVERT: E 296 MET cc_start: 0.8278 (tpt) cc_final: 0.8027 (tpp) REVERT: E 460 ASP cc_start: 0.7799 (m-30) cc_final: 0.7501 (m-30) REVERT: E 780 ARG cc_start: 0.8118 (mtm180) cc_final: 0.7557 (ptp-170) REVERT: E 805 ASP cc_start: 0.8045 (t0) cc_final: 0.7828 (t0) REVERT: E 819 LYS cc_start: 0.8580 (mmtm) cc_final: 0.8271 (mmtt) REVERT: E 1060 ARG cc_start: 0.8201 (mmp80) cc_final: 0.7972 (mmm-85) REVERT: E 1229 MET cc_start: 0.7692 (mmm) cc_final: 0.7472 (mmm) REVERT: E 1246 LEU cc_start: 0.8744 (tp) cc_final: 0.8536 (tp) REVERT: E 1256 MET cc_start: 0.8820 (mtp) cc_final: 0.8408 (mtm) REVERT: F 324 MET cc_start: 0.8324 (tpp) cc_final: 0.7817 (ttt) REVERT: F 512 ASP cc_start: 0.8070 (p0) cc_final: 0.6419 (p0) REVERT: F 1100 MET cc_start: 0.8176 (mtp) cc_final: 0.7897 (mtp) REVERT: F 1256 MET cc_start: 0.8322 (mtp) cc_final: 0.8044 (mtp) REVERT: F 1291 ASP cc_start: 0.8402 (p0) cc_final: 0.8141 (p0) REVERT: G 6 MET cc_start: 0.8534 (ptm) cc_final: 0.7955 (ptp) REVERT: G 409 ASN cc_start: 0.7728 (m-40) cc_final: 0.7412 (m110) REVERT: H 5 ARG cc_start: 0.7375 (mtm110) cc_final: 0.7060 (ptp90) REVERT: H 6 MET cc_start: 0.8421 (ptp) cc_final: 0.8088 (ptp) REVERT: H 149 LEU cc_start: 0.7196 (mt) cc_final: 0.6918 (mt) REVERT: H 204 ARG cc_start: 0.7475 (tpp-160) cc_final: 0.7182 (mtt-85) REVERT: H 218 ASN cc_start: 0.7819 (m-40) cc_final: 0.7533 (m110) REVERT: H 303 MET cc_start: 0.5953 (mmp) cc_final: 0.5306 (mmm) REVERT: H 324 ASP cc_start: 0.5213 (t0) cc_final: 0.4926 (p0) REVERT: H 328 MET cc_start: 0.8107 (tpt) cc_final: 0.7528 (mtt) REVERT: H 334 GLU cc_start: 0.7419 (mp0) cc_final: 0.6955 (pt0) REVERT: H 415 GLU cc_start: 0.7342 (mt-10) cc_final: 0.6837 (tt0) REVERT: H 429 ARG cc_start: 0.7445 (mmm160) cc_final: 0.7047 (tpt90) REVERT: I 435 MET cc_start: 0.6750 (mtt) cc_final: 0.6493 (mtt) REVERT: J 6 MET cc_start: 0.8194 (ptp) cc_final: 0.7642 (ptp) REVERT: J 145 ARG cc_start: 0.7613 (ttp80) cc_final: 0.7303 (ttp80) REVERT: K 432 MET cc_start: 0.8624 (ttp) cc_final: 0.8356 (ttp) REVERT: L 5 ARG cc_start: 0.7534 (mtm110) cc_final: 0.7003 (ptp90) REVERT: L 218 ASN cc_start: 0.7906 (m-40) cc_final: 0.7623 (m110) REVERT: L 303 MET cc_start: 0.5871 (mmp) cc_final: 0.5199 (mmm) REVERT: L 327 ASN cc_start: 0.7730 (OUTLIER) cc_final: 0.7413 (t0) REVERT: L 328 MET cc_start: 0.7868 (tpt) cc_final: 0.7446 (mtt) REVERT: L 334 GLU cc_start: 0.7607 (mp0) cc_final: 0.6883 (pt0) REVERT: L 415 GLU cc_start: 0.7473 (mt-10) cc_final: 0.6862 (tt0) REVERT: L 429 ARG cc_start: 0.7957 (tpt90) cc_final: 0.7735 (tpt90) outliers start: 118 outliers final: 64 residues processed: 957 average time/residue: 0.8205 time to fit residues: 1357.8853 Evaluate side-chains 817 residues out of total 9444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 751 time to evaluate : 7.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 273 ASP Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 796 HIS Chi-restraints excluded: chain B residue 1030 THR Chi-restraints excluded: chain B residue 1103 ILE Chi-restraints excluded: chain B residue 1131 THR Chi-restraints excluded: chain B residue 1187 LEU Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 511 ILE Chi-restraints excluded: chain C residue 971 HIS Chi-restraints excluded: chain C residue 1179 ASP Chi-restraints excluded: chain C residue 1229 MET Chi-restraints excluded: chain C residue 1248 SER Chi-restraints excluded: chain C residue 1268 LEU Chi-restraints excluded: chain C residue 1394 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 360 ASP Chi-restraints excluded: chain D residue 375 ASP Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 640 THR Chi-restraints excluded: chain D residue 708 MET Chi-restraints excluded: chain D residue 1178 LEU Chi-restraints excluded: chain E residue 42 ASP Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 521 SER Chi-restraints excluded: chain E residue 607 THR Chi-restraints excluded: chain E residue 640 THR Chi-restraints excluded: chain E residue 1103 ILE Chi-restraints excluded: chain E residue 1131 THR Chi-restraints excluded: chain E residue 1452 THR Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 273 ASP Chi-restraints excluded: chain F residue 304 THR Chi-restraints excluded: chain F residue 307 GLN Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 506 VAL Chi-restraints excluded: chain F residue 728 ILE Chi-restraints excluded: chain F residue 843 VAL Chi-restraints excluded: chain F residue 899 ASN Chi-restraints excluded: chain F residue 964 MET Chi-restraints excluded: chain F residue 1397 LEU Chi-restraints excluded: chain H residue 111 ILE Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 229 GLU Chi-restraints excluded: chain H residue 317 VAL Chi-restraints excluded: chain H residue 391 VAL Chi-restraints excluded: chain I residue 6 MET Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain J residue 360 VAL Chi-restraints excluded: chain K residue 129 ASN Chi-restraints excluded: chain K residue 360 VAL Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain L residue 286 LEU Chi-restraints excluded: chain L residue 327 ASN Chi-restraints excluded: chain L residue 391 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1164 random chunks: chunk 587 optimal weight: 0.7980 chunk 328 optimal weight: 7.9990 chunk 879 optimal weight: 9.9990 chunk 719 optimal weight: 8.9990 chunk 291 optimal weight: 9.9990 chunk 1058 optimal weight: 4.9990 chunk 1143 optimal weight: 9.9990 chunk 943 optimal weight: 0.3980 chunk 1050 optimal weight: 4.9990 chunk 361 optimal weight: 7.9990 chunk 849 optimal weight: 2.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 ASN A 899 ASN B 240 ASN B 539 GLN B 799 GLN B 876 ASN B1120 GLN ** C 876 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1406 ASN C1456 GLN D 240 ASN D 899 ASN E 240 ASN E 378 GLN ** E 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 799 GLN E1063 HIS E1195 ASN F 818 ASN ** F 876 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1195 ASN G 4 GLN G 86 GLN G 108 ASN H 14 GLN H 129 ASN H 434 ASN I 108 ASN ** I 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 434 ASN J 4 GLN J 86 GLN J 108 ASN K 64 ASN K 108 ASN ** L 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 92100 Z= 0.271 Angle : 0.832 82.529 124818 Z= 0.346 Chirality : 0.054 1.598 13890 Planarity : 0.004 0.054 16326 Dihedral : 5.917 158.688 13068 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.82 % Allowed : 11.77 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % 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: -1.30 (0.08), residues: 11640 helix: 0.51 (0.08), residues: 4188 sheet: -1.06 (0.12), residues: 1896 loop : -1.89 (0.08), residues: 5556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP K 69 HIS 0.043 0.001 HIS C 971 PHE 0.020 0.002 PHE G 36 TYR 0.018 0.002 TYR I 82 ARG 0.007 0.000 ARG I 231 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23280 Ramachandran restraints generated. 11640 Oldfield, 0 Emsley, 11640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23280 Ramachandran restraints generated. 11640 Oldfield, 0 Emsley, 11640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 974 residues out of total 9444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 802 time to evaluate : 7.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLU cc_start: 0.8012 (tt0) cc_final: 0.7770 (tt0) REVERT: A 61 VAL cc_start: 0.9095 (OUTLIER) cc_final: 0.8810 (t) REVERT: A 296 MET cc_start: 0.8986 (tpp) cc_final: 0.8443 (tpp) REVERT: A 473 LYS cc_start: 0.8576 (ptpt) cc_final: 0.8316 (mttm) REVERT: A 1229 MET cc_start: 0.8889 (mmm) cc_final: 0.8648 (mmt) REVERT: A 1368 MET cc_start: 0.8670 (ttt) cc_final: 0.8428 (ttp) REVERT: B 84 ASP cc_start: 0.8171 (OUTLIER) cc_final: 0.7697 (t70) REVERT: B 96 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.7842 (mp0) REVERT: B 162 GLU cc_start: 0.7214 (tp30) cc_final: 0.6904 (tp30) REVERT: B 182 MET cc_start: 0.8166 (mmt) cc_final: 0.7920 (mmt) REVERT: B 235 ASN cc_start: 0.7896 (m-40) cc_final: 0.7564 (m-40) REVERT: B 284 MET cc_start: 0.8773 (mtp) cc_final: 0.8519 (mtp) REVERT: B 375 ASP cc_start: 0.7539 (p0) cc_final: 0.7036 (p0) REVERT: B 786 ASP cc_start: 0.8205 (OUTLIER) cc_final: 0.7929 (m-30) REVERT: B 823 MET cc_start: 0.7201 (mtp) cc_final: 0.6789 (mtp) REVERT: B 929 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7759 (tm-30) REVERT: C 165 ASN cc_start: 0.8601 (m-40) cc_final: 0.8288 (m110) REVERT: C 391 ILE cc_start: 0.9000 (tt) cc_final: 0.8770 (tp) REVERT: C 446 GLU cc_start: 0.7579 (tp30) cc_final: 0.7097 (tm-30) REVERT: C 687 MET cc_start: 0.7406 (ptp) cc_final: 0.7160 (ptp) REVERT: C 747 SER cc_start: 0.8855 (m) cc_final: 0.8611 (p) REVERT: C 1051 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.6608 (mp0) REVERT: C 1242 ILE cc_start: 0.9008 (mt) cc_final: 0.8740 (tp) REVERT: D 460 ASP cc_start: 0.8198 (m-30) cc_final: 0.7813 (m-30) REVERT: D 819 LYS cc_start: 0.8511 (mmtm) cc_final: 0.8071 (mmmt) REVERT: D 952 MET cc_start: 0.7927 (ttt) cc_final: 0.7617 (ttt) REVERT: D 1229 MET cc_start: 0.8929 (mmm) cc_final: 0.8695 (mmt) REVERT: D 1368 MET cc_start: 0.8659 (ttt) cc_final: 0.8412 (ttm) REVERT: D 1391 MET cc_start: 0.8604 (ttm) cc_final: 0.8346 (ttm) REVERT: E 233 GLU cc_start: 0.7292 (tm-30) cc_final: 0.6722 (tm-30) REVERT: E 708 MET cc_start: 0.8426 (ttp) cc_final: 0.8216 (ttp) REVERT: E 780 ARG cc_start: 0.8160 (mtm180) cc_final: 0.7636 (ptp-170) REVERT: E 860 MET cc_start: 0.8376 (ttm) cc_final: 0.8163 (tpp) REVERT: E 1047 MET cc_start: 0.8388 (mtt) cc_final: 0.8032 (mtp) REVERT: E 1060 ARG cc_start: 0.8194 (mmp80) cc_final: 0.7981 (mmm-85) REVERT: E 1206 GLU cc_start: 0.7417 (pm20) cc_final: 0.7124 (pp20) REVERT: E 1289 MET cc_start: 0.7048 (mmt) cc_final: 0.6768 (mmt) REVERT: E 1397 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.8037 (tp) REVERT: F 84 ASP cc_start: 0.7528 (m-30) cc_final: 0.7250 (t0) REVERT: F 493 ARG cc_start: 0.8026 (mmt-90) cc_final: 0.7743 (mmt180) REVERT: F 971 HIS cc_start: 0.9362 (OUTLIER) cc_final: 0.8574 (t70) REVERT: F 1256 MET cc_start: 0.8385 (mtp) cc_final: 0.8058 (mtp) REVERT: F 1291 ASP cc_start: 0.8499 (p0) cc_final: 0.8224 (p0) REVERT: G 6 MET cc_start: 0.8393 (ptm) cc_final: 0.7983 (ptp) REVERT: H 5 ARG cc_start: 0.7755 (mtm110) cc_final: 0.7186 (ptp90) REVERT: H 204 ARG cc_start: 0.7394 (tpp-160) cc_final: 0.7093 (mtt-85) REVERT: H 218 ASN cc_start: 0.8132 (m-40) cc_final: 0.7906 (m110) REVERT: H 303 MET cc_start: 0.6196 (mmp) cc_final: 0.5628 (mmm) REVERT: H 328 MET cc_start: 0.8022 (tpt) cc_final: 0.7774 (tpt) REVERT: H 332 GLN cc_start: 0.6958 (mp10) cc_final: 0.6635 (mm-40) REVERT: H 334 GLU cc_start: 0.7482 (mp0) cc_final: 0.6882 (pt0) REVERT: H 415 GLU cc_start: 0.7420 (mt-10) cc_final: 0.6856 (tt0) REVERT: H 429 ARG cc_start: 0.7508 (mmm160) cc_final: 0.7127 (tpt90) REVERT: J 6 MET cc_start: 0.8267 (ptp) cc_final: 0.7735 (ptp) REVERT: J 317 VAL cc_start: 0.7732 (OUTLIER) cc_final: 0.7517 (t) REVERT: K 316 SER cc_start: 0.8453 (t) cc_final: 0.8010 (p) REVERT: K 412 ASP cc_start: 0.7161 (t0) cc_final: 0.6821 (t0) REVERT: K 432 MET cc_start: 0.8626 (ttp) cc_final: 0.8323 (ttp) REVERT: L 5 ARG cc_start: 0.7753 (mtm110) cc_final: 0.7136 (ptp90) REVERT: L 6 MET cc_start: 0.8415 (ptp) cc_final: 0.8189 (ptp) REVERT: L 218 ASN cc_start: 0.8081 (m-40) cc_final: 0.7833 (m110) REVERT: L 303 MET cc_start: 0.5914 (mmp) cc_final: 0.5258 (mmm) REVERT: L 328 MET cc_start: 0.7865 (tpt) cc_final: 0.7432 (mtt) REVERT: L 334 GLU cc_start: 0.7284 (mp0) cc_final: 0.6660 (pt0) REVERT: L 415 GLU cc_start: 0.7203 (mt-10) cc_final: 0.6906 (tt0) REVERT: L 429 ARG cc_start: 0.8041 (tpt90) cc_final: 0.7817 (tpt90) outliers start: 172 outliers final: 109 residues processed: 930 average time/residue: 0.8007 time to fit residues: 1293.1794 Evaluate side-chains 841 residues out of total 9444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 723 time to evaluate : 7.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 728 ILE Chi-restraints excluded: chain A residue 971 HIS Chi-restraints excluded: chain A residue 977 ILE Chi-restraints excluded: chain A residue 1265 THR Chi-restraints excluded: chain A residue 1355 VAL Chi-restraints excluded: chain A residue 1468 VAL Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 273 ASP Chi-restraints excluded: chain B residue 564 ASP Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 786 ASP Chi-restraints excluded: chain B residue 882 SER Chi-restraints excluded: chain B residue 929 GLU Chi-restraints excluded: chain B residue 971 HIS Chi-restraints excluded: chain B residue 1030 THR Chi-restraints excluded: chain B residue 1103 ILE Chi-restraints excluded: chain B residue 1131 THR Chi-restraints excluded: chain B residue 1187 LEU Chi-restraints excluded: chain B residue 1265 THR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 461 MET Chi-restraints excluded: chain C residue 640 THR Chi-restraints excluded: chain C residue 1051 GLU Chi-restraints excluded: chain C residue 1179 ASP Chi-restraints excluded: chain C residue 1201 LEU Chi-restraints excluded: chain C residue 1248 SER Chi-restraints excluded: chain C residue 1268 LEU Chi-restraints excluded: chain C residue 1276 LEU Chi-restraints excluded: chain C residue 1294 ASP Chi-restraints excluded: chain C residue 1313 SER Chi-restraints excluded: chain C residue 1394 VAL Chi-restraints excluded: chain D residue 42 ASP Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 375 ASP Chi-restraints excluded: chain D residue 478 SER Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 708 MET Chi-restraints excluded: chain D residue 728 ILE Chi-restraints excluded: chain D residue 844 GLU Chi-restraints excluded: chain D residue 971 HIS Chi-restraints excluded: chain D residue 1265 THR Chi-restraints excluded: chain D residue 1468 VAL Chi-restraints excluded: chain E residue 42 ASP Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 335 MET Chi-restraints excluded: chain E residue 607 THR Chi-restraints excluded: chain E residue 640 THR Chi-restraints excluded: chain E residue 747 SER Chi-restraints excluded: chain E residue 771 VAL Chi-restraints excluded: chain E residue 847 THR Chi-restraints excluded: chain E residue 1002 SER Chi-restraints excluded: chain E residue 1103 ILE Chi-restraints excluded: chain E residue 1131 THR Chi-restraints excluded: chain E residue 1201 LEU Chi-restraints excluded: chain E residue 1307 VAL Chi-restraints excluded: chain E residue 1397 LEU Chi-restraints excluded: chain E residue 1405 ILE Chi-restraints excluded: chain E residue 1452 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 273 ASP Chi-restraints excluded: chain F residue 304 THR Chi-restraints excluded: chain F residue 307 GLN Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain F residue 506 VAL Chi-restraints excluded: chain F residue 607 THR Chi-restraints excluded: chain F residue 650 LEU Chi-restraints excluded: chain F residue 711 MET Chi-restraints excluded: chain F residue 747 SER Chi-restraints excluded: chain F residue 843 VAL Chi-restraints excluded: chain F residue 964 MET Chi-restraints excluded: chain F residue 971 HIS Chi-restraints excluded: chain F residue 1265 THR Chi-restraints excluded: chain F residue 1276 LEU Chi-restraints excluded: chain F residue 1397 LEU Chi-restraints excluded: chain G residue 396 VAL Chi-restraints excluded: chain H residue 111 ILE Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 277 THR Chi-restraints excluded: chain H residue 389 PHE Chi-restraints excluded: chain H residue 391 VAL Chi-restraints excluded: chain H residue 418 VAL Chi-restraints excluded: chain H residue 451 VAL Chi-restraints excluded: chain I residue 6 MET Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 424 LEU Chi-restraints excluded: chain I residue 433 THR Chi-restraints excluded: chain J residue 317 VAL Chi-restraints excluded: chain K residue 6 MET Chi-restraints excluded: chain K residue 300 ASP Chi-restraints excluded: chain K residue 360 VAL Chi-restraints excluded: chain K residue 424 LEU Chi-restraints excluded: chain L residue 98 ILE Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain L residue 142 THR Chi-restraints excluded: chain L residue 277 THR Chi-restraints excluded: chain L residue 286 LEU Chi-restraints excluded: chain L residue 315 THR Chi-restraints excluded: chain L residue 389 PHE Chi-restraints excluded: chain L residue 391 VAL Chi-restraints excluded: chain L residue 407 LEU Chi-restraints excluded: chain L residue 451 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1164 random chunks: chunk 1046 optimal weight: 8.9990 chunk 796 optimal weight: 5.9990 chunk 549 optimal weight: 0.8980 chunk 117 optimal weight: 6.9990 chunk 505 optimal weight: 1.9990 chunk 711 optimal weight: 5.9990 chunk 1062 optimal weight: 10.0000 chunk 1125 optimal weight: 0.9990 chunk 555 optimal weight: 0.9990 chunk 1007 optimal weight: 10.0000 chunk 303 optimal weight: 0.8980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 HIS A1177 HIS B 818 ASN B1189 GLN B1456 GLN C1195 ASN C1406 ASN C1413 GLN C1456 GLN D 240 ASN D1177 HIS E 240 ASN ** E 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 818 ASN ** F 876 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1456 GLN G 4 GLN H 129 ASN H 434 ASN I 64 ASN ** I 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 434 ASN J 4 GLN K 64 ASN K 129 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.106 92100 Z= 0.162 Angle : 0.787 82.295 124818 Z= 0.316 Chirality : 0.051 1.515 13890 Planarity : 0.003 0.043 16326 Dihedral : 5.517 158.204 13068 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.72 % Allowed : 13.03 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % 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: -0.89 (0.08), residues: 11640 helix: 0.79 (0.09), residues: 4200 sheet: -0.79 (0.12), residues: 1854 loop : -1.62 (0.08), residues: 5586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP L 69 HIS 0.006 0.001 HIS C 971 PHE 0.015 0.001 PHE I 36 TYR 0.013 0.001 TYR B 211 ARG 0.006 0.000 ARG G 378 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23280 Ramachandran restraints generated. 11640 Oldfield, 0 Emsley, 11640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23280 Ramachandran restraints generated. 11640 Oldfield, 0 Emsley, 11640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 959 residues out of total 9444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 797 time to evaluate : 7.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 VAL cc_start: 0.9046 (t) cc_final: 0.8767 (t) REVERT: A 244 MET cc_start: 0.8895 (tpp) cc_final: 0.8449 (tpt) REVERT: A 296 MET cc_start: 0.8984 (tpp) cc_final: 0.8482 (tpp) REVERT: A 473 LYS cc_start: 0.8538 (ptpt) cc_final: 0.8305 (mttm) REVERT: A 1229 MET cc_start: 0.8960 (mmm) cc_final: 0.8736 (mmt) REVERT: A 1368 MET cc_start: 0.8674 (ttt) cc_final: 0.8433 (ttp) REVERT: A 1391 MET cc_start: 0.8596 (ttm) cc_final: 0.8310 (ttm) REVERT: B 84 ASP cc_start: 0.7939 (OUTLIER) cc_final: 0.7153 (t0) REVERT: B 96 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.7816 (mp0) REVERT: B 162 GLU cc_start: 0.7414 (tp30) cc_final: 0.7098 (tp30) REVERT: B 182 MET cc_start: 0.8210 (mmt) cc_final: 0.7949 (mmt) REVERT: B 235 ASN cc_start: 0.7967 (m-40) cc_final: 0.7614 (m-40) REVERT: B 375 ASP cc_start: 0.7463 (p0) cc_final: 0.6931 (p0) REVERT: B 786 ASP cc_start: 0.8149 (OUTLIER) cc_final: 0.7910 (m-30) REVERT: B 823 MET cc_start: 0.7168 (mtp) cc_final: 0.6770 (mtp) REVERT: B 829 LEU cc_start: 0.9516 (mp) cc_final: 0.9289 (mp) REVERT: C 165 ASN cc_start: 0.8537 (m-40) cc_final: 0.8208 (m110) REVERT: C 442 MET cc_start: 0.6419 (tpp) cc_final: 0.5854 (tpp) REVERT: C 687 MET cc_start: 0.7384 (ptp) cc_final: 0.7158 (ptp) REVERT: C 747 SER cc_start: 0.8799 (m) cc_final: 0.8505 (p) REVERT: C 964 MET cc_start: 0.7718 (tpp) cc_final: 0.7415 (tpp) REVERT: C 1051 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.6588 (mp0) REVERT: C 1242 ILE cc_start: 0.9008 (mt) cc_final: 0.8728 (tp) REVERT: C 1248 SER cc_start: 0.9171 (OUTLIER) cc_final: 0.8903 (p) REVERT: D 296 MET cc_start: 0.8936 (tpp) cc_final: 0.8539 (tpp) REVERT: D 460 ASP cc_start: 0.8220 (m-30) cc_final: 0.7831 (m-30) REVERT: D 693 MET cc_start: 0.8714 (mmm) cc_final: 0.8413 (mmm) REVERT: D 819 LYS cc_start: 0.8446 (mmtm) cc_final: 0.8026 (mmmt) REVERT: D 952 MET cc_start: 0.7931 (ttt) cc_final: 0.7645 (ttt) REVERT: D 1229 MET cc_start: 0.8977 (mmm) cc_final: 0.8721 (mmt) REVERT: D 1368 MET cc_start: 0.8637 (ttt) cc_final: 0.8388 (ttp) REVERT: D 1391 MET cc_start: 0.8566 (ttm) cc_final: 0.8262 (ttm) REVERT: E 345 MET cc_start: 0.7976 (tpp) cc_final: 0.7687 (mtp) REVERT: E 360 ASP cc_start: 0.7680 (OUTLIER) cc_final: 0.7016 (t0) REVERT: E 558 MET cc_start: 0.7966 (ttp) cc_final: 0.7619 (ttp) REVERT: E 606 LEU cc_start: 0.9018 (tt) cc_final: 0.8811 (tp) REVERT: E 726 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7260 (mt-10) REVERT: E 780 ARG cc_start: 0.8320 (mtm180) cc_final: 0.7798 (ptp-170) REVERT: E 986 ASP cc_start: 0.8827 (t0) cc_final: 0.8597 (t0) REVERT: E 1047 MET cc_start: 0.8209 (mtt) cc_final: 0.7502 (mtp) REVERT: E 1051 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7370 (mp0) REVERT: E 1060 ARG cc_start: 0.8156 (mmp80) cc_final: 0.7955 (mmm-85) REVERT: E 1397 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.8062 (tp) REVERT: F 84 ASP cc_start: 0.7772 (m-30) cc_final: 0.6994 (t0) REVERT: F 353 MET cc_start: 0.8308 (tpt) cc_final: 0.8104 (mmm) REVERT: F 811 LYS cc_start: 0.8535 (ttmt) cc_final: 0.8298 (mtpp) REVERT: F 971 HIS cc_start: 0.9256 (OUTLIER) cc_final: 0.8379 (t70) REVERT: F 1256 MET cc_start: 0.8309 (mtp) cc_final: 0.7981 (mtp) REVERT: F 1291 ASP cc_start: 0.8426 (p0) cc_final: 0.8143 (p0) REVERT: G 6 MET cc_start: 0.8462 (ptm) cc_final: 0.7937 (ptp) REVERT: G 230 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8575 (mt) REVERT: H 5 ARG cc_start: 0.7674 (mtm110) cc_final: 0.7071 (ptp90) REVERT: H 204 ARG cc_start: 0.7473 (tpp-160) cc_final: 0.7161 (mtt-85) REVERT: H 218 ASN cc_start: 0.8111 (m-40) cc_final: 0.7890 (m110) REVERT: H 303 MET cc_start: 0.6392 (mmp) cc_final: 0.5923 (mmm) REVERT: H 324 ASP cc_start: 0.5519 (t0) cc_final: 0.4983 (p0) REVERT: H 328 MET cc_start: 0.7983 (tpt) cc_final: 0.7770 (tpt) REVERT: H 332 GLN cc_start: 0.6902 (mp10) cc_final: 0.6621 (mm-40) REVERT: H 334 GLU cc_start: 0.7519 (mp0) cc_final: 0.6917 (mt-10) REVERT: H 415 GLU cc_start: 0.7422 (mt-10) cc_final: 0.6768 (tt0) REVERT: H 429 ARG cc_start: 0.7457 (mmm160) cc_final: 0.7087 (tpt90) REVERT: I 167 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8646 (mt) REVERT: I 434 ASN cc_start: 0.7657 (OUTLIER) cc_final: 0.7434 (p0) REVERT: J 6 MET cc_start: 0.8189 (ptp) cc_final: 0.7788 (ptp) REVERT: J 230 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8733 (mt) REVERT: J 394 ASP cc_start: 0.7909 (t0) cc_final: 0.7631 (t0) REVERT: K 167 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8431 (mt) REVERT: K 180 TYR cc_start: 0.8821 (m-80) cc_final: 0.8569 (m-80) REVERT: K 316 SER cc_start: 0.8430 (t) cc_final: 0.8012 (p) REVERT: K 412 ASP cc_start: 0.7234 (t0) cc_final: 0.6905 (t0) REVERT: K 432 MET cc_start: 0.8619 (ttp) cc_final: 0.8356 (ttp) REVERT: L 5 ARG cc_start: 0.7749 (mtm110) cc_final: 0.7125 (ptp90) REVERT: L 39 GLU cc_start: 0.7567 (tm-30) cc_final: 0.7338 (tm-30) REVERT: L 218 ASN cc_start: 0.8061 (m-40) cc_final: 0.7804 (m110) REVERT: L 303 MET cc_start: 0.6254 (mmp) cc_final: 0.5592 (mmm) REVERT: L 328 MET cc_start: 0.7917 (tpt) cc_final: 0.7572 (mtt) REVERT: L 334 GLU cc_start: 0.7264 (mp0) cc_final: 0.6810 (pt0) REVERT: L 415 GLU cc_start: 0.7193 (mt-10) cc_final: 0.6970 (tt0) REVERT: L 429 ARG cc_start: 0.8106 (tpt90) cc_final: 0.7884 (tpt90) outliers start: 162 outliers final: 98 residues processed: 912 average time/residue: 0.7975 time to fit residues: 1270.8894 Evaluate side-chains 833 residues out of total 9444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 722 time to evaluate : 8.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 971 HIS Chi-restraints excluded: chain A residue 977 ILE Chi-restraints excluded: chain A residue 1468 VAL Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 273 ASP Chi-restraints excluded: chain B residue 381 GLU Chi-restraints excluded: chain B residue 786 ASP Chi-restraints excluded: chain B residue 882 SER Chi-restraints excluded: chain B residue 971 HIS Chi-restraints excluded: chain B residue 1030 THR Chi-restraints excluded: chain B residue 1033 SER Chi-restraints excluded: chain B residue 1103 ILE Chi-restraints excluded: chain B residue 1131 THR Chi-restraints excluded: chain B residue 1179 ASP Chi-restraints excluded: chain B residue 1187 LEU Chi-restraints excluded: chain B residue 1355 VAL Chi-restraints excluded: chain B residue 1415 ILE Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 461 MET Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 607 THR Chi-restraints excluded: chain C residue 640 THR Chi-restraints excluded: chain C residue 726 GLU Chi-restraints excluded: chain C residue 971 HIS Chi-restraints excluded: chain C residue 1002 SER Chi-restraints excluded: chain C residue 1051 GLU Chi-restraints excluded: chain C residue 1115 VAL Chi-restraints excluded: chain C residue 1179 ASP Chi-restraints excluded: chain C residue 1201 LEU Chi-restraints excluded: chain C residue 1246 LEU Chi-restraints excluded: chain C residue 1248 SER Chi-restraints excluded: chain C residue 1268 LEU Chi-restraints excluded: chain C residue 1276 LEU Chi-restraints excluded: chain C residue 1394 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 360 ASP Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 375 ASP Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 551 THR Chi-restraints excluded: chain D residue 640 THR Chi-restraints excluded: chain D residue 708 MET Chi-restraints excluded: chain D residue 971 HIS Chi-restraints excluded: chain D residue 1178 LEU Chi-restraints excluded: chain E residue 42 ASP Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 335 MET Chi-restraints excluded: chain E residue 360 ASP Chi-restraints excluded: chain E residue 607 THR Chi-restraints excluded: chain E residue 847 THR Chi-restraints excluded: chain E residue 971 HIS Chi-restraints excluded: chain E residue 1103 ILE Chi-restraints excluded: chain E residue 1131 THR Chi-restraints excluded: chain E residue 1201 LEU Chi-restraints excluded: chain E residue 1307 VAL Chi-restraints excluded: chain E residue 1397 LEU Chi-restraints excluded: chain E residue 1405 ILE Chi-restraints excluded: chain E residue 1452 THR Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 273 ASP Chi-restraints excluded: chain F residue 304 THR Chi-restraints excluded: chain F residue 307 GLN Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain F residue 506 VAL Chi-restraints excluded: chain F residue 747 SER Chi-restraints excluded: chain F residue 843 VAL Chi-restraints excluded: chain F residue 964 MET Chi-restraints excluded: chain F residue 971 HIS Chi-restraints excluded: chain F residue 1276 LEU Chi-restraints excluded: chain F residue 1397 LEU Chi-restraints excluded: chain F residue 1415 ILE Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 433 THR Chi-restraints excluded: chain H residue 111 ILE Chi-restraints excluded: chain H residue 286 LEU Chi-restraints excluded: chain H residue 391 VAL Chi-restraints excluded: chain I residue 167 LEU Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 424 LEU Chi-restraints excluded: chain I residue 433 THR Chi-restraints excluded: chain I residue 434 ASN Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 433 THR Chi-restraints excluded: chain K residue 129 ASN Chi-restraints excluded: chain K residue 167 LEU Chi-restraints excluded: chain K residue 360 VAL Chi-restraints excluded: chain K residue 424 LEU Chi-restraints excluded: chain K residue 444 ILE Chi-restraints excluded: chain L residue 98 ILE Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain L residue 277 THR Chi-restraints excluded: chain L residue 286 LEU Chi-restraints excluded: chain L residue 315 THR Chi-restraints excluded: chain L residue 391 VAL Chi-restraints excluded: chain L residue 407 LEU Chi-restraints excluded: chain L residue 451 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1164 random chunks: chunk 937 optimal weight: 9.9990 chunk 638 optimal weight: 6.9990 chunk 16 optimal weight: 0.0470 chunk 837 optimal weight: 8.9990 chunk 464 optimal weight: 10.0000 chunk 960 optimal weight: 9.9990 chunk 777 optimal weight: 10.0000 chunk 1 optimal weight: 0.3980 chunk 574 optimal weight: 7.9990 chunk 1009 optimal weight: 0.9990 chunk 283 optimal weight: 10.0000 overall best weight: 3.2884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 ASN A1177 HIS B 818 ASN B 899 ASN C 421 GLN C 505 GLN C1406 ASN C1456 GLN D 240 ASN D1177 HIS E 240 ASN ** E 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 818 ASN ** F 876 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1054 GLN G 4 GLN H 129 ASN I 64 ASN ** I 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 337 HIS I 434 ASN J 4 GLN K 64 ASN K 434 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 92100 Z= 0.296 Angle : 0.834 82.366 124818 Z= 0.346 Chirality : 0.053 1.507 13890 Planarity : 0.004 0.042 16326 Dihedral : 5.656 164.026 13068 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.27 % Allowed : 13.75 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % 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: -0.84 (0.08), residues: 11640 helix: 0.79 (0.08), residues: 4212 sheet: -0.66 (0.12), residues: 1800 loop : -1.59 (0.08), residues: 5628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP K 69 HIS 0.005 0.001 HIS C1063 PHE 0.017 0.002 PHE I 36 TYR 0.020 0.002 TYR F 211 ARG 0.014 0.000 ARG J 364 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23280 Ramachandran restraints generated. 11640 Oldfield, 0 Emsley, 11640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23280 Ramachandran restraints generated. 11640 Oldfield, 0 Emsley, 11640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 973 residues out of total 9444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 759 time to evaluate : 7.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 MET cc_start: 0.9087 (tpp) cc_final: 0.8554 (tpp) REVERT: A 473 LYS cc_start: 0.8540 (ptpt) cc_final: 0.8277 (mttm) REVERT: A 1229 MET cc_start: 0.8995 (mmm) cc_final: 0.8732 (mmt) REVERT: A 1368 MET cc_start: 0.8663 (ttt) cc_final: 0.8454 (ttm) REVERT: B 65 ARG cc_start: 0.7691 (ttm110) cc_final: 0.7280 (mtm180) REVERT: B 84 ASP cc_start: 0.8239 (OUTLIER) cc_final: 0.7316 (t0) REVERT: B 96 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.7932 (mp0) REVERT: B 162 GLU cc_start: 0.7689 (tp30) cc_final: 0.7438 (tp30) REVERT: B 182 MET cc_start: 0.8152 (mmt) cc_final: 0.7889 (mmt) REVERT: B 235 ASN cc_start: 0.8038 (m-40) cc_final: 0.7789 (m-40) REVERT: B 562 MET cc_start: 0.8010 (mtm) cc_final: 0.7514 (mtp) REVERT: B 829 LEU cc_start: 0.9501 (mp) cc_final: 0.9260 (mp) REVERT: B 832 ARG cc_start: 0.7780 (ttm110) cc_final: 0.7553 (ttm-80) REVERT: B 860 MET cc_start: 0.8094 (tpp) cc_final: 0.7660 (tpp) REVERT: C 115 ASP cc_start: 0.7957 (m-30) cc_final: 0.7459 (p0) REVERT: C 165 ASN cc_start: 0.8585 (m-40) cc_final: 0.8253 (m110) REVERT: C 441 ASP cc_start: 0.4784 (m-30) cc_final: 0.3665 (p0) REVERT: C 687 MET cc_start: 0.7638 (ptp) cc_final: 0.7415 (ptp) REVERT: C 747 SER cc_start: 0.8831 (m) cc_final: 0.8591 (p) REVERT: C 1051 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.6640 (mp0) REVERT: C 1248 SER cc_start: 0.9305 (OUTLIER) cc_final: 0.9047 (p) REVERT: D 296 MET cc_start: 0.9094 (tpp) cc_final: 0.8769 (tpp) REVERT: D 460 ASP cc_start: 0.8342 (m-30) cc_final: 0.7921 (m-30) REVERT: D 819 LYS cc_start: 0.8577 (mmtm) cc_final: 0.8094 (mmmt) REVERT: D 1229 MET cc_start: 0.8999 (mmm) cc_final: 0.8726 (mmt) REVERT: D 1368 MET cc_start: 0.8647 (ttt) cc_final: 0.8439 (ttm) REVERT: E 363 ILE cc_start: 0.8514 (OUTLIER) cc_final: 0.8291 (tt) REVERT: E 391 ILE cc_start: 0.9147 (tt) cc_final: 0.8851 (tp) REVERT: E 558 MET cc_start: 0.8109 (ttp) cc_final: 0.7684 (ttp) REVERT: E 708 MET cc_start: 0.8456 (ttp) cc_final: 0.8219 (ttp) REVERT: E 780 ARG cc_start: 0.8177 (mtm180) cc_final: 0.7689 (ptp-170) REVERT: E 1047 MET cc_start: 0.8322 (mtt) cc_final: 0.7728 (mtp) REVERT: E 1051 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7389 (mp0) REVERT: E 1060 ARG cc_start: 0.8174 (mmp80) cc_final: 0.7973 (mmm-85) REVERT: E 1397 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8247 (tp) REVERT: F 84 ASP cc_start: 0.7802 (m-30) cc_final: 0.7301 (t0) REVERT: F 860 MET cc_start: 0.8139 (tpp) cc_final: 0.7754 (tpp) REVERT: F 971 HIS cc_start: 0.9270 (OUTLIER) cc_final: 0.8405 (t70) REVERT: F 1100 MET cc_start: 0.8212 (OUTLIER) cc_final: 0.7991 (ttp) REVERT: F 1256 MET cc_start: 0.8385 (mtp) cc_final: 0.7989 (mtp) REVERT: F 1291 ASP cc_start: 0.8504 (p0) cc_final: 0.8210 (p0) REVERT: G 6 MET cc_start: 0.8521 (ptm) cc_final: 0.8038 (ptp) REVERT: G 165 GLU cc_start: 0.8374 (tp30) cc_final: 0.8030 (tp30) REVERT: H 5 ARG cc_start: 0.7630 (mtm110) cc_final: 0.7005 (ptp90) REVERT: H 204 ARG cc_start: 0.7364 (tpp-160) cc_final: 0.7071 (mtt-85) REVERT: H 303 MET cc_start: 0.6601 (mmp) cc_final: 0.6122 (mmm) REVERT: H 328 MET cc_start: 0.8005 (tpt) cc_final: 0.7791 (tpt) REVERT: H 332 GLN cc_start: 0.6923 (mp10) cc_final: 0.6681 (mm-40) REVERT: H 334 GLU cc_start: 0.7497 (mp0) cc_final: 0.6862 (mt-10) REVERT: H 415 GLU cc_start: 0.7485 (mt-10) cc_final: 0.6887 (tt0) REVERT: I 167 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8677 (mt) REVERT: J 6 MET cc_start: 0.8371 (ptp) cc_final: 0.7954 (ptp) REVERT: J 394 ASP cc_start: 0.8041 (t0) cc_final: 0.7727 (t0) REVERT: K 167 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8377 (mt) REVERT: K 180 TYR cc_start: 0.8817 (m-80) cc_final: 0.8590 (m-80) REVERT: K 316 SER cc_start: 0.8598 (t) cc_final: 0.8320 (p) REVERT: K 412 ASP cc_start: 0.7438 (t0) cc_final: 0.7181 (t0) REVERT: K 432 MET cc_start: 0.8719 (ttp) cc_final: 0.8469 (ttp) REVERT: L 5 ARG cc_start: 0.7593 (mtm110) cc_final: 0.6929 (ptp90) REVERT: L 218 ASN cc_start: 0.8210 (m-40) cc_final: 0.7993 (m110) REVERT: L 303 MET cc_start: 0.6128 (mmp) cc_final: 0.5520 (mmm) REVERT: L 334 GLU cc_start: 0.7578 (mp0) cc_final: 0.7121 (pt0) REVERT: L 415 GLU cc_start: 0.7422 (mt-10) cc_final: 0.7011 (tt0) REVERT: L 438 VAL cc_start: 0.7351 (OUTLIER) cc_final: 0.7091 (m) outliers start: 214 outliers final: 148 residues processed: 921 average time/residue: 0.8202 time to fit residues: 1320.2496 Evaluate side-chains 864 residues out of total 9444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 705 time to evaluate : 7.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 728 ILE Chi-restraints excluded: chain A residue 971 HIS Chi-restraints excluded: chain A residue 977 ILE Chi-restraints excluded: chain A residue 1019 ASP Chi-restraints excluded: chain A residue 1265 THR Chi-restraints excluded: chain A residue 1355 VAL Chi-restraints excluded: chain A residue 1468 VAL Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 273 ASP Chi-restraints excluded: chain B residue 381 GLU Chi-restraints excluded: chain B residue 458 MET Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 560 ASP Chi-restraints excluded: chain B residue 564 ASP Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain B residue 687 MET Chi-restraints excluded: chain B residue 882 SER Chi-restraints excluded: chain B residue 971 HIS Chi-restraints excluded: chain B residue 987 LEU Chi-restraints excluded: chain B residue 1030 THR Chi-restraints excluded: chain B residue 1033 SER Chi-restraints excluded: chain B residue 1103 ILE Chi-restraints excluded: chain B residue 1131 THR Chi-restraints excluded: chain B residue 1153 LEU Chi-restraints excluded: chain B residue 1179 ASP Chi-restraints excluded: chain B residue 1181 LEU Chi-restraints excluded: chain B residue 1187 LEU Chi-restraints excluded: chain B residue 1265 THR Chi-restraints excluded: chain B residue 1276 LEU Chi-restraints excluded: chain B residue 1355 VAL Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain C residue 461 MET Chi-restraints excluded: chain C residue 607 THR Chi-restraints excluded: chain C residue 640 THR Chi-restraints excluded: chain C residue 726 GLU Chi-restraints excluded: chain C residue 971 HIS Chi-restraints excluded: chain C residue 1002 SER Chi-restraints excluded: chain C residue 1051 GLU Chi-restraints excluded: chain C residue 1115 VAL Chi-restraints excluded: chain C residue 1179 ASP Chi-restraints excluded: chain C residue 1201 LEU Chi-restraints excluded: chain C residue 1229 MET Chi-restraints excluded: chain C residue 1248 SER Chi-restraints excluded: chain C residue 1276 LEU Chi-restraints excluded: chain C residue 1394 VAL Chi-restraints excluded: chain C residue 1456 GLN Chi-restraints excluded: chain D residue 42 ASP Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 360 ASP Chi-restraints excluded: chain D residue 375 ASP Chi-restraints excluded: chain D residue 468 MET Chi-restraints excluded: chain D residue 478 SER Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 551 THR Chi-restraints excluded: chain D residue 640 THR Chi-restraints excluded: chain D residue 708 MET Chi-restraints excluded: chain D residue 728 ILE Chi-restraints excluded: chain D residue 971 HIS Chi-restraints excluded: chain D residue 1019 ASP Chi-restraints excluded: chain D residue 1178 LEU Chi-restraints excluded: chain D residue 1265 THR Chi-restraints excluded: chain D residue 1355 VAL Chi-restraints excluded: chain E residue 42 ASP Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 335 MET Chi-restraints excluded: chain E residue 360 ASP Chi-restraints excluded: chain E residue 363 ILE Chi-restraints excluded: chain E residue 607 THR Chi-restraints excluded: chain E residue 640 THR Chi-restraints excluded: chain E residue 747 SER Chi-restraints excluded: chain E residue 847 THR Chi-restraints excluded: chain E residue 971 HIS Chi-restraints excluded: chain E residue 1002 SER Chi-restraints excluded: chain E residue 1103 ILE Chi-restraints excluded: chain E residue 1131 THR Chi-restraints excluded: chain E residue 1201 LEU Chi-restraints excluded: chain E residue 1307 VAL Chi-restraints excluded: chain E residue 1397 LEU Chi-restraints excluded: chain E residue 1452 THR Chi-restraints excluded: chain F residue 273 ASP Chi-restraints excluded: chain F residue 304 THR Chi-restraints excluded: chain F residue 307 GLN Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 336 THR Chi-restraints excluded: chain F residue 381 GLU Chi-restraints excluded: chain F residue 458 MET Chi-restraints excluded: chain F residue 506 VAL Chi-restraints excluded: chain F residue 607 THR Chi-restraints excluded: chain F residue 611 MET Chi-restraints excluded: chain F residue 687 MET Chi-restraints excluded: chain F residue 711 MET Chi-restraints excluded: chain F residue 747 SER Chi-restraints excluded: chain F residue 780 ARG Chi-restraints excluded: chain F residue 843 VAL Chi-restraints excluded: chain F residue 964 MET Chi-restraints excluded: chain F residue 971 HIS Chi-restraints excluded: chain F residue 987 LEU Chi-restraints excluded: chain F residue 1100 MET Chi-restraints excluded: chain F residue 1265 THR Chi-restraints excluded: chain F residue 1276 LEU Chi-restraints excluded: chain F residue 1397 LEU Chi-restraints excluded: chain G residue 383 VAL Chi-restraints excluded: chain G residue 424 LEU Chi-restraints excluded: chain G residue 433 THR Chi-restraints excluded: chain H residue 111 ILE Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 277 THR Chi-restraints excluded: chain H residue 389 PHE Chi-restraints excluded: chain H residue 391 VAL Chi-restraints excluded: chain H residue 407 LEU Chi-restraints excluded: chain H residue 418 VAL Chi-restraints excluded: chain H residue 451 VAL Chi-restraints excluded: chain I residue 167 LEU Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 424 LEU Chi-restraints excluded: chain I residue 433 THR Chi-restraints excluded: chain I residue 444 ILE Chi-restraints excluded: chain J residue 383 VAL Chi-restraints excluded: chain J residue 424 LEU Chi-restraints excluded: chain J residue 433 THR Chi-restraints excluded: chain K residue 167 LEU Chi-restraints excluded: chain K residue 300 ASP Chi-restraints excluded: chain K residue 360 VAL Chi-restraints excluded: chain K residue 433 THR Chi-restraints excluded: chain K residue 444 ILE Chi-restraints excluded: chain L residue 98 ILE Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain L residue 142 THR Chi-restraints excluded: chain L residue 277 THR Chi-restraints excluded: chain L residue 286 LEU Chi-restraints excluded: chain L residue 315 THR Chi-restraints excluded: chain L residue 389 PHE Chi-restraints excluded: chain L residue 391 VAL Chi-restraints excluded: chain L residue 407 LEU Chi-restraints excluded: chain L residue 428 HIS Chi-restraints excluded: chain L residue 438 VAL Chi-restraints excluded: chain L residue 451 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1164 random chunks: chunk 378 optimal weight: 4.9990 chunk 1013 optimal weight: 7.9990 chunk 222 optimal weight: 3.9990 chunk 660 optimal weight: 10.0000 chunk 277 optimal weight: 6.9990 chunk 1126 optimal weight: 0.3980 chunk 934 optimal weight: 4.9990 chunk 521 optimal weight: 5.9990 chunk 93 optimal weight: 7.9990 chunk 372 optimal weight: 5.9990 chunk 591 optimal weight: 20.0000 overall best weight: 4.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 ASN A1177 HIS B 818 ASN C 643 ASN C1413 GLN C1456 GLN D 240 ASN D1177 HIS E1406 ASN E1413 GLN F 378 GLN F 818 ASN F 876 ASN F 902 ASN F1120 GLN G 4 GLN G 434 ASN H 129 ASN ** I 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 434 ASN J 4 GLN J 434 ASN K 64 ASN K 434 ASN L 108 ASN L 216 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 92100 Z= 0.348 Angle : 0.854 82.492 124818 Z= 0.359 Chirality : 0.054 1.508 13890 Planarity : 0.004 0.048 16326 Dihedral : 5.817 169.956 13068 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.54 % Allowed : 14.65 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % 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: -0.87 (0.08), residues: 11640 helix: 0.77 (0.08), residues: 4170 sheet: -0.64 (0.12), residues: 1860 loop : -1.61 (0.08), residues: 5610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP K 69 HIS 0.006 0.001 HIS C1063 PHE 0.019 0.002 PHE I 36 TYR 0.020 0.002 TYR B 211 ARG 0.009 0.000 ARG G 378 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23280 Ramachandran restraints generated. 11640 Oldfield, 0 Emsley, 11640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23280 Ramachandran restraints generated. 11640 Oldfield, 0 Emsley, 11640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 964 residues out of total 9444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 240 poor density : 724 time to evaluate : 7.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 473 LYS cc_start: 0.8564 (ptpt) cc_final: 0.8278 (mttm) REVERT: A 606 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8517 (tt) REVERT: A 1142 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8827 (mp) REVERT: A 1153 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.8967 (mp) REVERT: A 1229 MET cc_start: 0.8991 (mmm) cc_final: 0.8740 (mmt) REVERT: A 1368 MET cc_start: 0.8675 (ttt) cc_final: 0.8473 (ttm) REVERT: B 84 ASP cc_start: 0.8425 (OUTLIER) cc_final: 0.7440 (t0) REVERT: B 96 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.7813 (mp0) REVERT: B 162 GLU cc_start: 0.7843 (tp30) cc_final: 0.7588 (tp30) REVERT: B 182 MET cc_start: 0.8247 (mmt) cc_final: 0.7891 (mmt) REVERT: B 235 ASN cc_start: 0.8180 (m-40) cc_final: 0.7922 (m-40) REVERT: B 786 ASP cc_start: 0.8040 (t0) cc_final: 0.7691 (m-30) REVERT: B 823 MET cc_start: 0.7225 (mtp) cc_final: 0.6625 (mtp) REVERT: B 829 LEU cc_start: 0.9504 (mp) cc_final: 0.9223 (mp) REVERT: B 832 ARG cc_start: 0.7681 (ttm110) cc_final: 0.7469 (ttm-80) REVERT: B 858 MET cc_start: 0.8272 (mmt) cc_final: 0.7368 (mmm) REVERT: C 165 ASN cc_start: 0.8605 (m-40) cc_final: 0.8263 (m110) REVERT: C 441 ASP cc_start: 0.4887 (m-30) cc_final: 0.3751 (p0) REVERT: C 687 MET cc_start: 0.7873 (ptp) cc_final: 0.7534 (ptp) REVERT: C 693 MET cc_start: 0.8443 (mmm) cc_final: 0.8066 (mmm) REVERT: C 747 SER cc_start: 0.8807 (m) cc_final: 0.8575 (p) REVERT: C 964 MET cc_start: 0.8034 (tpp) cc_final: 0.7759 (tpp) REVERT: C 1047 MET cc_start: 0.8478 (mtt) cc_final: 0.7488 (mtp) REVERT: C 1051 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.6679 (mp0) REVERT: C 1248 SER cc_start: 0.9371 (OUTLIER) cc_final: 0.9093 (p) REVERT: D 296 MET cc_start: 0.9126 (tpp) cc_final: 0.8804 (tpp) REVERT: D 460 ASP cc_start: 0.8149 (m-30) cc_final: 0.7688 (m-30) REVERT: D 606 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8538 (tt) REVERT: D 819 LYS cc_start: 0.8639 (mmtm) cc_final: 0.8106 (mmmt) REVERT: D 854 ILE cc_start: 0.9286 (OUTLIER) cc_final: 0.8933 (pt) REVERT: D 1153 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.8992 (mp) REVERT: D 1229 MET cc_start: 0.8982 (mmm) cc_final: 0.8731 (mmt) REVERT: E 115 ASP cc_start: 0.7710 (m-30) cc_final: 0.7470 (p0) REVERT: E 166 ASP cc_start: 0.7727 (t0) cc_final: 0.7456 (t0) REVERT: E 251 MET cc_start: 0.7934 (ptp) cc_final: 0.7722 (ptp) REVERT: E 391 ILE cc_start: 0.9159 (tt) cc_final: 0.8907 (tp) REVERT: E 564 ASP cc_start: 0.7078 (t0) cc_final: 0.6866 (t0) REVERT: E 726 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7317 (mt-10) REVERT: E 780 ARG cc_start: 0.8200 (mtm180) cc_final: 0.7794 (ptp-170) REVERT: E 1047 MET cc_start: 0.8443 (mtt) cc_final: 0.7906 (mtp) REVERT: E 1051 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7437 (mp0) REVERT: E 1060 ARG cc_start: 0.8186 (mmp80) cc_final: 0.7953 (mmm-85) REVERT: F 84 ASP cc_start: 0.8351 (m-30) cc_final: 0.7809 (t0) REVERT: F 490 ASP cc_start: 0.9010 (OUTLIER) cc_final: 0.8790 (p0) REVERT: F 693 MET cc_start: 0.8564 (mmp) cc_final: 0.8291 (mmm) REVERT: F 823 MET cc_start: 0.7099 (mtp) cc_final: 0.6702 (mtp) REVERT: F 971 HIS cc_start: 0.9285 (OUTLIER) cc_final: 0.8954 (t70) REVERT: F 1291 ASP cc_start: 0.8586 (p0) cc_final: 0.8262 (p0) REVERT: F 1462 MET cc_start: 0.7991 (tpp) cc_final: 0.7679 (tpt) REVERT: G 6 MET cc_start: 0.8467 (ptm) cc_final: 0.8108 (ptp) REVERT: H 204 ARG cc_start: 0.7346 (tpp-160) cc_final: 0.7077 (mtt-85) REVERT: H 303 MET cc_start: 0.6470 (mmp) cc_final: 0.5989 (mmm) REVERT: H 328 MET cc_start: 0.8012 (tpt) cc_final: 0.7488 (ptp) REVERT: H 332 GLN cc_start: 0.7417 (mp10) cc_final: 0.7205 (mp10) REVERT: H 334 GLU cc_start: 0.7647 (mp0) cc_final: 0.6912 (mt-10) REVERT: H 415 GLU cc_start: 0.7541 (mt-10) cc_final: 0.6902 (tt0) REVERT: I 167 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8731 (mt) REVERT: I 435 MET cc_start: 0.6873 (mtt) cc_final: 0.6647 (mtm) REVERT: J 6 MET cc_start: 0.8299 (ptp) cc_final: 0.7958 (ptp) REVERT: J 394 ASP cc_start: 0.8078 (t0) cc_final: 0.7750 (t0) REVERT: K 167 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8642 (mt) REVERT: K 429 ARG cc_start: 0.8672 (mmm160) cc_final: 0.8060 (mmm160) REVERT: L 6 MET cc_start: 0.8466 (ptp) cc_final: 0.7867 (ptt) REVERT: L 303 MET cc_start: 0.6416 (mmp) cc_final: 0.5780 (mmm) REVERT: L 328 MET cc_start: 0.7819 (tpt) cc_final: 0.7415 (mtp) REVERT: L 334 GLU cc_start: 0.7635 (mp0) cc_final: 0.7161 (pt0) REVERT: L 415 GLU cc_start: 0.7528 (mt-10) cc_final: 0.7013 (tt0) REVERT: L 416 LEU cc_start: 0.6968 (mt) cc_final: 0.6727 (tt) REVERT: L 438 VAL cc_start: 0.7273 (OUTLIER) cc_final: 0.6997 (m) outliers start: 240 outliers final: 167 residues processed: 914 average time/residue: 0.7822 time to fit residues: 1255.5835 Evaluate side-chains 868 residues out of total 9444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 686 time to evaluate : 7.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 728 ILE Chi-restraints excluded: chain A residue 971 HIS Chi-restraints excluded: chain A residue 977 ILE Chi-restraints excluded: chain A residue 1019 ASP Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1265 THR Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain A residue 1355 VAL Chi-restraints excluded: chain A residue 1468 VAL Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 273 ASP Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 360 ASP Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 381 GLU Chi-restraints excluded: chain B residue 458 MET Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 564 ASP Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain B residue 687 MET Chi-restraints excluded: chain B residue 711 MET Chi-restraints excluded: chain B residue 882 SER Chi-restraints excluded: chain B residue 971 HIS Chi-restraints excluded: chain B residue 987 LEU Chi-restraints excluded: chain B residue 1030 THR Chi-restraints excluded: chain B residue 1033 SER Chi-restraints excluded: chain B residue 1103 ILE Chi-restraints excluded: chain B residue 1131 THR Chi-restraints excluded: chain B residue 1153 LEU Chi-restraints excluded: chain B residue 1179 ASP Chi-restraints excluded: chain B residue 1181 LEU Chi-restraints excluded: chain B residue 1187 LEU Chi-restraints excluded: chain B residue 1265 THR Chi-restraints excluded: chain B residue 1276 LEU Chi-restraints excluded: chain B residue 1355 VAL Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 607 THR Chi-restraints excluded: chain C residue 726 GLU Chi-restraints excluded: chain C residue 987 LEU Chi-restraints excluded: chain C residue 1002 SER Chi-restraints excluded: chain C residue 1051 GLU Chi-restraints excluded: chain C residue 1179 ASP Chi-restraints excluded: chain C residue 1201 LEU Chi-restraints excluded: chain C residue 1248 SER Chi-restraints excluded: chain C residue 1276 LEU Chi-restraints excluded: chain C residue 1313 SER Chi-restraints excluded: chain C residue 1394 VAL Chi-restraints excluded: chain C residue 1456 GLN Chi-restraints excluded: chain D residue 42 ASP Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 375 ASP Chi-restraints excluded: chain D residue 468 MET Chi-restraints excluded: chain D residue 478 SER Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 551 THR Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 640 THR Chi-restraints excluded: chain D residue 708 MET Chi-restraints excluded: chain D residue 728 ILE Chi-restraints excluded: chain D residue 854 ILE Chi-restraints excluded: chain D residue 971 HIS Chi-restraints excluded: chain D residue 1019 ASP Chi-restraints excluded: chain D residue 1038 ILE Chi-restraints excluded: chain D residue 1153 LEU Chi-restraints excluded: chain D residue 1178 LEU Chi-restraints excluded: chain D residue 1265 THR Chi-restraints excluded: chain D residue 1281 VAL Chi-restraints excluded: chain D residue 1355 VAL Chi-restraints excluded: chain E residue 42 ASP Chi-restraints excluded: chain E residue 69 ASN Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 218 THR Chi-restraints excluded: chain E residue 335 MET Chi-restraints excluded: chain E residue 357 ILE Chi-restraints excluded: chain E residue 360 ASP Chi-restraints excluded: chain E residue 363 ILE Chi-restraints excluded: chain E residue 400 LEU Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 458 MET Chi-restraints excluded: chain E residue 607 THR Chi-restraints excluded: chain E residue 640 THR Chi-restraints excluded: chain E residue 747 SER Chi-restraints excluded: chain E residue 847 THR Chi-restraints excluded: chain E residue 971 HIS Chi-restraints excluded: chain E residue 1002 SER Chi-restraints excluded: chain E residue 1103 ILE Chi-restraints excluded: chain E residue 1131 THR Chi-restraints excluded: chain E residue 1201 LEU Chi-restraints excluded: chain E residue 1307 VAL Chi-restraints excluded: chain E residue 1452 THR Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 273 ASP Chi-restraints excluded: chain F residue 304 THR Chi-restraints excluded: chain F residue 307 GLN Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain F residue 336 THR Chi-restraints excluded: chain F residue 363 ILE Chi-restraints excluded: chain F residue 381 GLU Chi-restraints excluded: chain F residue 458 MET Chi-restraints excluded: chain F residue 490 ASP Chi-restraints excluded: chain F residue 506 VAL Chi-restraints excluded: chain F residue 607 THR Chi-restraints excluded: chain F residue 611 MET Chi-restraints excluded: chain F residue 687 MET Chi-restraints excluded: chain F residue 706 LYS Chi-restraints excluded: chain F residue 711 MET Chi-restraints excluded: chain F residue 747 SER Chi-restraints excluded: chain F residue 780 ARG Chi-restraints excluded: chain F residue 843 VAL Chi-restraints excluded: chain F residue 971 HIS Chi-restraints excluded: chain F residue 987 LEU Chi-restraints excluded: chain F residue 1181 LEU Chi-restraints excluded: chain F residue 1265 THR Chi-restraints excluded: chain F residue 1276 LEU Chi-restraints excluded: chain F residue 1355 VAL Chi-restraints excluded: chain F residue 1397 LEU Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 383 VAL Chi-restraints excluded: chain G residue 396 VAL Chi-restraints excluded: chain G residue 424 LEU Chi-restraints excluded: chain G residue 433 THR Chi-restraints excluded: chain H residue 111 ILE Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 277 THR Chi-restraints excluded: chain H residue 389 PHE Chi-restraints excluded: chain H residue 391 VAL Chi-restraints excluded: chain H residue 407 LEU Chi-restraints excluded: chain H residue 418 VAL Chi-restraints excluded: chain H residue 451 VAL Chi-restraints excluded: chain I residue 167 LEU Chi-restraints excluded: chain I residue 300 ASP Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 407 LEU Chi-restraints excluded: chain I residue 433 THR Chi-restraints excluded: chain I residue 444 ILE Chi-restraints excluded: chain J residue 383 VAL Chi-restraints excluded: chain J residue 424 LEU Chi-restraints excluded: chain J residue 433 THR Chi-restraints excluded: chain K residue 167 LEU Chi-restraints excluded: chain K residue 300 ASP Chi-restraints excluded: chain K residue 360 VAL Chi-restraints excluded: chain K residue 444 ILE Chi-restraints excluded: chain L residue 98 ILE Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain L residue 142 THR Chi-restraints excluded: chain L residue 277 THR Chi-restraints excluded: chain L residue 315 THR Chi-restraints excluded: chain L residue 391 VAL Chi-restraints excluded: chain L residue 407 LEU Chi-restraints excluded: chain L residue 438 VAL Chi-restraints excluded: chain L residue 451 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1164 random chunks: chunk 1085 optimal weight: 0.9990 chunk 126 optimal weight: 6.9990 chunk 641 optimal weight: 7.9990 chunk 822 optimal weight: 6.9990 chunk 637 optimal weight: 8.9990 chunk 948 optimal weight: 3.9990 chunk 628 optimal weight: 9.9990 chunk 1121 optimal weight: 2.9990 chunk 702 optimal weight: 0.8980 chunk 683 optimal weight: 6.9990 chunk 517 optimal weight: 6.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1177 HIS B 818 ASN B1054 GLN D 240 ASN D1177 HIS F 818 ASN F1234 ASN G 4 GLN H 129 ASN ** I 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 434 ASN J 4 GLN K 64 ASN K 337 HIS K 434 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 92100 Z= 0.284 Angle : 0.830 82.431 124818 Z= 0.344 Chirality : 0.053 1.509 13890 Planarity : 0.004 0.042 16326 Dihedral : 5.722 171.266 13068 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.33 % Allowed : 15.52 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % 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 (0.08), residues: 11640 helix: 0.86 (0.08), residues: 4164 sheet: -0.58 (0.12), residues: 1812 loop : -1.53 (0.08), residues: 5664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP K 69 HIS 0.005 0.001 HIS C1063 PHE 0.017 0.001 PHE K 36 TYR 0.016 0.001 TYR B 211 ARG 0.007 0.000 ARG F 65 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23280 Ramachandran restraints generated. 11640 Oldfield, 0 Emsley, 11640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23280 Ramachandran restraints generated. 11640 Oldfield, 0 Emsley, 11640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 930 residues out of total 9444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 710 time to evaluate : 7.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 MET cc_start: 0.9094 (tpp) cc_final: 0.8572 (tpp) REVERT: A 473 LYS cc_start: 0.8549 (ptpt) cc_final: 0.8276 (mttm) REVERT: A 606 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8492 (tt) REVERT: A 1142 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8919 (mp) REVERT: A 1153 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8902 (mp) REVERT: A 1229 MET cc_start: 0.8992 (mmm) cc_final: 0.8731 (mmt) REVERT: A 1368 MET cc_start: 0.8651 (ttt) cc_final: 0.8407 (ttp) REVERT: B 84 ASP cc_start: 0.8469 (OUTLIER) cc_final: 0.7511 (t0) REVERT: B 96 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.7939 (mp0) REVERT: B 156 GLU cc_start: 0.8352 (mt-10) cc_final: 0.8148 (mt-10) REVERT: B 162 GLU cc_start: 0.7875 (tp30) cc_final: 0.7394 (tp30) REVERT: B 182 MET cc_start: 0.8329 (mmt) cc_final: 0.8015 (mmt) REVERT: B 562 MET cc_start: 0.8093 (mtm) cc_final: 0.7657 (mtp) REVERT: B 786 ASP cc_start: 0.8012 (t0) cc_final: 0.7720 (m-30) REVERT: B 820 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7475 (mtm-85) REVERT: B 823 MET cc_start: 0.7226 (mtp) cc_final: 0.6620 (mtp) REVERT: B 829 LEU cc_start: 0.9505 (mp) cc_final: 0.9233 (mp) REVERT: B 858 MET cc_start: 0.8241 (mmt) cc_final: 0.7226 (mmm) REVERT: C 165 ASN cc_start: 0.8570 (m-40) cc_final: 0.8303 (m110) REVERT: C 297 MET cc_start: 0.8449 (tpp) cc_final: 0.8234 (mmm) REVERT: C 441 ASP cc_start: 0.5116 (m-30) cc_final: 0.3630 (p0) REVERT: C 687 MET cc_start: 0.7903 (ptp) cc_final: 0.7575 (ptp) REVERT: C 747 SER cc_start: 0.8773 (m) cc_final: 0.8545 (p) REVERT: C 964 MET cc_start: 0.8016 (tpp) cc_final: 0.7710 (tpp) REVERT: C 1047 MET cc_start: 0.8517 (mtt) cc_final: 0.7420 (mtp) REVERT: C 1051 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.6640 (mp0) REVERT: C 1248 SER cc_start: 0.9380 (OUTLIER) cc_final: 0.9104 (p) REVERT: C 1387 MET cc_start: 0.8996 (ttp) cc_final: 0.8727 (ttp) REVERT: C 1456 GLN cc_start: 0.8713 (OUTLIER) cc_final: 0.8233 (tm-30) REVERT: D 296 MET cc_start: 0.9135 (tpp) cc_final: 0.8802 (tpp) REVERT: D 606 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8502 (tt) REVERT: D 819 LYS cc_start: 0.8651 (mmtm) cc_final: 0.8138 (mmmt) REVERT: D 1153 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.8944 (mp) REVERT: D 1229 MET cc_start: 0.8991 (mmm) cc_final: 0.8731 (mmt) REVERT: E 726 GLU cc_start: 0.7685 (mt-10) cc_final: 0.7334 (mt-10) REVERT: E 780 ARG cc_start: 0.8228 (mtm180) cc_final: 0.7946 (ptp-170) REVERT: E 1047 MET cc_start: 0.8372 (mtt) cc_final: 0.7801 (mtp) REVERT: E 1051 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7390 (mp0) REVERT: E 1060 ARG cc_start: 0.8196 (mmp80) cc_final: 0.7938 (mmm-85) REVERT: F 84 ASP cc_start: 0.8461 (m-30) cc_final: 0.7919 (t0) REVERT: F 490 ASP cc_start: 0.9026 (OUTLIER) cc_final: 0.8804 (p0) REVERT: F 693 MET cc_start: 0.8535 (mmp) cc_final: 0.8246 (mmm) REVERT: F 823 MET cc_start: 0.7128 (mtp) cc_final: 0.6737 (mtp) REVERT: F 832 ARG cc_start: 0.8055 (mtp-110) cc_final: 0.7848 (mtm110) REVERT: F 899 ASN cc_start: 0.7493 (t0) cc_final: 0.7165 (t0) REVERT: F 971 HIS cc_start: 0.9267 (OUTLIER) cc_final: 0.8968 (t70) REVERT: F 1291 ASP cc_start: 0.8598 (p0) cc_final: 0.8284 (p0) REVERT: F 1462 MET cc_start: 0.8012 (tpp) cc_final: 0.7602 (tpt) REVERT: G 6 MET cc_start: 0.8465 (ptm) cc_final: 0.8115 (ptp) REVERT: H 204 ARG cc_start: 0.7280 (tpp-160) cc_final: 0.6995 (mtt-85) REVERT: H 303 MET cc_start: 0.6445 (mmp) cc_final: 0.5987 (mmm) REVERT: H 328 MET cc_start: 0.8010 (tpt) cc_final: 0.7347 (ptp) REVERT: H 332 GLN cc_start: 0.7471 (mp10) cc_final: 0.7088 (mm-40) REVERT: H 334 GLU cc_start: 0.7653 (mp0) cc_final: 0.6942 (mt-10) REVERT: H 415 GLU cc_start: 0.7560 (mt-10) cc_final: 0.6491 (tm-30) REVERT: I 167 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8706 (mt) REVERT: J 6 MET cc_start: 0.8270 (ptp) cc_final: 0.7917 (ptp) REVERT: J 394 ASP cc_start: 0.8103 (t0) cc_final: 0.7734 (t0) REVERT: K 167 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8643 (mt) REVERT: K 432 MET cc_start: 0.8631 (ttp) cc_final: 0.8334 (ttp) REVERT: K 435 MET cc_start: 0.7348 (OUTLIER) cc_final: 0.7105 (mmt) REVERT: L 146 GLU cc_start: 0.6587 (mm-30) cc_final: 0.5522 (mm-30) REVERT: L 303 MET cc_start: 0.6754 (mmp) cc_final: 0.6496 (mmm) REVERT: L 328 MET cc_start: 0.7768 (tpt) cc_final: 0.7434 (mtm) REVERT: L 334 GLU cc_start: 0.7631 (mp0) cc_final: 0.7084 (pp20) REVERT: L 415 GLU cc_start: 0.7542 (mt-10) cc_final: 0.7014 (tt0) outliers start: 220 outliers final: 164 residues processed: 883 average time/residue: 0.8178 time to fit residues: 1264.0015 Evaluate side-chains 864 residues out of total 9444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 684 time to evaluate : 7.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 728 ILE Chi-restraints excluded: chain A residue 971 HIS Chi-restraints excluded: chain A residue 977 ILE Chi-restraints excluded: chain A residue 1019 ASP Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1265 THR Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain A residue 1355 VAL Chi-restraints excluded: chain A residue 1462 MET Chi-restraints excluded: chain A residue 1468 VAL Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 273 ASP Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 360 ASP Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 381 GLU Chi-restraints excluded: chain B residue 458 MET Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 560 ASP Chi-restraints excluded: chain B residue 564 ASP Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain B residue 687 MET Chi-restraints excluded: chain B residue 711 MET Chi-restraints excluded: chain B residue 806 SER Chi-restraints excluded: chain B residue 820 ARG Chi-restraints excluded: chain B residue 971 HIS Chi-restraints excluded: chain B residue 987 LEU Chi-restraints excluded: chain B residue 1030 THR Chi-restraints excluded: chain B residue 1033 SER Chi-restraints excluded: chain B residue 1103 ILE Chi-restraints excluded: chain B residue 1131 THR Chi-restraints excluded: chain B residue 1153 LEU Chi-restraints excluded: chain B residue 1179 ASP Chi-restraints excluded: chain B residue 1181 LEU Chi-restraints excluded: chain B residue 1187 LEU Chi-restraints excluded: chain B residue 1265 THR Chi-restraints excluded: chain B residue 1276 LEU Chi-restraints excluded: chain B residue 1355 VAL Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 607 THR Chi-restraints excluded: chain C residue 640 THR Chi-restraints excluded: chain C residue 726 GLU Chi-restraints excluded: chain C residue 971 HIS Chi-restraints excluded: chain C residue 987 LEU Chi-restraints excluded: chain C residue 1002 SER Chi-restraints excluded: chain C residue 1051 GLU Chi-restraints excluded: chain C residue 1100 MET Chi-restraints excluded: chain C residue 1115 VAL Chi-restraints excluded: chain C residue 1179 ASP Chi-restraints excluded: chain C residue 1201 LEU Chi-restraints excluded: chain C residue 1248 SER Chi-restraints excluded: chain C residue 1276 LEU Chi-restraints excluded: chain C residue 1313 SER Chi-restraints excluded: chain C residue 1394 VAL Chi-restraints excluded: chain C residue 1456 GLN Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 375 ASP Chi-restraints excluded: chain D residue 468 MET Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 551 THR Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 611 MET Chi-restraints excluded: chain D residue 640 THR Chi-restraints excluded: chain D residue 708 MET Chi-restraints excluded: chain D residue 728 ILE Chi-restraints excluded: chain D residue 971 HIS Chi-restraints excluded: chain D residue 1019 ASP Chi-restraints excluded: chain D residue 1038 ILE Chi-restraints excluded: chain D residue 1153 LEU Chi-restraints excluded: chain D residue 1201 LEU Chi-restraints excluded: chain D residue 1265 THR Chi-restraints excluded: chain D residue 1355 VAL Chi-restraints excluded: chain E residue 42 ASP Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 335 MET Chi-restraints excluded: chain E residue 360 ASP Chi-restraints excluded: chain E residue 363 ILE Chi-restraints excluded: chain E residue 458 MET Chi-restraints excluded: chain E residue 607 THR Chi-restraints excluded: chain E residue 640 THR Chi-restraints excluded: chain E residue 747 SER Chi-restraints excluded: chain E residue 1002 SER Chi-restraints excluded: chain E residue 1103 ILE Chi-restraints excluded: chain E residue 1131 THR Chi-restraints excluded: chain E residue 1201 LEU Chi-restraints excluded: chain E residue 1452 THR Chi-restraints excluded: chain F residue 42 ASP Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 273 ASP Chi-restraints excluded: chain F residue 304 THR Chi-restraints excluded: chain F residue 307 GLN Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain F residue 336 THR Chi-restraints excluded: chain F residue 363 ILE Chi-restraints excluded: chain F residue 381 GLU Chi-restraints excluded: chain F residue 458 MET Chi-restraints excluded: chain F residue 490 ASP Chi-restraints excluded: chain F residue 607 THR Chi-restraints excluded: chain F residue 706 LYS Chi-restraints excluded: chain F residue 711 MET Chi-restraints excluded: chain F residue 780 ARG Chi-restraints excluded: chain F residue 843 VAL Chi-restraints excluded: chain F residue 964 MET Chi-restraints excluded: chain F residue 971 HIS Chi-restraints excluded: chain F residue 987 LEU Chi-restraints excluded: chain F residue 1181 LEU Chi-restraints excluded: chain F residue 1265 THR Chi-restraints excluded: chain F residue 1276 LEU Chi-restraints excluded: chain F residue 1355 VAL Chi-restraints excluded: chain F residue 1397 LEU Chi-restraints excluded: chain G residue 5 ARG Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 383 VAL Chi-restraints excluded: chain G residue 396 VAL Chi-restraints excluded: chain G residue 424 LEU Chi-restraints excluded: chain G residue 433 THR Chi-restraints excluded: chain H residue 111 ILE Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 277 THR Chi-restraints excluded: chain H residue 286 LEU Chi-restraints excluded: chain H residue 389 PHE Chi-restraints excluded: chain H residue 391 VAL Chi-restraints excluded: chain H residue 407 LEU Chi-restraints excluded: chain H residue 418 VAL Chi-restraints excluded: chain H residue 451 VAL Chi-restraints excluded: chain I residue 116 HIS Chi-restraints excluded: chain I residue 167 LEU Chi-restraints excluded: chain I residue 300 ASP Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 433 THR Chi-restraints excluded: chain I residue 444 ILE Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 383 VAL Chi-restraints excluded: chain J residue 424 LEU Chi-restraints excluded: chain J residue 433 THR Chi-restraints excluded: chain K residue 167 LEU Chi-restraints excluded: chain K residue 360 VAL Chi-restraints excluded: chain K residue 433 THR Chi-restraints excluded: chain K residue 435 MET Chi-restraints excluded: chain K residue 444 ILE Chi-restraints excluded: chain L residue 36 PHE Chi-restraints excluded: chain L residue 98 ILE Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain L residue 142 THR Chi-restraints excluded: chain L residue 277 THR Chi-restraints excluded: chain L residue 391 VAL Chi-restraints excluded: chain L residue 451 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1164 random chunks: chunk 694 optimal weight: 3.9990 chunk 448 optimal weight: 0.9990 chunk 670 optimal weight: 4.9990 chunk 337 optimal weight: 2.9990 chunk 220 optimal weight: 6.9990 chunk 217 optimal weight: 3.9990 chunk 713 optimal weight: 20.0000 chunk 764 optimal weight: 0.9990 chunk 554 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 881 optimal weight: 7.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 HIS A1177 HIS B 539 GLN B 818 ASN B1054 GLN C1456 GLN D 240 ASN D1177 HIS E 261 GLN F 818 ASN G 4 GLN H 129 ASN H 337 HIS ** I 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 434 ASN J 4 GLN K 64 ASN K 434 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 92100 Z= 0.209 Angle : 0.810 82.406 124818 Z= 0.330 Chirality : 0.052 1.512 13890 Planarity : 0.003 0.042 16326 Dihedral : 5.555 172.094 13068 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.19 % Allowed : 15.94 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % 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: -0.59 (0.08), residues: 11640 helix: 1.02 (0.09), residues: 4158 sheet: -0.52 (0.12), residues: 1818 loop : -1.43 (0.08), residues: 5664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP L 69 HIS 0.008 0.001 HIS E 788 PHE 0.016 0.001 PHE I 36 TYR 0.012 0.001 TYR B1198 ARG 0.008 0.000 ARG A1186 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23280 Ramachandran restraints generated. 11640 Oldfield, 0 Emsley, 11640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23280 Ramachandran restraints generated. 11640 Oldfield, 0 Emsley, 11640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 927 residues out of total 9444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 720 time to evaluate : 7.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7386 (mt-10) REVERT: A 473 LYS cc_start: 0.8524 (ptpt) cc_final: 0.8263 (mttm) REVERT: A 606 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8498 (tt) REVERT: A 1153 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8727 (mp) REVERT: A 1184 ASN cc_start: 0.8482 (t0) cc_final: 0.8177 (m110) REVERT: A 1229 MET cc_start: 0.8988 (mmm) cc_final: 0.8717 (mmt) REVERT: A 1368 MET cc_start: 0.8643 (ttt) cc_final: 0.8433 (ttp) REVERT: B 84 ASP cc_start: 0.8434 (OUTLIER) cc_final: 0.7523 (t0) REVERT: B 96 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.7924 (mp0) REVERT: B 156 GLU cc_start: 0.8317 (mt-10) cc_final: 0.8116 (mt-10) REVERT: B 162 GLU cc_start: 0.7923 (tp30) cc_final: 0.7438 (tp30) REVERT: B 182 MET cc_start: 0.8361 (mmt) cc_final: 0.8033 (mmt) REVERT: B 562 MET cc_start: 0.8081 (mtm) cc_final: 0.7861 (mtp) REVERT: B 786 ASP cc_start: 0.7977 (t0) cc_final: 0.7578 (m-30) REVERT: B 823 MET cc_start: 0.7387 (mtp) cc_final: 0.6843 (mtp) REVERT: B 829 LEU cc_start: 0.9516 (mp) cc_final: 0.9234 (mp) REVERT: B 858 MET cc_start: 0.8246 (mmt) cc_final: 0.7261 (mmm) REVERT: B 899 ASN cc_start: 0.7933 (t0) cc_final: 0.7521 (t0) REVERT: C 165 ASN cc_start: 0.8475 (m-40) cc_final: 0.8268 (m110) REVERT: C 297 MET cc_start: 0.8314 (tpp) cc_final: 0.7977 (mmm) REVERT: C 441 ASP cc_start: 0.5114 (m-30) cc_final: 0.3608 (p0) REVERT: C 687 MET cc_start: 0.7926 (ptp) cc_final: 0.7687 (ptp) REVERT: C 964 MET cc_start: 0.7981 (tpp) cc_final: 0.7698 (tpp) REVERT: C 1047 MET cc_start: 0.8514 (mtt) cc_final: 0.7300 (mtp) REVERT: C 1051 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.6570 (mp0) REVERT: C 1248 SER cc_start: 0.9162 (OUTLIER) cc_final: 0.8919 (p) REVERT: C 1387 MET cc_start: 0.8994 (ttp) cc_final: 0.8738 (ttp) REVERT: C 1456 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.7677 (tm130) REVERT: D 296 MET cc_start: 0.9086 (tpp) cc_final: 0.8740 (tpp) REVERT: D 606 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8497 (tt) REVERT: D 819 LYS cc_start: 0.8615 (mmtm) cc_final: 0.8109 (mmmt) REVERT: D 1153 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8907 (mp) REVERT: D 1184 ASN cc_start: 0.8516 (t0) cc_final: 0.8194 (m110) REVERT: D 1229 MET cc_start: 0.8989 (mmm) cc_final: 0.8721 (mmt) REVERT: E 297 MET cc_start: 0.8152 (mmm) cc_final: 0.7934 (mmm) REVERT: E 558 MET cc_start: 0.8303 (tmm) cc_final: 0.7854 (ttp) REVERT: E 726 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7425 (mt-10) REVERT: E 780 ARG cc_start: 0.8260 (mtm180) cc_final: 0.7993 (ptp-170) REVERT: E 860 MET cc_start: 0.8402 (tpp) cc_final: 0.8177 (tpp) REVERT: E 1047 MET cc_start: 0.8362 (mtt) cc_final: 0.7635 (mtp) REVERT: E 1051 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7310 (mp0) REVERT: F 84 ASP cc_start: 0.8496 (m-30) cc_final: 0.7810 (t0) REVERT: F 307 GLN cc_start: 0.8000 (OUTLIER) cc_final: 0.7520 (mp10) REVERT: F 490 ASP cc_start: 0.9032 (OUTLIER) cc_final: 0.8740 (p0) REVERT: F 693 MET cc_start: 0.8419 (mmp) cc_final: 0.8175 (mmm) REVERT: F 823 MET cc_start: 0.7096 (mtp) cc_final: 0.6704 (mtp) REVERT: F 829 LEU cc_start: 0.9414 (mp) cc_final: 0.9211 (mp) REVERT: F 899 ASN cc_start: 0.7440 (t0) cc_final: 0.7178 (t0) REVERT: F 1291 ASP cc_start: 0.8588 (p0) cc_final: 0.8258 (p0) REVERT: F 1462 MET cc_start: 0.8036 (tpp) cc_final: 0.7447 (tpt) REVERT: G 6 MET cc_start: 0.8573 (ptm) cc_final: 0.8136 (ptp) REVERT: H 204 ARG cc_start: 0.7281 (tpp-160) cc_final: 0.7009 (mtt-85) REVERT: H 303 MET cc_start: 0.6402 (mmp) cc_final: 0.5988 (mmm) REVERT: H 328 MET cc_start: 0.7979 (tpt) cc_final: 0.7369 (ptp) REVERT: H 332 GLN cc_start: 0.7597 (mp10) cc_final: 0.7390 (mm-40) REVERT: H 334 GLU cc_start: 0.7486 (mp0) cc_final: 0.6982 (mt-10) REVERT: H 415 GLU cc_start: 0.7483 (mt-10) cc_final: 0.6406 (tm-30) REVERT: I 167 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8667 (mt) REVERT: I 259 ILE cc_start: 0.5605 (pt) cc_final: 0.5127 (pt) REVERT: J 6 MET cc_start: 0.8282 (ptp) cc_final: 0.7988 (ptp) REVERT: J 394 ASP cc_start: 0.8028 (t0) cc_final: 0.7664 (t0) REVERT: K 167 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8606 (mt) REVERT: K 435 MET cc_start: 0.7199 (OUTLIER) cc_final: 0.6987 (mmt) REVERT: L 146 GLU cc_start: 0.6683 (mm-30) cc_final: 0.5718 (mm-30) REVERT: L 328 MET cc_start: 0.7790 (tpt) cc_final: 0.7514 (mtm) REVERT: L 334 GLU cc_start: 0.7601 (mp0) cc_final: 0.7025 (pp20) REVERT: L 415 GLU cc_start: 0.7588 (mt-10) cc_final: 0.7020 (tt0) REVERT: L 438 VAL cc_start: 0.7184 (OUTLIER) cc_final: 0.6866 (m) outliers start: 207 outliers final: 165 residues processed: 880 average time/residue: 0.8213 time to fit residues: 1262.9927 Evaluate side-chains 867 residues out of total 9444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 686 time to evaluate : 7.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 728 ILE Chi-restraints excluded: chain A residue 971 HIS Chi-restraints excluded: chain A residue 977 ILE Chi-restraints excluded: chain A residue 1019 ASP Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1265 THR Chi-restraints excluded: chain A residue 1355 VAL Chi-restraints excluded: chain A residue 1462 MET Chi-restraints excluded: chain A residue 1468 VAL Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 273 ASP Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 360 ASP Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 381 GLU Chi-restraints excluded: chain B residue 458 MET Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 520 MET Chi-restraints excluded: chain B residue 560 ASP Chi-restraints excluded: chain B residue 564 ASP Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain B residue 687 MET Chi-restraints excluded: chain B residue 711 MET Chi-restraints excluded: chain B residue 971 HIS Chi-restraints excluded: chain B residue 987 LEU Chi-restraints excluded: chain B residue 1030 THR Chi-restraints excluded: chain B residue 1033 SER Chi-restraints excluded: chain B residue 1103 ILE Chi-restraints excluded: chain B residue 1131 THR Chi-restraints excluded: chain B residue 1153 LEU Chi-restraints excluded: chain B residue 1179 ASP Chi-restraints excluded: chain B residue 1181 LEU Chi-restraints excluded: chain B residue 1187 LEU Chi-restraints excluded: chain B residue 1265 THR Chi-restraints excluded: chain B residue 1276 LEU Chi-restraints excluded: chain B residue 1355 VAL Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 607 THR Chi-restraints excluded: chain C residue 640 THR Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 726 GLU Chi-restraints excluded: chain C residue 971 HIS Chi-restraints excluded: chain C residue 987 LEU Chi-restraints excluded: chain C residue 1002 SER Chi-restraints excluded: chain C residue 1051 GLU Chi-restraints excluded: chain C residue 1201 LEU Chi-restraints excluded: chain C residue 1248 SER Chi-restraints excluded: chain C residue 1276 LEU Chi-restraints excluded: chain C residue 1313 SER Chi-restraints excluded: chain C residue 1394 VAL Chi-restraints excluded: chain C residue 1456 GLN Chi-restraints excluded: chain D residue 42 ASP Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 375 ASP Chi-restraints excluded: chain D residue 478 SER Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 551 THR Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 611 MET Chi-restraints excluded: chain D residue 640 THR Chi-restraints excluded: chain D residue 708 MET Chi-restraints excluded: chain D residue 728 ILE Chi-restraints excluded: chain D residue 971 HIS Chi-restraints excluded: chain D residue 1019 ASP Chi-restraints excluded: chain D residue 1153 LEU Chi-restraints excluded: chain D residue 1265 THR Chi-restraints excluded: chain D residue 1281 VAL Chi-restraints excluded: chain D residue 1355 VAL Chi-restraints excluded: chain E residue 42 ASP Chi-restraints excluded: chain E residue 69 ASN Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 335 MET Chi-restraints excluded: chain E residue 360 ASP Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 607 THR Chi-restraints excluded: chain E residue 640 THR Chi-restraints excluded: chain E residue 747 SER Chi-restraints excluded: chain E residue 771 VAL Chi-restraints excluded: chain E residue 1103 ILE Chi-restraints excluded: chain E residue 1131 THR Chi-restraints excluded: chain E residue 1201 LEU Chi-restraints excluded: chain E residue 1452 THR Chi-restraints excluded: chain F residue 42 ASP Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 273 ASP Chi-restraints excluded: chain F residue 304 THR Chi-restraints excluded: chain F residue 307 GLN Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain F residue 336 THR Chi-restraints excluded: chain F residue 363 ILE Chi-restraints excluded: chain F residue 381 GLU Chi-restraints excluded: chain F residue 490 ASP Chi-restraints excluded: chain F residue 506 VAL Chi-restraints excluded: chain F residue 607 THR Chi-restraints excluded: chain F residue 687 MET Chi-restraints excluded: chain F residue 706 LYS Chi-restraints excluded: chain F residue 711 MET Chi-restraints excluded: chain F residue 780 ARG Chi-restraints excluded: chain F residue 843 VAL Chi-restraints excluded: chain F residue 964 MET Chi-restraints excluded: chain F residue 987 LEU Chi-restraints excluded: chain F residue 1181 LEU Chi-restraints excluded: chain F residue 1265 THR Chi-restraints excluded: chain F residue 1276 LEU Chi-restraints excluded: chain F residue 1355 VAL Chi-restraints excluded: chain F residue 1397 LEU Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 383 VAL Chi-restraints excluded: chain G residue 424 LEU Chi-restraints excluded: chain G residue 433 THR Chi-restraints excluded: chain H residue 36 PHE Chi-restraints excluded: chain H residue 111 ILE Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 277 THR Chi-restraints excluded: chain H residue 286 LEU Chi-restraints excluded: chain H residue 391 VAL Chi-restraints excluded: chain H residue 407 LEU Chi-restraints excluded: chain H residue 418 VAL Chi-restraints excluded: chain H residue 445 VAL Chi-restraints excluded: chain H residue 451 VAL Chi-restraints excluded: chain I residue 6 MET Chi-restraints excluded: chain I residue 116 HIS Chi-restraints excluded: chain I residue 167 LEU Chi-restraints excluded: chain I residue 300 ASP Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 433 THR Chi-restraints excluded: chain I residue 444 ILE Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 383 VAL Chi-restraints excluded: chain J residue 424 LEU Chi-restraints excluded: chain K residue 116 HIS Chi-restraints excluded: chain K residue 167 LEU Chi-restraints excluded: chain K residue 300 ASP Chi-restraints excluded: chain K residue 360 VAL Chi-restraints excluded: chain K residue 435 MET Chi-restraints excluded: chain K residue 444 ILE Chi-restraints excluded: chain L residue 36 PHE Chi-restraints excluded: chain L residue 98 ILE Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain L residue 142 THR Chi-restraints excluded: chain L residue 277 THR Chi-restraints excluded: chain L residue 286 LEU Chi-restraints excluded: chain L residue 391 VAL Chi-restraints excluded: chain L residue 438 VAL Chi-restraints excluded: chain L residue 451 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1164 random chunks: chunk 1020 optimal weight: 0.8980 chunk 1074 optimal weight: 0.0370 chunk 980 optimal weight: 6.9990 chunk 1045 optimal weight: 3.9990 chunk 629 optimal weight: 9.9990 chunk 455 optimal weight: 2.9990 chunk 820 optimal weight: 9.9990 chunk 320 optimal weight: 8.9990 chunk 944 optimal weight: 20.0000 chunk 988 optimal weight: 0.6980 chunk 1041 optimal weight: 1.9990 overall best weight: 1.3262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1177 HIS B 934 GLN B1202 GLN C 672 GLN C1456 GLN D1177 HIS F 818 ASN G 4 GLN H 129 ASN ** I 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 4 GLN K 64 ASN K 434 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 92100 Z= 0.173 Angle : 0.800 82.440 124818 Z= 0.324 Chirality : 0.051 1.509 13890 Planarity : 0.003 0.042 16326 Dihedral : 5.433 172.497 13068 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.97 % Allowed : 16.20 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % 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: -0.43 (0.08), residues: 11640 helix: 1.13 (0.09), residues: 4152 sheet: -0.43 (0.12), residues: 1848 loop : -1.33 (0.08), residues: 5640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 69 HIS 0.004 0.001 HIS A 230 PHE 0.015 0.001 PHE I 36 TYR 0.013 0.001 TYR B1198 ARG 0.009 0.000 ARG I 429 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23280 Ramachandran restraints generated. 11640 Oldfield, 0 Emsley, 11640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23280 Ramachandran restraints generated. 11640 Oldfield, 0 Emsley, 11640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 907 residues out of total 9444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 721 time to evaluate : 7.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7377 (mt-10) REVERT: A 606 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8465 (tt) REVERT: A 1153 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8657 (mp) REVERT: A 1184 ASN cc_start: 0.8363 (t0) cc_final: 0.8121 (m110) REVERT: A 1229 MET cc_start: 0.9009 (mmm) cc_final: 0.8737 (mmt) REVERT: A 1368 MET cc_start: 0.8623 (ttt) cc_final: 0.8410 (ttp) REVERT: B 84 ASP cc_start: 0.8440 (OUTLIER) cc_final: 0.7519 (t0) REVERT: B 96 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8034 (mp0) REVERT: B 156 GLU cc_start: 0.8294 (mt-10) cc_final: 0.8063 (mt-10) REVERT: B 162 GLU cc_start: 0.7890 (tp30) cc_final: 0.7407 (tp30) REVERT: B 182 MET cc_start: 0.8326 (mmt) cc_final: 0.8027 (mmt) REVERT: B 786 ASP cc_start: 0.7950 (t0) cc_final: 0.7598 (m-30) REVERT: B 823 MET cc_start: 0.7359 (mtp) cc_final: 0.6825 (mtp) REVERT: B 829 LEU cc_start: 0.9468 (mp) cc_final: 0.9185 (mp) REVERT: B 858 MET cc_start: 0.8227 (mmt) cc_final: 0.7225 (mmm) REVERT: C 1 CYS cc_start: 0.7976 (t) cc_final: 0.7639 (p) REVERT: C 165 ASN cc_start: 0.8448 (m-40) cc_final: 0.8235 (m110) REVERT: C 225 PHE cc_start: 0.8454 (m-80) cc_final: 0.8246 (m-10) REVERT: C 297 MET cc_start: 0.8209 (tpp) cc_final: 0.7825 (mmm) REVERT: C 441 ASP cc_start: 0.5124 (m-30) cc_final: 0.3653 (p0) REVERT: C 687 MET cc_start: 0.7881 (ptp) cc_final: 0.7666 (ptp) REVERT: C 964 MET cc_start: 0.7980 (tpp) cc_final: 0.7704 (tpp) REVERT: C 971 HIS cc_start: 0.8732 (OUTLIER) cc_final: 0.7935 (t-90) REVERT: C 1047 MET cc_start: 0.8440 (mtt) cc_final: 0.7233 (mtp) REVERT: C 1051 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.6605 (mp0) REVERT: C 1248 SER cc_start: 0.9099 (OUTLIER) cc_final: 0.8833 (p) REVERT: C 1387 MET cc_start: 0.8939 (ttp) cc_final: 0.8656 (ttp) REVERT: D 296 MET cc_start: 0.9109 (tpp) cc_final: 0.8763 (tpp) REVERT: D 562 MET cc_start: 0.8999 (mmm) cc_final: 0.8760 (mmm) REVERT: D 606 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8446 (tt) REVERT: D 819 LYS cc_start: 0.8596 (mmtm) cc_final: 0.8131 (mmmt) REVERT: D 1153 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8694 (mp) REVERT: D 1184 ASN cc_start: 0.8387 (t0) cc_final: 0.8105 (m110) REVERT: D 1229 MET cc_start: 0.8985 (mmm) cc_final: 0.8712 (mmt) REVERT: D 1391 MET cc_start: 0.8646 (ttm) cc_final: 0.8363 (ttm) REVERT: E 297 MET cc_start: 0.8246 (mmm) cc_final: 0.7973 (mmm) REVERT: E 558 MET cc_start: 0.8282 (tmm) cc_final: 0.7811 (ttp) REVERT: E 726 GLU cc_start: 0.7717 (mt-10) cc_final: 0.7409 (mt-10) REVERT: E 780 ARG cc_start: 0.8227 (mtm180) cc_final: 0.7944 (ptp-170) REVERT: E 860 MET cc_start: 0.8423 (tpp) cc_final: 0.8218 (tpp) REVERT: E 1047 MET cc_start: 0.8360 (mtt) cc_final: 0.7561 (mtp) REVERT: E 1051 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7493 (mp0) REVERT: F 84 ASP cc_start: 0.8445 (m-30) cc_final: 0.7742 (t0) REVERT: F 307 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.7489 (mp10) REVERT: F 458 MET cc_start: 0.8121 (OUTLIER) cc_final: 0.7751 (ttt) REVERT: F 490 ASP cc_start: 0.9047 (OUTLIER) cc_final: 0.8740 (p0) REVERT: F 693 MET cc_start: 0.8465 (mmp) cc_final: 0.8201 (mmm) REVERT: F 823 MET cc_start: 0.6969 (mtp) cc_final: 0.6553 (mtp) REVERT: F 829 LEU cc_start: 0.9363 (mp) cc_final: 0.9154 (mp) REVERT: F 1291 ASP cc_start: 0.8607 (p0) cc_final: 0.8280 (p0) REVERT: F 1462 MET cc_start: 0.8030 (tpp) cc_final: 0.7441 (tpt) REVERT: G 6 MET cc_start: 0.8566 (ptm) cc_final: 0.8129 (ptp) REVERT: H 204 ARG cc_start: 0.7433 (tpp-160) cc_final: 0.7185 (mtt-85) REVERT: H 303 MET cc_start: 0.6349 (mmp) cc_final: 0.5970 (mmm) REVERT: H 324 ASP cc_start: 0.5536 (t0) cc_final: 0.4620 (p0) REVERT: H 328 MET cc_start: 0.7970 (tpt) cc_final: 0.7500 (ptt) REVERT: H 334 GLU cc_start: 0.7460 (mp0) cc_final: 0.6962 (mt-10) REVERT: H 415 GLU cc_start: 0.7482 (mt-10) cc_final: 0.6711 (tt0) REVERT: I 167 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8696 (mt) REVERT: I 259 ILE cc_start: 0.5473 (pt) cc_final: 0.4995 (pt) REVERT: I 435 MET cc_start: 0.7468 (mtt) cc_final: 0.7149 (mtm) REVERT: J 6 MET cc_start: 0.8296 (ptp) cc_final: 0.8004 (ptp) REVERT: J 394 ASP cc_start: 0.8002 (t0) cc_final: 0.7624 (t0) REVERT: L 146 GLU cc_start: 0.6651 (mm-30) cc_final: 0.5691 (mm-30) REVERT: L 334 GLU cc_start: 0.7487 (mp0) cc_final: 0.7057 (pp20) REVERT: L 415 GLU cc_start: 0.7541 (mt-10) cc_final: 0.7073 (tt0) REVERT: L 438 VAL cc_start: 0.7106 (OUTLIER) cc_final: 0.6758 (m) outliers start: 186 outliers final: 154 residues processed: 866 average time/residue: 0.7910 time to fit residues: 1207.5224 Evaluate side-chains 867 residues out of total 9444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 698 time to evaluate : 7.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 728 ILE Chi-restraints excluded: chain A residue 971 HIS Chi-restraints excluded: chain A residue 977 ILE Chi-restraints excluded: chain A residue 1019 ASP Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1265 THR Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain A residue 1355 VAL Chi-restraints excluded: chain A residue 1462 MET Chi-restraints excluded: chain A residue 1468 VAL Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 273 ASP Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 360 ASP Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 381 GLU Chi-restraints excluded: chain B residue 458 MET Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 520 MET Chi-restraints excluded: chain B residue 560 ASP Chi-restraints excluded: chain B residue 564 ASP Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain B residue 711 MET Chi-restraints excluded: chain B residue 971 HIS Chi-restraints excluded: chain B residue 987 LEU Chi-restraints excluded: chain B residue 1030 THR Chi-restraints excluded: chain B residue 1033 SER Chi-restraints excluded: chain B residue 1103 ILE Chi-restraints excluded: chain B residue 1131 THR Chi-restraints excluded: chain B residue 1153 LEU Chi-restraints excluded: chain B residue 1179 ASP Chi-restraints excluded: chain B residue 1181 LEU Chi-restraints excluded: chain B residue 1187 LEU Chi-restraints excluded: chain B residue 1265 THR Chi-restraints excluded: chain B residue 1276 LEU Chi-restraints excluded: chain B residue 1355 VAL Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 607 THR Chi-restraints excluded: chain C residue 640 THR Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 726 GLU Chi-restraints excluded: chain C residue 971 HIS Chi-restraints excluded: chain C residue 1002 SER Chi-restraints excluded: chain C residue 1051 GLU Chi-restraints excluded: chain C residue 1201 LEU Chi-restraints excluded: chain C residue 1248 SER Chi-restraints excluded: chain C residue 1276 LEU Chi-restraints excluded: chain C residue 1375 ILE Chi-restraints excluded: chain C residue 1394 VAL Chi-restraints excluded: chain D residue 42 ASP Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 375 ASP Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 551 THR Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 611 MET Chi-restraints excluded: chain D residue 640 THR Chi-restraints excluded: chain D residue 708 MET Chi-restraints excluded: chain D residue 728 ILE Chi-restraints excluded: chain D residue 971 HIS Chi-restraints excluded: chain D residue 1019 ASP Chi-restraints excluded: chain D residue 1038 ILE Chi-restraints excluded: chain D residue 1153 LEU Chi-restraints excluded: chain D residue 1265 THR Chi-restraints excluded: chain D residue 1281 VAL Chi-restraints excluded: chain E residue 42 ASP Chi-restraints excluded: chain E residue 69 ASN Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 335 MET Chi-restraints excluded: chain E residue 360 ASP Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 607 THR Chi-restraints excluded: chain E residue 640 THR Chi-restraints excluded: chain E residue 747 SER Chi-restraints excluded: chain E residue 771 VAL Chi-restraints excluded: chain E residue 971 HIS Chi-restraints excluded: chain E residue 1103 ILE Chi-restraints excluded: chain E residue 1131 THR Chi-restraints excluded: chain E residue 1201 LEU Chi-restraints excluded: chain E residue 1452 THR Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 273 ASP Chi-restraints excluded: chain F residue 304 THR Chi-restraints excluded: chain F residue 307 GLN Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain F residue 336 THR Chi-restraints excluded: chain F residue 363 ILE Chi-restraints excluded: chain F residue 381 GLU Chi-restraints excluded: chain F residue 458 MET Chi-restraints excluded: chain F residue 490 ASP Chi-restraints excluded: chain F residue 506 VAL Chi-restraints excluded: chain F residue 607 THR Chi-restraints excluded: chain F residue 706 LYS Chi-restraints excluded: chain F residue 711 MET Chi-restraints excluded: chain F residue 780 ARG Chi-restraints excluded: chain F residue 964 MET Chi-restraints excluded: chain F residue 987 LEU Chi-restraints excluded: chain F residue 1181 LEU Chi-restraints excluded: chain F residue 1265 THR Chi-restraints excluded: chain F residue 1276 LEU Chi-restraints excluded: chain F residue 1355 VAL Chi-restraints excluded: chain F residue 1397 LEU Chi-restraints excluded: chain G residue 5 ARG Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 383 VAL Chi-restraints excluded: chain G residue 433 THR Chi-restraints excluded: chain H residue 36 PHE Chi-restraints excluded: chain H residue 111 ILE Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 277 THR Chi-restraints excluded: chain H residue 286 LEU Chi-restraints excluded: chain H residue 391 VAL Chi-restraints excluded: chain H residue 418 VAL Chi-restraints excluded: chain H residue 451 VAL Chi-restraints excluded: chain I residue 167 LEU Chi-restraints excluded: chain I residue 300 ASP Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 444 ILE Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 360 VAL Chi-restraints excluded: chain J residue 383 VAL Chi-restraints excluded: chain J residue 424 LEU Chi-restraints excluded: chain J residue 433 THR Chi-restraints excluded: chain K residue 6 MET Chi-restraints excluded: chain K residue 300 ASP Chi-restraints excluded: chain K residue 360 VAL Chi-restraints excluded: chain K residue 444 ILE Chi-restraints excluded: chain L residue 36 PHE Chi-restraints excluded: chain L residue 98 ILE Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain L residue 142 THR Chi-restraints excluded: chain L residue 277 THR Chi-restraints excluded: chain L residue 286 LEU Chi-restraints excluded: chain L residue 391 VAL Chi-restraints excluded: chain L residue 438 VAL Chi-restraints excluded: chain L residue 451 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1164 random chunks: chunk 686 optimal weight: 0.8980 chunk 1105 optimal weight: 10.0000 chunk 674 optimal weight: 3.9990 chunk 524 optimal weight: 0.1980 chunk 768 optimal weight: 7.9990 chunk 1159 optimal weight: 9.9990 chunk 1067 optimal weight: 0.5980 chunk 923 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 chunk 713 optimal weight: 0.6980 chunk 566 optimal weight: 8.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 ASN A 497 HIS A1177 HIS B 818 ASN B1202 GLN C1456 GLN D1177 HIS E1406 ASN F 818 ASN F 934 GLN G 4 GLN G 50 GLN H 129 ASN I 64 ASN ** I 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 4 GLN K 64 ASN K 434 ASN L 337 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.105 92100 Z= 0.148 Angle : 0.791 82.470 124818 Z= 0.317 Chirality : 0.051 1.507 13890 Planarity : 0.003 0.042 16326 Dihedral : 5.257 172.770 13068 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.73 % Allowed : 16.57 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % 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: -0.29 (0.08), residues: 11640 helix: 1.21 (0.09), residues: 4188 sheet: -0.21 (0.13), residues: 1716 loop : -1.27 (0.08), residues: 5736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 69 HIS 0.005 0.000 HIS A 603 PHE 0.014 0.001 PHE I 36 TYR 0.013 0.001 TYR B1198 ARG 0.009 0.000 ARG F 832 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23280 Ramachandran restraints generated. 11640 Oldfield, 0 Emsley, 11640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23280 Ramachandran restraints generated. 11640 Oldfield, 0 Emsley, 11640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 924 residues out of total 9444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 761 time to evaluate : 8.045 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 94 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7329 (mt-10) REVERT: A 296 MET cc_start: 0.8896 (tpp) cc_final: 0.8395 (tpp) REVERT: A 606 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8333 (tt) REVERT: A 1184 ASN cc_start: 0.8399 (t0) cc_final: 0.8085 (m110) REVERT: A 1229 MET cc_start: 0.8998 (mmm) cc_final: 0.8725 (mmt) REVERT: A 1368 MET cc_start: 0.8564 (ttt) cc_final: 0.8299 (ttm) REVERT: A 1391 MET cc_start: 0.8637 (ttm) cc_final: 0.8342 (ttm) REVERT: B 84 ASP cc_start: 0.8432 (OUTLIER) cc_final: 0.7503 (t0) REVERT: B 96 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.8037 (mp0) REVERT: B 147 ASP cc_start: 0.7613 (m-30) cc_final: 0.7350 (m-30) REVERT: B 156 GLU cc_start: 0.8261 (mt-10) cc_final: 0.8017 (mt-10) REVERT: B 162 GLU cc_start: 0.7989 (tp30) cc_final: 0.7753 (tp30) REVERT: B 182 MET cc_start: 0.8326 (mmt) cc_final: 0.8050 (mmt) REVERT: B 562 MET cc_start: 0.8046 (mtm) cc_final: 0.7802 (mtp) REVERT: B 767 ASN cc_start: 0.7926 (m-40) cc_final: 0.7522 (t0) REVERT: B 786 ASP cc_start: 0.7921 (t0) cc_final: 0.7493 (m-30) REVERT: B 820 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.7784 (mtm-85) REVERT: B 823 MET cc_start: 0.7228 (mtp) cc_final: 0.6652 (mtp) REVERT: B 829 LEU cc_start: 0.9393 (mp) cc_final: 0.9134 (mp) REVERT: B 858 MET cc_start: 0.8211 (mmt) cc_final: 0.7240 (mmm) REVERT: B 899 ASN cc_start: 0.7623 (t0) cc_final: 0.7343 (t0) REVERT: C 1 CYS cc_start: 0.7928 (t) cc_final: 0.7650 (p) REVERT: C 165 ASN cc_start: 0.8490 (m-40) cc_final: 0.8249 (m110) REVERT: C 182 MET cc_start: 0.7603 (mmt) cc_final: 0.7003 (mmt) REVERT: C 297 MET cc_start: 0.8149 (tpp) cc_final: 0.7784 (mmm) REVERT: C 558 MET cc_start: 0.8337 (tmm) cc_final: 0.7825 (ttp) REVERT: C 964 MET cc_start: 0.7876 (tpp) cc_final: 0.7620 (tpp) REVERT: C 971 HIS cc_start: 0.8590 (OUTLIER) cc_final: 0.8043 (t-90) REVERT: C 1047 MET cc_start: 0.8416 (mtt) cc_final: 0.6954 (mtp) REVERT: C 1051 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.7048 (mp0) REVERT: C 1248 SER cc_start: 0.9108 (OUTLIER) cc_final: 0.8871 (p) REVERT: C 1387 MET cc_start: 0.8956 (ttp) cc_final: 0.8676 (ttp) REVERT: C 1456 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.7855 (tm130) REVERT: D 442 MET cc_start: 0.7079 (ttp) cc_final: 0.6719 (ttp) REVERT: D 562 MET cc_start: 0.8974 (mmm) cc_final: 0.8698 (mmm) REVERT: D 606 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8332 (tt) REVERT: D 819 LYS cc_start: 0.8525 (mmtm) cc_final: 0.8075 (mmmt) REVERT: D 1153 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8586 (mp) REVERT: D 1184 ASN cc_start: 0.8351 (t0) cc_final: 0.8056 (m110) REVERT: D 1229 MET cc_start: 0.8993 (mmm) cc_final: 0.8720 (mmt) REVERT: D 1391 MET cc_start: 0.8615 (ttm) cc_final: 0.8334 (ttm) REVERT: E 221 LEU cc_start: 0.9191 (mt) cc_final: 0.8989 (mt) REVERT: E 297 MET cc_start: 0.8165 (mmm) cc_final: 0.7915 (mmm) REVERT: E 360 ASP cc_start: 0.7594 (OUTLIER) cc_final: 0.6899 (t0) REVERT: E 558 MET cc_start: 0.8252 (tmm) cc_final: 0.7792 (ttp) REVERT: E 726 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7391 (mt-10) REVERT: E 780 ARG cc_start: 0.8280 (mtm180) cc_final: 0.7994 (ptp-170) REVERT: E 1047 MET cc_start: 0.8356 (mtt) cc_final: 0.7434 (mtp) REVERT: E 1051 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7406 (mp0) REVERT: E 1246 LEU cc_start: 0.8646 (tp) cc_final: 0.8438 (tp) REVERT: F 42 ASP cc_start: 0.7785 (OUTLIER) cc_final: 0.7581 (p0) REVERT: F 84 ASP cc_start: 0.8444 (m-30) cc_final: 0.7735 (t0) REVERT: F 458 MET cc_start: 0.8080 (OUTLIER) cc_final: 0.7735 (ttt) REVERT: F 693 MET cc_start: 0.8424 (mmp) cc_final: 0.8159 (mmm) REVERT: F 829 LEU cc_start: 0.9331 (mp) cc_final: 0.9122 (mp) REVERT: F 1218 ASP cc_start: 0.8214 (m-30) cc_final: 0.7980 (m-30) REVERT: F 1291 ASP cc_start: 0.8518 (p0) cc_final: 0.8213 (p0) REVERT: F 1462 MET cc_start: 0.8024 (tpp) cc_final: 0.7463 (tpt) REVERT: G 6 MET cc_start: 0.8601 (ptm) cc_final: 0.8160 (ptp) REVERT: H 204 ARG cc_start: 0.7426 (tpp-160) cc_final: 0.7186 (mtt-85) REVERT: H 324 ASP cc_start: 0.5812 (t0) cc_final: 0.4936 (p0) REVERT: H 328 MET cc_start: 0.7963 (tpt) cc_final: 0.7507 (ptt) REVERT: H 334 GLU cc_start: 0.7431 (mp0) cc_final: 0.6978 (mt-10) REVERT: H 415 GLU cc_start: 0.7466 (mt-10) cc_final: 0.6708 (tt0) REVERT: I 259 ILE cc_start: 0.5817 (pt) cc_final: 0.5354 (pt) REVERT: J 6 MET cc_start: 0.8307 (ptp) cc_final: 0.8007 (ptp) REVERT: J 394 ASP cc_start: 0.8001 (t0) cc_final: 0.7630 (t0) REVERT: K 259 ILE cc_start: 0.5861 (pt) cc_final: 0.5365 (pt) REVERT: K 316 SER cc_start: 0.8705 (t) cc_final: 0.8388 (m) REVERT: L 146 GLU cc_start: 0.6606 (mm-30) cc_final: 0.5646 (mm-30) REVERT: L 303 MET cc_start: 0.6201 (mmt) cc_final: 0.5828 (mmm) REVERT: L 334 GLU cc_start: 0.7435 (mp0) cc_final: 0.7155 (pp20) REVERT: L 415 GLU cc_start: 0.7542 (mt-10) cc_final: 0.7093 (tt0) REVERT: L 438 VAL cc_start: 0.7074 (OUTLIER) cc_final: 0.6720 (m) outliers start: 163 outliers final: 126 residues processed: 887 average time/residue: 0.8146 time to fit residues: 1273.8876 Evaluate side-chains 861 residues out of total 9444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 720 time to evaluate : 7.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 1019 ASP Chi-restraints excluded: chain A residue 1265 THR Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain A residue 1468 VAL Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 273 ASP Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 360 ASP Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 381 GLU Chi-restraints excluded: chain B residue 458 MET Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 560 ASP Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain B residue 716 ILE Chi-restraints excluded: chain B residue 820 ARG Chi-restraints excluded: chain B residue 971 HIS Chi-restraints excluded: chain B residue 1030 THR Chi-restraints excluded: chain B residue 1103 ILE Chi-restraints excluded: chain B residue 1131 THR Chi-restraints excluded: chain B residue 1179 ASP Chi-restraints excluded: chain B residue 1181 LEU Chi-restraints excluded: chain B residue 1187 LEU Chi-restraints excluded: chain B residue 1265 THR Chi-restraints excluded: chain B residue 1276 LEU Chi-restraints excluded: chain B residue 1355 VAL Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 607 THR Chi-restraints excluded: chain C residue 640 THR Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 726 GLU Chi-restraints excluded: chain C residue 771 VAL Chi-restraints excluded: chain C residue 971 HIS Chi-restraints excluded: chain C residue 1002 SER Chi-restraints excluded: chain C residue 1051 GLU Chi-restraints excluded: chain C residue 1201 LEU Chi-restraints excluded: chain C residue 1248 SER Chi-restraints excluded: chain C residue 1276 LEU Chi-restraints excluded: chain C residue 1375 ILE Chi-restraints excluded: chain C residue 1394 VAL Chi-restraints excluded: chain C residue 1456 GLN Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 375 ASP Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 551 THR Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 640 THR Chi-restraints excluded: chain D residue 708 MET Chi-restraints excluded: chain D residue 728 ILE Chi-restraints excluded: chain D residue 971 HIS Chi-restraints excluded: chain D residue 1019 ASP Chi-restraints excluded: chain D residue 1153 LEU Chi-restraints excluded: chain D residue 1265 THR Chi-restraints excluded: chain D residue 1281 VAL Chi-restraints excluded: chain E residue 42 ASP Chi-restraints excluded: chain E residue 69 ASN Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 335 MET Chi-restraints excluded: chain E residue 360 ASP Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 607 THR Chi-restraints excluded: chain E residue 640 THR Chi-restraints excluded: chain E residue 747 SER Chi-restraints excluded: chain E residue 771 VAL Chi-restraints excluded: chain E residue 971 HIS Chi-restraints excluded: chain E residue 1103 ILE Chi-restraints excluded: chain E residue 1131 THR Chi-restraints excluded: chain E residue 1201 LEU Chi-restraints excluded: chain E residue 1452 THR Chi-restraints excluded: chain F residue 42 ASP Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 273 ASP Chi-restraints excluded: chain F residue 304 THR Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain F residue 336 THR Chi-restraints excluded: chain F residue 363 ILE Chi-restraints excluded: chain F residue 381 GLU Chi-restraints excluded: chain F residue 458 MET Chi-restraints excluded: chain F residue 506 VAL Chi-restraints excluded: chain F residue 607 THR Chi-restraints excluded: chain F residue 706 LYS Chi-restraints excluded: chain F residue 711 MET Chi-restraints excluded: chain F residue 780 ARG Chi-restraints excluded: chain F residue 964 MET Chi-restraints excluded: chain F residue 1265 THR Chi-restraints excluded: chain F residue 1276 LEU Chi-restraints excluded: chain F residue 1355 VAL Chi-restraints excluded: chain F residue 1397 LEU Chi-restraints excluded: chain G residue 5 ARG Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 424 LEU Chi-restraints excluded: chain H residue 36 PHE Chi-restraints excluded: chain H residue 111 ILE Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 277 THR Chi-restraints excluded: chain H residue 286 LEU Chi-restraints excluded: chain H residue 391 VAL Chi-restraints excluded: chain H residue 407 LEU Chi-restraints excluded: chain H residue 418 VAL Chi-restraints excluded: chain H residue 451 VAL Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 433 THR Chi-restraints excluded: chain I residue 444 ILE Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 360 VAL Chi-restraints excluded: chain J residue 424 LEU Chi-restraints excluded: chain J residue 433 THR Chi-restraints excluded: chain K residue 300 ASP Chi-restraints excluded: chain K residue 360 VAL Chi-restraints excluded: chain L residue 36 PHE Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain L residue 142 THR Chi-restraints excluded: chain L residue 286 LEU Chi-restraints excluded: chain L residue 391 VAL Chi-restraints excluded: chain L residue 438 VAL Chi-restraints excluded: chain L residue 451 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1164 random chunks: chunk 733 optimal weight: 4.9990 chunk 983 optimal weight: 7.9990 chunk 282 optimal weight: 7.9990 chunk 851 optimal weight: 8.9990 chunk 136 optimal weight: 9.9990 chunk 256 optimal weight: 5.9990 chunk 924 optimal weight: 7.9990 chunk 387 optimal weight: 6.9990 chunk 949 optimal weight: 8.9990 chunk 117 optimal weight: 0.6980 chunk 170 optimal weight: 10.0000 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 ASN A1177 HIS B 635 ASN B 818 ASN B1184 ASN D 240 ASN E1406 ASN F 818 ASN G 4 GLN G 57 GLN H 108 ASN H 129 ASN I 64 ASN ** I 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 4 GLN K 64 ASN K 434 ASN ** L 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.103454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.080382 restraints weight = 170744.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.082439 restraints weight = 101108.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.083831 restraints weight = 69556.683| |-----------------------------------------------------------------------------| r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.103 92100 Z= 0.446 Angle : 0.896 82.569 124818 Z= 0.384 Chirality : 0.056 1.532 13890 Planarity : 0.004 0.044 16326 Dihedral : 5.784 177.423 13068 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 1.96 % Allowed : 16.45 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % 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: -0.65 (0.08), residues: 11640 helix: 0.90 (0.08), residues: 4140 sheet: -0.47 (0.12), residues: 1800 loop : -1.44 (0.08), residues: 5700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP K 69 HIS 0.006 0.001 HIS E 230 PHE 0.031 0.002 PHE C 225 TYR 0.027 0.002 TYR A 211 ARG 0.018 0.001 ARG C1414 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20465.57 seconds wall clock time: 360 minutes 39.07 seconds (21639.07 seconds total)