Starting phenix.real_space_refine on Fri Mar 15 18:34:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfz_33802/03_2024/7yfz_33802.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfz_33802/03_2024/7yfz_33802.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfz_33802/03_2024/7yfz_33802.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfz_33802/03_2024/7yfz_33802.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfz_33802/03_2024/7yfz_33802.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfz_33802/03_2024/7yfz_33802.pdb" } resolution = 3.19 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 342 5.16 5 C 42255 2.51 5 N 11547 2.21 5 O 13236 1.98 5 H 61470 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 70": "OE1" <-> "OE2" Residue "B GLU 92": "OE1" <-> "OE2" Residue "B GLU 180": "OE1" <-> "OE2" Residue "B GLU 253": "OE1" <-> "OE2" Residue "C GLU 9": "OE1" <-> "OE2" Residue "C GLU 18": "OE1" <-> "OE2" Residue "C GLU 42": "OE1" <-> "OE2" Residue "C GLU 105": "OE1" <-> "OE2" Residue "C GLU 159": "OE1" <-> "OE2" Residue "D GLU 13": "OE1" <-> "OE2" Residue "D GLU 52": "OE1" <-> "OE2" Residue "D GLU 105": "OE1" <-> "OE2" Residue "D GLU 151": "OE1" <-> "OE2" Residue "D GLU 183": "OE1" <-> "OE2" Residue "E TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 95": "OE1" <-> "OE2" Residue "E GLU 241": "OE1" <-> "OE2" Residue "E GLU 296": "OE1" <-> "OE2" Residue "F GLU 23": "OE1" <-> "OE2" Residue "F GLU 133": "OE1" <-> "OE2" Residue "F GLU 180": "OE1" <-> "OE2" Residue "F GLU 203": "OE1" <-> "OE2" Residue "G GLU 13": "OE1" <-> "OE2" Residue "G GLU 52": "OE1" <-> "OE2" Residue "G GLU 105": "OE1" <-> "OE2" Residue "G GLU 120": "OE1" <-> "OE2" Residue "G GLU 151": "OE1" <-> "OE2" Residue "H GLU 92": "OE1" <-> "OE2" Residue "H GLU 180": "OE1" <-> "OE2" Residue "H GLU 203": "OE1" <-> "OE2" Residue "H GLU 296": "OE1" <-> "OE2" Residue "I GLU 21": "OE1" <-> "OE2" Residue "I GLU 61": "OE1" <-> "OE2" Residue "I GLU 133": "OE1" <-> "OE2" Residue "I GLU 158": "OE1" <-> "OE2" Residue "I GLU 180": "OE1" <-> "OE2" Residue "I GLU 296": "OE1" <-> "OE2" Residue "J GLU 25": "OE1" <-> "OE2" Residue "J GLU 42": "OE1" <-> "OE2" Residue "J GLU 52": "OE1" <-> "OE2" Residue "J GLU 105": "OE1" <-> "OE2" Residue "J GLU 125": "OE1" <-> "OE2" Residue "K GLU 23": "OE1" <-> "OE2" Residue "K GLU 70": "OE1" <-> "OE2" Residue "K GLU 92": "OE1" <-> "OE2" Residue "K GLU 296": "OE1" <-> "OE2" Residue "L GLU 133": "OE1" <-> "OE2" Residue "L GLU 241": "OE1" <-> "OE2" Residue "L GLU 260": "OE1" <-> "OE2" Residue "M GLU 125": "OE1" <-> "OE2" Residue "M GLU 159": "OE1" <-> "OE2" Residue "O GLU 23": "OE1" <-> "OE2" Residue "O GLU 58": "OE1" <-> "OE2" Residue "O GLU 70": "OE1" <-> "OE2" Residue "O GLU 92": "OE1" <-> "OE2" Residue "O GLU 180": "OE1" <-> "OE2" Residue "O GLU 296": "OE1" <-> "OE2" Residue "P GLU 158": "OE1" <-> "OE2" Residue "P GLU 180": "OE1" <-> "OE2" Residue "P GLU 253": "OE1" <-> "OE2" Residue "P GLU 296": "OE1" <-> "OE2" Residue "Q GLU 58": "OE1" <-> "OE2" Residue "Q GLU 95": "OE1" <-> "OE2" Residue "Q GLU 133": "OE1" <-> "OE2" Residue "Q GLU 241": "OE1" <-> "OE2" Residue "Q GLU 260": "OE1" <-> "OE2" Residue "Q GLU 296": "OE1" <-> "OE2" Residue "R GLU 23": "OE1" <-> "OE2" Residue "R GLU 61": "OE1" <-> "OE2" Residue "R ASP 62": "OD1" <-> "OD2" Residue "R GLU 70": "OE1" <-> "OE2" Residue "R GLU 180": "OE1" <-> "OE2" Residue "R GLU 296": "OE1" <-> "OE2" Residue "S GLU 42": "OE1" <-> "OE2" Residue "S GLU 120": "OE1" <-> "OE2" Residue "X GLU 84": "OE1" <-> "OE2" Residue "X GLU 118": "OE1" <-> "OE2" Residue "b GLU 27": "OE1" <-> "OE2" Residue "c GLU 71": "OE1" <-> "OE2" Residue "c GLU 92": "OE1" <-> "OE2" Residue "c GLU 113": "OE1" <-> "OE2" Residue "d GLU 49": "OE1" <-> "OE2" Residue "e GLU 51": "OE1" <-> "OE2" Residue "e GLU 53": "OE1" <-> "OE2" Residue "e GLU 113": "OE1" <-> "OE2" Residue "f GLU 27": "OE1" <-> "OE2" Residue "f GLU 49": "OE1" <-> "OE2" Residue "h GLU 9": "OE1" <-> "OE2" Residue "h GLU 99": "OE1" <-> "OE2" Residue "i GLU 5": "OE1" <-> "OE2" Residue "i GLU 26": "OE1" <-> "OE2" Residue "j GLU 3": "OE1" <-> "OE2" Residue "j GLU 26": "OE1" <-> "OE2" Residue "k GLU 3": "OE1" <-> "OE2" Residue "k GLU 99": "OE1" <-> "OE2" Residue "l ASP 34": "OD1" <-> "OD2" Residue "m GLU 3": "OE1" <-> "OE2" Residue "m PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "n GLU 78": "OE1" <-> "OE2" Residue "n GLU 84": "OE1" <-> "OE2" Residue "n GLU 93": "OE1" <-> "OE2" Residue "n GLU 114": "OE1" <-> "OE2" Residue "o GLU 36": "OE1" <-> "OE2" Residue "o GLU 84": "OE1" <-> "OE2" Residue "p GLU 36": "OE1" <-> "OE2" Residue "p GLU 84": "OE1" <-> "OE2" Residue "p GLU 93": "OE1" <-> "OE2" Residue "p GLU 109": "OE1" <-> "OE2" Residue "q GLU 84": "OE1" <-> "OE2" Residue "q GLU 93": "OE1" <-> "OE2" Residue "r GLU 93": "OE1" <-> "OE2" Residue "t GLU 3": "OE1" <-> "OE2" Residue "t GLU 31": "OE1" <-> "OE2" Residue "t GLU 77": "OE1" <-> "OE2" Residue "t GLU 83": "OE1" <-> "OE2" Residue "t GLU 125": "OE1" <-> "OE2" Residue "u GLU 3": "OE1" <-> "OE2" Residue "u GLU 31": "OE1" <-> "OE2" Residue "u GLU 83": "OE1" <-> "OE2" Residue "u GLU 125": "OE1" <-> "OE2" Residue "v TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "v GLU 83": "OE1" <-> "OE2" Residue "v GLU 125": "OE1" <-> "OE2" Residue "x GLU 169": "OE1" <-> "OE2" Residue "y GLU 169": "OE1" <-> "OE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 128850 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 4519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 4519 Classifications: {'peptide': 299} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 276} Chain: "B" Number of atoms: 4565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 4565 Classifications: {'peptide': 299} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 276} Chain: "C" Number of atoms: 3339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 3339 Classifications: {'peptide': 238} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 13, 'TRANS': 224} Chain: "D" Number of atoms: 3339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 3339 Classifications: {'peptide': 238} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 13, 'TRANS': 224} Chain: "E" Number of atoms: 4519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 4519 Classifications: {'peptide': 299} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 276} Chain: "F" Number of atoms: 4565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 4565 Classifications: {'peptide': 299} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 276} Chain: "G" Number of atoms: 3339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 3339 Classifications: {'peptide': 238} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 13, 'TRANS': 224} Chain: "H" Number of atoms: 4519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 4519 Classifications: {'peptide': 299} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 276} Chain: "I" Number of atoms: 4565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 4565 Classifications: {'peptide': 299} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 276} Chain: "J" Number of atoms: 3339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 3339 Classifications: {'peptide': 238} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 13, 'TRANS': 224} Chain: "K" Number of atoms: 4519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 4519 Classifications: {'peptide': 299} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 276} Chain: "L" Number of atoms: 4551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 4551 Classifications: {'peptide': 299} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 276} Chain: "M" Number of atoms: 3339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 3339 Classifications: {'peptide': 238} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 13, 'TRANS': 224} Chain: "O" Number of atoms: 4512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 4512 Classifications: {'peptide': 299} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 276} Chain: "P" Number of atoms: 4565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 4565 Classifications: {'peptide': 299} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 276} Chain: "Q" Number of atoms: 4519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 4519 Classifications: {'peptide': 299} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 276} Chain: "R" Number of atoms: 4565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 4565 Classifications: {'peptide': 299} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 276} Chain: "S" Number of atoms: 3339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 3339 Classifications: {'peptide': 238} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 13, 'TRANS': 224} Chain: "X" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1869 Classifications: {'peptide': 120} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "a" Number of atoms: 2119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 2119 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 6, 'TRANS': 175} Chain: "b" Number of atoms: 2119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 2119 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 6, 'TRANS': 175} Chain: "c" Number of atoms: 2119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 2119 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 6, 'TRANS': 175} Chain: "d" Number of atoms: 2119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 2119 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 6, 'TRANS': 175} Chain: "e" Number of atoms: 2119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 2119 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 6, 'TRANS': 175} Chain: "f" Number of atoms: 2119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 2119 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 6, 'TRANS': 175} Chain: "h" Number of atoms: 1660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 1660 Classifications: {'peptide': 106} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 101} Chain: "i" Number of atoms: 1660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 1660 Classifications: {'peptide': 106} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 101} Chain: "j" Number of atoms: 1660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 1660 Classifications: {'peptide': 106} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 101} Chain: "k" Number of atoms: 1660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 1660 Classifications: {'peptide': 106} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 101} Chain: "l" Number of atoms: 1660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 1660 Classifications: {'peptide': 106} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 101} Chain: "m" Number of atoms: 1660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 1660 Classifications: {'peptide': 106} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 101} Chain: "n" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1869 Classifications: {'peptide': 120} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "o" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1869 Classifications: {'peptide': 120} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "p" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1869 Classifications: {'peptide': 120} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "q" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1869 Classifications: {'peptide': 120} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "r" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1869 Classifications: {'peptide': 120} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "t" Number of atoms: 3538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 3538 Classifications: {'peptide': 229} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 216} Chain: "u" Number of atoms: 3538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 3538 Classifications: {'peptide': 229} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 216} Chain: "v" Number of atoms: 3538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 3538 Classifications: {'peptide': 229} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 216} Chain: "w" Number of atoms: 3277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 3277 Classifications: {'peptide': 221} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 208} Chain: "x" Number of atoms: 3277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 3277 Classifications: {'peptide': 221} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 208} Chain: "y" Number of atoms: 3277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 3277 Classifications: {'peptide': 221} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 208} Time building chain proxies: 40.54, per 1000 atoms: 0.31 Number of scatterers: 128850 At special positions: 0 Unit cell: (234.33, 221.49, 192.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 342 16.00 O 13236 8.00 N 11547 7.00 C 42255 6.00 H 61470 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=25, symmetry=0 Simple disulfide: pdb=" SG CYS A 187 " - pdb=" SG CYS E 215 " distance=2.03 Simple disulfide: pdb=" SG CYS B 215 " - pdb=" SG CYS G 78 " distance=2.03 Simple disulfide: pdb=" SG CYS C 5 " - pdb=" SG CYS C 48 " distance=2.03 Simple disulfide: pdb=" SG CYS C 76 " - pdb=" SG CYS C 122 " distance=2.05 Simple disulfide: pdb=" SG CYS C 78 " - pdb=" SG CYS R 215 " distance=2.03 Simple disulfide: pdb=" SG CYS C 80 " - pdb=" SG CYS C 237 " distance=2.03 Simple disulfide: pdb=" SG CYS D 5 " - pdb=" SG CYS D 48 " distance=2.03 Simple disulfide: pdb=" SG CYS D 76 " - pdb=" SG CYS D 122 " distance=2.05 Simple disulfide: pdb=" SG CYS D 80 " - pdb=" SG CYS D 237 " distance=2.03 Simple disulfide: pdb=" SG CYS G 5 " - pdb=" SG CYS G 48 " distance=2.01 Simple disulfide: pdb=" SG CYS G 76 " - pdb=" SG CYS G 122 " distance=2.03 Simple disulfide: pdb=" SG CYS G 80 " - pdb=" SG CYS G 237 " distance=2.03 Simple disulfide: pdb=" SG CYS H 187 " - pdb=" SG CYS K 215 " distance=2.04 Simple disulfide: pdb=" SG CYS H 215 " - pdb=" SG CYS O 187 " distance=2.04 Simple disulfide: pdb=" SG CYS I 215 " - pdb=" SG CYS M 78 " distance=2.03 Simple disulfide: pdb=" SG CYS J 5 " - pdb=" SG CYS J 48 " distance=2.02 Simple disulfide: pdb=" SG CYS J 76 " - pdb=" SG CYS J 122 " distance=2.04 Simple disulfide: pdb=" SG CYS J 78 " - pdb=" SG CYS P 215 " distance=2.03 Simple disulfide: pdb=" SG CYS J 80 " - pdb=" SG CYS J 237 " distance=2.03 Simple disulfide: pdb=" SG CYS M 5 " - pdb=" SG CYS M 48 " distance=2.03 Simple disulfide: pdb=" SG CYS M 76 " - pdb=" SG CYS M 122 " distance=2.06 Simple disulfide: pdb=" SG CYS M 80 " - pdb=" SG CYS M 237 " distance=2.03 Simple disulfide: pdb=" SG CYS S 5 " - pdb=" SG CYS S 48 " distance=2.02 Simple disulfide: pdb=" SG CYS S 76 " - pdb=" SG CYS S 122 " distance=2.03 Simple disulfide: pdb=" SG CYS S 80 " - pdb=" SG CYS S 237 " distance=2.02 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: 74.68 Conformation dependent library (CDL) restraints added in 10.3 seconds 17460 Ramachandran restraints generated. 8730 Oldfield, 0 Emsley, 8730 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16074 Finding SS restraints... Secondary structure from input PDB file: 241 helices and 130 sheets defined 32.9% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.30 Creating SS restraints... Processing helix chain 'A' and resid 14 through 31 Processing helix chain 'A' and resid 40 through 66 Processing helix chain 'A' and resid 74 through 82 Processing helix chain 'A' and resid 93 through 103 Processing helix chain 'A' and resid 111 through 121 Processing helix chain 'A' and resid 155 through 167 removed outlier: 3.529A pdb=" N ARG A 165 " --> pdb=" O GLN A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 214 Processing helix chain 'A' and resid 219 through 233 Processing helix chain 'A' and resid 244 through 256 removed outlier: 3.591A pdb=" N PHE A 248 " --> pdb=" O THR A 244 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG A 254 " --> pdb=" O LYS A 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 31 removed outlier: 3.587A pdb=" N ILE B 22 " --> pdb=" O HIS B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 66 Processing helix chain 'B' and resid 74 through 82 Processing helix chain 'B' and resid 93 through 101 Processing helix chain 'B' and resid 110 through 121 Processing helix chain 'B' and resid 155 through 167 Processing helix chain 'B' and resid 219 through 232 Processing helix chain 'B' and resid 244 through 256 removed outlier: 3.550A pdb=" N PHE B 248 " --> pdb=" O THR B 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 17 Processing helix chain 'C' and resid 18 through 19 No H-bonds generated for 'chain 'C' and resid 18 through 19' Processing helix chain 'C' and resid 20 through 24 Processing helix chain 'C' and resid 26 through 46 removed outlier: 3.758A pdb=" N LYS C 39 " --> pdb=" O ALA C 35 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU C 40 " --> pdb=" O TYR C 36 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER C 46 " --> pdb=" O GLU C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 50 Processing helix chain 'C' and resid 61 through 72 Processing helix chain 'C' and resid 113 through 118 removed outlier: 3.771A pdb=" N ASN C 118 " --> pdb=" O SER C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 142 removed outlier: 3.666A pdb=" N SER C 131 " --> pdb=" O GLU C 127 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N TYR C 138 " --> pdb=" O LYS C 134 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN C 139 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU C 141 " --> pdb=" O ARG C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 157 removed outlier: 3.751A pdb=" N GLU C 151 " --> pdb=" O GLU C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 194 Proline residue: C 188 - end of helix removed outlier: 3.526A pdb=" N PHE C 191 " --> pdb=" O LEU C 187 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG C 192 " --> pdb=" O PRO C 188 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA C 193 " --> pdb=" O ILE C 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 17 Processing helix chain 'D' and resid 18 through 19 No H-bonds generated for 'chain 'D' and resid 18 through 19' Processing helix chain 'D' and resid 20 through 24 Processing helix chain 'D' and resid 26 through 46 removed outlier: 3.648A pdb=" N LYS D 39 " --> pdb=" O ALA D 35 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU D 40 " --> pdb=" O TYR D 36 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER D 46 " --> pdb=" O GLU D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 50 Processing helix chain 'D' and resid 51 through 55 removed outlier: 4.039A pdb=" N PHE D 54 " --> pdb=" O VAL D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 72 Processing helix chain 'D' and resid 113 through 118 removed outlier: 3.568A pdb=" N ASN D 118 " --> pdb=" O SER D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 142 removed outlier: 3.880A pdb=" N SER D 131 " --> pdb=" O GLU D 127 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N TYR D 138 " --> pdb=" O LYS D 134 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU D 141 " --> pdb=" O ARG D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 157 removed outlier: 4.089A pdb=" N GLU D 151 " --> pdb=" O GLU D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 194 Proline residue: D 188 - end of helix removed outlier: 3.724A pdb=" N ARG D 192 " --> pdb=" O PRO D 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 31 Processing helix chain 'E' and resid 40 through 66 Processing helix chain 'E' and resid 74 through 82 Processing helix chain 'E' and resid 93 through 103 Processing helix chain 'E' and resid 111 through 120 Processing helix chain 'E' and resid 155 through 167 removed outlier: 3.574A pdb=" N TYR E 166 " --> pdb=" O LEU E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 219 through 232 Processing helix chain 'E' and resid 244 through 256 removed outlier: 3.512A pdb=" N PHE E 248 " --> pdb=" O THR E 244 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG E 254 " --> pdb=" O LYS E 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 31 Processing helix chain 'F' and resid 40 through 66 Processing helix chain 'F' and resid 74 through 82 Processing helix chain 'F' and resid 83 through 85 No H-bonds generated for 'chain 'F' and resid 83 through 85' Processing helix chain 'F' and resid 93 through 101 Processing helix chain 'F' and resid 110 through 121 removed outlier: 3.584A pdb=" N ILE F 121 " --> pdb=" O ALA F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 165 Processing helix chain 'F' and resid 219 through 233 Processing helix chain 'F' and resid 244 through 256 Processing helix chain 'F' and resid 289 through 291 No H-bonds generated for 'chain 'F' and resid 289 through 291' Processing helix chain 'G' and resid 7 through 17 Processing helix chain 'G' and resid 18 through 19 No H-bonds generated for 'chain 'G' and resid 18 through 19' Processing helix chain 'G' and resid 20 through 24 Processing helix chain 'G' and resid 26 through 46 removed outlier: 3.528A pdb=" N LYS G 39 " --> pdb=" O ALA G 35 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU G 40 " --> pdb=" O TYR G 36 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER G 46 " --> pdb=" O GLU G 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 50 Processing helix chain 'G' and resid 61 through 72 removed outlier: 3.690A pdb=" N ILE G 67 " --> pdb=" O GLN G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 118 removed outlier: 3.563A pdb=" N ASN G 118 " --> pdb=" O SER G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 142 removed outlier: 3.719A pdb=" N SER G 131 " --> pdb=" O GLU G 127 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N TYR G 138 " --> pdb=" O LYS G 134 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN G 139 " --> pdb=" O ALA G 135 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 157 removed outlier: 3.971A pdb=" N GLU G 151 " --> pdb=" O GLU G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 191 Proline residue: G 188 - end of helix Processing helix chain 'H' and resid 14 through 31 Processing helix chain 'H' and resid 40 through 66 Processing helix chain 'H' and resid 74 through 82 Processing helix chain 'H' and resid 93 through 103 Processing helix chain 'H' and resid 111 through 121 Processing helix chain 'H' and resid 155 through 167 Processing helix chain 'H' and resid 210 through 214 Processing helix chain 'H' and resid 219 through 233 Processing helix chain 'H' and resid 244 through 256 removed outlier: 3.706A pdb=" N PHE H 248 " --> pdb=" O THR H 244 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLU H 253 " --> pdb=" O ARG H 249 " (cutoff:3.500A) Processing helix chain 'I' and resid 14 through 31 Processing helix chain 'I' and resid 40 through 66 Processing helix chain 'I' and resid 74 through 82 Processing helix chain 'I' and resid 93 through 101 Processing helix chain 'I' and resid 110 through 121 Processing helix chain 'I' and resid 155 through 167 Processing helix chain 'I' and resid 219 through 233 Processing helix chain 'I' and resid 244 through 256 removed outlier: 3.775A pdb=" N PHE I 248 " --> pdb=" O THR I 244 " (cutoff:3.500A) Processing helix chain 'I' and resid 289 through 291 No H-bonds generated for 'chain 'I' and resid 289 through 291' Processing helix chain 'J' and resid 7 through 17 Processing helix chain 'J' and resid 18 through 19 No H-bonds generated for 'chain 'J' and resid 18 through 19' Processing helix chain 'J' and resid 20 through 24 Processing helix chain 'J' and resid 26 through 46 removed outlier: 3.817A pdb=" N LEU J 40 " --> pdb=" O TYR J 36 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER J 46 " --> pdb=" O GLU J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 47 through 50 Processing helix chain 'J' and resid 61 through 72 removed outlier: 3.660A pdb=" N ILE J 67 " --> pdb=" O GLN J 63 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 118 removed outlier: 3.873A pdb=" N ASN J 118 " --> pdb=" O SER J 114 " (cutoff:3.500A) Processing helix chain 'J' and resid 125 through 142 removed outlier: 4.140A pdb=" N TYR J 138 " --> pdb=" O LYS J 134 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN J 139 " --> pdb=" O ALA J 135 " (cutoff:3.500A) Processing helix chain 'J' and resid 145 through 157 removed outlier: 3.814A pdb=" N GLU J 151 " --> pdb=" O GLU J 147 " (cutoff:3.500A) Processing helix chain 'J' and resid 180 through 191 Proline residue: J 188 - end of helix Processing helix chain 'K' and resid 14 through 31 Processing helix chain 'K' and resid 40 through 66 Processing helix chain 'K' and resid 74 through 82 Processing helix chain 'K' and resid 93 through 103 Processing helix chain 'K' and resid 111 through 120 Processing helix chain 'K' and resid 155 through 167 removed outlier: 3.949A pdb=" N ARG K 165 " --> pdb=" O GLN K 161 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR K 166 " --> pdb=" O LEU K 162 " (cutoff:3.500A) Processing helix chain 'K' and resid 210 through 214 removed outlier: 3.511A pdb=" N ASN K 213 " --> pdb=" O PRO K 210 " (cutoff:3.500A) Processing helix chain 'K' and resid 219 through 233 removed outlier: 3.807A pdb=" N GLY K 226 " --> pdb=" O ALA K 222 " (cutoff:3.500A) Processing helix chain 'K' and resid 244 through 256 removed outlier: 3.682A pdb=" N ILE K 251 " --> pdb=" O LEU K 247 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG K 254 " --> pdb=" O LYS K 250 " (cutoff:3.500A) Processing helix chain 'L' and resid 14 through 31 removed outlier: 3.675A pdb=" N ILE L 22 " --> pdb=" O HIS L 18 " (cutoff:3.500A) Processing helix chain 'L' and resid 40 through 66 Processing helix chain 'L' and resid 74 through 82 Processing helix chain 'L' and resid 93 through 101 Processing helix chain 'L' and resid 110 through 121 removed outlier: 3.575A pdb=" N ILE L 121 " --> pdb=" O ALA L 117 " (cutoff:3.500A) Processing helix chain 'L' and resid 155 through 167 Processing helix chain 'L' and resid 219 through 232 Processing helix chain 'L' and resid 244 through 256 Processing helix chain 'M' and resid 7 through 17 Processing helix chain 'M' and resid 18 through 19 No H-bonds generated for 'chain 'M' and resid 18 through 19' Processing helix chain 'M' and resid 20 through 24 Processing helix chain 'M' and resid 26 through 46 removed outlier: 3.675A pdb=" N LYS M 39 " --> pdb=" O ALA M 35 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU M 40 " --> pdb=" O TYR M 36 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER M 46 " --> pdb=" O GLU M 42 " (cutoff:3.500A) Processing helix chain 'M' and resid 47 through 50 Processing helix chain 'M' and resid 61 through 72 Processing helix chain 'M' and resid 113 through 118 removed outlier: 3.576A pdb=" N ASN M 118 " --> pdb=" O SER M 114 " (cutoff:3.500A) Processing helix chain 'M' and resid 125 through 142 removed outlier: 3.895A pdb=" N SER M 131 " --> pdb=" O GLU M 127 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N TYR M 138 " --> pdb=" O LYS M 134 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN M 139 " --> pdb=" O ALA M 135 " (cutoff:3.500A) Processing helix chain 'M' and resid 145 through 157 removed outlier: 4.667A pdb=" N GLU M 151 " --> pdb=" O GLU M 147 " (cutoff:3.500A) Processing helix chain 'M' and resid 180 through 194 Proline residue: M 188 - end of helix removed outlier: 3.797A pdb=" N ARG M 192 " --> pdb=" O PRO M 188 " (cutoff:3.500A) Processing helix chain 'O' and resid 14 through 31 Processing helix chain 'O' and resid 40 through 66 Processing helix chain 'O' and resid 74 through 82 Processing helix chain 'O' and resid 93 through 103 Processing helix chain 'O' and resid 111 through 120 Processing helix chain 'O' and resid 155 through 165 removed outlier: 3.871A pdb=" N ARG O 165 " --> pdb=" O GLN O 161 " (cutoff:3.500A) Processing helix chain 'O' and resid 210 through 214 Processing helix chain 'O' and resid 219 through 233 removed outlier: 3.605A pdb=" N GLY O 226 " --> pdb=" O ALA O 222 " (cutoff:3.500A) Processing helix chain 'O' and resid 244 through 256 removed outlier: 3.684A pdb=" N ILE O 251 " --> pdb=" O LEU O 247 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG O 254 " --> pdb=" O LYS O 250 " (cutoff:3.500A) Processing helix chain 'P' and resid 14 through 31 removed outlier: 3.532A pdb=" N ILE P 22 " --> pdb=" O HIS P 18 " (cutoff:3.500A) Processing helix chain 'P' and resid 40 through 66 Processing helix chain 'P' and resid 74 through 82 Processing helix chain 'P' and resid 93 through 101 Processing helix chain 'P' and resid 110 through 120 removed outlier: 3.640A pdb=" N ALA P 117 " --> pdb=" O ASP P 113 " (cutoff:3.500A) Processing helix chain 'P' and resid 155 through 167 Processing helix chain 'P' and resid 219 through 232 removed outlier: 3.658A pdb=" N LEU P 227 " --> pdb=" O MET P 223 " (cutoff:3.500A) Processing helix chain 'P' and resid 244 through 256 Processing helix chain 'Q' and resid 14 through 31 removed outlier: 3.573A pdb=" N LEU Q 29 " --> pdb=" O SER Q 25 " (cutoff:3.500A) Processing helix chain 'Q' and resid 40 through 66 Processing helix chain 'Q' and resid 74 through 82 Processing helix chain 'Q' and resid 93 through 103 Processing helix chain 'Q' and resid 111 through 120 Processing helix chain 'Q' and resid 155 through 165 Processing helix chain 'Q' and resid 210 through 214 Processing helix chain 'Q' and resid 219 through 233 Processing helix chain 'Q' and resid 244 through 256 removed outlier: 3.504A pdb=" N PHE Q 248 " --> pdb=" O THR Q 244 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG Q 254 " --> pdb=" O LYS Q 250 " (cutoff:3.500A) Processing helix chain 'R' and resid 14 through 31 Processing helix chain 'R' and resid 40 through 66 Processing helix chain 'R' and resid 74 through 82 Processing helix chain 'R' and resid 93 through 101 Processing helix chain 'R' and resid 110 through 120 Processing helix chain 'R' and resid 155 through 167 Processing helix chain 'R' and resid 219 through 233 Processing helix chain 'R' and resid 244 through 256 Processing helix chain 'R' and resid 289 through 291 No H-bonds generated for 'chain 'R' and resid 289 through 291' Processing helix chain 'S' and resid 7 through 17 removed outlier: 4.697A pdb=" N GLU S 13 " --> pdb=" O GLU S 9 " (cutoff:3.500A) Processing helix chain 'S' and resid 18 through 19 No H-bonds generated for 'chain 'S' and resid 18 through 19' Processing helix chain 'S' and resid 20 through 24 Processing helix chain 'S' and resid 26 through 46 removed outlier: 3.608A pdb=" N LYS S 39 " --> pdb=" O ALA S 35 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU S 40 " --> pdb=" O TYR S 36 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER S 46 " --> pdb=" O GLU S 42 " (cutoff:3.500A) Processing helix chain 'S' and resid 47 through 50 Processing helix chain 'S' and resid 60 through 72 removed outlier: 3.640A pdb=" N ILE S 67 " --> pdb=" O GLN S 63 " (cutoff:3.500A) Processing helix chain 'S' and resid 113 through 118 removed outlier: 3.625A pdb=" N ASN S 118 " --> pdb=" O SER S 114 " (cutoff:3.500A) Processing helix chain 'S' and resid 125 through 142 removed outlier: 3.651A pdb=" N SER S 131 " --> pdb=" O GLU S 127 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N TYR S 138 " --> pdb=" O LYS S 134 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN S 139 " --> pdb=" O ALA S 135 " (cutoff:3.500A) Processing helix chain 'S' and resid 145 through 157 removed outlier: 4.090A pdb=" N GLU S 151 " --> pdb=" O GLU S 147 " (cutoff:3.500A) Processing helix chain 'S' and resid 180 through 191 Proline residue: S 188 - end of helix Processing helix chain 'X' and resid 33 through 47 Processing helix chain 'X' and resid 62 through 67 Processing helix chain 'X' and resid 73 through 87 Processing helix chain 'a' and resid 58 through 73 removed outlier: 3.700A pdb=" N ARG a 73 " --> pdb=" O PHE a 69 " (cutoff:3.500A) Processing helix chain 'a' and resid 146 through 154 Processing helix chain 'a' and resid 168 through 181 Processing helix chain 'b' and resid 58 through 73 removed outlier: 3.723A pdb=" N ARG b 73 " --> pdb=" O PHE b 69 " (cutoff:3.500A) Processing helix chain 'b' and resid 146 through 154 Processing helix chain 'b' and resid 168 through 181 Processing helix chain 'c' and resid 58 through 73 removed outlier: 3.717A pdb=" N ARG c 73 " --> pdb=" O PHE c 69 " (cutoff:3.500A) Processing helix chain 'c' and resid 146 through 154 Processing helix chain 'c' and resid 168 through 181 Processing helix chain 'd' and resid 58 through 73 removed outlier: 3.814A pdb=" N ARG d 73 " --> pdb=" O PHE d 69 " (cutoff:3.500A) Processing helix chain 'd' and resid 146 through 154 Processing helix chain 'd' and resid 168 through 181 Processing helix chain 'e' and resid 58 through 73 removed outlier: 3.701A pdb=" N ARG e 73 " --> pdb=" O PHE e 69 " (cutoff:3.500A) Processing helix chain 'e' and resid 140 through 144 Processing helix chain 'e' and resid 146 through 154 Processing helix chain 'e' and resid 168 through 181 Processing helix chain 'f' and resid 58 through 73 removed outlier: 3.668A pdb=" N ARG f 73 " --> pdb=" O PHE f 69 " (cutoff:3.500A) Processing helix chain 'f' and resid 146 through 154 Processing helix chain 'f' and resid 168 through 181 Processing helix chain 'h' and resid 60 through 64 removed outlier: 3.935A pdb=" N GLY h 64 " --> pdb=" O ALA h 61 " (cutoff:3.500A) Processing helix chain 'h' and resid 96 through 106 Processing helix chain 'i' and resid 60 through 64 removed outlier: 3.721A pdb=" N GLY i 64 " --> pdb=" O ALA i 61 " (cutoff:3.500A) Processing helix chain 'i' and resid 96 through 106 Processing helix chain 'j' and resid 60 through 64 removed outlier: 3.651A pdb=" N GLY j 64 " --> pdb=" O ALA j 61 " (cutoff:3.500A) Processing helix chain 'j' and resid 96 through 106 Processing helix chain 'k' and resid 60 through 64 removed outlier: 3.905A pdb=" N GLY k 64 " --> pdb=" O ALA k 61 " (cutoff:3.500A) Processing helix chain 'k' and resid 96 through 106 Processing helix chain 'l' and resid 60 through 64 removed outlier: 3.760A pdb=" N GLY l 64 " --> pdb=" O ALA l 61 " (cutoff:3.500A) Processing helix chain 'l' and resid 96 through 106 Processing helix chain 'm' and resid 60 through 64 removed outlier: 3.853A pdb=" N GLY m 64 " --> pdb=" O ALA m 61 " (cutoff:3.500A) Processing helix chain 'm' and resid 96 through 106 Processing helix chain 'n' and resid 33 through 47 removed outlier: 3.589A pdb=" N VAL n 38 " --> pdb=" O ASN n 34 " (cutoff:3.500A) Processing helix chain 'n' and resid 62 through 67 Processing helix chain 'n' and resid 73 through 88 Processing helix chain 'o' and resid 33 through 47 Processing helix chain 'o' and resid 62 through 67 Processing helix chain 'o' and resid 73 through 87 Processing helix chain 'p' and resid 33 through 47 removed outlier: 3.573A pdb=" N VAL p 38 " --> pdb=" O ASN p 34 " (cutoff:3.500A) Processing helix chain 'p' and resid 62 through 67 Processing helix chain 'p' and resid 73 through 88 removed outlier: 3.629A pdb=" N THR p 88 " --> pdb=" O GLU p 84 " (cutoff:3.500A) Processing helix chain 'q' and resid 33 through 47 removed outlier: 3.527A pdb=" N VAL q 38 " --> pdb=" O ASN q 34 " (cutoff:3.500A) Processing helix chain 'q' and resid 62 through 67 Processing helix chain 'q' and resid 73 through 87 Processing helix chain 'r' and resid 33 through 47 Processing helix chain 'r' and resid 62 through 67 Processing helix chain 'r' and resid 73 through 88 removed outlier: 3.589A pdb=" N THR r 88 " --> pdb=" O GLU r 84 " (cutoff:3.500A) Processing helix chain 't' and resid 46 through 51 removed outlier: 3.604A pdb=" N ALA t 51 " --> pdb=" O ALA t 47 " (cutoff:3.500A) Processing helix chain 't' and resid 64 through 77 removed outlier: 3.586A pdb=" N GLU t 73 " --> pdb=" O GLU t 69 " (cutoff:3.500A) Processing helix chain 't' and resid 87 through 92 removed outlier: 3.564A pdb=" N ASN t 92 " --> pdb=" O ASP t 88 " (cutoff:3.500A) Processing helix chain 't' and resid 104 through 117 Processing helix chain 'u' and resid 46 through 51 removed outlier: 3.735A pdb=" N ALA u 51 " --> pdb=" O ALA u 47 " (cutoff:3.500A) Processing helix chain 'u' and resid 64 through 77 removed outlier: 3.575A pdb=" N GLU u 73 " --> pdb=" O GLU u 69 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU u 77 " --> pdb=" O GLU u 73 " (cutoff:3.500A) Processing helix chain 'u' and resid 87 through 92 removed outlier: 3.636A pdb=" N ASN u 92 " --> pdb=" O ASP u 88 " (cutoff:3.500A) Processing helix chain 'u' and resid 104 through 117 Processing helix chain 'v' and resid 46 through 51 removed outlier: 3.661A pdb=" N ALA v 51 " --> pdb=" O ALA v 47 " (cutoff:3.500A) Processing helix chain 'v' and resid 64 through 77 removed outlier: 3.505A pdb=" N GLU v 77 " --> pdb=" O GLU v 73 " (cutoff:3.500A) Processing helix chain 'v' and resid 87 through 92 removed outlier: 3.532A pdb=" N ASN v 92 " --> pdb=" O ASP v 88 " (cutoff:3.500A) Processing helix chain 'v' and resid 104 through 117 Processing helix chain 'w' and resid 13 through 27 removed outlier: 4.103A pdb=" N VAL w 19 " --> pdb=" O VAL w 15 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL w 27 " --> pdb=" O GLU w 23 " (cutoff:3.500A) Processing helix chain 'w' and resid 99 through 105 Processing helix chain 'w' and resid 171 through 185 Processing helix chain 'w' and resid 204 through 218 removed outlier: 3.557A pdb=" N ARG w 216 " --> pdb=" O ALA w 212 " (cutoff:3.500A) Processing helix chain 'x' and resid 11 through 27 removed outlier: 3.748A pdb=" N VAL x 19 " --> pdb=" O VAL x 15 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL x 27 " --> pdb=" O GLU x 23 " (cutoff:3.500A) Processing helix chain 'x' and resid 99 through 105 Processing helix chain 'x' and resid 117 through 121 removed outlier: 3.903A pdb=" N MET x 121 " --> pdb=" O LEU x 118 " (cutoff:3.500A) Processing helix chain 'x' and resid 171 through 185 Processing helix chain 'x' and resid 204 through 218 removed outlier: 3.608A pdb=" N ARG x 216 " --> pdb=" O ALA x 212 " (cutoff:3.500A) Processing helix chain 'y' and resid 13 through 26 removed outlier: 4.247A pdb=" N VAL y 19 " --> pdb=" O VAL y 15 " (cutoff:3.500A) Processing helix chain 'y' and resid 99 through 105 Processing helix chain 'y' and resid 117 through 121 removed outlier: 3.796A pdb=" N MET y 121 " --> pdb=" O LEU y 118 " (cutoff:3.500A) Processing helix chain 'y' and resid 171 through 185 removed outlier: 3.848A pdb=" N LEU y 182 " --> pdb=" O ASP y 178 " (cutoff:3.500A) Processing helix chain 'y' and resid 204 through 218 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 6 Processing sheet with id=AA2, first strand: chain 'A' and resid 126 through 132 removed outlier: 3.818A pdb=" N TRP A 126 " --> pdb=" O ILE A 152 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 177 through 183 Processing sheet with id=AA4, first strand: chain 'A' and resid 196 through 208 removed outlier: 4.764A pdb=" N GLN A 268 " --> pdb=" O PRO A 199 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N SER A 201 " --> pdb=" O LEU A 266 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LEU A 266 " --> pdb=" O SER A 201 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N GLU A 203 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N VAL A 264 " --> pdb=" O GLU A 203 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ASP A 205 " --> pdb=" O VAL A 262 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 4 through 6 Processing sheet with id=AA6, first strand: chain 'B' and resid 124 through 132 removed outlier: 3.882A pdb=" N TRP B 126 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR B 174 " --> pdb=" O VAL B 147 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N VAL B 149 " --> pdb=" O TYR B 174 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 177 through 183 removed outlier: 3.593A pdb=" N THR B 181 " --> pdb=" O ARG B 188 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE B 183 " --> pdb=" O PHE B 186 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 196 through 208 removed outlier: 4.691A pdb=" N GLN B 268 " --> pdb=" O PRO B 199 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N SER B 201 " --> pdb=" O LEU B 266 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LEU B 266 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N GLU B 203 " --> pdb=" O VAL B 264 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N VAL B 264 " --> pdb=" O GLU B 203 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASP B 205 " --> pdb=" O VAL B 262 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 76 through 78 Processing sheet with id=AB1, first strand: chain 'C' and resid 85 through 86 removed outlier: 6.770A pdb=" N VAL C 85 " --> pdb=" O ALA C 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 162 through 166 removed outlier: 6.603A pdb=" N VAL C 172 " --> pdb=" O ALA C 164 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N THR C 166 " --> pdb=" O GLN C 170 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N GLN C 170 " --> pdb=" O THR C 166 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL C 171 " --> pdb=" O MET C 203 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N HIS C 205 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N VAL C 173 " --> pdb=" O HIS C 205 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 76 through 78 Processing sheet with id=AB4, first strand: chain 'D' and resid 85 through 86 removed outlier: 6.828A pdb=" N VAL D 85 " --> pdb=" O ALA D 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'D' and resid 162 through 166 removed outlier: 6.528A pdb=" N VAL D 172 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N THR D 166 " --> pdb=" O GLN D 170 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N GLN D 170 " --> pdb=" O THR D 166 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VAL D 171 " --> pdb=" O MET D 203 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N HIS D 205 " --> pdb=" O VAL D 171 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N VAL D 173 " --> pdb=" O HIS D 205 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 4 through 6 Processing sheet with id=AB7, first strand: chain 'E' and resid 126 through 132 removed outlier: 3.773A pdb=" N TRP E 126 " --> pdb=" O ILE E 152 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 177 through 180 Processing sheet with id=AB9, first strand: chain 'E' and resid 196 through 208 removed outlier: 6.355A pdb=" N GLN E 207 " --> pdb=" O VAL E 261 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N VAL E 261 " --> pdb=" O GLN E 207 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 4 through 6 Processing sheet with id=AC2, first strand: chain 'F' and resid 124 through 132 removed outlier: 3.808A pdb=" N TRP F 126 " --> pdb=" O ILE F 152 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 177 through 183 removed outlier: 3.648A pdb=" N THR F 181 " --> pdb=" O ARG F 188 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 196 through 208 removed outlier: 4.707A pdb=" N GLN F 268 " --> pdb=" O PRO F 199 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N SER F 201 " --> pdb=" O LEU F 266 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LEU F 266 " --> pdb=" O SER F 201 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLU F 203 " --> pdb=" O VAL F 264 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N VAL F 264 " --> pdb=" O GLU F 203 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ASP F 205 " --> pdb=" O VAL F 262 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 76 through 78 Processing sheet with id=AC6, first strand: chain 'G' and resid 85 through 86 removed outlier: 6.897A pdb=" N VAL G 85 " --> pdb=" O ALA G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'G' and resid 162 through 166 removed outlier: 6.687A pdb=" N VAL G 172 " --> pdb=" O ALA G 164 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N THR G 166 " --> pdb=" O GLN G 170 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLN G 170 " --> pdb=" O THR G 166 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 204 through 205 Processing sheet with id=AC9, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AD1, first strand: chain 'H' and resid 124 through 132 removed outlier: 3.594A pdb=" N TRP H 126 " --> pdb=" O ILE H 152 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 177 through 180 Processing sheet with id=AD3, first strand: chain 'H' and resid 196 through 208 removed outlier: 4.654A pdb=" N GLN H 268 " --> pdb=" O PRO H 199 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N SER H 201 " --> pdb=" O LEU H 266 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU H 266 " --> pdb=" O SER H 201 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLU H 203 " --> pdb=" O VAL H 264 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N VAL H 264 " --> pdb=" O GLU H 203 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ASP H 205 " --> pdb=" O VAL H 262 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 4 through 6 Processing sheet with id=AD5, first strand: chain 'I' and resid 124 through 132 removed outlier: 3.809A pdb=" N TRP I 126 " --> pdb=" O ILE I 152 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TYR I 174 " --> pdb=" O VAL I 147 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VAL I 149 " --> pdb=" O TYR I 174 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 177 through 183 removed outlier: 3.538A pdb=" N THR I 181 " --> pdb=" O ARG I 188 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 196 through 208 removed outlier: 4.880A pdb=" N GLN I 268 " --> pdb=" O PRO I 199 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N SER I 201 " --> pdb=" O LEU I 266 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU I 266 " --> pdb=" O SER I 201 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N GLU I 203 " --> pdb=" O VAL I 264 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N VAL I 264 " --> pdb=" O GLU I 203 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ASP I 205 " --> pdb=" O VAL I 262 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 76 through 78 Processing sheet with id=AD9, first strand: chain 'J' and resid 85 through 86 removed outlier: 6.957A pdb=" N VAL J 85 " --> pdb=" O ALA J 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'J' and resid 162 through 166 removed outlier: 6.728A pdb=" N VAL J 172 " --> pdb=" O ALA J 164 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N THR J 166 " --> pdb=" O GLN J 170 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLN J 170 " --> pdb=" O THR J 166 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 204 through 205 Processing sheet with id=AE3, first strand: chain 'K' and resid 4 through 6 Processing sheet with id=AE4, first strand: chain 'K' and resid 126 through 132 removed outlier: 3.797A pdb=" N TRP K 126 " --> pdb=" O ILE K 152 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N VAL K 149 " --> pdb=" O TYR K 174 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 177 through 183 Processing sheet with id=AE6, first strand: chain 'K' and resid 196 through 208 removed outlier: 4.650A pdb=" N GLN K 268 " --> pdb=" O PRO K 199 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N SER K 201 " --> pdb=" O LEU K 266 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LEU K 266 " --> pdb=" O SER K 201 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLU K 203 " --> pdb=" O VAL K 264 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N VAL K 264 " --> pdb=" O GLU K 203 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ASP K 205 " --> pdb=" O VAL K 262 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AE8, first strand: chain 'L' and resid 126 through 132 removed outlier: 3.694A pdb=" N TRP L 126 " --> pdb=" O ILE L 152 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR L 174 " --> pdb=" O VAL L 147 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N VAL L 149 " --> pdb=" O TYR L 174 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'L' and resid 177 through 183 removed outlier: 4.022A pdb=" N THR L 181 " --> pdb=" O ARG L 188 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE L 183 " --> pdb=" O PHE L 186 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 196 through 208 removed outlier: 4.564A pdb=" N GLN L 268 " --> pdb=" O PRO L 199 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N SER L 201 " --> pdb=" O LEU L 266 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LEU L 266 " --> pdb=" O SER L 201 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N GLU L 203 " --> pdb=" O VAL L 264 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N VAL L 264 " --> pdb=" O GLU L 203 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ASP L 205 " --> pdb=" O VAL L 262 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'M' and resid 76 through 78 Processing sheet with id=AF3, first strand: chain 'M' and resid 85 through 86 removed outlier: 7.003A pdb=" N VAL M 85 " --> pdb=" O ALA M 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'M' and resid 162 through 166 removed outlier: 6.550A pdb=" N VAL M 172 " --> pdb=" O ALA M 164 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N THR M 166 " --> pdb=" O GLN M 170 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLN M 170 " --> pdb=" O THR M 166 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'M' and resid 204 through 205 Processing sheet with id=AF6, first strand: chain 'O' and resid 4 through 6 Processing sheet with id=AF7, first strand: chain 'O' and resid 126 through 132 removed outlier: 3.804A pdb=" N TRP O 126 " --> pdb=" O ILE O 152 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N VAL O 149 " --> pdb=" O TYR O 174 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'O' and resid 177 through 180 Processing sheet with id=AF9, first strand: chain 'O' and resid 196 through 208 removed outlier: 6.520A pdb=" N GLN O 207 " --> pdb=" O VAL O 261 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N VAL O 261 " --> pdb=" O GLN O 207 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'P' and resid 4 through 6 Processing sheet with id=AG2, first strand: chain 'P' and resid 124 through 132 removed outlier: 3.783A pdb=" N TRP P 126 " --> pdb=" O ILE P 152 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TYR P 174 " --> pdb=" O VAL P 147 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N VAL P 149 " --> pdb=" O TYR P 174 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'P' and resid 177 through 183 removed outlier: 3.774A pdb=" N THR P 181 " --> pdb=" O ARG P 188 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE P 183 " --> pdb=" O PHE P 186 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'P' and resid 196 through 208 removed outlier: 4.568A pdb=" N GLN P 268 " --> pdb=" O PRO P 199 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N SER P 201 " --> pdb=" O LEU P 266 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LEU P 266 " --> pdb=" O SER P 201 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLU P 203 " --> pdb=" O VAL P 264 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N VAL P 264 " --> pdb=" O GLU P 203 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ASP P 205 " --> pdb=" O VAL P 262 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'Q' and resid 4 through 6 Processing sheet with id=AG6, first strand: chain 'Q' and resid 126 through 132 removed outlier: 3.658A pdb=" N TRP Q 126 " --> pdb=" O ILE Q 152 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Q' and resid 177 through 180 Processing sheet with id=AG8, first strand: chain 'Q' and resid 196 through 208 removed outlier: 6.242A pdb=" N GLN Q 207 " --> pdb=" O VAL Q 261 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N VAL Q 261 " --> pdb=" O GLN Q 207 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'R' and resid 4 through 6 Processing sheet with id=AH1, first strand: chain 'R' and resid 126 through 132 removed outlier: 3.756A pdb=" N TRP R 126 " --> pdb=" O ILE R 152 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'R' and resid 177 through 183 removed outlier: 3.640A pdb=" N THR R 181 " --> pdb=" O ARG R 188 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'R' and resid 196 through 208 removed outlier: 4.796A pdb=" N GLN R 268 " --> pdb=" O PRO R 199 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N SER R 201 " --> pdb=" O LEU R 266 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LEU R 266 " --> pdb=" O SER R 201 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N GLU R 203 " --> pdb=" O VAL R 264 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL R 264 " --> pdb=" O GLU R 203 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ASP R 205 " --> pdb=" O VAL R 262 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'S' and resid 76 through 78 Processing sheet with id=AH5, first strand: chain 'S' and resid 162 through 166 removed outlier: 6.713A pdb=" N VAL S 172 " --> pdb=" O ALA S 164 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N THR S 166 " --> pdb=" O GLN S 170 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N GLN S 170 " --> pdb=" O THR S 166 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'S' and resid 204 through 205 Processing sheet with id=AH7, first strand: chain 'X' and resid 8 through 9 Processing sheet with id=AH8, first strand: chain 'X' and resid 11 through 13 Processing sheet with id=AH9, first strand: chain 'X' and resid 91 through 102 removed outlier: 6.710A pdb=" N THR X 116 " --> pdb=" O THR X 92 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ILE X 94 " --> pdb=" O GLU X 114 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLU X 114 " --> pdb=" O ILE X 94 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N SER X 96 " --> pdb=" O ASP X 112 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ASP X 112 " --> pdb=" O SER X 96 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N SER X 98 " --> pdb=" O ALA X 110 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ALA X 110 " --> pdb=" O SER X 98 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ARG X 100 " --> pdb=" O LEU X 108 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N LEU X 108 " --> pdb=" O ARG X 100 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'a' and resid 8 through 9 Processing sheet with id=AI2, first strand: chain 'a' and resid 16 through 28 WARNING: can't find start of bonding for strands! previous: chain 'a' and resid 43 through 45 current: chain 'a' and resid 84 through 97 removed outlier: 5.441A pdb=" N ILE a 90 " --> pdb=" O ARG a 112 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ARG a 112 " --> pdb=" O ILE a 90 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N LYS a 106 " --> pdb=" O THR a 96 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'a' and resid 105 through 113 current: chain 'b' and resid 43 through 45 WARNING: can't find start of bonding for strands! previous: chain 'b' and resid 43 through 45 current: chain 'b' and resid 84 through 97 removed outlier: 5.565A pdb=" N ILE b 90 " --> pdb=" O ARG b 112 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ARG b 112 " --> pdb=" O ILE b 90 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU b 92 " --> pdb=" O ARG b 110 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N LYS b 106 " --> pdb=" O THR b 96 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'b' and resid 105 through 113 current: chain 'c' and resid 43 through 45 WARNING: can't find start of bonding for strands! previous: chain 'c' and resid 43 through 45 current: chain 'c' and resid 84 through 97 removed outlier: 5.446A pdb=" N ILE c 90 " --> pdb=" O ARG c 112 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ARG c 112 " --> pdb=" O ILE c 90 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N LYS c 106 " --> pdb=" O THR c 96 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'c' and resid 105 through 113 current: chain 'd' and resid 43 through 45 WARNING: can't find start of bonding for strands! previous: chain 'd' and resid 43 through 45 current: chain 'd' and resid 84 through 97 removed outlier: 5.504A pdb=" N ILE d 90 " --> pdb=" O ARG d 112 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ARG d 112 " --> pdb=" O ILE d 90 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU d 92 " --> pdb=" O ARG d 110 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LYS d 106 " --> pdb=" O THR d 96 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'd' and resid 105 through 113 current: chain 'e' and resid 43 through 45 WARNING: can't find start of bonding for strands! previous: chain 'e' and resid 43 through 45 current: chain 'e' and resid 84 through 97 removed outlier: 5.423A pdb=" N ILE e 90 " --> pdb=" O ARG e 112 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ARG e 112 " --> pdb=" O ILE e 90 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N LYS e 106 " --> pdb=" O THR e 96 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'e' and resid 105 through 113 current: chain 'f' and resid 43 through 45 WARNING: can't find start of bonding for strands! previous: chain 'f' and resid 43 through 45 current: chain 'f' and resid 84 through 97 removed outlier: 5.489A pdb=" N ILE f 90 " --> pdb=" O ARG f 112 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ARG f 112 " --> pdb=" O ILE f 90 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N LYS f 106 " --> pdb=" O THR f 96 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'a' and resid 157 through 161 removed outlier: 4.469A pdb=" N SER l 15 " --> pdb=" O ALA a 159 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ASP a 161 " --> pdb=" O SER l 15 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N ILE l 17 " --> pdb=" O ASP a 161 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N TRP l 36 " --> pdb=" O ARG l 52 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ARG l 52 " --> pdb=" O TRP l 36 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N PHE l 38 " --> pdb=" O GLY l 50 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU l 42 " --> pdb=" O ASN l 46 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N ASN l 46 " --> pdb=" O LEU l 42 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'a' and resid 165 through 166 Processing sheet with id=AI5, first strand: chain 'b' and resid 157 through 161 removed outlier: 3.793A pdb=" N ALA b 159 " --> pdb=" O LYS m 13 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N SER m 15 " --> pdb=" O ALA b 159 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ASP b 161 " --> pdb=" O SER m 15 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ILE m 17 " --> pdb=" O ASP b 161 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU m 40 " --> pdb=" O THR m 49 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N THR m 49 " --> pdb=" O LEU m 40 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N LEU m 42 " --> pdb=" O VAL m 47 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL m 47 " --> pdb=" O LEU m 42 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'b' and resid 165 through 166 removed outlier: 4.437A pdb=" N LEU m 92 " --> pdb=" O LEU m 4 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'c' and resid 8 through 9 Processing sheet with id=AI8, first strand: chain 'c' and resid 157 through 161 removed outlier: 4.751A pdb=" N SER j 15 " --> pdb=" O ALA c 159 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ASP c 161 " --> pdb=" O SER j 15 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ILE j 17 " --> pdb=" O ASP c 161 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N LEU j 40 " --> pdb=" O THR j 49 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N THR j 49 " --> pdb=" O LEU j 40 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N LEU j 42 " --> pdb=" O VAL j 47 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL j 47 " --> pdb=" O LEU j 42 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'c' and resid 165 through 166 removed outlier: 4.588A pdb=" N LEU j 92 " --> pdb=" O LEU j 4 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'd' and resid 8 through 9 removed outlier: 3.504A pdb=" N ILE d 9 " --> pdb=" O VAL d 12 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'd' and resid 157 through 161 removed outlier: 3.914A pdb=" N ALA d 159 " --> pdb=" O LYS k 13 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N SER k 15 " --> pdb=" O ALA d 159 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ASP d 161 " --> pdb=" O SER k 15 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N ILE k 17 " --> pdb=" O ASP d 161 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N LEU k 40 " --> pdb=" O THR k 49 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N THR k 49 " --> pdb=" O LEU k 40 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N LEU k 42 " --> pdb=" O VAL k 47 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL k 47 " --> pdb=" O LEU k 42 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'd' and resid 165 through 166 removed outlier: 4.424A pdb=" N LEU k 92 " --> pdb=" O LEU k 4 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'e' and resid 8 through 9 Processing sheet with id=AJ5, first strand: chain 'e' and resid 157 through 161 removed outlier: 6.332A pdb=" N VAL e 157 " --> pdb=" O LYS i 13 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N SER i 15 " --> pdb=" O VAL e 157 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N ALA e 159 " --> pdb=" O SER i 15 " (cutoff:3.500A) removed outlier: 11.103A pdb=" N ILE i 17 " --> pdb=" O ALA e 159 " (cutoff:3.500A) removed outlier: 11.360A pdb=" N ASP e 161 " --> pdb=" O ILE i 17 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LEU i 40 " --> pdb=" O THR i 49 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N THR i 49 " --> pdb=" O LEU i 40 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N LEU i 42 " --> pdb=" O VAL i 47 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL i 47 " --> pdb=" O LEU i 42 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'e' and resid 165 through 166 removed outlier: 4.536A pdb=" N LEU i 92 " --> pdb=" O LEU i 4 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'f' and resid 8 through 9 Processing sheet with id=AJ8, first strand: chain 'f' and resid 157 through 161 removed outlier: 3.891A pdb=" N ALA f 159 " --> pdb=" O LYS h 13 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N SER h 15 " --> pdb=" O ALA f 159 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ASP f 161 " --> pdb=" O SER h 15 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N ILE h 17 " --> pdb=" O ASP f 161 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N TRP h 36 " --> pdb=" O ARG h 52 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ARG h 52 " --> pdb=" O TRP h 36 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N PHE h 38 " --> pdb=" O GLY h 50 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY h 50 " --> pdb=" O PHE h 38 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU h 42 " --> pdb=" O ASN h 46 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N ASN h 46 " --> pdb=" O LEU h 42 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'f' and resid 165 through 166 removed outlier: 4.528A pdb=" N LEU h 92 " --> pdb=" O LEU h 4 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'n' and resid 8 through 9 Processing sheet with id=AK2, first strand: chain 'n' and resid 11 through 13 Processing sheet with id=AK3, first strand: chain 'n' and resid 91 through 102 removed outlier: 6.710A pdb=" N THR n 116 " --> pdb=" O THR n 92 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ILE n 94 " --> pdb=" O GLU n 114 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N GLU n 114 " --> pdb=" O ILE n 94 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N SER n 96 " --> pdb=" O ASP n 112 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ASP n 112 " --> pdb=" O SER n 96 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N SER n 98 " --> pdb=" O ALA n 110 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ALA n 110 " --> pdb=" O SER n 98 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ARG n 100 " --> pdb=" O LEU n 108 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N LEU n 108 " --> pdb=" O ARG n 100 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'o' and resid 8 through 9 Processing sheet with id=AK5, first strand: chain 'o' and resid 11 through 13 Processing sheet with id=AK6, first strand: chain 'o' and resid 91 through 102 removed outlier: 6.416A pdb=" N GLU o 114 " --> pdb=" O THR o 95 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ASP o 112 " --> pdb=" O PHE o 97 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE o 99 " --> pdb=" O ALA o 110 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ALA o 110 " --> pdb=" O ILE o 99 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N PHE o 101 " --> pdb=" O LEU o 108 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LEU o 108 " --> pdb=" O PHE o 101 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'p' and resid 8 through 9 Processing sheet with id=AK8, first strand: chain 'p' and resid 11 through 13 Processing sheet with id=AK9, first strand: chain 'p' and resid 91 through 102 removed outlier: 6.694A pdb=" N THR p 116 " --> pdb=" O THR p 92 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE p 94 " --> pdb=" O GLU p 114 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N GLU p 114 " --> pdb=" O ILE p 94 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N SER p 96 " --> pdb=" O ASP p 112 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ASP p 112 " --> pdb=" O SER p 96 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N SER p 98 " --> pdb=" O ALA p 110 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ALA p 110 " --> pdb=" O SER p 98 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ARG p 100 " --> pdb=" O LEU p 108 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N LEU p 108 " --> pdb=" O ARG p 100 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'q' and resid 8 through 9 Processing sheet with id=AL2, first strand: chain 'q' and resid 12 through 13 Processing sheet with id=AL3, first strand: chain 'q' and resid 91 through 102 removed outlier: 6.724A pdb=" N THR q 116 " --> pdb=" O THR q 92 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ILE q 94 " --> pdb=" O GLU q 114 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N GLU q 114 " --> pdb=" O ILE q 94 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N SER q 96 " --> pdb=" O ASP q 112 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ASP q 112 " --> pdb=" O SER q 96 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N SER q 98 " --> pdb=" O ALA q 110 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ALA q 110 " --> pdb=" O SER q 98 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ARG q 100 " --> pdb=" O LEU q 108 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N LEU q 108 " --> pdb=" O ARG q 100 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'r' and resid 8 through 9 Processing sheet with id=AL5, first strand: chain 'r' and resid 11 through 13 Processing sheet with id=AL6, first strand: chain 'r' and resid 91 through 102 removed outlier: 6.653A pdb=" N THR r 116 " --> pdb=" O THR r 92 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ILE r 94 " --> pdb=" O GLU r 114 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N GLU r 114 " --> pdb=" O ILE r 94 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N SER r 96 " --> pdb=" O ASP r 112 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ASP r 112 " --> pdb=" O SER r 96 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N SER r 98 " --> pdb=" O ALA r 110 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ALA r 110 " --> pdb=" O SER r 98 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ARG r 100 " --> pdb=" O LEU r 108 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N LEU r 108 " --> pdb=" O ARG r 100 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 't' and resid 2 through 4 removed outlier: 6.986A pdb=" N LEU t 2 " --> pdb=" O ILE t 18 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 't' and resid 80 through 84 removed outlier: 6.249A pdb=" N ILE t 129 " --> pdb=" O GLY t 82 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N TRP t 84 " --> pdb=" O ILE t 129 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 't' and resid 139 through 142 removed outlier: 6.204A pdb=" N LEU t 140 " --> pdb=" O LYS t 176 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 't' and resid 148 through 154 removed outlier: 7.225A pdb=" N THR t 151 " --> pdb=" O LYS t 162 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N LYS t 162 " --> pdb=" O THR t 151 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'u' and resid 2 through 4 removed outlier: 7.047A pdb=" N LEU u 2 " --> pdb=" O ILE u 18 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'u' and resid 25 through 27 Processing sheet with id=AM4, first strand: chain 'u' and resid 80 through 84 removed outlier: 6.333A pdb=" N ILE u 129 " --> pdb=" O GLY u 82 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N TRP u 84 " --> pdb=" O ILE u 129 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'u' and resid 139 through 142 Processing sheet with id=AM6, first strand: chain 'u' and resid 148 through 154 removed outlier: 7.180A pdb=" N THR u 151 " --> pdb=" O LYS u 162 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N LYS u 162 " --> pdb=" O THR u 151 " (cutoff:3.500A) Processing sheet with id=AM7, first strand: chain 'v' and resid 2 through 4 removed outlier: 6.973A pdb=" N LEU v 2 " --> pdb=" O ILE v 18 " (cutoff:3.500A) Processing sheet with id=AM8, first strand: chain 'v' and resid 80 through 84 removed outlier: 6.397A pdb=" N ILE v 129 " --> pdb=" O GLY v 82 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N TRP v 84 " --> pdb=" O ILE v 129 " (cutoff:3.500A) Processing sheet with id=AM9, first strand: chain 'v' and resid 139 through 142 removed outlier: 6.181A pdb=" N LEU v 140 " --> pdb=" O LYS v 176 " (cutoff:3.500A) Processing sheet with id=AN1, first strand: chain 'v' and resid 148 through 154 removed outlier: 7.425A pdb=" N THR v 151 " --> pdb=" O LYS v 162 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N LYS v 162 " --> pdb=" O THR v 151 " (cutoff:3.500A) Processing sheet with id=AN2, first strand: chain 'w' and resid 65 through 69 removed outlier: 4.196A pdb=" N GLU w 67 " --> pdb=" O VAL w 45 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N VAL w 45 " --> pdb=" O GLU w 67 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N THR w 44 " --> pdb=" O VAL w 38 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N VAL w 38 " --> pdb=" O THR w 44 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N THR w 46 " --> pdb=" O VAL w 36 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET w 31 " --> pdb=" O LEU w 92 " (cutoff:3.500A) Processing sheet with id=AN3, first strand: chain 'w' and resid 54 through 55 Processing sheet with id=AN4, first strand: chain 'w' and resid 74 through 75 Processing sheet with id=AN5, first strand: chain 'w' and resid 143 through 146 Processing sheet with id=AN6, first strand: chain 'x' and resid 65 through 69 removed outlier: 5.162A pdb=" N GLN x 66 " --> pdb=" O VAL x 47 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL x 47 " --> pdb=" O GLN x 66 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N THR x 44 " --> pdb=" O VAL x 38 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N VAL x 38 " --> pdb=" O THR x 44 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N THR x 46 " --> pdb=" O VAL x 36 " (cutoff:3.500A) Processing sheet with id=AN7, first strand: chain 'x' and resid 74 through 75 Processing sheet with id=AN8, first strand: chain 'x' and resid 143 through 146 Processing sheet with id=AN9, first strand: chain 'x' and resid 188 through 189 removed outlier: 3.975A pdb=" N ALA x 201 " --> pdb=" O GLN x 189 " (cutoff:3.500A) Processing sheet with id=AO1, first strand: chain 'y' and resid 65 through 69 removed outlier: 5.130A pdb=" N GLN y 66 " --> pdb=" O VAL y 47 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL y 47 " --> pdb=" O GLN y 66 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N THR y 44 " --> pdb=" O VAL y 38 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N VAL y 38 " --> pdb=" O THR y 44 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N THR y 46 " --> pdb=" O VAL y 36 " (cutoff:3.500A) Processing sheet with id=AO2, first strand: chain 'y' and resid 74 through 75 Processing sheet with id=AO3, first strand: chain 'y' and resid 143 through 146 Processing sheet with id=AO4, first strand: chain 'y' and resid 188 through 189 removed outlier: 4.071A pdb=" N ALA y 201 " --> pdb=" O GLN y 189 " (cutoff:3.500A) 2550 hydrogen bonds defined for protein. 7110 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: 49.14 Time building geometry restraints manager: 78.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.04: 61264 1.04 - 1.26: 11995 1.26 - 1.48: 26827 1.48 - 1.70: 29412 1.70 - 1.92: 579 Bond restraints: 130077 Sorted by residual: bond pdb=" N VAL L 279 " pdb=" H VAL L 279 " ideal model delta sigma weight residual 0.860 1.053 -0.193 2.00e-02 2.50e+03 9.27e+01 bond pdb=" N THR L 275 " pdb=" H THR L 275 " ideal model delta sigma weight residual 0.860 1.039 -0.179 2.00e-02 2.50e+03 7.98e+01 bond pdb=" N THR L 274 " pdb=" H THR L 274 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.82e+01 bond pdb=" N LYS f 115 " pdb=" H LYS f 115 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.80e+01 bond pdb=" N VAL f 114 " pdb=" H VAL f 114 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.80e+01 ... (remaining 130072 not shown) Histogram of bond angle deviations from ideal: 4.14 - 30.59: 19 30.59 - 57.04: 11 57.04 - 83.50: 32 83.50 - 109.95: 105993 109.95 - 136.40: 126964 Bond angle restraints: 233019 Sorted by residual: angle pdb=" H1 MET S 1 " pdb=" N MET S 1 " pdb=" H2 MET S 1 " ideal model delta sigma weight residual 109.47 4.14 105.33 3.00e+00 1.11e-01 1.23e+03 angle pdb=" H1 MET q 1 " pdb=" N MET q 1 " pdb=" H2 MET q 1 " ideal model delta sigma weight residual 109.47 5.01 104.46 3.00e+00 1.11e-01 1.21e+03 angle pdb=" H1 MET D 1 " pdb=" N MET D 1 " pdb=" H2 MET D 1 " ideal model delta sigma weight residual 109.47 5.09 104.38 3.00e+00 1.11e-01 1.21e+03 angle pdb=" H1 MET n 1 " pdb=" N MET n 1 " pdb=" H2 MET n 1 " ideal model delta sigma weight residual 109.47 6.23 103.24 3.00e+00 1.11e-01 1.18e+03 angle pdb=" H1 MET r 1 " pdb=" N MET r 1 " pdb=" H2 MET r 1 " ideal model delta sigma weight residual 109.47 6.68 102.79 3.00e+00 1.11e-01 1.17e+03 ... (remaining 233014 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 56869 17.96 - 35.92: 3477 35.92 - 53.88: 1164 53.88 - 71.84: 288 71.84 - 89.80: 80 Dihedral angle restraints: 61878 sinusoidal: 33945 harmonic: 27933 Sorted by residual: dihedral pdb=" CB CYS C 5 " pdb=" SG CYS C 5 " pdb=" SG CYS C 48 " pdb=" CB CYS C 48 " ideal model delta sinusoidal sigma weight residual 93.00 178.82 -85.82 1 1.00e+01 1.00e-02 8.90e+01 dihedral pdb=" CA ASN t 166 " pdb=" C ASN t 166 " pdb=" N PRO t 167 " pdb=" CA PRO t 167 " ideal model delta harmonic sigma weight residual -180.00 -133.58 -46.42 0 5.00e+00 4.00e-02 8.62e+01 dihedral pdb=" CB CYS M 5 " pdb=" SG CYS M 5 " pdb=" SG CYS M 48 " pdb=" CB CYS M 48 " ideal model delta sinusoidal sigma weight residual 93.00 176.45 -83.45 1 1.00e+01 1.00e-02 8.51e+01 ... (remaining 61875 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 9511 0.085 - 0.170: 1088 0.170 - 0.255: 31 0.255 - 0.340: 8 0.340 - 0.425: 3 Chirality restraints: 10641 Sorted by residual: chirality pdb=" CG LEU v 112 " pdb=" CB LEU v 112 " pdb=" CD1 LEU v 112 " pdb=" CD2 LEU v 112 " both_signs ideal model delta sigma weight residual False -2.59 -2.16 -0.42 2.00e-01 2.50e+01 4.51e+00 chirality pdb=" CA PRO v 98 " pdb=" N PRO v 98 " pdb=" C PRO v 98 " pdb=" CB PRO v 98 " both_signs ideal model delta sigma weight residual False 2.72 2.32 0.40 2.00e-01 2.50e+01 4.02e+00 chirality pdb=" CA PRO u 98 " pdb=" N PRO u 98 " pdb=" C PRO u 98 " pdb=" CB PRO u 98 " both_signs ideal model delta sigma weight residual False 2.72 2.37 0.35 2.00e-01 2.50e+01 3.12e+00 ... (remaining 10638 not shown) Planarity restraints: 19809 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL d 114 " -0.069 2.00e-02 2.50e+03 1.23e-01 1.52e+02 pdb=" C VAL d 114 " 0.214 2.00e-02 2.50e+03 pdb=" O VAL d 114 " -0.076 2.00e-02 2.50e+03 pdb=" N LYS d 115 " -0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL c 114 " -0.066 2.00e-02 2.50e+03 1.20e-01 1.44e+02 pdb=" C VAL c 114 " 0.207 2.00e-02 2.50e+03 pdb=" O VAL c 114 " -0.075 2.00e-02 2.50e+03 pdb=" N LYS c 115 " -0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL b 114 " 0.067 2.00e-02 2.50e+03 1.19e-01 1.41e+02 pdb=" C VAL b 114 " -0.206 2.00e-02 2.50e+03 pdb=" O VAL b 114 " 0.072 2.00e-02 2.50e+03 pdb=" N LYS b 115 " 0.066 2.00e-02 2.50e+03 ... (remaining 19806 not shown) Histogram of nonbonded interaction distances: 1.29 - 1.95: 1055 1.95 - 2.61: 152538 2.61 - 3.28: 384954 3.28 - 3.94: 501746 3.94 - 4.60: 779966 Nonbonded interactions: 1820259 Sorted by model distance: nonbonded pdb="HH22 ARG v 97 " pdb=" O MET x 62 " model vdw 1.291 1.850 nonbonded pdb=" O ASN S 3 " pdb="HD21 ASN S 3 " model vdw 1.327 1.850 nonbonded pdb=" H GLY u 103 " pdb=" OD1 ASP x 112 " model vdw 1.329 1.850 nonbonded pdb=" H LYS u 96 " pdb=" OD2 ASP w 61 " model vdw 1.357 1.850 nonbonded pdb=" OH TYR t 99 " pdb=" H PHE y 55 " model vdw 1.376 1.850 ... (remaining 1820254 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 275 or (resid 276 through 277 and (name N or nam \ e CA or name C or name O or name CB or name CG or name CD )) or resid 278 throug \ h 299)) selection = (chain 'B' and (resid 1 through 105 or (resid 106 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 \ or name NH2)) or (resid 107 and (name N or name CA or name C or name O or name C \ B )) or (resid 108 and (name N or name CA or name C or name O or name CB or name \ CG or name CD or name NE or name CZ or name NH1 or name NH2)) or (resid 109 and \ (name N or name CA or name C or name O or name CB or name CG1 or name CG2 or na \ me CD1)) or (resid 110 and (name N or name CA or name C or name O or name CB or \ name CG or name OD1 or name OD2)) or resid 111 through 275 or (resid 276 through \ 277 and (name N or name CA or name C or name O or name CB or name CG or name CD \ )) or resid 278 through 299)) selection = (chain 'E' and (resid 1 through 275 or (resid 276 through 277 and (name N or nam \ e CA or name C or name O or name CB or name CG or name CD )) or resid 278 throug \ h 299)) selection = (chain 'F' and (resid 1 through 105 or (resid 106 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 \ or name NH2)) or (resid 107 and (name N or name CA or name C or name O or name C \ B )) or (resid 108 and (name N or name CA or name C or name O or name CB or name \ CG or name CD or name NE or name CZ or name NH1 or name NH2)) or (resid 109 and \ (name N or name CA or name C or name O or name CB or name CG1 or name CG2 or na \ me CD1)) or (resid 110 and (name N or name CA or name C or name O or name CB or \ name CG or name OD1 or name OD2)) or resid 111 through 275 or (resid 276 through \ 277 and (name N or name CA or name C or name O or name CB or name CG or name CD \ )) or resid 278 through 299)) selection = (chain 'H' and (resid 1 through 275 or (resid 276 through 277 and (name N or nam \ e CA or name C or name O or name CB or name CG or name CD )) or resid 278 throug \ h 299)) selection = (chain 'I' and (resid 1 through 105 or (resid 106 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 \ or name NH2)) or (resid 107 and (name N or name CA or name C or name O or name C \ B )) or (resid 108 and (name N or name CA or name C or name O or name CB or name \ CG or name CD or name NE or name CZ or name NH1 or name NH2)) or (resid 109 and \ (name N or name CA or name C or name O or name CB or name CG1 or name CG2 or na \ me CD1)) or (resid 110 and (name N or name CA or name C or name O or name CB or \ name CG or name OD1 or name OD2)) or resid 111 through 275 or (resid 276 through \ 277 and (name N or name CA or name C or name O or name CB or name CG or name CD \ )) or resid 278 through 299)) selection = (chain 'K' and (resid 1 through 275 or (resid 276 through 277 and (name N or nam \ e CA or name C or name O or name CB or name CG or name CD )) or resid 278 throug \ h 299)) selection = (chain 'L' and (resid 1 through 105 or (resid 106 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 \ or name NH2)) or (resid 107 and (name N or name CA or name C or name O or name C \ B )) or (resid 108 and (name N or name CA or name C or name O or name CB or name \ CG or name CD or name NE or name CZ or name NH1 or name NH2)) or (resid 109 and \ (name N or name CA or name C or name O or name CB or name CG1 or name CG2 or na \ me CD1)) or (resid 110 and (name N or name CA or name C or name O or name CB or \ name CG or name OD1 or name OD2)) or resid 111 through 299)) selection = (chain 'O' and (resid 1 through 275 or (resid 276 through 277 and (name N or nam \ e CA or name C or name O or name CB or name CG or name CD )) or resid 278 throug \ h 299)) selection = (chain 'P' and (resid 1 through 105 or (resid 106 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 \ or name NH2)) or (resid 107 and (name N or name CA or name C or name O or name C \ B )) or (resid 108 and (name N or name CA or name C or name O or name CB or name \ CG or name CD or name NE or name CZ or name NH1 or name NH2)) or (resid 109 and \ (name N or name CA or name C or name O or name CB or name CG1 or name CG2 or na \ me CD1)) or (resid 110 and (name N or name CA or name C or name O or name CB or \ name CG or name OD1 or name OD2)) or resid 111 through 275 or (resid 276 through \ 277 and (name N or name CA or name C or name O or name CB or name CG or name CD \ )) or resid 278 through 299)) selection = (chain 'Q' and (resid 1 through 275 or (resid 276 through 277 and (name N or nam \ e CA or name C or name O or name CB or name CG or name CD )) or resid 278 throug \ h 299)) selection = (chain 'R' and (resid 1 through 105 or (resid 106 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 \ or name NH2)) or (resid 107 and (name N or name CA or name C or name O or name C \ B )) or (resid 108 and (name N or name CA or name C or name O or name CB or name \ CG or name CD or name NE or name CZ or name NH1 or name NH2)) or (resid 109 and \ (name N or name CA or name C or name O or name CB or name CG1 or name CG2 or na \ me CD1)) or (resid 110 and (name N or name CA or name C or name O or name CB or \ name CG or name OD1 or name OD2)) or resid 111 through 275 or (resid 276 through \ 277 and (name N or name CA or name C or name O or name CB or name CG or name CD \ )) or resid 278 through 299)) } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'G' selection = chain 'J' selection = chain 'M' selection = chain 'S' } ncs_group { reference = chain 'X' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' } ncs_group { reference = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' } ncs_group { reference = chain 't' selection = chain 'u' selection = chain 'v' } ncs_group { reference = chain 'w' selection = chain 'x' selection = chain 'y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 1.480 Extract box with map and model: 26.230 Check model and map are aligned: 1.410 Set scattering table: 0.880 Process input model: 299.930 Find NCS groups from input model: 4.920 Set up NCS constraints: 1.060 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:2.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 342.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 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 : 0.006 0.142 68607 Z= 0.391 Angle : 0.865 16.979 93228 Z= 0.505 Chirality : 0.051 0.425 10641 Planarity : 0.007 0.128 12279 Dihedral : 12.310 89.726 25527 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 18.46 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.21 % Favored : 93.57 % Rotamer: Outliers : 0.20 % Allowed : 0.22 % Favored : 99.58 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 4.47 % Cis-general : 0.00 % Twisted Proline : 0.81 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.09), residues: 8730 helix: 0.21 (0.10), residues: 2703 sheet: -0.36 (0.13), residues: 1461 loop : -1.18 (0.09), residues: 4566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP t 207 HIS 0.012 0.002 HIS t 116 PHE 0.025 0.003 PHE H 67 TYR 0.037 0.002 TYR t 99 ARG 0.015 0.001 ARG f 112 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17460 Ramachandran restraints generated. 8730 Oldfield, 0 Emsley, 8730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17460 Ramachandran restraints generated. 8730 Oldfield, 0 Emsley, 8730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Evaluate side-chains 1280 residues out of total 7326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 1265 time to evaluate : 8.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4892 (ttm) cc_final: 0.4414 (tmm) REVERT: A 26 MET cc_start: 0.8230 (mmt) cc_final: 0.7775 (mmt) REVERT: C 103 TYR cc_start: 0.7531 (m-10) cc_final: 0.6314 (t80) REVERT: C 221 TYR cc_start: 0.4284 (m-10) cc_final: 0.3987 (t80) REVERT: D 221 TYR cc_start: 0.4527 (m-10) cc_final: 0.4086 (t80) REVERT: H 26 MET cc_start: 0.8326 (mmt) cc_final: 0.7924 (mmt) REVERT: K 26 MET cc_start: 0.7965 (mmt) cc_final: 0.7493 (mmt) REVERT: M 103 TYR cc_start: 0.7477 (m-10) cc_final: 0.6047 (t80) REVERT: M 221 TYR cc_start: 0.4635 (m-10) cc_final: 0.4037 (t80) REVERT: O 26 MET cc_start: 0.8266 (mmp) cc_final: 0.8037 (mmt) REVERT: P 215 CYS cc_start: 0.5398 (m) cc_final: 0.5126 (m) REVERT: i 8 ASP cc_start: 0.7886 (t0) cc_final: 0.7646 (t0) REVERT: m 91 LYS cc_start: 0.8634 (mttt) cc_final: 0.8431 (mttt) REVERT: o 1 MET cc_start: 0.1028 (ppp) cc_final: 0.0384 (ppp) REVERT: t 26 TYR cc_start: 0.5949 (p90) cc_final: 0.5706 (p90) REVERT: t 173 ARG cc_start: 0.7403 (mmt-90) cc_final: 0.7055 (mmt-90) REVERT: u 204 GLU cc_start: 0.6584 (mp0) cc_final: 0.6266 (mp0) REVERT: v 23 ILE cc_start: 0.7726 (mm) cc_final: 0.7464 (pt) REVERT: v 26 TYR cc_start: 0.6338 (p90) cc_final: 0.5876 (p90) REVERT: w 14 ASP cc_start: 0.5903 (m-30) cc_final: 0.5097 (m-30) REVERT: x 62 MET cc_start: 0.3618 (pmm) cc_final: 0.2338 (mmt) outliers start: 15 outliers final: 5 residues processed: 1278 average time/residue: 1.6154 time to fit residues: 3269.5340 Evaluate side-chains 888 residues out of total 7326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 883 time to evaluate : 7.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 116 ILE Chi-restraints excluded: chain b residue 116 ILE Chi-restraints excluded: chain c residue 115 LYS Chi-restraints excluded: chain e residue 116 ILE Chi-restraints excluded: chain f residue 115 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 858 random chunks: chunk 724 optimal weight: 0.9980 chunk 650 optimal weight: 3.9990 chunk 360 optimal weight: 7.9990 chunk 222 optimal weight: 8.9990 chunk 438 optimal weight: 3.9990 chunk 347 optimal weight: 2.9990 chunk 672 optimal weight: 1.9990 chunk 260 optimal weight: 8.9990 chunk 408 optimal weight: 0.8980 chunk 500 optimal weight: 1.9990 chunk 779 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 GLN F 46 ASN H 132 ASN K 122 ASN L 161 GLN M 99 GLN O 122 ASN a 58 ASN b 158 ASN c 42 HIS c 173 GLN d 31 ASN e 173 GLN h 19 ASN j 76 ASN l 76 ASN m 19 ASN m 76 ASN ** n 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 103 GLN p 56 ASN q 44 GLN ** t 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 94 GLN ** v 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 95 GLN ** w 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 68607 Z= 0.217 Angle : 0.642 15.496 93228 Z= 0.338 Chirality : 0.046 0.408 10641 Planarity : 0.005 0.128 12279 Dihedral : 6.086 89.489 9647 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.14 % Favored : 94.75 % Rotamer: Outliers : 0.93 % Allowed : 5.27 % Favored : 93.80 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 4.47 % Cis-general : 0.00 % Twisted Proline : 0.81 % Twisted General : 0.08 % 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: -0.48 (0.09), residues: 8730 helix: 0.61 (0.10), residues: 2763 sheet: -0.14 (0.13), residues: 1548 loop : -0.95 (0.09), residues: 4419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 218 HIS 0.008 0.001 HIS y 200 PHE 0.028 0.001 PHE y 55 TYR 0.031 0.001 TYR t 99 ARG 0.007 0.001 ARG v 114 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17460 Ramachandran restraints generated. 8730 Oldfield, 0 Emsley, 8730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17460 Ramachandran restraints generated. 8730 Oldfield, 0 Emsley, 8730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Evaluate side-chains 1014 residues out of total 7326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 946 time to evaluate : 8.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.8276 (mmt) cc_final: 0.7821 (mmt) REVERT: C 103 TYR cc_start: 0.7382 (m-10) cc_final: 0.6336 (t80) REVERT: C 203 MET cc_start: 0.8162 (mmm) cc_final: 0.7498 (mmm) REVERT: C 221 TYR cc_start: 0.4324 (m-10) cc_final: 0.3795 (t80) REVERT: D 103 TYR cc_start: 0.7502 (m-80) cc_final: 0.6118 (t80) REVERT: D 221 TYR cc_start: 0.4513 (m-80) cc_final: 0.4159 (t80) REVERT: E 26 MET cc_start: 0.8254 (mmt) cc_final: 0.7991 (mmt) REVERT: F 26 MET cc_start: 0.8106 (mmm) cc_final: 0.7877 (mmm) REVERT: H 26 MET cc_start: 0.8290 (mmt) cc_final: 0.7998 (mmt) REVERT: K 26 MET cc_start: 0.8026 (mmt) cc_final: 0.7542 (mmt) REVERT: M 45 MET cc_start: 0.6296 (mmp) cc_final: 0.6011 (mmp) REVERT: M 103 TYR cc_start: 0.7413 (m-10) cc_final: 0.6096 (t80) REVERT: M 221 TYR cc_start: 0.4837 (m-10) cc_final: 0.4277 (t80) REVERT: P 215 CYS cc_start: 0.5402 (m) cc_final: 0.5169 (m) REVERT: Q 26 MET cc_start: 0.8337 (mmt) cc_final: 0.8036 (mmt) REVERT: a 56 ASP cc_start: 0.7819 (t70) cc_final: 0.7546 (t0) REVERT: d 51 GLU cc_start: 0.6952 (tt0) cc_final: 0.6681 (tt0) REVERT: d 110 ARG cc_start: 0.8059 (mtt90) cc_final: 0.7626 (mtt90) REVERT: f 115 LYS cc_start: 0.4078 (OUTLIER) cc_final: 0.3807 (pptt) REVERT: i 8 ASP cc_start: 0.7813 (t0) cc_final: 0.7533 (t0) REVERT: r 22 TYR cc_start: 0.4450 (t80) cc_final: 0.4037 (t80) REVERT: t 184 MET cc_start: 0.5143 (mmp) cc_final: 0.4707 (mmt) REVERT: v 23 ILE cc_start: 0.7690 (mm) cc_final: 0.7368 (pt) REVERT: v 26 TYR cc_start: 0.6251 (p90) cc_final: 0.5891 (p90) REVERT: v 220 LYS cc_start: 0.7978 (mmtm) cc_final: 0.7541 (mtmm) REVERT: w 160 GLU cc_start: 0.6487 (OUTLIER) cc_final: 0.6171 (pm20) REVERT: x 62 MET cc_start: 0.3304 (pmm) cc_final: 0.1832 (mmt) outliers start: 68 outliers final: 50 residues processed: 982 average time/residue: 1.6412 time to fit residues: 2636.9565 Evaluate side-chains 903 residues out of total 7326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 851 time to evaluate : 7.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain G residue 99 GLN Chi-restraints excluded: chain H residue 157 ASP Chi-restraints excluded: chain H residue 187 CYS Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 122 ASN Chi-restraints excluded: chain J residue 99 GLN Chi-restraints excluded: chain L residue 183 ILE Chi-restraints excluded: chain O residue 189 ARG Chi-restraints excluded: chain O residue 253 GLU Chi-restraints excluded: chain O residue 291 ASP Chi-restraints excluded: chain P residue 211 LEU Chi-restraints excluded: chain Q residue 118 LEU Chi-restraints excluded: chain b residue 116 ILE Chi-restraints excluded: chain b residue 124 ASP Chi-restraints excluded: chain b residue 131 THR Chi-restraints excluded: chain c residue 9 ILE Chi-restraints excluded: chain c residue 161 ASP Chi-restraints excluded: chain d residue 124 ASP Chi-restraints excluded: chain d residue 142 ASP Chi-restraints excluded: chain d residue 157 VAL Chi-restraints excluded: chain e residue 42 HIS Chi-restraints excluded: chain e residue 121 THR Chi-restraints excluded: chain f residue 115 LYS Chi-restraints excluded: chain f residue 142 ASP Chi-restraints excluded: chain h residue 19 ASN Chi-restraints excluded: chain j residue 96 THR Chi-restraints excluded: chain k residue 104 ILE Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain n residue 23 LEU Chi-restraints excluded: chain r residue 93 GLU Chi-restraints excluded: chain t residue 7 THR Chi-restraints excluded: chain t residue 53 ILE Chi-restraints excluded: chain t residue 112 LEU Chi-restraints excluded: chain t residue 161 VAL Chi-restraints excluded: chain t residue 174 MET Chi-restraints excluded: chain t residue 197 SER Chi-restraints excluded: chain t residue 211 LEU Chi-restraints excluded: chain u residue 7 THR Chi-restraints excluded: chain u residue 161 VAL Chi-restraints excluded: chain u residue 197 SER Chi-restraints excluded: chain v residue 7 THR Chi-restraints excluded: chain v residue 197 SER Chi-restraints excluded: chain v residue 207 TRP Chi-restraints excluded: chain w residue 112 ASP Chi-restraints excluded: chain w residue 160 GLU Chi-restraints excluded: chain x residue 112 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 858 random chunks: chunk 433 optimal weight: 10.0000 chunk 241 optimal weight: 5.9990 chunk 648 optimal weight: 6.9990 chunk 530 optimal weight: 10.0000 chunk 214 optimal weight: 4.9990 chunk 780 optimal weight: 3.9990 chunk 843 optimal weight: 9.9990 chunk 695 optimal weight: 4.9990 chunk 774 optimal weight: 10.0000 chunk 266 optimal weight: 6.9990 chunk 626 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 161 GLN ** C 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 HIS C 208 GLN E 39 GLN G 139 GLN I 46 ASN I 145 ASN I 213 ASN ** J 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 122 ASN ** M 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 145 ASN S 208 GLN ** X 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 158 ASN h 19 ASN p 44 GLN t 28 HIS ** t 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 95 GLN ** y 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.139 68607 Z= 0.422 Angle : 0.690 14.525 93228 Z= 0.365 Chirality : 0.047 0.412 10641 Planarity : 0.006 0.092 12279 Dihedral : 6.003 89.864 9639 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.15 % Favored : 93.71 % Rotamer: Outliers : 1.72 % Allowed : 6.44 % Favored : 91.84 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 4.47 % Cis-general : 0.00 % Twisted Proline : 0.81 % Twisted General : 0.08 % 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: -0.53 (0.09), residues: 8730 helix: 0.65 (0.10), residues: 2796 sheet: -0.17 (0.13), residues: 1617 loop : -1.07 (0.09), residues: 4317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP y 28 HIS 0.008 0.002 HIS u 28 PHE 0.025 0.002 PHE H 67 TYR 0.039 0.002 TYR t 99 ARG 0.006 0.001 ARG u 97 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17460 Ramachandran restraints generated. 8730 Oldfield, 0 Emsley, 8730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17460 Ramachandran restraints generated. 8730 Oldfield, 0 Emsley, 8730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Evaluate side-chains 965 residues out of total 7326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 839 time to evaluate : 7.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 26 MET cc_start: 0.8337 (mmt) cc_final: 0.7970 (mmt) REVERT: C 103 TYR cc_start: 0.7625 (m-10) cc_final: 0.6346 (t80) REVERT: D 103 TYR cc_start: 0.7665 (m-80) cc_final: 0.6189 (t80) REVERT: E 26 MET cc_start: 0.8457 (mmt) cc_final: 0.7921 (mmt) REVERT: F 26 MET cc_start: 0.8323 (mmm) cc_final: 0.8047 (mmm) REVERT: G 208 GLN cc_start: 0.7415 (mp-120) cc_final: 0.7084 (mp-120) REVERT: H 26 MET cc_start: 0.8443 (mmt) cc_final: 0.8111 (mmt) REVERT: H 67 PHE cc_start: 0.5006 (m-80) cc_final: 0.3981 (m-80) REVERT: K 26 MET cc_start: 0.8086 (mmt) cc_final: 0.7589 (mmt) REVERT: M 221 TYR cc_start: 0.4959 (m-80) cc_final: 0.4302 (t80) REVERT: O 26 MET cc_start: 0.8377 (mmm) cc_final: 0.7825 (mmt) REVERT: Q 26 MET cc_start: 0.8427 (mmt) cc_final: 0.8138 (mmt) REVERT: R 274 THR cc_start: 0.7147 (m) cc_final: 0.6901 (p) REVERT: b 157 VAL cc_start: 0.8440 (OUTLIER) cc_final: 0.8170 (t) REVERT: d 51 GLU cc_start: 0.7018 (tt0) cc_final: 0.6806 (tt0) REVERT: d 71 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7306 (mp0) REVERT: d 110 ARG cc_start: 0.8196 (mtt90) cc_final: 0.7857 (mtt90) REVERT: f 71 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7136 (mp0) REVERT: f 115 LYS cc_start: 0.5698 (OUTLIER) cc_final: 0.4347 (pttm) REVERT: r 22 TYR cc_start: 0.4634 (t80) cc_final: 0.4304 (t80) REVERT: v 23 ILE cc_start: 0.7921 (mm) cc_final: 0.7498 (pt) REVERT: v 219 ASP cc_start: 0.7250 (m-30) cc_final: 0.6852 (m-30) REVERT: v 220 LYS cc_start: 0.8046 (mmtm) cc_final: 0.7642 (mtmm) REVERT: w 169 GLU cc_start: 0.6530 (mt-10) cc_final: 0.6256 (mt-10) REVERT: x 62 MET cc_start: 0.3456 (pmm) cc_final: 0.2012 (mmt) REVERT: y 208 MET cc_start: 0.4288 (mtt) cc_final: 0.4069 (mtt) outliers start: 126 outliers final: 88 residues processed: 905 average time/residue: 1.5492 time to fit residues: 2307.3395 Evaluate side-chains 892 residues out of total 7326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 800 time to evaluate : 7.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain G residue 99 GLN Chi-restraints excluded: chain G residue 206 ILE Chi-restraints excluded: chain H residue 157 ASP Chi-restraints excluded: chain I residue 122 ASN Chi-restraints excluded: chain I residue 213 ASN Chi-restraints excluded: chain J residue 50 MET Chi-restraints excluded: chain J residue 99 GLN Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain L residue 183 ILE Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 206 ILE Chi-restraints excluded: chain O residue 189 ARG Chi-restraints excluded: chain O residue 253 GLU Chi-restraints excluded: chain O residue 291 ASP Chi-restraints excluded: chain P residue 183 ILE Chi-restraints excluded: chain P residue 211 LEU Chi-restraints excluded: chain Q residue 118 LEU Chi-restraints excluded: chain R residue 87 SER Chi-restraints excluded: chain S residue 48 CYS Chi-restraints excluded: chain X residue 1 MET Chi-restraints excluded: chain a residue 146 ASP Chi-restraints excluded: chain a residue 161 ASP Chi-restraints excluded: chain b residue 116 ILE Chi-restraints excluded: chain b residue 131 THR Chi-restraints excluded: chain b residue 142 ASP Chi-restraints excluded: chain b residue 146 ASP Chi-restraints excluded: chain b residue 157 VAL Chi-restraints excluded: chain c residue 146 ASP Chi-restraints excluded: chain c residue 161 ASP Chi-restraints excluded: chain d residue 41 ASP Chi-restraints excluded: chain d residue 71 GLU Chi-restraints excluded: chain d residue 124 ASP Chi-restraints excluded: chain d residue 131 THR Chi-restraints excluded: chain d residue 142 ASP Chi-restraints excluded: chain e residue 121 THR Chi-restraints excluded: chain e residue 146 ASP Chi-restraints excluded: chain e residue 161 ASP Chi-restraints excluded: chain f residue 71 GLU Chi-restraints excluded: chain f residue 115 LYS Chi-restraints excluded: chain f residue 117 VAL Chi-restraints excluded: chain f residue 131 THR Chi-restraints excluded: chain f residue 142 ASP Chi-restraints excluded: chain f residue 157 VAL Chi-restraints excluded: chain h residue 91 LYS Chi-restraints excluded: chain i residue 75 GLU Chi-restraints excluded: chain i residue 100 ILE Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 96 THR Chi-restraints excluded: chain k residue 104 ILE Chi-restraints excluded: chain l residue 20 ASP Chi-restraints excluded: chain l residue 96 THR Chi-restraints excluded: chain m residue 105 SER Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain n residue 109 GLU Chi-restraints excluded: chain o residue 22 TYR Chi-restraints excluded: chain r residue 93 GLU Chi-restraints excluded: chain t residue 7 THR Chi-restraints excluded: chain t residue 53 ILE Chi-restraints excluded: chain t residue 90 VAL Chi-restraints excluded: chain t residue 111 THR Chi-restraints excluded: chain t residue 112 LEU Chi-restraints excluded: chain t residue 161 VAL Chi-restraints excluded: chain t residue 174 MET Chi-restraints excluded: chain t residue 179 SER Chi-restraints excluded: chain t residue 197 SER Chi-restraints excluded: chain t residue 207 TRP Chi-restraints excluded: chain u residue 7 THR Chi-restraints excluded: chain u residue 61 THR Chi-restraints excluded: chain u residue 111 THR Chi-restraints excluded: chain u residue 161 VAL Chi-restraints excluded: chain u residue 197 SER Chi-restraints excluded: chain u residue 207 TRP Chi-restraints excluded: chain v residue 7 THR Chi-restraints excluded: chain v residue 56 THR Chi-restraints excluded: chain v residue 112 LEU Chi-restraints excluded: chain v residue 156 ASP Chi-restraints excluded: chain v residue 197 SER Chi-restraints excluded: chain v residue 207 TRP Chi-restraints excluded: chain v residue 211 LEU Chi-restraints excluded: chain w residue 26 SER Chi-restraints excluded: chain w residue 112 ASP Chi-restraints excluded: chain w residue 187 LYS Chi-restraints excluded: chain x residue 112 ASP Chi-restraints excluded: chain x residue 198 THR Chi-restraints excluded: chain y residue 112 ASP Chi-restraints excluded: chain y residue 198 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 858 random chunks: chunk 771 optimal weight: 5.9990 chunk 586 optimal weight: 9.9990 chunk 405 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 372 optimal weight: 7.9990 chunk 524 optimal weight: 0.9990 chunk 783 optimal weight: 10.0000 chunk 829 optimal weight: 6.9990 chunk 409 optimal weight: 3.9990 chunk 742 optimal weight: 0.8980 chunk 223 optimal weight: 6.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN K 122 ASN M 139 GLN ** f 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 76 ASN ** t 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 95 GLN ** y 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 88 GLN ** y 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 68607 Z= 0.273 Angle : 0.616 13.830 93228 Z= 0.324 Chirality : 0.046 0.403 10641 Planarity : 0.005 0.078 12279 Dihedral : 5.765 84.527 9639 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.44 % Favored : 94.44 % Rotamer: Outliers : 1.52 % Allowed : 7.62 % Favored : 90.87 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 4.47 % Cis-general : 0.00 % Twisted Proline : 0.81 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.09), residues: 8730 helix: 0.85 (0.10), residues: 2796 sheet: -0.08 (0.13), residues: 1626 loop : -0.97 (0.09), residues: 4308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP x 28 HIS 0.005 0.001 HIS v 71 PHE 0.022 0.001 PHE y 179 TYR 0.036 0.001 TYR t 99 ARG 0.006 0.000 ARG a 110 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17460 Ramachandran restraints generated. 8730 Oldfield, 0 Emsley, 8730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17460 Ramachandran restraints generated. 8730 Oldfield, 0 Emsley, 8730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Evaluate side-chains 935 residues out of total 7326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 824 time to evaluate : 8.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 26 MET cc_start: 0.8273 (mmt) cc_final: 0.7825 (mmt) REVERT: C 103 TYR cc_start: 0.7422 (m-10) cc_final: 0.6243 (t80) REVERT: D 103 TYR cc_start: 0.7665 (m-80) cc_final: 0.6264 (t80) REVERT: E 26 MET cc_start: 0.8425 (mmt) cc_final: 0.7761 (mmt) REVERT: F 252 MET cc_start: 0.8910 (mmm) cc_final: 0.8512 (mmm) REVERT: G 208 GLN cc_start: 0.7469 (mp-120) cc_final: 0.7247 (mp10) REVERT: H 26 MET cc_start: 0.8492 (mmt) cc_final: 0.8151 (mmt) REVERT: K 26 MET cc_start: 0.8074 (mmt) cc_final: 0.7623 (mmt) REVERT: M 221 TYR cc_start: 0.4955 (m-80) cc_final: 0.4279 (t80) REVERT: O 26 MET cc_start: 0.8237 (mmm) cc_final: 0.7696 (mmt) REVERT: Q 26 MET cc_start: 0.8476 (mmt) cc_final: 0.8118 (mmt) REVERT: b 34 GLU cc_start: 0.0751 (OUTLIER) cc_final: 0.0433 (pm20) REVERT: d 38 ASP cc_start: 0.5894 (OUTLIER) cc_final: 0.5399 (p0) REVERT: d 51 GLU cc_start: 0.7002 (tt0) cc_final: 0.6765 (tt0) REVERT: d 71 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7289 (mp0) REVERT: d 110 ARG cc_start: 0.8270 (mtt90) cc_final: 0.7924 (mtt90) REVERT: f 71 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.7067 (mp0) REVERT: f 115 LYS cc_start: 0.5593 (OUTLIER) cc_final: 0.4101 (pttm) REVERT: h 91 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8359 (mttt) REVERT: r 22 TYR cc_start: 0.4601 (t80) cc_final: 0.4336 (t80) REVERT: t 184 MET cc_start: 0.4954 (mmp) cc_final: 0.4588 (mmt) REVERT: v 23 ILE cc_start: 0.7901 (mm) cc_final: 0.7440 (pt) REVERT: v 114 ARG cc_start: 0.3477 (tpt170) cc_final: 0.2986 (tpt170) REVERT: v 220 LYS cc_start: 0.8092 (mmtm) cc_final: 0.7769 (mtmm) REVERT: w 160 GLU cc_start: 0.6679 (pm20) cc_final: 0.6018 (pm20) REVERT: x 62 MET cc_start: 0.3268 (pmm) cc_final: 0.2052 (mmt) REVERT: x 165 PHE cc_start: 0.6947 (m-80) cc_final: 0.6719 (m-80) outliers start: 111 outliers final: 85 residues processed: 883 average time/residue: 1.5487 time to fit residues: 2250.5091 Evaluate side-chains 883 residues out of total 7326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 792 time to evaluate : 7.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain G residue 99 GLN Chi-restraints excluded: chain G residue 206 ILE Chi-restraints excluded: chain H residue 58 GLU Chi-restraints excluded: chain H residue 157 ASP Chi-restraints excluded: chain I residue 122 ASN Chi-restraints excluded: chain J residue 99 GLN Chi-restraints excluded: chain L residue 183 ILE Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 139 GLN Chi-restraints excluded: chain O residue 189 ARG Chi-restraints excluded: chain O residue 253 GLU Chi-restraints excluded: chain O residue 291 ASP Chi-restraints excluded: chain P residue 118 LEU Chi-restraints excluded: chain P residue 183 ILE Chi-restraints excluded: chain Q residue 118 LEU Chi-restraints excluded: chain S residue 48 CYS Chi-restraints excluded: chain S residue 109 SER Chi-restraints excluded: chain S residue 206 ILE Chi-restraints excluded: chain a residue 31 ASN Chi-restraints excluded: chain a residue 121 THR Chi-restraints excluded: chain a residue 161 ASP Chi-restraints excluded: chain b residue 34 GLU Chi-restraints excluded: chain b residue 116 ILE Chi-restraints excluded: chain b residue 131 THR Chi-restraints excluded: chain b residue 142 ASP Chi-restraints excluded: chain b residue 146 ASP Chi-restraints excluded: chain c residue 161 ASP Chi-restraints excluded: chain d residue 38 ASP Chi-restraints excluded: chain d residue 41 ASP Chi-restraints excluded: chain d residue 71 GLU Chi-restraints excluded: chain d residue 124 ASP Chi-restraints excluded: chain d residue 131 THR Chi-restraints excluded: chain d residue 142 ASP Chi-restraints excluded: chain e residue 121 THR Chi-restraints excluded: chain e residue 161 ASP Chi-restraints excluded: chain f residue 41 ASP Chi-restraints excluded: chain f residue 71 GLU Chi-restraints excluded: chain f residue 115 LYS Chi-restraints excluded: chain f residue 117 VAL Chi-restraints excluded: chain f residue 131 THR Chi-restraints excluded: chain f residue 142 ASP Chi-restraints excluded: chain h residue 26 GLU Chi-restraints excluded: chain h residue 91 LYS Chi-restraints excluded: chain j residue 96 THR Chi-restraints excluded: chain k residue 5 GLU Chi-restraints excluded: chain k residue 104 ILE Chi-restraints excluded: chain l residue 20 ASP Chi-restraints excluded: chain l residue 96 THR Chi-restraints excluded: chain m residue 104 ILE Chi-restraints excluded: chain m residue 105 SER Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain n residue 109 GLU Chi-restraints excluded: chain r residue 93 GLU Chi-restraints excluded: chain t residue 7 THR Chi-restraints excluded: chain t residue 53 ILE Chi-restraints excluded: chain t residue 90 VAL Chi-restraints excluded: chain t residue 111 THR Chi-restraints excluded: chain t residue 112 LEU Chi-restraints excluded: chain t residue 156 ASP Chi-restraints excluded: chain t residue 161 VAL Chi-restraints excluded: chain t residue 197 SER Chi-restraints excluded: chain t residue 207 TRP Chi-restraints excluded: chain t residue 211 LEU Chi-restraints excluded: chain u residue 7 THR Chi-restraints excluded: chain u residue 61 THR Chi-restraints excluded: chain u residue 63 LEU Chi-restraints excluded: chain u residue 93 THR Chi-restraints excluded: chain u residue 111 THR Chi-restraints excluded: chain u residue 156 ASP Chi-restraints excluded: chain u residue 161 VAL Chi-restraints excluded: chain u residue 197 SER Chi-restraints excluded: chain u residue 207 TRP Chi-restraints excluded: chain v residue 7 THR Chi-restraints excluded: chain v residue 56 THR Chi-restraints excluded: chain v residue 112 LEU Chi-restraints excluded: chain v residue 197 SER Chi-restraints excluded: chain v residue 207 TRP Chi-restraints excluded: chain v residue 211 LEU Chi-restraints excluded: chain w residue 26 SER Chi-restraints excluded: chain w residue 112 ASP Chi-restraints excluded: chain w residue 187 LYS Chi-restraints excluded: chain x residue 95 GLN Chi-restraints excluded: chain x residue 112 ASP Chi-restraints excluded: chain y residue 112 ASP Chi-restraints excluded: chain y residue 180 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 858 random chunks: chunk 690 optimal weight: 3.9990 chunk 470 optimal weight: 5.9990 chunk 12 optimal weight: 9.9990 chunk 617 optimal weight: 3.9990 chunk 342 optimal weight: 0.1980 chunk 707 optimal weight: 4.9990 chunk 573 optimal weight: 0.0670 chunk 0 optimal weight: 6.9990 chunk 423 optimal weight: 3.9990 chunk 744 optimal weight: 10.0000 chunk 209 optimal weight: 10.0000 overall best weight: 2.4524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN K 122 ASN ** f 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 101 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 68607 Z= 0.245 Angle : 0.587 13.108 93228 Z= 0.307 Chirality : 0.045 0.405 10641 Planarity : 0.005 0.076 12279 Dihedral : 5.545 80.436 9639 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.57 % Favored : 94.32 % Rotamer: Outliers : 1.60 % Allowed : 8.03 % Favored : 90.38 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 4.47 % Cis-general : 0.00 % Twisted Proline : 0.61 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.09), residues: 8730 helix: 1.05 (0.10), residues: 2799 sheet: -0.01 (0.13), residues: 1626 loop : -0.88 (0.09), residues: 4305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP r 63 HIS 0.006 0.001 HIS v 71 PHE 0.018 0.001 PHE w 55 TYR 0.036 0.001 TYR t 99 ARG 0.008 0.000 ARG a 110 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17460 Ramachandran restraints generated. 8730 Oldfield, 0 Emsley, 8730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17460 Ramachandran restraints generated. 8730 Oldfield, 0 Emsley, 8730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Evaluate side-chains 952 residues out of total 7326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 835 time to evaluate : 8.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.8334 (mmt) cc_final: 0.7883 (mmt) REVERT: C 103 TYR cc_start: 0.7434 (m-10) cc_final: 0.6079 (t80) REVERT: C 118 ASN cc_start: 0.8439 (OUTLIER) cc_final: 0.8185 (p0) REVERT: D 103 TYR cc_start: 0.7637 (m-80) cc_final: 0.6164 (t80) REVERT: E 26 MET cc_start: 0.8539 (mmt) cc_final: 0.8131 (mmt) REVERT: E 280 MET cc_start: 0.6240 (mtm) cc_final: 0.5901 (mtm) REVERT: F 252 MET cc_start: 0.8895 (mmm) cc_final: 0.8521 (mmm) REVERT: H 26 MET cc_start: 0.8501 (mmt) cc_final: 0.8144 (mmt) REVERT: K 26 MET cc_start: 0.8073 (mmt) cc_final: 0.7595 (mmt) REVERT: M 103 TYR cc_start: 0.7451 (m-10) cc_final: 0.5847 (t80) REVERT: M 221 TYR cc_start: 0.4942 (m-80) cc_final: 0.4278 (t80) REVERT: O 26 MET cc_start: 0.8197 (mmm) cc_final: 0.7707 (mmt) REVERT: Q 26 MET cc_start: 0.8484 (mmt) cc_final: 0.8086 (mmt) REVERT: S 45 MET cc_start: 0.6736 (mmp) cc_final: 0.6509 (mmp) REVERT: b 34 GLU cc_start: 0.0873 (OUTLIER) cc_final: 0.0641 (pm20) REVERT: b 157 VAL cc_start: 0.8482 (OUTLIER) cc_final: 0.8279 (t) REVERT: d 51 GLU cc_start: 0.7004 (tt0) cc_final: 0.6779 (tt0) REVERT: d 71 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7279 (mp0) REVERT: d 110 ARG cc_start: 0.8303 (mtt90) cc_final: 0.7951 (mtt90) REVERT: e 79 MET cc_start: 0.7453 (mmt) cc_final: 0.7107 (mmt) REVERT: f 71 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.7016 (mp0) REVERT: f 115 LYS cc_start: 0.5643 (OUTLIER) cc_final: 0.4045 (pttm) REVERT: h 91 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8398 (mttt) REVERT: r 1 MET cc_start: 0.2945 (tmm) cc_final: 0.1597 (tmm) REVERT: t 63 LEU cc_start: 0.5990 (OUTLIER) cc_final: 0.5727 (mp) REVERT: v 23 ILE cc_start: 0.7804 (mm) cc_final: 0.7296 (pt) REVERT: v 56 THR cc_start: 0.3388 (OUTLIER) cc_final: 0.3148 (t) REVERT: v 114 ARG cc_start: 0.3198 (tpt170) cc_final: 0.2879 (tpt170) REVERT: v 219 ASP cc_start: 0.7213 (m-30) cc_final: 0.6708 (m-30) REVERT: v 220 LYS cc_start: 0.8067 (mmtm) cc_final: 0.7774 (mtmm) REVERT: w 160 GLU cc_start: 0.6530 (pm20) cc_final: 0.6063 (pm20) REVERT: x 62 MET cc_start: 0.3266 (pmm) cc_final: 0.2220 (mmt) REVERT: x 95 GLN cc_start: 0.5145 (OUTLIER) cc_final: 0.3800 (tp40) REVERT: x 165 PHE cc_start: 0.6850 (m-80) cc_final: 0.6579 (m-80) outliers start: 117 outliers final: 85 residues processed: 903 average time/residue: 1.4591 time to fit residues: 2159.3821 Evaluate side-chains 889 residues out of total 7326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 794 time to evaluate : 7.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain G residue 99 GLN Chi-restraints excluded: chain G residue 206 ILE Chi-restraints excluded: chain H residue 58 GLU Chi-restraints excluded: chain H residue 157 ASP Chi-restraints excluded: chain I residue 122 ASN Chi-restraints excluded: chain J residue 50 MET Chi-restraints excluded: chain J residue 78 CYS Chi-restraints excluded: chain J residue 99 GLN Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain L residue 183 ILE Chi-restraints excluded: chain O residue 189 ARG Chi-restraints excluded: chain O residue 291 ASP Chi-restraints excluded: chain P residue 183 ILE Chi-restraints excluded: chain R residue 87 SER Chi-restraints excluded: chain S residue 48 CYS Chi-restraints excluded: chain S residue 206 ILE Chi-restraints excluded: chain a residue 31 ASN Chi-restraints excluded: chain a residue 121 THR Chi-restraints excluded: chain a residue 161 ASP Chi-restraints excluded: chain b residue 34 GLU Chi-restraints excluded: chain b residue 116 ILE Chi-restraints excluded: chain b residue 131 THR Chi-restraints excluded: chain b residue 142 ASP Chi-restraints excluded: chain b residue 146 ASP Chi-restraints excluded: chain b residue 157 VAL Chi-restraints excluded: chain c residue 12 VAL Chi-restraints excluded: chain c residue 124 ASP Chi-restraints excluded: chain c residue 161 ASP Chi-restraints excluded: chain d residue 41 ASP Chi-restraints excluded: chain d residue 71 GLU Chi-restraints excluded: chain d residue 124 ASP Chi-restraints excluded: chain d residue 142 ASP Chi-restraints excluded: chain e residue 161 ASP Chi-restraints excluded: chain f residue 41 ASP Chi-restraints excluded: chain f residue 71 GLU Chi-restraints excluded: chain f residue 115 LYS Chi-restraints excluded: chain f residue 117 VAL Chi-restraints excluded: chain f residue 131 THR Chi-restraints excluded: chain f residue 142 ASP Chi-restraints excluded: chain f residue 157 VAL Chi-restraints excluded: chain h residue 26 GLU Chi-restraints excluded: chain h residue 91 LYS Chi-restraints excluded: chain j residue 96 THR Chi-restraints excluded: chain k residue 5 GLU Chi-restraints excluded: chain k residue 104 ILE Chi-restraints excluded: chain l residue 20 ASP Chi-restraints excluded: chain l residue 96 THR Chi-restraints excluded: chain m residue 105 SER Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain n residue 109 GLU Chi-restraints excluded: chain o residue 22 TYR Chi-restraints excluded: chain r residue 93 GLU Chi-restraints excluded: chain t residue 7 THR Chi-restraints excluded: chain t residue 53 ILE Chi-restraints excluded: chain t residue 63 LEU Chi-restraints excluded: chain t residue 90 VAL Chi-restraints excluded: chain t residue 111 THR Chi-restraints excluded: chain t residue 112 LEU Chi-restraints excluded: chain t residue 156 ASP Chi-restraints excluded: chain t residue 161 VAL Chi-restraints excluded: chain t residue 174 MET Chi-restraints excluded: chain t residue 179 SER Chi-restraints excluded: chain t residue 197 SER Chi-restraints excluded: chain t residue 207 TRP Chi-restraints excluded: chain t residue 211 LEU Chi-restraints excluded: chain u residue 7 THR Chi-restraints excluded: chain u residue 93 THR Chi-restraints excluded: chain u residue 111 THR Chi-restraints excluded: chain u residue 112 LEU Chi-restraints excluded: chain u residue 156 ASP Chi-restraints excluded: chain u residue 161 VAL Chi-restraints excluded: chain u residue 197 SER Chi-restraints excluded: chain u residue 207 TRP Chi-restraints excluded: chain v residue 7 THR Chi-restraints excluded: chain v residue 56 THR Chi-restraints excluded: chain v residue 111 THR Chi-restraints excluded: chain v residue 112 LEU Chi-restraints excluded: chain v residue 156 ASP Chi-restraints excluded: chain v residue 197 SER Chi-restraints excluded: chain v residue 207 TRP Chi-restraints excluded: chain v residue 211 LEU Chi-restraints excluded: chain w residue 26 SER Chi-restraints excluded: chain w residue 112 ASP Chi-restraints excluded: chain x residue 95 GLN Chi-restraints excluded: chain x residue 112 ASP Chi-restraints excluded: chain x residue 114 ARG Chi-restraints excluded: chain y residue 112 ASP Chi-restraints excluded: chain y residue 180 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 858 random chunks: chunk 279 optimal weight: 8.9990 chunk 746 optimal weight: 0.8980 chunk 163 optimal weight: 5.9990 chunk 486 optimal weight: 3.9990 chunk 204 optimal weight: 2.9990 chunk 830 optimal weight: 0.9980 chunk 689 optimal weight: 5.9990 chunk 384 optimal weight: 5.9990 chunk 69 optimal weight: 0.9990 chunk 274 optimal weight: 0.8980 chunk 435 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN K 122 ASN ** f 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 68607 Z= 0.180 Angle : 0.558 12.287 93228 Z= 0.291 Chirality : 0.044 0.395 10641 Planarity : 0.004 0.076 12279 Dihedral : 5.302 75.749 9639 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.89 % Favored : 94.99 % Rotamer: Outliers : 1.47 % Allowed : 8.35 % Favored : 90.17 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 4.47 % Cis-general : 0.00 % Twisted Proline : 0.61 % Twisted General : 0.05 % 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: 0.09 (0.09), residues: 8730 helix: 1.32 (0.10), residues: 2763 sheet: 0.12 (0.13), residues: 1620 loop : -0.76 (0.10), residues: 4347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP r 63 HIS 0.006 0.001 HIS v 71 PHE 0.015 0.001 PHE w 55 TYR 0.033 0.001 TYR t 99 ARG 0.008 0.000 ARG a 110 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17460 Ramachandran restraints generated. 8730 Oldfield, 0 Emsley, 8730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17460 Ramachandran restraints generated. 8730 Oldfield, 0 Emsley, 8730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Evaluate side-chains 942 residues out of total 7326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 834 time to evaluate : 8.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.8330 (mmt) cc_final: 0.7792 (mmt) REVERT: C 103 TYR cc_start: 0.7436 (m-10) cc_final: 0.6144 (t80) REVERT: C 118 ASN cc_start: 0.8323 (OUTLIER) cc_final: 0.8089 (p0) REVERT: E 26 MET cc_start: 0.8536 (mmt) cc_final: 0.8152 (mmt) REVERT: E 280 MET cc_start: 0.6368 (mtm) cc_final: 0.6086 (mtm) REVERT: F 252 MET cc_start: 0.8887 (mmm) cc_final: 0.8494 (mmm) REVERT: H 26 MET cc_start: 0.8482 (mmt) cc_final: 0.8155 (mmt) REVERT: K 26 MET cc_start: 0.8052 (mmt) cc_final: 0.7589 (mmt) REVERT: M 103 TYR cc_start: 0.7466 (m-10) cc_final: 0.6212 (t80) REVERT: M 162 MET cc_start: 0.7683 (ptp) cc_final: 0.7434 (ptp) REVERT: M 221 TYR cc_start: 0.5011 (m-80) cc_final: 0.4328 (t80) REVERT: O 26 MET cc_start: 0.8181 (mmm) cc_final: 0.7656 (mmt) REVERT: P 215 CYS cc_start: 0.5641 (m) cc_final: 0.5350 (m) REVERT: Q 26 MET cc_start: 0.8493 (mmt) cc_final: 0.8063 (mmt) REVERT: b 157 VAL cc_start: 0.8480 (OUTLIER) cc_final: 0.8274 (t) REVERT: d 38 ASP cc_start: 0.5643 (OUTLIER) cc_final: 0.5174 (p0) REVERT: d 71 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7244 (mp0) REVERT: d 110 ARG cc_start: 0.8306 (mtt90) cc_final: 0.7987 (mtt90) REVERT: f 71 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.7018 (mp0) REVERT: r 1 MET cc_start: 0.2940 (tmm) cc_final: 0.1624 (tmm) REVERT: t 55 LYS cc_start: 0.4550 (tppt) cc_final: 0.4309 (tppt) REVERT: t 184 MET cc_start: 0.5044 (mmp) cc_final: 0.4460 (mmt) REVERT: v 23 ILE cc_start: 0.7775 (mm) cc_final: 0.7238 (pt) REVERT: v 114 ARG cc_start: 0.3063 (tpt170) cc_final: 0.2762 (tpt170) REVERT: v 220 LYS cc_start: 0.8000 (mmtm) cc_final: 0.7608 (mtmm) REVERT: w 160 GLU cc_start: 0.6661 (pm20) cc_final: 0.6355 (pm20) REVERT: x 62 MET cc_start: 0.3028 (pmm) cc_final: 0.2087 (mmt) REVERT: x 95 GLN cc_start: 0.5302 (OUTLIER) cc_final: 0.4567 (tp40) REVERT: x 165 PHE cc_start: 0.6709 (m-80) cc_final: 0.6413 (m-80) outliers start: 108 outliers final: 86 residues processed: 897 average time/residue: 1.4229 time to fit residues: 2087.4635 Evaluate side-chains 897 residues out of total 7326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 805 time to evaluate : 7.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 CYS Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 99 GLN Chi-restraints excluded: chain G residue 206 ILE Chi-restraints excluded: chain H residue 58 GLU Chi-restraints excluded: chain I residue 122 ASN Chi-restraints excluded: chain J residue 50 MET Chi-restraints excluded: chain J residue 78 CYS Chi-restraints excluded: chain J residue 99 GLN Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain L residue 183 ILE Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain O residue 189 ARG Chi-restraints excluded: chain O residue 253 GLU Chi-restraints excluded: chain O residue 291 ASP Chi-restraints excluded: chain P residue 211 LEU Chi-restraints excluded: chain S residue 48 CYS Chi-restraints excluded: chain S residue 206 ILE Chi-restraints excluded: chain X residue 36 GLU Chi-restraints excluded: chain a residue 31 ASN Chi-restraints excluded: chain a residue 161 ASP Chi-restraints excluded: chain b residue 116 ILE Chi-restraints excluded: chain b residue 142 ASP Chi-restraints excluded: chain b residue 146 ASP Chi-restraints excluded: chain b residue 157 VAL Chi-restraints excluded: chain c residue 12 VAL Chi-restraints excluded: chain c residue 124 ASP Chi-restraints excluded: chain c residue 161 ASP Chi-restraints excluded: chain d residue 38 ASP Chi-restraints excluded: chain d residue 71 GLU Chi-restraints excluded: chain d residue 124 ASP Chi-restraints excluded: chain d residue 142 ASP Chi-restraints excluded: chain d residue 157 VAL Chi-restraints excluded: chain e residue 42 HIS Chi-restraints excluded: chain e residue 121 THR Chi-restraints excluded: chain e residue 161 ASP Chi-restraints excluded: chain f residue 71 GLU Chi-restraints excluded: chain f residue 115 LYS Chi-restraints excluded: chain f residue 117 VAL Chi-restraints excluded: chain f residue 131 THR Chi-restraints excluded: chain f residue 142 ASP Chi-restraints excluded: chain f residue 157 VAL Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 96 THR Chi-restraints excluded: chain k residue 5 GLU Chi-restraints excluded: chain k residue 104 ILE Chi-restraints excluded: chain l residue 20 ASP Chi-restraints excluded: chain l residue 96 THR Chi-restraints excluded: chain m residue 19 ASN Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain n residue 109 GLU Chi-restraints excluded: chain o residue 22 TYR Chi-restraints excluded: chain r residue 93 GLU Chi-restraints excluded: chain t residue 7 THR Chi-restraints excluded: chain t residue 90 VAL Chi-restraints excluded: chain t residue 111 THR Chi-restraints excluded: chain t residue 112 LEU Chi-restraints excluded: chain t residue 161 VAL Chi-restraints excluded: chain t residue 174 MET Chi-restraints excluded: chain t residue 207 TRP Chi-restraints excluded: chain t residue 211 LEU Chi-restraints excluded: chain u residue 7 THR Chi-restraints excluded: chain u residue 61 THR Chi-restraints excluded: chain u residue 93 THR Chi-restraints excluded: chain u residue 111 THR Chi-restraints excluded: chain u residue 112 LEU Chi-restraints excluded: chain u residue 151 THR Chi-restraints excluded: chain u residue 161 VAL Chi-restraints excluded: chain u residue 207 TRP Chi-restraints excluded: chain v residue 7 THR Chi-restraints excluded: chain v residue 95 LEU Chi-restraints excluded: chain v residue 111 THR Chi-restraints excluded: chain v residue 112 LEU Chi-restraints excluded: chain v residue 197 SER Chi-restraints excluded: chain v residue 207 TRP Chi-restraints excluded: chain v residue 211 LEU Chi-restraints excluded: chain w residue 26 SER Chi-restraints excluded: chain w residue 61 ASP Chi-restraints excluded: chain w residue 105 GLU Chi-restraints excluded: chain w residue 112 ASP Chi-restraints excluded: chain x residue 61 ASP Chi-restraints excluded: chain x residue 95 GLN Chi-restraints excluded: chain x residue 112 ASP Chi-restraints excluded: chain x residue 114 ARG Chi-restraints excluded: chain y residue 112 ASP Chi-restraints excluded: chain y residue 180 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 858 random chunks: chunk 800 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 472 optimal weight: 9.9990 chunk 606 optimal weight: 4.9990 chunk 469 optimal weight: 4.9990 chunk 698 optimal weight: 4.9990 chunk 463 optimal weight: 0.6980 chunk 826 optimal weight: 7.9990 chunk 517 optimal weight: 2.9990 chunk 504 optimal weight: 4.9990 chunk 381 optimal weight: 4.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN K 122 ASN ** M 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 173 GLN ** f 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 16 GLN ** n 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 68607 Z= 0.325 Angle : 0.605 12.255 93228 Z= 0.317 Chirality : 0.045 0.398 10641 Planarity : 0.005 0.080 12279 Dihedral : 5.411 81.704 9639 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.90 % Favored : 94.01 % Rotamer: Outliers : 1.60 % Allowed : 8.83 % Favored : 89.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.47 % Cis-general : 0.00 % Twisted Proline : 0.41 % Twisted General : 0.05 % 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: 0.03 (0.09), residues: 8730 helix: 1.24 (0.10), residues: 2799 sheet: 0.10 (0.13), residues: 1605 loop : -0.81 (0.09), residues: 4326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP y 28 HIS 0.007 0.001 HIS v 71 PHE 0.016 0.002 PHE y 179 TYR 0.036 0.002 TYR t 99 ARG 0.010 0.001 ARG a 110 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17460 Ramachandran restraints generated. 8730 Oldfield, 0 Emsley, 8730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17460 Ramachandran restraints generated. 8730 Oldfield, 0 Emsley, 8730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Evaluate side-chains 907 residues out of total 7326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 790 time to evaluate : 8.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.8320 (mmt) cc_final: 0.7877 (mmt) REVERT: A 286 MET cc_start: 0.7935 (mtm) cc_final: 0.7648 (mtm) REVERT: C 103 TYR cc_start: 0.7474 (m-10) cc_final: 0.6067 (t80) REVERT: C 118 ASN cc_start: 0.8481 (OUTLIER) cc_final: 0.8226 (p0) REVERT: E 26 MET cc_start: 0.8535 (mmt) cc_final: 0.8054 (mmt) REVERT: F 252 MET cc_start: 0.8869 (mmm) cc_final: 0.8488 (mmm) REVERT: H 26 MET cc_start: 0.8471 (mmt) cc_final: 0.8146 (mmt) REVERT: K 26 MET cc_start: 0.8088 (mmt) cc_final: 0.7652 (mmt) REVERT: M 103 TYR cc_start: 0.7560 (m-10) cc_final: 0.5977 (t80) REVERT: M 221 TYR cc_start: 0.5031 (m-80) cc_final: 0.4307 (t80) REVERT: O 26 MET cc_start: 0.8158 (mmm) cc_final: 0.7708 (mmt) REVERT: O 291 ASP cc_start: 0.7084 (OUTLIER) cc_final: 0.6877 (t70) REVERT: Q 26 MET cc_start: 0.8472 (mmt) cc_final: 0.8185 (mmt) REVERT: d 38 ASP cc_start: 0.5629 (OUTLIER) cc_final: 0.5218 (p0) REVERT: d 71 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7305 (mp0) REVERT: f 71 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7151 (mp0) REVERT: r 1 MET cc_start: 0.3114 (tmm) cc_final: 0.1881 (tmm) REVERT: v 23 ILE cc_start: 0.7864 (mm) cc_final: 0.7264 (pt) REVERT: v 114 ARG cc_start: 0.3082 (tpt170) cc_final: 0.2869 (tpt170) REVERT: v 220 LYS cc_start: 0.7875 (mmtm) cc_final: 0.7540 (mtmm) REVERT: w 160 GLU cc_start: 0.6651 (pm20) cc_final: 0.6236 (pm20) REVERT: x 62 MET cc_start: 0.3452 (pmm) cc_final: 0.2508 (mmt) REVERT: x 95 GLN cc_start: 0.5345 (OUTLIER) cc_final: 0.4512 (tp40) REVERT: x 165 PHE cc_start: 0.6673 (m-80) cc_final: 0.6386 (m-80) outliers start: 117 outliers final: 94 residues processed: 860 average time/residue: 1.5855 time to fit residues: 2241.2515 Evaluate side-chains 875 residues out of total 7326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 775 time to evaluate : 7.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 187 CYS Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 99 GLN Chi-restraints excluded: chain H residue 58 GLU Chi-restraints excluded: chain H residue 157 ASP Chi-restraints excluded: chain J residue 50 MET Chi-restraints excluded: chain J residue 78 CYS Chi-restraints excluded: chain J residue 99 GLN Chi-restraints excluded: chain J residue 124 ASP Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain L residue 183 ILE Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 78 CYS Chi-restraints excluded: chain O residue 189 ARG Chi-restraints excluded: chain O residue 253 GLU Chi-restraints excluded: chain O residue 291 ASP Chi-restraints excluded: chain P residue 211 LEU Chi-restraints excluded: chain R residue 87 SER Chi-restraints excluded: chain S residue 48 CYS Chi-restraints excluded: chain X residue 22 TYR Chi-restraints excluded: chain X residue 36 GLU Chi-restraints excluded: chain a residue 31 ASN Chi-restraints excluded: chain a residue 121 THR Chi-restraints excluded: chain a residue 161 ASP Chi-restraints excluded: chain b residue 34 GLU Chi-restraints excluded: chain b residue 116 ILE Chi-restraints excluded: chain b residue 131 THR Chi-restraints excluded: chain b residue 142 ASP Chi-restraints excluded: chain b residue 146 ASP Chi-restraints excluded: chain c residue 12 VAL Chi-restraints excluded: chain c residue 124 ASP Chi-restraints excluded: chain c residue 161 ASP Chi-restraints excluded: chain d residue 38 ASP Chi-restraints excluded: chain d residue 41 ASP Chi-restraints excluded: chain d residue 71 GLU Chi-restraints excluded: chain d residue 124 ASP Chi-restraints excluded: chain d residue 131 THR Chi-restraints excluded: chain d residue 142 ASP Chi-restraints excluded: chain e residue 121 THR Chi-restraints excluded: chain e residue 161 ASP Chi-restraints excluded: chain f residue 71 GLU Chi-restraints excluded: chain f residue 115 LYS Chi-restraints excluded: chain f residue 131 THR Chi-restraints excluded: chain f residue 142 ASP Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 96 THR Chi-restraints excluded: chain k residue 5 GLU Chi-restraints excluded: chain k residue 104 ILE Chi-restraints excluded: chain l residue 20 ASP Chi-restraints excluded: chain l residue 96 THR Chi-restraints excluded: chain m residue 19 ASN Chi-restraints excluded: chain m residue 104 ILE Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain o residue 22 TYR Chi-restraints excluded: chain r residue 93 GLU Chi-restraints excluded: chain t residue 7 THR Chi-restraints excluded: chain t residue 111 THR Chi-restraints excluded: chain t residue 112 LEU Chi-restraints excluded: chain t residue 156 ASP Chi-restraints excluded: chain t residue 161 VAL Chi-restraints excluded: chain t residue 174 MET Chi-restraints excluded: chain t residue 179 SER Chi-restraints excluded: chain t residue 197 SER Chi-restraints excluded: chain t residue 207 TRP Chi-restraints excluded: chain t residue 211 LEU Chi-restraints excluded: chain u residue 7 THR Chi-restraints excluded: chain u residue 24 ARG Chi-restraints excluded: chain u residue 61 THR Chi-restraints excluded: chain u residue 93 THR Chi-restraints excluded: chain u residue 95 LEU Chi-restraints excluded: chain u residue 111 THR Chi-restraints excluded: chain u residue 112 LEU Chi-restraints excluded: chain u residue 156 ASP Chi-restraints excluded: chain u residue 161 VAL Chi-restraints excluded: chain u residue 207 TRP Chi-restraints excluded: chain v residue 7 THR Chi-restraints excluded: chain v residue 95 LEU Chi-restraints excluded: chain v residue 111 THR Chi-restraints excluded: chain v residue 112 LEU Chi-restraints excluded: chain v residue 156 ASP Chi-restraints excluded: chain v residue 197 SER Chi-restraints excluded: chain v residue 207 TRP Chi-restraints excluded: chain v residue 211 LEU Chi-restraints excluded: chain w residue 26 SER Chi-restraints excluded: chain w residue 52 LYS Chi-restraints excluded: chain w residue 61 ASP Chi-restraints excluded: chain w residue 105 GLU Chi-restraints excluded: chain w residue 112 ASP Chi-restraints excluded: chain x residue 61 ASP Chi-restraints excluded: chain x residue 95 GLN Chi-restraints excluded: chain x residue 112 ASP Chi-restraints excluded: chain x residue 114 ARG Chi-restraints excluded: chain y residue 112 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 858 random chunks: chunk 511 optimal weight: 9.9990 chunk 330 optimal weight: 4.9990 chunk 493 optimal weight: 0.3980 chunk 249 optimal weight: 4.9990 chunk 162 optimal weight: 3.9990 chunk 160 optimal weight: 0.7980 chunk 525 optimal weight: 0.3980 chunk 563 optimal weight: 1.9990 chunk 408 optimal weight: 0.6980 chunk 77 optimal weight: 5.9990 chunk 650 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN K 122 ASN f 42 HIS ** n 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 71 HIS ** v 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 68607 Z= 0.161 Angle : 0.551 13.489 93228 Z= 0.285 Chirality : 0.045 0.397 10641 Planarity : 0.004 0.077 12279 Dihedral : 5.128 73.964 9639 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.71 % Favored : 95.19 % Rotamer: Outliers : 1.23 % Allowed : 9.39 % Favored : 89.38 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 4.47 % Cis-general : 0.00 % Twisted Proline : 0.41 % Twisted General : 0.05 % 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 (0.09), residues: 8730 helix: 1.47 (0.10), residues: 2763 sheet: 0.25 (0.13), residues: 1593 loop : -0.64 (0.10), residues: 4374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP j 28 HIS 0.005 0.001 HIS v 71 PHE 0.021 0.001 PHE H 186 TYR 0.029 0.001 TYR t 99 ARG 0.011 0.000 ARG a 110 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17460 Ramachandran restraints generated. 8730 Oldfield, 0 Emsley, 8730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17460 Ramachandran restraints generated. 8730 Oldfield, 0 Emsley, 8730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Evaluate side-chains 907 residues out of total 7326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 817 time to evaluate : 7.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.8304 (mmt) cc_final: 0.7781 (mmt) REVERT: A 286 MET cc_start: 0.7897 (mtm) cc_final: 0.7626 (mtm) REVERT: C 45 MET cc_start: 0.6918 (mmp) cc_final: 0.6641 (mmp) REVERT: C 103 TYR cc_start: 0.7382 (m-10) cc_final: 0.6063 (t80) REVERT: C 118 ASN cc_start: 0.8316 (OUTLIER) cc_final: 0.8104 (p0) REVERT: E 26 MET cc_start: 0.8536 (mmt) cc_final: 0.8151 (mmt) REVERT: F 252 MET cc_start: 0.8875 (mmm) cc_final: 0.8540 (mmm) REVERT: H 26 MET cc_start: 0.8466 (mmt) cc_final: 0.8078 (mmt) REVERT: K 26 MET cc_start: 0.8063 (mmt) cc_final: 0.7619 (mmt) REVERT: M 103 TYR cc_start: 0.7464 (m-10) cc_final: 0.6252 (t80) REVERT: M 162 MET cc_start: 0.7695 (ptp) cc_final: 0.7425 (ptp) REVERT: M 221 TYR cc_start: 0.4849 (m-80) cc_final: 0.4166 (t80) REVERT: O 26 MET cc_start: 0.8180 (mmm) cc_final: 0.7724 (mmt) REVERT: Q 26 MET cc_start: 0.8482 (mmt) cc_final: 0.8066 (mmt) REVERT: d 71 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7242 (mp0) REVERT: f 71 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.7053 (mp0) REVERT: r 1 MET cc_start: 0.3071 (tmm) cc_final: 0.1958 (tmm) REVERT: v 23 ILE cc_start: 0.7719 (mm) cc_final: 0.7207 (pt) REVERT: v 114 ARG cc_start: 0.3084 (tpt170) cc_final: 0.2800 (tpt170) REVERT: v 220 LYS cc_start: 0.7865 (mmtm) cc_final: 0.7475 (mptt) REVERT: w 160 GLU cc_start: 0.6556 (pm20) cc_final: 0.6351 (pm20) REVERT: x 62 MET cc_start: 0.3094 (pmm) cc_final: 0.2261 (mmt) REVERT: x 165 PHE cc_start: 0.6797 (m-80) cc_final: 0.6539 (m-80) outliers start: 90 outliers final: 74 residues processed: 868 average time/residue: 1.4596 time to fit residues: 2066.0180 Evaluate side-chains 871 residues out of total 7326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 794 time to evaluate : 7.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 CYS Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain G residue 47 TYR Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 99 GLN Chi-restraints excluded: chain H residue 58 GLU Chi-restraints excluded: chain J residue 50 MET Chi-restraints excluded: chain J residue 78 CYS Chi-restraints excluded: chain J residue 99 GLN Chi-restraints excluded: chain L residue 183 ILE Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain O residue 189 ARG Chi-restraints excluded: chain O residue 253 GLU Chi-restraints excluded: chain O residue 291 ASP Chi-restraints excluded: chain R residue 87 SER Chi-restraints excluded: chain S residue 48 CYS Chi-restraints excluded: chain S residue 109 SER Chi-restraints excluded: chain X residue 22 TYR Chi-restraints excluded: chain a residue 31 ASN Chi-restraints excluded: chain a residue 161 ASP Chi-restraints excluded: chain b residue 34 GLU Chi-restraints excluded: chain b residue 116 ILE Chi-restraints excluded: chain b residue 131 THR Chi-restraints excluded: chain b residue 142 ASP Chi-restraints excluded: chain b residue 146 ASP Chi-restraints excluded: chain c residue 12 VAL Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 161 ASP Chi-restraints excluded: chain d residue 71 GLU Chi-restraints excluded: chain d residue 124 ASP Chi-restraints excluded: chain d residue 157 VAL Chi-restraints excluded: chain e residue 42 HIS Chi-restraints excluded: chain e residue 161 ASP Chi-restraints excluded: chain f residue 71 GLU Chi-restraints excluded: chain f residue 115 LYS Chi-restraints excluded: chain j residue 96 THR Chi-restraints excluded: chain k residue 5 GLU Chi-restraints excluded: chain k residue 104 ILE Chi-restraints excluded: chain l residue 96 THR Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain o residue 22 TYR Chi-restraints excluded: chain r residue 93 GLU Chi-restraints excluded: chain t residue 7 THR Chi-restraints excluded: chain t residue 111 THR Chi-restraints excluded: chain t residue 112 LEU Chi-restraints excluded: chain t residue 156 ASP Chi-restraints excluded: chain t residue 161 VAL Chi-restraints excluded: chain t residue 174 MET Chi-restraints excluded: chain t residue 179 SER Chi-restraints excluded: chain t residue 197 SER Chi-restraints excluded: chain t residue 207 TRP Chi-restraints excluded: chain t residue 211 LEU Chi-restraints excluded: chain u residue 7 THR Chi-restraints excluded: chain u residue 24 ARG Chi-restraints excluded: chain u residue 61 THR Chi-restraints excluded: chain u residue 111 THR Chi-restraints excluded: chain u residue 112 LEU Chi-restraints excluded: chain u residue 116 HIS Chi-restraints excluded: chain u residue 161 VAL Chi-restraints excluded: chain u residue 207 TRP Chi-restraints excluded: chain v residue 7 THR Chi-restraints excluded: chain v residue 95 LEU Chi-restraints excluded: chain v residue 111 THR Chi-restraints excluded: chain v residue 112 LEU Chi-restraints excluded: chain v residue 207 TRP Chi-restraints excluded: chain v residue 211 LEU Chi-restraints excluded: chain w residue 26 SER Chi-restraints excluded: chain w residue 61 ASP Chi-restraints excluded: chain w residue 105 GLU Chi-restraints excluded: chain w residue 112 ASP Chi-restraints excluded: chain x residue 61 ASP Chi-restraints excluded: chain x residue 112 ASP Chi-restraints excluded: chain x residue 114 ARG Chi-restraints excluded: chain y residue 112 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 858 random chunks: chunk 752 optimal weight: 1.9990 chunk 792 optimal weight: 0.9990 chunk 722 optimal weight: 4.9990 chunk 770 optimal weight: 6.9990 chunk 463 optimal weight: 0.9980 chunk 335 optimal weight: 9.9990 chunk 605 optimal weight: 9.9990 chunk 236 optimal weight: 6.9990 chunk 696 optimal weight: 0.3980 chunk 728 optimal weight: 0.8980 chunk 767 optimal weight: 10.0000 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN K 122 ASN M 208 GLN ** n 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 68607 Z= 0.166 Angle : 0.539 12.630 93228 Z= 0.279 Chirality : 0.044 0.401 10641 Planarity : 0.004 0.076 12279 Dihedral : 4.950 73.206 9639 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.99 % Favored : 94.91 % Rotamer: Outliers : 1.05 % Allowed : 9.61 % Favored : 89.34 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 4.47 % Cis-general : 0.00 % Twisted Proline : 0.20 % Twisted General : 0.05 % 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: 0.44 (0.09), residues: 8730 helix: 1.61 (0.10), residues: 2763 sheet: 0.30 (0.13), residues: 1593 loop : -0.55 (0.10), residues: 4374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 218 HIS 0.005 0.001 HIS v 71 PHE 0.014 0.001 PHE H 67 TYR 0.028 0.001 TYR t 99 ARG 0.011 0.000 ARG a 110 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17460 Ramachandran restraints generated. 8730 Oldfield, 0 Emsley, 8730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17460 Ramachandran restraints generated. 8730 Oldfield, 0 Emsley, 8730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Evaluate side-chains 887 residues out of total 7326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 810 time to evaluate : 8.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.8320 (mmt) cc_final: 0.7802 (mmt) REVERT: A 286 MET cc_start: 0.7910 (mtm) cc_final: 0.7650 (mtm) REVERT: C 45 MET cc_start: 0.6929 (mmp) cc_final: 0.6670 (mmp) REVERT: C 103 TYR cc_start: 0.7339 (m-10) cc_final: 0.6090 (t80) REVERT: C 118 ASN cc_start: 0.8304 (OUTLIER) cc_final: 0.8083 (p0) REVERT: E 26 MET cc_start: 0.8534 (mmt) cc_final: 0.8153 (mmt) REVERT: F 252 MET cc_start: 0.8901 (mmm) cc_final: 0.8558 (mmm) REVERT: H 26 MET cc_start: 0.8460 (mmt) cc_final: 0.8078 (mmt) REVERT: K 26 MET cc_start: 0.8046 (mmt) cc_final: 0.7609 (mmt) REVERT: M 103 TYR cc_start: 0.7491 (m-10) cc_final: 0.6338 (t80) REVERT: M 162 MET cc_start: 0.7688 (ptp) cc_final: 0.7421 (ptp) REVERT: M 221 TYR cc_start: 0.4845 (m-80) cc_final: 0.4164 (t80) REVERT: O 26 MET cc_start: 0.8174 (mmm) cc_final: 0.7733 (mmt) REVERT: Q 26 MET cc_start: 0.8476 (mmt) cc_final: 0.8080 (mmt) REVERT: c 79 MET cc_start: 0.7281 (mmt) cc_final: 0.6988 (mmt) REVERT: d 71 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7252 (mp0) REVERT: d 110 ARG cc_start: 0.8165 (mtt90) cc_final: 0.7915 (mtt90) REVERT: f 71 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.7055 (mp0) REVERT: o 1 MET cc_start: 0.1692 (mtm) cc_final: 0.1316 (mtt) REVERT: r 1 MET cc_start: 0.3076 (tmm) cc_final: 0.1966 (tmm) REVERT: u 45 ASP cc_start: 0.5450 (t0) cc_final: 0.5187 (t0) REVERT: v 23 ILE cc_start: 0.7761 (mm) cc_final: 0.7221 (pt) REVERT: v 204 GLU cc_start: 0.6121 (mm-30) cc_final: 0.5391 (mm-30) REVERT: v 220 LYS cc_start: 0.7803 (mmtm) cc_final: 0.7429 (mptt) REVERT: w 202 MET cc_start: 0.6577 (mpp) cc_final: 0.6051 (mpp) REVERT: x 62 MET cc_start: 0.2941 (pmm) cc_final: 0.2205 (mmt) REVERT: x 165 PHE cc_start: 0.6745 (m-80) cc_final: 0.6432 (m-80) outliers start: 77 outliers final: 65 residues processed: 855 average time/residue: 1.4996 time to fit residues: 2098.2399 Evaluate side-chains 861 residues out of total 7326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 793 time to evaluate : 7.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 CYS Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 99 GLN Chi-restraints excluded: chain H residue 58 GLU Chi-restraints excluded: chain J residue 50 MET Chi-restraints excluded: chain J residue 78 CYS Chi-restraints excluded: chain J residue 99 GLN Chi-restraints excluded: chain L residue 183 ILE Chi-restraints excluded: chain M residue 78 CYS Chi-restraints excluded: chain O residue 291 ASP Chi-restraints excluded: chain P residue 211 LEU Chi-restraints excluded: chain S residue 48 CYS Chi-restraints excluded: chain X residue 36 GLU Chi-restraints excluded: chain a residue 31 ASN Chi-restraints excluded: chain a residue 121 THR Chi-restraints excluded: chain a residue 161 ASP Chi-restraints excluded: chain b residue 34 GLU Chi-restraints excluded: chain b residue 131 THR Chi-restraints excluded: chain b residue 142 ASP Chi-restraints excluded: chain b residue 146 ASP Chi-restraints excluded: chain c residue 12 VAL Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 161 ASP Chi-restraints excluded: chain d residue 71 GLU Chi-restraints excluded: chain d residue 157 VAL Chi-restraints excluded: chain e residue 42 HIS Chi-restraints excluded: chain e residue 161 ASP Chi-restraints excluded: chain f residue 34 GLU Chi-restraints excluded: chain f residue 71 GLU Chi-restraints excluded: chain f residue 115 LYS Chi-restraints excluded: chain j residue 96 THR Chi-restraints excluded: chain k residue 104 ILE Chi-restraints excluded: chain l residue 96 THR Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain o residue 22 TYR Chi-restraints excluded: chain r residue 93 GLU Chi-restraints excluded: chain t residue 7 THR Chi-restraints excluded: chain t residue 111 THR Chi-restraints excluded: chain t residue 112 LEU Chi-restraints excluded: chain t residue 161 VAL Chi-restraints excluded: chain t residue 174 MET Chi-restraints excluded: chain t residue 179 SER Chi-restraints excluded: chain t residue 197 SER Chi-restraints excluded: chain t residue 207 TRP Chi-restraints excluded: chain t residue 211 LEU Chi-restraints excluded: chain u residue 24 ARG Chi-restraints excluded: chain u residue 111 THR Chi-restraints excluded: chain u residue 112 LEU Chi-restraints excluded: chain u residue 116 HIS Chi-restraints excluded: chain u residue 161 VAL Chi-restraints excluded: chain u residue 207 TRP Chi-restraints excluded: chain v residue 7 THR Chi-restraints excluded: chain v residue 95 LEU Chi-restraints excluded: chain v residue 111 THR Chi-restraints excluded: chain v residue 112 LEU Chi-restraints excluded: chain v residue 207 TRP Chi-restraints excluded: chain v residue 211 LEU Chi-restraints excluded: chain w residue 26 SER Chi-restraints excluded: chain w residue 61 ASP Chi-restraints excluded: chain w residue 105 GLU Chi-restraints excluded: chain w residue 112 ASP Chi-restraints excluded: chain x residue 61 ASP Chi-restraints excluded: chain x residue 114 ARG Chi-restraints excluded: chain y residue 112 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 858 random chunks: chunk 506 optimal weight: 3.9990 chunk 814 optimal weight: 9.9990 chunk 497 optimal weight: 0.9990 chunk 386 optimal weight: 6.9990 chunk 566 optimal weight: 10.0000 chunk 854 optimal weight: 1.9990 chunk 786 optimal weight: 5.9990 chunk 680 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 525 optimal weight: 0.8980 chunk 417 optimal weight: 0.0570 overall best weight: 1.5904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN M 77 HIS ** n 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 144 HIS ** y 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 68607 Z= 0.183 Angle : 0.541 13.301 93228 Z= 0.280 Chirality : 0.044 0.401 10641 Planarity : 0.004 0.088 12279 Dihedral : 4.901 73.440 9637 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.93 % Favored : 94.98 % Rotamer: Outliers : 1.01 % Allowed : 9.79 % Favored : 89.20 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 4.47 % Cis-general : 0.00 % Twisted Proline : 0.20 % Twisted General : 0.05 % 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: 0.49 (0.09), residues: 8730 helix: 1.66 (0.10), residues: 2763 sheet: 0.32 (0.13), residues: 1593 loop : -0.52 (0.10), residues: 4374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP r 63 HIS 0.006 0.001 HIS u 135 PHE 0.013 0.001 PHE H 67 TYR 0.025 0.001 TYR t 99 ARG 0.012 0.000 ARG a 110 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17460 Ramachandran restraints generated. 8730 Oldfield, 0 Emsley, 8730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17460 Ramachandran restraints generated. 8730 Oldfield, 0 Emsley, 8730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Evaluate side-chains 871 residues out of total 7326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 797 time to evaluate : 10.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 26 MET cc_start: 0.8328 (mmt) cc_final: 0.7804 (mmt) REVERT: A 286 MET cc_start: 0.7914 (mtm) cc_final: 0.7660 (mtm) REVERT: C 103 TYR cc_start: 0.7359 (m-10) cc_final: 0.6090 (t80) REVERT: C 118 ASN cc_start: 0.8336 (OUTLIER) cc_final: 0.8108 (p0) REVERT: E 26 MET cc_start: 0.8542 (mmt) cc_final: 0.8149 (mmt) REVERT: F 252 MET cc_start: 0.8897 (mmm) cc_final: 0.8560 (mmm) REVERT: H 26 MET cc_start: 0.8465 (mmt) cc_final: 0.8157 (mmt) REVERT: K 26 MET cc_start: 0.8047 (mmt) cc_final: 0.7595 (mmt) REVERT: M 103 TYR cc_start: 0.7479 (m-10) cc_final: 0.6332 (t80) REVERT: M 162 MET cc_start: 0.7750 (ptp) cc_final: 0.7494 (ptp) REVERT: M 221 TYR cc_start: 0.4847 (m-80) cc_final: 0.4161 (t80) REVERT: O 26 MET cc_start: 0.8172 (mmm) cc_final: 0.7735 (mmt) REVERT: Q 26 MET cc_start: 0.8476 (mmt) cc_final: 0.8114 (mmt) REVERT: c 79 MET cc_start: 0.7290 (mmt) cc_final: 0.7040 (mmt) REVERT: d 71 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7270 (mp0) REVERT: f 71 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.7066 (mp0) REVERT: o 1 MET cc_start: 0.1639 (mtm) cc_final: 0.1258 (mtt) REVERT: q 24 ASP cc_start: 0.6858 (p0) cc_final: 0.6590 (p0) REVERT: r 1 MET cc_start: 0.3039 (tmm) cc_final: 0.1825 (tmm) REVERT: t 184 MET cc_start: 0.5814 (mmp) cc_final: 0.5059 (mmt) REVERT: u 45 ASP cc_start: 0.5482 (t0) cc_final: 0.5182 (t0) REVERT: v 23 ILE cc_start: 0.7788 (mm) cc_final: 0.7231 (pt) REVERT: v 220 LYS cc_start: 0.7795 (mmtm) cc_final: 0.7429 (mptt) REVERT: w 202 MET cc_start: 0.6611 (mpp) cc_final: 0.6108 (mpp) REVERT: x 62 MET cc_start: 0.2921 (pmm) cc_final: 0.2280 (mmt) outliers start: 74 outliers final: 68 residues processed: 840 average time/residue: 1.5421 time to fit residues: 2129.9528 Evaluate side-chains 851 residues out of total 7326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 780 time to evaluate : 7.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 CYS Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 99 GLN Chi-restraints excluded: chain H residue 58 GLU Chi-restraints excluded: chain J residue 50 MET Chi-restraints excluded: chain J residue 78 CYS Chi-restraints excluded: chain J residue 99 GLN Chi-restraints excluded: chain L residue 183 ILE Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 78 CYS Chi-restraints excluded: chain O residue 291 ASP Chi-restraints excluded: chain R residue 87 SER Chi-restraints excluded: chain S residue 48 CYS Chi-restraints excluded: chain X residue 36 GLU Chi-restraints excluded: chain a residue 31 ASN Chi-restraints excluded: chain a residue 121 THR Chi-restraints excluded: chain a residue 161 ASP Chi-restraints excluded: chain b residue 34 GLU Chi-restraints excluded: chain b residue 131 THR Chi-restraints excluded: chain b residue 142 ASP Chi-restraints excluded: chain b residue 146 ASP Chi-restraints excluded: chain c residue 12 VAL Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 161 ASP Chi-restraints excluded: chain d residue 71 GLU Chi-restraints excluded: chain d residue 157 VAL Chi-restraints excluded: chain e residue 42 HIS Chi-restraints excluded: chain e residue 161 ASP Chi-restraints excluded: chain f residue 34 GLU Chi-restraints excluded: chain f residue 71 GLU Chi-restraints excluded: chain f residue 115 LYS Chi-restraints excluded: chain j residue 96 THR Chi-restraints excluded: chain k residue 104 ILE Chi-restraints excluded: chain l residue 96 THR Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain n residue 23 LEU Chi-restraints excluded: chain n residue 109 GLU Chi-restraints excluded: chain o residue 22 TYR Chi-restraints excluded: chain r residue 93 GLU Chi-restraints excluded: chain t residue 7 THR Chi-restraints excluded: chain t residue 111 THR Chi-restraints excluded: chain t residue 112 LEU Chi-restraints excluded: chain t residue 161 VAL Chi-restraints excluded: chain t residue 174 MET Chi-restraints excluded: chain t residue 179 SER Chi-restraints excluded: chain t residue 197 SER Chi-restraints excluded: chain t residue 207 TRP Chi-restraints excluded: chain t residue 211 LEU Chi-restraints excluded: chain u residue 24 ARG Chi-restraints excluded: chain u residue 111 THR Chi-restraints excluded: chain u residue 112 LEU Chi-restraints excluded: chain u residue 116 HIS Chi-restraints excluded: chain u residue 161 VAL Chi-restraints excluded: chain u residue 207 TRP Chi-restraints excluded: chain v residue 7 THR Chi-restraints excluded: chain v residue 95 LEU Chi-restraints excluded: chain v residue 111 THR Chi-restraints excluded: chain v residue 112 LEU Chi-restraints excluded: chain v residue 207 TRP Chi-restraints excluded: chain v residue 211 LEU Chi-restraints excluded: chain w residue 52 LYS Chi-restraints excluded: chain w residue 61 ASP Chi-restraints excluded: chain w residue 105 GLU Chi-restraints excluded: chain x residue 61 ASP Chi-restraints excluded: chain x residue 112 ASP Chi-restraints excluded: chain x residue 114 ARG Chi-restraints excluded: chain y residue 112 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 858 random chunks: chunk 540 optimal weight: 4.9990 chunk 725 optimal weight: 6.9990 chunk 208 optimal weight: 2.9990 chunk 627 optimal weight: 4.9990 chunk 100 optimal weight: 0.1980 chunk 189 optimal weight: 4.9990 chunk 681 optimal weight: 0.0980 chunk 285 optimal weight: 0.6980 chunk 700 optimal weight: 4.9990 chunk 86 optimal weight: 6.9990 chunk 125 optimal weight: 0.3980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 208 GLN Q 39 GLN ** n 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 103 GLN ** t 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.104738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.085317 restraints weight = 424665.048| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.74 r_work: 0.3065 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 68607 Z= 0.154 Angle : 0.525 11.547 93228 Z= 0.271 Chirality : 0.044 0.398 10641 Planarity : 0.004 0.088 12279 Dihedral : 4.741 70.786 9637 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.73 % Favored : 95.18 % Rotamer: Outliers : 0.94 % Allowed : 9.87 % Favored : 89.19 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 4.47 % Cis-general : 0.00 % Twisted Proline : 0.20 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.09), residues: 8730 helix: 1.75 (0.10), residues: 2763 sheet: 0.38 (0.13), residues: 1593 loop : -0.44 (0.10), residues: 4374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP j 28 HIS 0.005 0.001 HIS u 135 PHE 0.021 0.001 PHE w 165 TYR 0.020 0.001 TYR t 99 ARG 0.013 0.000 ARG a 110 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 34413.74 seconds wall clock time: 590 minutes 46.51 seconds (35446.51 seconds total)