Starting phenix.real_space_refine on Wed Feb 21 19:49:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eon_28405/02_2024/8eon_28405.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eon_28405/02_2024/8eon_28405.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eon_28405/02_2024/8eon_28405.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eon_28405/02_2024/8eon_28405.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eon_28405/02_2024/8eon_28405.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eon_28405/02_2024/8eon_28405.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 408 5.16 5 C 60357 2.51 5 N 16329 2.21 5 O 18594 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 41": "OD1" <-> "OD2" Residue "G TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 18": "OD1" <-> "OD2" Residue "H GLU 45": "OE1" <-> "OE2" Residue "H ASP 49": "OD1" <-> "OD2" Residue "H GLU 58": "OE1" <-> "OE2" Residue "H ASP 76": "OD1" <-> "OD2" Residue "H GLU 88": "OE1" <-> "OE2" Residue "I GLU 32": "OE1" <-> "OE2" Residue "I GLU 41": "OE1" <-> "OE2" Residue "I PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 51": "OE1" <-> "OE2" Residue "J PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 187": "OD1" <-> "OD2" Residue "J GLU 346": "OE1" <-> "OE2" Residue "J GLU 359": "OE1" <-> "OE2" Residue "K PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 125": "OE1" <-> "OE2" Residue "K GLU 162": "OE1" <-> "OE2" Residue "K GLU 191": "OE1" <-> "OE2" Residue "K TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 37": "OD1" <-> "OD2" Residue "L TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 67": "OD1" <-> "OD2" Residue "L TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 13": "OD1" <-> "OD2" Residue "M GLU 45": "OE1" <-> "OE2" Residue "M ASP 76": "OD1" <-> "OD2" Residue "M GLU 97": "OE1" <-> "OE2" Residue "N PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 39": "OE1" <-> "OE2" Residue "N ASP 98": "OD1" <-> "OD2" Residue "N TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 27": "OE1" <-> "OE2" Residue "O GLU 51": "OE1" <-> "OE2" Residue "O PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 162": "OD1" <-> "OD2" Residue "O GLU 344": "OE1" <-> "OE2" Residue "O GLU 367": "OE1" <-> "OE2" Residue "P PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 156": "OD1" <-> "OD2" Residue "P PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 181": "OE1" <-> "OE2" Residue "P TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 292": "OD1" <-> "OD2" Residue "P ASP 298": "OD1" <-> "OD2" Residue "P PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 498": "OD1" <-> "OD2" Residue "Q TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 58": "OE1" <-> "OE2" Residue "R ASP 68": "OD1" <-> "OD2" Residue "R GLU 97": "OE1" <-> "OE2" Residue "S PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 32": "OE1" <-> "OE2" Residue "S GLU 46": "OE1" <-> "OE2" Residue "T ASP 187": "OD1" <-> "OD2" Residue "T TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 346": "OE1" <-> "OE2" Residue "T ARG 366": "NH1" <-> "NH2" Residue "T PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 36": "OD1" <-> "OD2" Residue "U PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 298": "OD1" <-> "OD2" Residue "U GLU 353": "OE1" <-> "OE2" Residue "U PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 419": "OE1" <-> "OE2" Residue "V ASP 41": "OD1" <-> "OD2" Residue "V TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 13": "OD1" <-> "OD2" Residue "W GLU 45": "OE1" <-> "OE2" Residue "W ASP 49": "OD1" <-> "OD2" Residue "W TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 76": "OD1" <-> "OD2" Residue "W GLU 97": "OE1" <-> "OE2" Residue "X GLU 32": "OE1" <-> "OE2" Residue "X GLU 39": "OE1" <-> "OE2" Residue "X GLU 63": "OE1" <-> "OE2" Residue "X PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 27": "OE1" <-> "OE2" Residue "Y PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 367": "OE1" <-> "OE2" Residue "Y PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 47": "OE1" <-> "OE2" Residue "Z ASP 49": "OD1" <-> "OD2" Residue "Z PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 119": "OE1" <-> "OE2" Residue "Z ASP 124": "OD1" <-> "OD2" Residue "Z TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 156": "OD1" <-> "OD2" Residue "Z GLU 158": "OE1" <-> "OE2" Residue "Z GLU 176": "OE1" <-> "OE2" Residue "Z TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 298": "OD1" <-> "OD2" Residue "Z PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 377": "OE1" <-> "OE2" Residue "Z PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 485": "OD1" <-> "OD2" Residue "a TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 37": "OD1" <-> "OD2" Residue "a TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 84": "OD1" <-> "OD2" Residue "a GLU 98": "OE1" <-> "OE2" Residue "b ASP 13": "OD1" <-> "OD2" Residue "b ASP 49": "OD1" <-> "OD2" Residue "b ASP 69": "OD1" <-> "OD2" Residue "b ASP 76": "OD1" <-> "OD2" Residue "b GLU 88": "OE1" <-> "OE2" Residue "b GLU 97": "OE1" <-> "OE2" Residue "c PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 39": "OE1" <-> "OE2" Residue "c GLU 46": "OE1" <-> "OE2" Residue "c PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 108": "OD1" <-> "OD2" Residue "c TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 25": "OE1" <-> "OE2" Residue "d PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 261": "OD1" <-> "OD2" Residue "d ASP 285": "OD1" <-> "OD2" Residue "d GLU 346": "OE1" <-> "OE2" Residue "d GLU 347": "OE1" <-> "OE2" Residue "d GLU 359": "OE1" <-> "OE2" Residue "d ARG 366": "NH1" <-> "NH2" Residue "d TYR 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 36": "OD1" <-> "OD2" Residue "e PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 158": "OE1" <-> "OE2" Residue "e GLU 162": "OE1" <-> "OE2" Residue "e PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 298": "OD1" <-> "OD2" Residue "e PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 368": "OD1" <-> "OD2" Residue "e PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 41": "OD1" <-> "OD2" Residue "f ASP 67": "OD1" <-> "OD2" Residue "f ASP 78": "OD1" <-> "OD2" Residue "f ASP 92": "OD1" <-> "OD2" Residue "g ASP 27": "OD1" <-> "OD2" Residue "g GLU 29": "OE1" <-> "OE2" Residue "g GLU 45": "OE1" <-> "OE2" Residue "g GLU 58": "OE1" <-> "OE2" Residue "g TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 76": "OD1" <-> "OD2" Residue "g GLU 97": "OE1" <-> "OE2" Residue "h ASP 50": "OD1" <-> "OD2" Residue "h PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 63": "OE1" <-> "OE2" Residue "h TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ASP 23": "OD1" <-> "OD2" Residue "i PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 344": "OE1" <-> "OE2" Residue "i GLU 347": "OE1" <-> "OE2" Residue "i GLU 359": "OE1" <-> "OE2" Residue "i GLU 367": "OE1" <-> "OE2" Residue "i ASP 392": "OD1" <-> "OD2" Residue "i PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 47": "OE1" <-> "OE2" Residue "j PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 119": "OE1" <-> "OE2" Residue "j TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 181": "OE1" <-> "OE2" Residue "j PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ASP 485": "OD1" <-> "OD2" Residue "B TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 48": "OE1" <-> "OE2" Residue "C PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 155": "OE1" <-> "OE2" Residue "D ASP 19": "OD1" <-> "OD2" Residue "D GLU 90": "OE1" <-> "OE2" Residue "E GLU 72": "OE1" <-> "OE2" Residue "E ASP 198": "OD1" <-> "OD2" Residue "E PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 274": "OD1" <-> "OD2" Residue "F GLU 47": "OE1" <-> "OE2" Residue "k ASP 19": "OD1" <-> "OD2" Residue "k GLU 90": "OE1" <-> "OE2" Residue "k GLU 139": "OE1" <-> "OE2" Residue "l GLU 21": "OE1" <-> "OE2" Residue "l TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 250": "OE1" <-> "OE2" Residue "m GLU 72": "OE1" <-> "OE2" Residue "m PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ASP 19": "OD1" <-> "OD2" Residue "o GLU 90": "OE1" <-> "OE2" Residue "o ASP 98": "OD1" <-> "OD2" Residue "p PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r GLU 189": "OE1" <-> "OE2" Residue "r TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r GLU 367": "OE1" <-> "OE2" Residue "s PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ASP 80": "OD1" <-> "OD2" Residue "s PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s GLU 367": "OE1" <-> "OE2" Residue "t ASP 80": "OD1" <-> "OD2" Residue "u PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.20s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 95688 Number of models: 1 Model: "" Number of chains: 48 Chain: "G" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 816 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "H" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 823 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 2, 'TRANS': 105} Chain: "I" Number of atoms: 1133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1133 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 8, 'TRANS': 143} Chain: "J" Number of atoms: 3036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3036 Classifications: {'peptide': 417} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 395} Chain: "K" Number of atoms: 3818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3818 Classifications: {'peptide': 500} Link IDs: {'PCIS': 2, 'PTRANS': 30, 'TRANS': 467} Chain: "L" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 816 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "M" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 823 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 2, 'TRANS': 105} Chain: "N" Number of atoms: 1133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1133 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 8, 'TRANS': 143} Chain: "O" Number of atoms: 3036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3036 Classifications: {'peptide': 417} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 395} Chain: "P" Number of atoms: 3818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3818 Classifications: {'peptide': 500} Link IDs: {'PCIS': 2, 'PTRANS': 30, 'TRANS': 467} Chain: "Q" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 816 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "R" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 823 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 2, 'TRANS': 105} Chain: "S" Number of atoms: 1133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1133 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 8, 'TRANS': 143} Chain: "T" Number of atoms: 3036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3036 Classifications: {'peptide': 417} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 395} Chain: "U" Number of atoms: 3818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3818 Classifications: {'peptide': 500} Link IDs: {'PCIS': 2, 'PTRANS': 30, 'TRANS': 467} Chain: "V" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 816 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "W" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 823 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 2, 'TRANS': 105} Chain: "X" Number of atoms: 1133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1133 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 8, 'TRANS': 143} Chain: "Y" Number of atoms: 3036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3036 Classifications: {'peptide': 417} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 395} Chain: "Z" Number of atoms: 3818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3818 Classifications: {'peptide': 500} Link IDs: {'PCIS': 2, 'PTRANS': 30, 'TRANS': 467} Chain: "a" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 816 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "b" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 823 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 2, 'TRANS': 105} Chain: "c" Number of atoms: 1133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1133 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 8, 'TRANS': 143} Chain: "d" Number of atoms: 3036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3036 Classifications: {'peptide': 417} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 395} Chain: "e" Number of atoms: 3818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3818 Classifications: {'peptide': 500} Link IDs: {'PCIS': 2, 'PTRANS': 30, 'TRANS': 467} Chain: "f" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 816 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "g" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 823 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 2, 'TRANS': 105} Chain: "h" Number of atoms: 1133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1133 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 8, 'TRANS': 143} Chain: "i" Number of atoms: 3036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3036 Classifications: {'peptide': 417} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 395} Chain: "j" Number of atoms: 3818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3818 Classifications: {'peptide': 500} Link IDs: {'PCIS': 2, 'PTRANS': 30, 'TRANS': 467} Chain: "A" Number of atoms: 1329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1329 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 6, 'TRANS': 165} Chain: "B" Number of atoms: 1329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1329 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 6, 'TRANS': 165} Chain: "C" Number of atoms: 1329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1329 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 6, 'TRANS': 165} Chain: "D" Number of atoms: 1482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1482 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 12, 'TRANS': 180} Chain: "E" Number of atoms: 2278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2278 Classifications: {'peptide': 287} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 271} Chain: "F" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1687 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 207} Chain: "k" Number of atoms: 1482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1482 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 12, 'TRANS': 180} Chain: "l" Number of atoms: 2278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2278 Classifications: {'peptide': 287} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 271} Chain: "m" Number of atoms: 2278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2278 Classifications: {'peptide': 287} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 271} Chain: "n" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1687 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 207} Chain: "o" Number of atoms: 1482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1482 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 12, 'TRANS': 180} Chain: "p" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1687 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 207} Chain: "q" Number of atoms: 2934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 2934 Classifications: {'peptide': 404} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 382} Chain: "r" Number of atoms: 2934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 2934 Classifications: {'peptide': 404} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 382} Chain: "s" Number of atoms: 2934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 2934 Classifications: {'peptide': 404} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 382} Chain: "t" Number of atoms: 2934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 2934 Classifications: {'peptide': 404} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 382} Chain breaks: 1 Chain: "u" Number of atoms: 2934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 2934 Classifications: {'peptide': 404} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 382} Chain breaks: 1 Chain: "v" Number of atoms: 2934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 2934 Classifications: {'peptide': 404} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 382} Chain breaks: 1 Time building chain proxies: 35.66, per 1000 atoms: 0.37 Number of scatterers: 95688 At special positions: 0 Unit cell: (273.28, 288.96, 236.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 408 16.00 O 18594 8.00 N 16329 7.00 C 60357 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 27.98 Conformation dependent library (CDL) restraints added in 13.1 seconds 25218 Ramachandran restraints generated. 12609 Oldfield, 0 Emsley, 12609 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 23220 Finding SS restraints... Secondary structure from input PDB file: 237 helices and 174 sheets defined 21.6% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.92 Creating SS restraints... Processing helix chain 'G' and resid 60 through 65 removed outlier: 3.879A pdb=" N ARG G 65 " --> pdb=" O SER G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 104 removed outlier: 3.808A pdb=" N THR G 104 " --> pdb=" O GLN G 100 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 40 removed outlier: 3.556A pdb=" N LEU H 40 " --> pdb=" O ARG H 36 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 60 Processing helix chain 'H' and resid 68 through 79 Processing helix chain 'I' and resid 72 through 84 Processing helix chain 'J' and resid 16 through 33 removed outlier: 3.570A pdb=" N VAL J 20 " --> pdb=" O ASP J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 42 through 65 removed outlier: 3.754A pdb=" N ILE J 65 " --> pdb=" O ASN J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 84 Processing helix chain 'J' and resid 188 through 203 removed outlier: 3.879A pdb=" N ARG J 203 " --> pdb=" O ALA J 199 " (cutoff:3.500A) Processing helix chain 'J' and resid 204 through 214 removed outlier: 3.745A pdb=" N LYS J 210 " --> pdb=" O THR J 206 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA J 211 " --> pdb=" O MET J 207 " (cutoff:3.500A) Processing helix chain 'J' and resid 255 through 266 removed outlier: 4.348A pdb=" N VAL J 259 " --> pdb=" O ASP J 255 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA J 260 " --> pdb=" O LYS J 256 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA J 266 " --> pdb=" O ALA J 262 " (cutoff:3.500A) Processing helix chain 'J' and resid 327 through 341 removed outlier: 3.679A pdb=" N ILE J 331 " --> pdb=" O ALA J 327 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN J 340 " --> pdb=" O VAL J 336 " (cutoff:3.500A) Processing helix chain 'J' and resid 357 through 368 Processing helix chain 'J' and resid 389 through 393 removed outlier: 4.107A pdb=" N PHE J 393 " --> pdb=" O PRO J 390 " (cutoff:3.500A) Processing helix chain 'K' and resid 9 through 14 Processing helix chain 'K' and resid 21 through 39 removed outlier: 3.847A pdb=" N THR K 25 " --> pdb=" O ALA K 21 " (cutoff:3.500A) Processing helix chain 'K' and resid 40 through 51 Processing helix chain 'K' and resid 57 through 69 removed outlier: 3.536A pdb=" N LEU K 61 " --> pdb=" O ASN K 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 123 through 139 removed outlier: 3.636A pdb=" N ARG K 127 " --> pdb=" O LEU K 123 " (cutoff:3.500A) Processing helix chain 'K' and resid 142 through 155 Processing helix chain 'K' and resid 476 through 484 removed outlier: 3.780A pdb=" N ILE K 480 " --> pdb=" O SER K 476 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASN K 484 " --> pdb=" O ILE K 480 " (cutoff:3.500A) Processing helix chain 'L' and resid 60 through 65 removed outlier: 3.741A pdb=" N TYR L 64 " --> pdb=" O TYR L 60 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ARG L 65 " --> pdb=" O SER L 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 60 through 65' Processing helix chain 'L' and resid 92 through 104 removed outlier: 3.908A pdb=" N THR L 104 " --> pdb=" O GLN L 100 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 40 removed outlier: 3.690A pdb=" N LEU M 40 " --> pdb=" O ARG M 36 " (cutoff:3.500A) Processing helix chain 'M' and resid 55 through 60 Processing helix chain 'M' and resid 67 through 79 removed outlier: 3.628A pdb=" N ARG M 71 " --> pdb=" O TYR M 67 " (cutoff:3.500A) Processing helix chain 'N' and resid 72 through 84 Processing helix chain 'O' and resid 16 through 32 Processing helix chain 'O' and resid 42 through 65 removed outlier: 3.696A pdb=" N ILE O 65 " --> pdb=" O ASN O 61 " (cutoff:3.500A) Processing helix chain 'O' and resid 76 through 84 removed outlier: 3.643A pdb=" N ASP O 80 " --> pdb=" O GLY O 76 " (cutoff:3.500A) Processing helix chain 'O' and resid 187 through 203 removed outlier: 3.875A pdb=" N ARG O 203 " --> pdb=" O ALA O 199 " (cutoff:3.500A) Processing helix chain 'O' and resid 204 through 216 removed outlier: 3.512A pdb=" N ILE O 209 " --> pdb=" O SER O 205 " (cutoff:3.500A) Processing helix chain 'O' and resid 255 through 266 removed outlier: 4.260A pdb=" N VAL O 259 " --> pdb=" O ASP O 255 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA O 260 " --> pdb=" O LYS O 256 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA O 266 " --> pdb=" O ALA O 262 " (cutoff:3.500A) Processing helix chain 'O' and resid 327 through 340 removed outlier: 3.767A pdb=" N GLN O 340 " --> pdb=" O VAL O 336 " (cutoff:3.500A) Processing helix chain 'O' and resid 356 through 368 Processing helix chain 'O' and resid 389 through 393 removed outlier: 3.569A pdb=" N PHE O 393 " --> pdb=" O PRO O 390 " (cutoff:3.500A) Processing helix chain 'P' and resid 9 through 14 Processing helix chain 'P' and resid 15 through 19 Processing helix chain 'P' and resid 21 through 40 removed outlier: 3.853A pdb=" N THR P 25 " --> pdb=" O ALA P 21 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG P 40 " --> pdb=" O ASP P 36 " (cutoff:3.500A) Processing helix chain 'P' and resid 40 through 51 Processing helix chain 'P' and resid 57 through 69 Processing helix chain 'P' and resid 122 through 139 removed outlier: 3.678A pdb=" N ILE P 126 " --> pdb=" O ASN P 122 " (cutoff:3.500A) Processing helix chain 'P' and resid 142 through 156 Processing helix chain 'P' and resid 161 through 165 Processing helix chain 'P' and resid 470 through 474 removed outlier: 3.716A pdb=" N LEU P 473 " --> pdb=" O GLY P 470 " (cutoff:3.500A) Processing helix chain 'P' and resid 476 through 484 Processing helix chain 'Q' and resid 60 through 65 removed outlier: 3.805A pdb=" N ARG Q 65 " --> pdb=" O SER Q 61 " (cutoff:3.500A) Processing helix chain 'Q' and resid 92 through 104 removed outlier: 3.873A pdb=" N THR Q 104 " --> pdb=" O GLN Q 100 " (cutoff:3.500A) Processing helix chain 'R' and resid 28 through 39 Processing helix chain 'R' and resid 55 through 60 Processing helix chain 'R' and resid 67 through 79 removed outlier: 3.696A pdb=" N ARG R 71 " --> pdb=" O TYR R 67 " (cutoff:3.500A) Processing helix chain 'S' and resid 72 through 84 removed outlier: 3.539A pdb=" N ILE S 76 " --> pdb=" O SER S 72 " (cutoff:3.500A) Processing helix chain 'T' and resid 16 through 32 Processing helix chain 'T' and resid 42 through 65 removed outlier: 3.746A pdb=" N ILE T 65 " --> pdb=" O ASN T 61 " (cutoff:3.500A) Processing helix chain 'T' and resid 76 through 84 Processing helix chain 'T' and resid 188 through 203 removed outlier: 3.959A pdb=" N ARG T 203 " --> pdb=" O ALA T 199 " (cutoff:3.500A) Processing helix chain 'T' and resid 204 through 216 removed outlier: 3.726A pdb=" N VAL T 216 " --> pdb=" O TYR T 212 " (cutoff:3.500A) Processing helix chain 'T' and resid 255 through 266 removed outlier: 4.113A pdb=" N VAL T 259 " --> pdb=" O ASP T 255 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA T 260 " --> pdb=" O LYS T 256 " (cutoff:3.500A) Processing helix chain 'T' and resid 327 through 341 Processing helix chain 'T' and resid 357 through 368 Processing helix chain 'T' and resid 389 through 393 removed outlier: 3.892A pdb=" N PHE T 393 " --> pdb=" O PRO T 390 " (cutoff:3.500A) Processing helix chain 'U' and resid 9 through 14 Processing helix chain 'U' and resid 21 through 39 removed outlier: 3.830A pdb=" N THR U 25 " --> pdb=" O ALA U 21 " (cutoff:3.500A) Processing helix chain 'U' and resid 40 through 51 Processing helix chain 'U' and resid 57 through 69 Processing helix chain 'U' and resid 123 through 139 Processing helix chain 'U' and resid 142 through 155 removed outlier: 3.541A pdb=" N ILE U 146 " --> pdb=" O SER U 142 " (cutoff:3.500A) Processing helix chain 'U' and resid 161 through 165 removed outlier: 3.517A pdb=" N THR U 164 " --> pdb=" O ASP U 161 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY U 165 " --> pdb=" O GLU U 162 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 161 through 165' Processing helix chain 'U' and resid 476 through 483 removed outlier: 3.610A pdb=" N ILE U 480 " --> pdb=" O SER U 476 " (cutoff:3.500A) Processing helix chain 'V' and resid 60 through 65 Processing helix chain 'V' and resid 92 through 104 removed outlier: 3.886A pdb=" N THR V 104 " --> pdb=" O GLN V 100 " (cutoff:3.500A) Processing helix chain 'W' and resid 28 through 40 removed outlier: 3.568A pdb=" N LEU W 40 " --> pdb=" O ARG W 36 " (cutoff:3.500A) Processing helix chain 'W' and resid 55 through 60 Processing helix chain 'W' and resid 67 through 79 removed outlier: 4.124A pdb=" N ARG W 71 " --> pdb=" O TYR W 67 " (cutoff:3.500A) Processing helix chain 'X' and resid 72 through 84 Processing helix chain 'Y' and resid 16 through 33 Processing helix chain 'Y' and resid 42 through 65 removed outlier: 3.888A pdb=" N ILE Y 65 " --> pdb=" O ASN Y 61 " (cutoff:3.500A) Processing helix chain 'Y' and resid 76 through 84 removed outlier: 3.582A pdb=" N ASP Y 80 " --> pdb=" O GLY Y 76 " (cutoff:3.500A) Processing helix chain 'Y' and resid 187 through 203 removed outlier: 3.651A pdb=" N LYS Y 191 " --> pdb=" O ASP Y 187 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG Y 203 " --> pdb=" O ALA Y 199 " (cutoff:3.500A) Processing helix chain 'Y' and resid 204 through 216 Processing helix chain 'Y' and resid 255 through 266 removed outlier: 3.869A pdb=" N VAL Y 259 " --> pdb=" O ASP Y 255 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA Y 266 " --> pdb=" O ALA Y 262 " (cutoff:3.500A) Processing helix chain 'Y' and resid 327 through 340 removed outlier: 3.706A pdb=" N ILE Y 331 " --> pdb=" O ALA Y 327 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLN Y 340 " --> pdb=" O VAL Y 336 " (cutoff:3.500A) Processing helix chain 'Y' and resid 357 through 368 Processing helix chain 'Y' and resid 389 through 393 removed outlier: 3.805A pdb=" N PHE Y 393 " --> pdb=" O PRO Y 390 " (cutoff:3.500A) Processing helix chain 'Z' and resid 9 through 14 Processing helix chain 'Z' and resid 22 through 40 Processing helix chain 'Z' and resid 40 through 51 Processing helix chain 'Z' and resid 52 through 55 Processing helix chain 'Z' and resid 57 through 69 Processing helix chain 'Z' and resid 122 through 139 removed outlier: 3.503A pdb=" N ILE Z 126 " --> pdb=" O ASN Z 122 " (cutoff:3.500A) Processing helix chain 'Z' and resid 142 through 156 Processing helix chain 'Z' and resid 470 through 474 Processing helix chain 'Z' and resid 476 through 484 removed outlier: 3.579A pdb=" N ASN Z 484 " --> pdb=" O ILE Z 480 " (cutoff:3.500A) Processing helix chain 'a' and resid 60 through 65 removed outlier: 3.703A pdb=" N ARG a 65 " --> pdb=" O SER a 61 " (cutoff:3.500A) Processing helix chain 'a' and resid 92 through 104 removed outlier: 4.022A pdb=" N THR a 104 " --> pdb=" O GLN a 100 " (cutoff:3.500A) Processing helix chain 'b' and resid 28 through 39 Processing helix chain 'b' and resid 55 through 60 Processing helix chain 'b' and resid 67 through 79 removed outlier: 3.631A pdb=" N ARG b 71 " --> pdb=" O TYR b 67 " (cutoff:3.500A) Processing helix chain 'c' and resid 72 through 84 Processing helix chain 'd' and resid 16 through 32 Processing helix chain 'd' and resid 42 through 65 removed outlier: 3.620A pdb=" N ILE d 65 " --> pdb=" O ASN d 61 " (cutoff:3.500A) Processing helix chain 'd' and resid 76 through 86 removed outlier: 4.135A pdb=" N LEU d 85 " --> pdb=" O ALA d 81 " (cutoff:3.500A) Processing helix chain 'd' and resid 188 through 203 removed outlier: 4.006A pdb=" N ARG d 203 " --> pdb=" O ALA d 199 " (cutoff:3.500A) Processing helix chain 'd' and resid 204 through 216 Processing helix chain 'd' and resid 257 through 266 removed outlier: 3.956A pdb=" N ASP d 261 " --> pdb=" O GLN d 257 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA d 266 " --> pdb=" O ALA d 262 " (cutoff:3.500A) Processing helix chain 'd' and resid 327 through 341 Processing helix chain 'd' and resid 357 through 368 Processing helix chain 'd' and resid 389 through 393 removed outlier: 4.121A pdb=" N PHE d 393 " --> pdb=" O PRO d 390 " (cutoff:3.500A) Processing helix chain 'e' and resid 9 through 13 removed outlier: 3.760A pdb=" N GLN e 12 " --> pdb=" O ASP e 9 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA e 13 " --> pdb=" O ILE e 10 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 9 through 13' Processing helix chain 'e' and resid 21 through 40 removed outlier: 3.773A pdb=" N THR e 25 " --> pdb=" O ALA e 21 " (cutoff:3.500A) Processing helix chain 'e' and resid 40 through 51 Processing helix chain 'e' and resid 57 through 69 removed outlier: 3.573A pdb=" N LEU e 61 " --> pdb=" O ASN e 57 " (cutoff:3.500A) Processing helix chain 'e' and resid 123 through 139 Processing helix chain 'e' and resid 142 through 155 Processing helix chain 'e' and resid 161 through 165 Processing helix chain 'e' and resid 476 through 484 removed outlier: 3.783A pdb=" N ILE e 480 " --> pdb=" O SER e 476 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN e 484 " --> pdb=" O ILE e 480 " (cutoff:3.500A) Processing helix chain 'f' and resid 60 through 65 Processing helix chain 'f' and resid 92 through 104 removed outlier: 3.851A pdb=" N THR f 104 " --> pdb=" O GLN f 100 " (cutoff:3.500A) Processing helix chain 'g' and resid 28 through 40 removed outlier: 3.583A pdb=" N LEU g 40 " --> pdb=" O ARG g 36 " (cutoff:3.500A) Processing helix chain 'g' and resid 55 through 60 Processing helix chain 'g' and resid 68 through 79 Processing helix chain 'h' and resid 72 through 84 removed outlier: 3.555A pdb=" N ILE h 76 " --> pdb=" O SER h 72 " (cutoff:3.500A) Processing helix chain 'i' and resid 16 through 33 Processing helix chain 'i' and resid 42 through 65 removed outlier: 4.030A pdb=" N ILE i 65 " --> pdb=" O ASN i 61 " (cutoff:3.500A) Processing helix chain 'i' and resid 76 through 84 removed outlier: 3.654A pdb=" N ASP i 80 " --> pdb=" O GLY i 76 " (cutoff:3.500A) Processing helix chain 'i' and resid 187 through 203 removed outlier: 3.625A pdb=" N LYS i 191 " --> pdb=" O ASP i 187 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ARG i 203 " --> pdb=" O ALA i 199 " (cutoff:3.500A) Processing helix chain 'i' and resid 204 through 216 removed outlier: 3.669A pdb=" N VAL i 216 " --> pdb=" O TYR i 212 " (cutoff:3.500A) Processing helix chain 'i' and resid 255 through 266 removed outlier: 3.919A pdb=" N ALA i 266 " --> pdb=" O ALA i 262 " (cutoff:3.500A) Processing helix chain 'i' and resid 327 through 340 removed outlier: 3.743A pdb=" N ILE i 331 " --> pdb=" O ALA i 327 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN i 340 " --> pdb=" O VAL i 336 " (cutoff:3.500A) Processing helix chain 'i' and resid 357 through 368 Processing helix chain 'i' and resid 389 through 393 removed outlier: 3.554A pdb=" N PHE i 393 " --> pdb=" O PRO i 390 " (cutoff:3.500A) Processing helix chain 'j' and resid 9 through 14 Processing helix chain 'j' and resid 22 through 39 Processing helix chain 'j' and resid 39 through 51 Processing helix chain 'j' and resid 52 through 55 removed outlier: 3.776A pdb=" N THR j 55 " --> pdb=" O HIS j 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 52 through 55' Processing helix chain 'j' and resid 57 through 69 removed outlier: 3.827A pdb=" N LEU j 61 " --> pdb=" O ASN j 57 " (cutoff:3.500A) Processing helix chain 'j' and resid 122 through 139 removed outlier: 3.848A pdb=" N ILE j 126 " --> pdb=" O ASN j 122 " (cutoff:3.500A) Processing helix chain 'j' and resid 143 through 156 Processing helix chain 'j' and resid 470 through 474 Processing helix chain 'j' and resid 476 through 483 Processing helix chain 'A' and resid 73 through 85 Processing helix chain 'A' and resid 160 through 171 removed outlier: 3.959A pdb=" N VAL A 169 " --> pdb=" O PHE A 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 85 Processing helix chain 'B' and resid 161 through 169 removed outlier: 3.577A pdb=" N PHE B 165 " --> pdb=" O ALA B 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 85 Processing helix chain 'C' and resid 140 through 144 Processing helix chain 'C' and resid 160 through 169 removed outlier: 3.621A pdb=" N LEU C 164 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE C 165 " --> pdb=" O ALA C 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 61 Processing helix chain 'D' and resid 86 through 98 Processing helix chain 'D' and resid 181 through 193 removed outlier: 4.146A pdb=" N VAL D 193 " --> pdb=" O LEU D 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 57 removed outlier: 3.871A pdb=" N SER E 57 " --> pdb=" O GLU E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 127 removed outlier: 3.748A pdb=" N ASP E 125 " --> pdb=" O ARG E 122 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR E 127 " --> pdb=" O ILE E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 152 Processing helix chain 'E' and resid 177 through 186 removed outlier: 4.383A pdb=" N ALA E 181 " --> pdb=" O SER E 177 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N MET E 186 " --> pdb=" O SER E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 258 removed outlier: 3.779A pdb=" N ASN E 258 " --> pdb=" O PRO E 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 31 removed outlier: 3.822A pdb=" N ALA F 20 " --> pdb=" O ARG F 16 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP F 31 " --> pdb=" O ARG F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 112 removed outlier: 3.912A pdb=" N SER F 111 " --> pdb=" O GLN F 107 " (cutoff:3.500A) Processing helix chain 'k' and resid 54 through 61 Processing helix chain 'k' and resid 86 through 97 Processing helix chain 'k' and resid 181 through 192 removed outlier: 3.776A pdb=" N ARG k 192 " --> pdb=" O SER k 188 " (cutoff:3.500A) Processing helix chain 'l' and resid 48 through 57 removed outlier: 3.905A pdb=" N SER l 57 " --> pdb=" O GLU l 53 " (cutoff:3.500A) Processing helix chain 'l' and resid 122 through 127 removed outlier: 3.727A pdb=" N ASP l 125 " --> pdb=" O ARG l 122 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR l 127 " --> pdb=" O ILE l 124 " (cutoff:3.500A) Processing helix chain 'l' and resid 140 through 152 Processing helix chain 'l' and resid 177 through 186 removed outlier: 4.312A pdb=" N ALA l 181 " --> pdb=" O SER l 177 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET l 186 " --> pdb=" O SER l 182 " (cutoff:3.500A) Processing helix chain 'l' and resid 254 through 258 removed outlier: 3.548A pdb=" N VAL l 257 " --> pdb=" O ASN l 254 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASN l 258 " --> pdb=" O PRO l 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 254 through 258' Processing helix chain 'm' and resid 48 through 57 removed outlier: 4.080A pdb=" N SER m 57 " --> pdb=" O GLU m 53 " (cutoff:3.500A) Processing helix chain 'm' and resid 122 through 127 removed outlier: 3.687A pdb=" N ASP m 125 " --> pdb=" O ARG m 122 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR m 127 " --> pdb=" O ILE m 124 " (cutoff:3.500A) Processing helix chain 'm' and resid 140 through 152 Processing helix chain 'm' and resid 177 through 186 removed outlier: 4.230A pdb=" N ALA m 181 " --> pdb=" O SER m 177 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N MET m 186 " --> pdb=" O SER m 182 " (cutoff:3.500A) Processing helix chain 'm' and resid 254 through 258 removed outlier: 3.503A pdb=" N VAL m 257 " --> pdb=" O ASN m 254 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASN m 258 " --> pdb=" O PRO m 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 254 through 258' Processing helix chain 'n' and resid 16 through 31 removed outlier: 3.641A pdb=" N ALA n 20 " --> pdb=" O ARG n 16 " (cutoff:3.500A) Processing helix chain 'n' and resid 105 through 112 removed outlier: 3.637A pdb=" N SER n 111 " --> pdb=" O GLN n 107 " (cutoff:3.500A) Processing helix chain 'n' and resid 141 through 145 removed outlier: 3.970A pdb=" N SER n 145 " --> pdb=" O SER n 142 " (cutoff:3.500A) Processing helix chain 'o' and resid 54 through 61 Processing helix chain 'o' and resid 86 through 98 removed outlier: 3.524A pdb=" N ASP o 98 " --> pdb=" O ASN o 94 " (cutoff:3.500A) Processing helix chain 'o' and resid 181 through 191 Processing helix chain 'p' and resid 16 through 31 removed outlier: 3.715A pdb=" N ALA p 20 " --> pdb=" O ARG p 16 " (cutoff:3.500A) Processing helix chain 'p' and resid 105 through 112 removed outlier: 3.937A pdb=" N SER p 111 " --> pdb=" O GLN p 107 " (cutoff:3.500A) Processing helix chain 'p' and resid 141 through 145 removed outlier: 3.981A pdb=" N SER p 145 " --> pdb=" O SER p 142 " (cutoff:3.500A) Processing helix chain 'q' and resid 19 through 22 removed outlier: 3.716A pdb=" N SER q 22 " --> pdb=" O ASP q 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 19 through 22' Processing helix chain 'q' and resid 23 through 34 Processing helix chain 'q' and resid 43 through 68 Processing helix chain 'q' and resid 77 through 84 removed outlier: 3.767A pdb=" N ALA q 81 " --> pdb=" O THR q 77 " (cutoff:3.500A) Processing helix chain 'q' and resid 185 through 196 removed outlier: 5.247A pdb=" N ARG q 194 " --> pdb=" O LEU q 190 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N VAL q 195 " --> pdb=" O LYS q 191 " (cutoff:3.500A) Processing helix chain 'q' and resid 206 through 214 removed outlier: 4.247A pdb=" N LYS q 210 " --> pdb=" O THR q 206 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA q 211 " --> pdb=" O MET q 207 " (cutoff:3.500A) Processing helix chain 'q' and resid 255 through 265 removed outlier: 4.107A pdb=" N VAL q 259 " --> pdb=" O ASP q 255 " (cutoff:3.500A) Processing helix chain 'q' and resid 327 through 341 removed outlier: 4.251A pdb=" N ILE q 331 " --> pdb=" O ALA q 327 " (cutoff:3.500A) Processing helix chain 'q' and resid 356 through 368 Processing helix chain 'q' and resid 389 through 393 removed outlier: 3.878A pdb=" N PHE q 393 " --> pdb=" O PRO q 390 " (cutoff:3.500A) Processing helix chain 'q' and resid 408 through 410 No H-bonds generated for 'chain 'q' and resid 408 through 410' Processing helix chain 'r' and resid 23 through 34 Processing helix chain 'r' and resid 43 through 68 removed outlier: 3.600A pdb=" N THR r 68 " --> pdb=" O ARG r 64 " (cutoff:3.500A) Processing helix chain 'r' and resid 77 through 84 removed outlier: 3.769A pdb=" N ALA r 81 " --> pdb=" O THR r 77 " (cutoff:3.500A) Processing helix chain 'r' and resid 185 through 196 removed outlier: 5.478A pdb=" N ARG r 194 " --> pdb=" O LEU r 190 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N VAL r 195 " --> pdb=" O LYS r 191 " (cutoff:3.500A) Processing helix chain 'r' and resid 206 through 215 removed outlier: 4.057A pdb=" N LYS r 210 " --> pdb=" O THR r 206 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA r 211 " --> pdb=" O MET r 207 " (cutoff:3.500A) Processing helix chain 'r' and resid 255 through 265 removed outlier: 4.126A pdb=" N VAL r 259 " --> pdb=" O ASP r 255 " (cutoff:3.500A) Processing helix chain 'r' and resid 327 through 341 removed outlier: 4.196A pdb=" N ILE r 331 " --> pdb=" O ALA r 327 " (cutoff:3.500A) Processing helix chain 'r' and resid 356 through 368 Processing helix chain 'r' and resid 389 through 393 removed outlier: 3.966A pdb=" N PHE r 393 " --> pdb=" O PRO r 390 " (cutoff:3.500A) Processing helix chain 's' and resid 21 through 34 removed outlier: 3.547A pdb=" N GLU s 25 " --> pdb=" O LEU s 21 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ALA s 26 " --> pdb=" O SER s 22 " (cutoff:3.500A) Processing helix chain 's' and resid 43 through 68 Processing helix chain 's' and resid 77 through 86 removed outlier: 3.812A pdb=" N ALA s 81 " --> pdb=" O THR s 77 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LEU s 85 " --> pdb=" O ALA s 81 " (cutoff:3.500A) Processing helix chain 's' and resid 185 through 196 removed outlier: 3.530A pdb=" N GLU s 189 " --> pdb=" O MET s 185 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ARG s 194 " --> pdb=" O LEU s 190 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N VAL s 195 " --> pdb=" O LYS s 191 " (cutoff:3.500A) Processing helix chain 's' and resid 206 through 215 removed outlier: 3.957A pdb=" N LYS s 210 " --> pdb=" O THR s 206 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA s 211 " --> pdb=" O MET s 207 " (cutoff:3.500A) Processing helix chain 's' and resid 255 through 265 removed outlier: 4.114A pdb=" N VAL s 259 " --> pdb=" O ASP s 255 " (cutoff:3.500A) Processing helix chain 's' and resid 327 through 341 removed outlier: 4.187A pdb=" N ILE s 331 " --> pdb=" O ALA s 327 " (cutoff:3.500A) Processing helix chain 's' and resid 356 through 368 Processing helix chain 's' and resid 389 through 393 removed outlier: 4.033A pdb=" N PHE s 393 " --> pdb=" O PRO s 390 " (cutoff:3.500A) Processing helix chain 's' and resid 408 through 410 No H-bonds generated for 'chain 's' and resid 408 through 410' Processing helix chain 't' and resid 21 through 34 removed outlier: 3.631A pdb=" N ALA t 26 " --> pdb=" O SER t 22 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA t 31 " --> pdb=" O GLU t 27 " (cutoff:3.500A) Processing helix chain 't' and resid 43 through 66 removed outlier: 4.212A pdb=" N LEU t 47 " --> pdb=" O PRO t 43 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL t 48 " --> pdb=" O GLN t 44 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG t 64 " --> pdb=" O ARG t 60 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA t 66 " --> pdb=" O GLU t 62 " (cutoff:3.500A) Processing helix chain 't' and resid 77 through 84 removed outlier: 4.043A pdb=" N ALA t 81 " --> pdb=" O THR t 77 " (cutoff:3.500A) Processing helix chain 't' and resid 185 through 193 removed outlier: 4.023A pdb=" N LYS t 191 " --> pdb=" O ASP t 187 " (cutoff:3.500A) Processing helix chain 't' and resid 205 through 215 Processing helix chain 't' and resid 257 through 266 removed outlier: 4.054A pdb=" N LEU t 263 " --> pdb=" O VAL t 259 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA t 266 " --> pdb=" O ALA t 262 " (cutoff:3.500A) Processing helix chain 't' and resid 329 through 341 removed outlier: 4.288A pdb=" N ASN t 333 " --> pdb=" O GLU t 329 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA t 334 " --> pdb=" O ALA t 330 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N VAL t 335 " --> pdb=" O ILE t 331 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL t 336 " --> pdb=" O GLN t 332 " (cutoff:3.500A) Processing helix chain 't' and resid 356 through 362 removed outlier: 3.588A pdb=" N VAL t 360 " --> pdb=" O SER t 356 " (cutoff:3.500A) Processing helix chain 't' and resid 363 through 367 removed outlier: 3.535A pdb=" N GLU t 367 " --> pdb=" O ILE t 364 " (cutoff:3.500A) Processing helix chain 'u' and resid 21 through 34 removed outlier: 3.622A pdb=" N ALA u 26 " --> pdb=" O SER u 22 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA u 31 " --> pdb=" O GLU u 27 " (cutoff:3.500A) Processing helix chain 'u' and resid 43 through 66 removed outlier: 4.279A pdb=" N LEU u 47 " --> pdb=" O PRO u 43 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL u 48 " --> pdb=" O GLN u 44 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER u 56 " --> pdb=" O ALA u 52 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG u 64 " --> pdb=" O ARG u 60 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA u 66 " --> pdb=" O GLU u 62 " (cutoff:3.500A) Processing helix chain 'u' and resid 77 through 84 removed outlier: 3.911A pdb=" N ALA u 81 " --> pdb=" O THR u 77 " (cutoff:3.500A) Processing helix chain 'u' and resid 185 through 193 removed outlier: 4.115A pdb=" N LYS u 191 " --> pdb=" O ASP u 187 " (cutoff:3.500A) Processing helix chain 'u' and resid 205 through 215 Processing helix chain 'u' and resid 257 through 266 removed outlier: 4.078A pdb=" N LEU u 263 " --> pdb=" O VAL u 259 " (cutoff:3.500A) Processing helix chain 'u' and resid 329 through 341 removed outlier: 4.093A pdb=" N ASN u 333 " --> pdb=" O GLU u 329 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA u 334 " --> pdb=" O ALA u 330 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL u 335 " --> pdb=" O ILE u 331 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL u 336 " --> pdb=" O GLN u 332 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN u 337 " --> pdb=" O ASN u 333 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR u 338 " --> pdb=" O ALA u 334 " (cutoff:3.500A) Processing helix chain 'u' and resid 357 through 362 Processing helix chain 'u' and resid 363 through 367 Processing helix chain 'v' and resid 21 through 34 removed outlier: 3.576A pdb=" N ALA v 26 " --> pdb=" O SER v 22 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA v 31 " --> pdb=" O GLU v 27 " (cutoff:3.500A) Processing helix chain 'v' and resid 43 through 66 removed outlier: 3.915A pdb=" N LEU v 47 " --> pdb=" O PRO v 43 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE v 53 " --> pdb=" O ALA v 49 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL v 58 " --> pdb=" O ALA v 54 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG v 64 " --> pdb=" O ARG v 60 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA v 66 " --> pdb=" O GLU v 62 " (cutoff:3.500A) Processing helix chain 'v' and resid 77 through 84 removed outlier: 3.712A pdb=" N ALA v 81 " --> pdb=" O THR v 77 " (cutoff:3.500A) Processing helix chain 'v' and resid 185 through 193 removed outlier: 4.082A pdb=" N LYS v 191 " --> pdb=" O ASP v 187 " (cutoff:3.500A) Processing helix chain 'v' and resid 205 through 215 removed outlier: 3.530A pdb=" N ALA v 215 " --> pdb=" O ALA v 211 " (cutoff:3.500A) Processing helix chain 'v' and resid 257 through 266 removed outlier: 4.028A pdb=" N LEU v 263 " --> pdb=" O VAL v 259 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA v 266 " --> pdb=" O ALA v 262 " (cutoff:3.500A) Processing helix chain 'v' and resid 329 through 341 removed outlier: 3.666A pdb=" N ASN v 333 " --> pdb=" O GLU v 329 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL v 335 " --> pdb=" O ILE v 331 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL v 336 " --> pdb=" O GLN v 332 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASN v 337 " --> pdb=" O ASN v 333 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N TYR v 338 " --> pdb=" O ALA v 334 " (cutoff:3.500A) Processing helix chain 'v' and resid 356 through 362 Processing helix chain 'v' and resid 363 through 367 Processing sheet with id=AA1, first strand: chain 'G' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 11 through 12 current: chain 'G' and resid 22 through 30 removed outlier: 7.267A pdb=" N MET G 34 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL G 49 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ALA G 36 " --> pdb=" O HIS G 47 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N HIS G 47 " --> pdb=" O ALA G 36 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ILE G 38 " --> pdb=" O VAL G 45 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 70 through 73 removed outlier: 3.543A pdb=" N VAL G 72 " --> pdb=" O PHE G 89 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE G 89 " --> pdb=" O VAL G 72 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 5 through 6 removed outlier: 3.533A pdb=" N THR H 5 " --> pdb=" O LEU H 25 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 84 through 90 removed outlier: 6.857A pdb=" N ILE H 106 " --> pdb=" O THR H 85 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ILE H 87 " --> pdb=" O LYS H 104 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N LYS H 104 " --> pdb=" O ILE H 87 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 23 through 25 removed outlier: 3.602A pdb=" N ILE I 11 " --> pdb=" O LEU I 25 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLY I 10 " --> pdb=" O THR I 105 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ASN I 116 " --> pdb=" O GLY I 144 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N THR I 140 " --> pdb=" O LEU I 120 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 43 through 47 removed outlier: 3.746A pdb=" N GLY I 44 " --> pdb=" O PHE I 56 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 101 through 104 removed outlier: 3.959A pdb=" N VAL J 103 " --> pdb=" O SER J 168 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N SER J 168 " --> pdb=" O VAL J 103 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 109 through 110 removed outlier: 3.810A pdb=" N ASP J 130 " --> pdb=" O ARG J 110 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 142 through 144 Processing sheet with id=AB1, first strand: chain 'J' and resid 219 through 226 Processing sheet with id=AB2, first strand: chain 'J' and resid 309 through 320 removed outlier: 6.491A pdb=" N GLN J 320 " --> pdb=" O ILE J 373 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N ILE J 373 " --> pdb=" O GLN J 320 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 355 through 356 removed outlier: 3.948A pdb=" N LEU J 355 " --> pdb=" O TYR J 397 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR J 397 " --> pdb=" O LEU J 355 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'K' and resid 181 through 185 removed outlier: 3.513A pdb=" N GLU K 181 " --> pdb=" O ASP K 425 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP K 425 " --> pdb=" O GLU K 181 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU K 183 " --> pdb=" O THR K 423 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N THR K 423 " --> pdb=" O LEU K 183 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VAL K 185 " --> pdb=" O TYR K 421 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N TYR K 421 " --> pdb=" O VAL K 185 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 218 through 219 removed outlier: 3.512A pdb=" N TYR K 256 " --> pdb=" O VAL K 219 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 229 through 231 removed outlier: 3.889A pdb=" N THR K 229 " --> pdb=" O THR K 248 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N ILE K 371 " --> pdb=" O LYS K 278 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N LYS K 278 " --> pdb=" O ILE K 371 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N GLY K 373 " --> pdb=" O PHE K 276 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE K 276 " --> pdb=" O GLY K 373 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLN K 375 " --> pdb=" O SER K 274 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TRP K 331 " --> pdb=" O ALA K 277 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 308 through 311 removed outlier: 6.450A pdb=" N VAL K 300 " --> pdb=" O ILE K 309 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ASP K 311 " --> pdb=" O ASP K 298 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ASP K 298 " --> pdb=" O ASP K 311 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 398 through 400 Processing sheet with id=AB9, first strand: chain 'K' and resid 464 through 465 Processing sheet with id=AC1, first strand: chain 'L' and resid 11 through 17 removed outlier: 6.989A pdb=" N ILE L 38 " --> pdb=" O HIS L 47 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N HIS L 47 " --> pdb=" O ILE L 38 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N ARG L 40 " --> pdb=" O VAL L 45 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VAL L 45 " --> pdb=" O ARG L 40 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 70 through 73 Processing sheet with id=AC3, first strand: chain 'M' and resid 5 through 6 removed outlier: 3.577A pdb=" N THR M 5 " --> pdb=" O LEU M 25 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'M' and resid 84 through 90 removed outlier: 6.991A pdb=" N ILE M 106 " --> pdb=" O THR M 85 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N ILE M 87 " --> pdb=" O LYS M 104 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N LYS M 104 " --> pdb=" O ILE M 87 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'N' and resid 23 through 25 removed outlier: 3.581A pdb=" N GLY N 10 " --> pdb=" O THR N 105 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'N' and resid 35 through 37 removed outlier: 4.183A pdb=" N LEU N 62 " --> pdb=" O PHE N 143 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N THR N 140 " --> pdb=" O LEU N 120 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'N' and resid 43 through 47 Processing sheet with id=AC8, first strand: chain 'O' and resid 103 through 104 removed outlier: 3.977A pdb=" N VAL O 103 " --> pdb=" O TRP O 167 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'O' and resid 142 through 144 removed outlier: 3.695A pdb=" N GLY O 122 " --> pdb=" O GLN O 118 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'O' and resid 219 through 226 removed outlier: 3.692A pdb=" N SER O 221 " --> pdb=" O CYS O 249 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE O 225 " --> pdb=" O ALA O 245 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'O' and resid 282 through 283 Processing sheet with id=AD3, first strand: chain 'O' and resid 309 through 320 removed outlier: 6.729A pdb=" N GLN O 320 " --> pdb=" O ILE O 373 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ILE O 373 " --> pdb=" O GLN O 320 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'P' and resid 195 through 196 removed outlier: 4.244A pdb=" N VAL P 185 " --> pdb=" O LEU P 196 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ASN P 182 " --> pdb=" O ASP P 425 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N ASP P 425 " --> pdb=" O ASN P 182 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA P 184 " --> pdb=" O THR P 423 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU P 419 " --> pdb=" O LYS P 188 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'P' and resid 218 through 219 removed outlier: 7.092A pdb=" N ASP P 298 " --> pdb=" O ASP P 311 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ASP P 311 " --> pdb=" O ASP P 298 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL P 300 " --> pdb=" O ILE P 309 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN P 307 " --> pdb=" O ASP P 302 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'P' and resid 230 through 231 removed outlier: 3.628A pdb=" N LEU P 247 " --> pdb=" O VAL P 369 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL P 369 " --> pdb=" O LEU P 247 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TRP P 372 " --> pdb=" O PHE P 276 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TRP P 331 " --> pdb=" O ALA P 277 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG P 332 " --> pdb=" O ILE P 324 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'P' and resid 272 through 273 Processing sheet with id=AD8, first strand: chain 'P' and resid 318 through 320 removed outlier: 7.173A pdb=" N THR P 336 " --> pdb=" O VAL P 319 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'P' and resid 398 through 402 removed outlier: 6.812A pdb=" N THR P 407 " --> pdb=" O GLN P 401 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'Q' and resid 11 through 17 removed outlier: 3.607A pdb=" N MET Q 33 " --> pdb=" O ASN Q 30 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N MET Q 34 " --> pdb=" O VAL Q 49 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL Q 49 " --> pdb=" O MET Q 34 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ALA Q 36 " --> pdb=" O HIS Q 47 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N HIS Q 47 " --> pdb=" O ALA Q 36 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ILE Q 38 " --> pdb=" O VAL Q 45 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'Q' and resid 70 through 73 Processing sheet with id=AE3, first strand: chain 'R' and resid 5 through 6 Processing sheet with id=AE4, first strand: chain 'R' and resid 84 through 90 removed outlier: 6.949A pdb=" N ILE R 106 " --> pdb=" O THR R 85 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N ILE R 87 " --> pdb=" O LYS R 104 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N LYS R 104 " --> pdb=" O ILE R 87 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'S' and resid 23 through 25 removed outlier: 3.542A pdb=" N ILE S 11 " --> pdb=" O LEU S 25 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLY S 10 " --> pdb=" O THR S 105 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY S 117 " --> pdb=" O THR S 100 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU S 102 " --> pdb=" O SER S 115 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N SER S 115 " --> pdb=" O LEU S 102 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N ALA S 104 " --> pdb=" O VAL S 113 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N VAL S 113 " --> pdb=" O ALA S 104 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N THR S 140 " --> pdb=" O LEU S 120 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'S' and resid 43 through 47 removed outlier: 3.644A pdb=" N GLY S 44 " --> pdb=" O PHE S 56 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'T' and resid 101 through 103 removed outlier: 3.876A pdb=" N VAL T 101 " --> pdb=" O ALA T 170 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA T 170 " --> pdb=" O VAL T 101 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL T 103 " --> pdb=" O SER T 168 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N SER T 168 " --> pdb=" O VAL T 103 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'T' and resid 109 through 110 removed outlier: 3.843A pdb=" N ASP T 130 " --> pdb=" O ARG T 110 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'T' and resid 142 through 144 removed outlier: 3.583A pdb=" N GLY T 122 " --> pdb=" O GLN T 118 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'T' and resid 219 through 226 Processing sheet with id=AF2, first strand: chain 'T' and resid 381 through 382 removed outlier: 6.251A pdb=" N ILE T 309 " --> pdb=" O GLN T 404 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'T' and resid 372 through 378 removed outlier: 5.524A pdb=" N ILE T 373 " --> pdb=" O GLN T 320 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLN T 320 " --> pdb=" O ILE T 373 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG T 413 " --> pdb=" O VAL T 315 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL T 317 " --> pdb=" O ARG T 413 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'T' and resid 355 through 356 removed outlier: 3.799A pdb=" N LEU T 355 " --> pdb=" O TYR T 397 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'U' and resid 181 through 189 removed outlier: 4.161A pdb=" N VAL U 185 " --> pdb=" O LEU U 196 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASP U 189 " --> pdb=" O GLY U 192 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 192 through 196 current: chain 'U' and resid 429 through 430 Processing sheet with id=AF6, first strand: chain 'U' and resid 218 through 219 Processing sheet with id=AF7, first strand: chain 'U' and resid 230 through 232 removed outlier: 3.767A pdb=" N GLU U 231 " --> pdb=" O LYS U 246 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS U 246 " --> pdb=" O GLU U 231 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 245 through 249 current: chain 'U' and resid 331 through 337 No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'U' and resid 308 through 312 removed outlier: 5.960A pdb=" N VAL U 308 " --> pdb=" O ASP U 302 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ASP U 302 " --> pdb=" O VAL U 308 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N SER U 310 " --> pdb=" O VAL U 300 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP U 298 " --> pdb=" O GLN U 312 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'U' and resid 398 through 402 removed outlier: 4.934A pdb=" N LEU U 400 " --> pdb=" O LYS U 409 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N LYS U 409 " --> pdb=" O LEU U 400 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL U 408 " --> pdb=" O PHE U 447 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE U 447 " --> pdb=" O VAL U 408 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'U' and resid 464 through 465 Processing sheet with id=AG2, first strand: chain 'V' and resid 11 through 17 removed outlier: 7.018A pdb=" N MET V 34 " --> pdb=" O VAL V 49 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL V 49 " --> pdb=" O MET V 34 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ALA V 36 " --> pdb=" O HIS V 47 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N HIS V 47 " --> pdb=" O ALA V 36 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ILE V 38 " --> pdb=" O VAL V 45 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'V' and resid 70 through 73 Processing sheet with id=AG4, first strand: chain 'W' and resid 5 through 6 Processing sheet with id=AG5, first strand: chain 'W' and resid 84 through 90 removed outlier: 6.829A pdb=" N ILE W 106 " --> pdb=" O THR W 85 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N ILE W 87 " --> pdb=" O LYS W 104 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N LYS W 104 " --> pdb=" O ILE W 87 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'X' and resid 23 through 25 removed outlier: 3.513A pdb=" N GLY X 10 " --> pdb=" O THR X 105 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N LEU X 114 " --> pdb=" O TYR X 146 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N TYR X 146 " --> pdb=" O LEU X 114 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ASN X 116 " --> pdb=" O GLY X 144 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N THR X 140 " --> pdb=" O LEU X 120 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'X' and resid 43 through 47 Processing sheet with id=AG8, first strand: chain 'Y' and resid 101 through 104 removed outlier: 3.886A pdb=" N VAL Y 101 " --> pdb=" O ALA Y 170 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA Y 170 " --> pdb=" O VAL Y 101 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N VAL Y 103 " --> pdb=" O SER Y 168 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N SER Y 168 " --> pdb=" O VAL Y 103 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG8 Processing sheet with id=AG9, first strand: chain 'Y' and resid 142 through 144 removed outlier: 6.324A pdb=" N SER Y 115 " --> pdb=" O ILE Y 160 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU Y 158 " --> pdb=" O VAL Y 117 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'Y' and resid 219 through 225 removed outlier: 6.687A pdb=" N CYS Y 249 " --> pdb=" O THR Y 220 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N VAL Y 222 " --> pdb=" O TRP Y 247 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N TRP Y 247 " --> pdb=" O VAL Y 222 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N VAL Y 224 " --> pdb=" O ALA Y 245 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ALA Y 245 " --> pdb=" O VAL Y 224 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'Y' and resid 282 through 283 Processing sheet with id=AH3, first strand: chain 'Y' and resid 309 through 319 Processing sheet with id=AH4, first strand: chain 'Y' and resid 355 through 356 Processing sheet with id=AH5, first strand: chain 'Z' and resid 181 through 188 removed outlier: 4.361A pdb=" N VAL Z 185 " --> pdb=" O LEU Z 196 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Z' and resid 195 through 196 current: chain 'Z' and resid 429 through 430 Processing sheet with id=AH6, first strand: chain 'Z' and resid 201 through 203 removed outlier: 3.549A pdb=" N ARG Z 201 " --> pdb=" O ILE Z 395 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE Z 395 " --> pdb=" O ARG Z 201 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN Z 203 " --> pdb=" O VAL Z 393 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL Z 393 " --> pdb=" O ASN Z 203 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH6 Processing sheet with id=AH7, first strand: chain 'Z' and resid 218 through 219 removed outlier: 3.822A pdb=" N ALA Z 350 " --> pdb=" O ALA Z 286 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA Z 299 " --> pdb=" O ILE Z 287 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ASP Z 298 " --> pdb=" O ASP Z 311 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ASP Z 311 " --> pdb=" O ASP Z 298 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N VAL Z 300 " --> pdb=" O ILE Z 309 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'Z' and resid 229 through 232 removed outlier: 4.150A pdb=" N THR Z 229 " --> pdb=" O THR Z 248 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR Z 248 " --> pdb=" O THR Z 229 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU Z 247 " --> pdb=" O VAL Z 369 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL Z 369 " --> pdb=" O LEU Z 247 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'Z' and resid 271 through 278 WARNING: can't find start of bonding for strands! previous: chain 'Z' and resid 271 through 278 current: chain 'Z' and resid 330 through 337 No H-bonds generated for sheet with id=AH9 Processing sheet with id=AI1, first strand: chain 'Z' and resid 398 through 402 removed outlier: 5.771A pdb=" N LEU Z 400 " --> pdb=" O LYS Z 409 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LYS Z 409 " --> pdb=" O LEU Z 400 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL Z 408 " --> pdb=" O PHE Z 447 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'a' and resid 11 through 18 removed outlier: 7.005A pdb=" N MET a 34 " --> pdb=" O VAL a 49 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL a 49 " --> pdb=" O MET a 34 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ALA a 36 " --> pdb=" O HIS a 47 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N HIS a 47 " --> pdb=" O ALA a 36 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ILE a 38 " --> pdb=" O VAL a 45 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'a' and resid 70 through 73 removed outlier: 3.512A pdb=" N VAL a 72 " --> pdb=" O PHE a 89 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'b' and resid 5 through 6 Processing sheet with id=AI5, first strand: chain 'b' and resid 84 through 90 removed outlier: 3.591A pdb=" N GLY b 86 " --> pdb=" O ILE b 106 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LYS b 104 " --> pdb=" O GLU b 88 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'c' and resid 23 through 25 removed outlier: 7.422A pdb=" N LEU c 114 " --> pdb=" O TYR c 146 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N TYR c 146 " --> pdb=" O LEU c 114 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ASN c 116 " --> pdb=" O GLY c 144 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N THR c 140 " --> pdb=" O LEU c 120 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'c' and resid 43 through 46 Processing sheet with id=AI8, first strand: chain 'd' and resid 7 through 8 Processing sheet with id=AI9, first strand: chain 'd' and resid 102 through 104 removed outlier: 3.765A pdb=" N VAL d 103 " --> pdb=" O TRP d 167 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'd' and resid 142 through 144 Processing sheet with id=AJ2, first strand: chain 'd' and resid 219 through 226 removed outlier: 3.516A pdb=" N SER d 221 " --> pdb=" O CYS d 249 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'd' and resid 282 through 283 Processing sheet with id=AJ4, first strand: chain 'd' and resid 381 through 382 removed outlier: 5.968A pdb=" N ILE d 309 " --> pdb=" O GLN d 404 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N THR d 406 " --> pdb=" O ILE d 309 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N TYR d 311 " --> pdb=" O THR d 406 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'd' and resid 372 through 378 removed outlier: 5.785A pdb=" N ILE d 373 " --> pdb=" O GLN d 320 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N GLN d 320 " --> pdb=" O ILE d 373 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL d 315 " --> pdb=" O ARG d 413 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N THR d 415 " --> pdb=" O VAL d 315 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N VAL d 317 " --> pdb=" O THR d 415 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'd' and resid 355 through 356 removed outlier: 3.912A pdb=" N LEU d 355 " --> pdb=" O TYR d 397 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'e' and resid 181 through 189 removed outlier: 3.848A pdb=" N ASP e 189 " --> pdb=" O GLY e 192 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'e' and resid 192 through 195 current: chain 'e' and resid 429 through 430 Processing sheet with id=AJ8, first strand: chain 'e' and resid 218 through 219 removed outlier: 3.561A pdb=" N TYR e 256 " --> pdb=" O VAL e 219 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'e' and resid 230 through 231 WARNING: can't find start of bonding for strands! previous: chain 'e' and resid 245 through 248 current: chain 'e' and resid 330 through 337 Processing sheet with id=AK1, first strand: chain 'e' and resid 308 through 311 removed outlier: 6.090A pdb=" N VAL e 308 " --> pdb=" O ASP e 302 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ASP e 302 " --> pdb=" O VAL e 308 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER e 310 " --> pdb=" O VAL e 300 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N PHE e 284 " --> pdb=" O ALA e 352 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'e' and resid 398 through 400 removed outlier: 3.678A pdb=" N VAL e 399 " --> pdb=" O LYS e 409 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'e' and resid 464 through 465 Processing sheet with id=AK4, first strand: chain 'f' and resid 11 through 17 removed outlier: 7.000A pdb=" N ILE f 38 " --> pdb=" O HIS f 47 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N HIS f 47 " --> pdb=" O ILE f 38 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N ARG f 40 " --> pdb=" O VAL f 45 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL f 45 " --> pdb=" O ARG f 40 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'f' and resid 70 through 73 Processing sheet with id=AK6, first strand: chain 'g' and resid 5 through 6 removed outlier: 3.802A pdb=" N THR g 5 " --> pdb=" O LEU g 25 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'g' and resid 84 through 90 removed outlier: 7.090A pdb=" N ILE g 106 " --> pdb=" O THR g 85 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N ILE g 87 " --> pdb=" O LYS g 104 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N LYS g 104 " --> pdb=" O ILE g 87 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'h' and resid 23 through 25 removed outlier: 3.523A pdb=" N ILE h 11 " --> pdb=" O LEU h 25 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY h 10 " --> pdb=" O THR h 105 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N ASN h 116 " --> pdb=" O GLY h 144 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR h 140 " --> pdb=" O LEU h 120 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'h' and resid 43 through 47 removed outlier: 3.657A pdb=" N GLY h 44 " --> pdb=" O PHE h 56 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'i' and resid 101 through 104 removed outlier: 4.021A pdb=" N VAL i 101 " --> pdb=" O ALA i 170 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N VAL i 103 " --> pdb=" O SER i 168 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N SER i 168 " --> pdb=" O VAL i 103 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'i' and resid 142 through 144 removed outlier: 3.789A pdb=" N GLY i 122 " --> pdb=" O GLN i 118 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'i' and resid 219 through 226 removed outlier: 4.143A pdb=" N SER i 221 " --> pdb=" O CYS i 249 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'i' and resid 282 through 283 Processing sheet with id=AL5, first strand: chain 'i' and resid 309 through 320 removed outlier: 3.768A pdb=" N VAL i 381 " --> pdb=" O ASP i 312 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLN i 320 " --> pdb=" O ILE i 373 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N ILE i 373 " --> pdb=" O GLN i 320 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'i' and resid 355 through 356 removed outlier: 3.552A pdb=" N LEU i 355 " --> pdb=" O TYR i 397 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'j' and resid 181 through 188 removed outlier: 4.138A pdb=" N VAL j 185 " --> pdb=" O LEU j 196 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'j' and resid 195 through 196 current: chain 'j' and resid 429 through 430 Processing sheet with id=AL8, first strand: chain 'j' and resid 218 through 219 removed outlier: 3.513A pdb=" N VAL j 349 " --> pdb=" O VAL j 257 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N PHE j 284 " --> pdb=" O ALA j 352 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE j 285 " --> pdb=" O PHE j 301 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ASP j 298 " --> pdb=" O ASP j 311 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ASP j 311 " --> pdb=" O ASP j 298 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL j 300 " --> pdb=" O ILE j 309 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'j' and resid 229 through 232 removed outlier: 3.908A pdb=" N THR j 229 " --> pdb=" O THR j 248 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR j 248 " --> pdb=" O THR j 229 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU j 247 " --> pdb=" O VAL j 369 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL j 369 " --> pdb=" O LEU j 247 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE j 367 " --> pdb=" O LYS j 249 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ILE j 371 " --> pdb=" O LYS j 278 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N LYS j 278 " --> pdb=" O ILE j 371 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N GLY j 373 " --> pdb=" O PHE j 276 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N PHE j 276 " --> pdb=" O GLY j 373 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLN j 375 " --> pdb=" O SER j 274 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU j 335 " --> pdb=" O PHE j 273 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA j 277 " --> pdb=" O TRP j 331 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TRP j 331 " --> pdb=" O ALA j 277 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG j 332 " --> pdb=" O ILE j 324 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE j 324 " --> pdb=" O ARG j 332 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL j 334 " --> pdb=" O ARG j 322 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG j 322 " --> pdb=" O VAL j 334 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N SER j 320 " --> pdb=" O THR j 336 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'j' and resid 398 through 402 removed outlier: 4.976A pdb=" N LEU j 400 " --> pdb=" O LYS j 409 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LYS j 409 " --> pdb=" O LEU j 400 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASN j 402 " --> pdb=" O THR j 407 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'j' and resid 464 through 466 Processing sheet with id=AM3, first strand: chain 'A' and resid 15 through 18 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 15 through 18 current: chain 'A' and resid 53 through 59 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 53 through 59 current: chain 'A' and resid 98 through 106 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 98 through 106 current: chain 'B' and resid 52 through 59 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 52 through 59 current: chain 'B' and resid 98 through 111 removed outlier: 6.541A pdb=" N THR B 124 " --> pdb=" O THR B 105 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLU B 107 " --> pdb=" O ARG B 122 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ARG B 122 " --> pdb=" O GLU B 107 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N LEU B 109 " --> pdb=" O PRO B 120 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 119 through 127 current: chain 'C' and resid 23 through 24 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 23 through 24 current: chain 'C' and resid 52 through 59 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 52 through 59 current: chain 'C' and resid 98 through 111 removed outlier: 6.861A pdb=" N THR C 124 " --> pdb=" O THR C 105 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLU C 107 " --> pdb=" O ARG C 122 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ARG C 122 " --> pdb=" O GLU C 107 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N LEU C 109 " --> pdb=" O PRO C 120 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 119 through 127 current: chain 'D' and resid 24 through 25 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 24 through 25 current: chain 'D' and resid 76 through 83 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 76 through 83 current: chain 'D' and resid 111 through 125 removed outlier: 5.788A pdb=" N SER D 125 " --> pdb=" O ALA D 131 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ALA D 131 " --> pdb=" O SER D 125 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 128 through 134 current: chain 'k' and resid 24 through 25 WARNING: can't find start of bonding for strands! previous: chain 'k' and resid 24 through 25 current: chain 'k' and resid 76 through 83 WARNING: can't find start of bonding for strands! previous: chain 'k' and resid 76 through 83 current: chain 'k' and resid 111 through 124 WARNING: can't find start of bonding for strands! previous: chain 'k' and resid 132 through 134 current: chain 'o' and resid 76 through 83 WARNING: can't find start of bonding for strands! previous: chain 'o' and resid 76 through 83 current: chain 'o' and resid 128 through 139 Processing sheet with id=AM4, first strand: chain 'D' and resid 40 through 42 removed outlier: 3.579A pdb=" N ILE D 71 " --> pdb=" O SER D 41 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'E' and resid 3 through 12 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 15 through 19 current: chain 'E' and resid 39 through 45 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 39 through 45 current: chain 'E' and resid 90 through 91 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 90 through 91 current: chain 'E' and resid 114 through 120 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 114 through 120 current: chain 'E' and resid 231 through 235 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 231 through 235 current: chain 'E' and resid 259 through 271 removed outlier: 6.944A pdb=" N MET E 282 " --> pdb=" O THR E 264 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LEU E 266 " --> pdb=" O LYS E 280 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LYS E 280 " --> pdb=" O LEU E 266 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N TYR E 268 " --> pdb=" O TYR E 278 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N TYR E 278 " --> pdb=" O TYR E 268 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'E' and resid 137 through 139 Processing sheet with id=AM7, first strand: chain 'E' and resid 154 through 158 removed outlier: 3.611A pdb=" N ASP E 204 " --> pdb=" O ASP E 158 " (cutoff:3.500A) Processing sheet with id=AM8, first strand: chain 'F' and resid 71 through 75 removed outlier: 4.016A pdb=" N ASP F 73 " --> pdb=" O ALA F 50 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N ALA F 50 " --> pdb=" O ASP F 73 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ILE F 49 " --> pdb=" O TYR F 43 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N TYR F 43 " --> pdb=" O ILE F 49 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N THR F 51 " --> pdb=" O VAL F 41 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE F 36 " --> pdb=" O ILE F 98 " (cutoff:3.500A) Processing sheet with id=AM9, first strand: chain 'F' and resid 58 through 59 Processing sheet with id=AN1, first strand: chain 'F' and resid 84 through 87 removed outlier: 3.759A pdb=" N ILE n 166 " --> pdb=" O ASN F 173 " (cutoff:3.500A) Processing sheet with id=AN2, first strand: chain 'F' and resid 149 through 152 Processing sheet with id=AN3, first strand: chain 'F' and resid 158 through 161 removed outlier: 6.491A pdb=" N ILE F 166 " --> pdb=" O THR p 175 " (cutoff:3.500A) Processing sheet with id=AN4, first strand: chain 'F' and resid 187 through 188 removed outlier: 6.309A pdb=" N VAL F 187 " --> pdb=" O VAL p 194 " (cutoff:3.500A) Processing sheet with id=AN5, first strand: chain 'F' and resid 198 through 199 Processing sheet with id=AN6, first strand: chain 'k' and resid 40 through 42 removed outlier: 3.591A pdb=" N ILE k 71 " --> pdb=" O SER k 41 " (cutoff:3.500A) Processing sheet with id=AN7, first strand: chain 'l' and resid 3 through 11 WARNING: can't find start of bonding for strands! previous: chain 'l' and resid 16 through 19 current: chain 'l' and resid 39 through 45 WARNING: can't find start of bonding for strands! previous: chain 'l' and resid 39 through 45 current: chain 'l' and resid 90 through 91 WARNING: can't find start of bonding for strands! previous: chain 'l' and resid 90 through 91 current: chain 'l' and resid 114 through 120 WARNING: can't find start of bonding for strands! previous: chain 'l' and resid 114 through 120 current: chain 'l' and resid 231 through 235 WARNING: can't find start of bonding for strands! previous: chain 'l' and resid 231 through 235 current: chain 'l' and resid 259 through 271 removed outlier: 6.851A pdb=" N MET l 282 " --> pdb=" O THR l 264 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LEU l 266 " --> pdb=" O LYS l 280 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LYS l 280 " --> pdb=" O LEU l 266 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N TYR l 268 " --> pdb=" O TYR l 278 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N TYR l 278 " --> pdb=" O TYR l 268 " (cutoff:3.500A) Processing sheet with id=AN8, first strand: chain 'l' and resid 137 through 139 Processing sheet with id=AN9, first strand: chain 'l' and resid 154 through 158 removed outlier: 3.680A pdb=" N ASP l 204 " --> pdb=" O ASP l 158 " (cutoff:3.500A) Processing sheet with id=AO1, first strand: chain 'm' and resid 3 through 12 WARNING: can't find start of bonding for strands! previous: chain 'm' and resid 15 through 19 current: chain 'm' and resid 39 through 45 WARNING: can't find start of bonding for strands! previous: chain 'm' and resid 39 through 45 current: chain 'm' and resid 90 through 91 WARNING: can't find start of bonding for strands! previous: chain 'm' and resid 90 through 91 current: chain 'm' and resid 114 through 120 WARNING: can't find start of bonding for strands! previous: chain 'm' and resid 114 through 120 current: chain 'm' and resid 231 through 235 WARNING: can't find start of bonding for strands! previous: chain 'm' and resid 231 through 235 current: chain 'm' and resid 259 through 271 removed outlier: 6.941A pdb=" N MET m 282 " --> pdb=" O THR m 264 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LEU m 266 " --> pdb=" O LYS m 280 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LYS m 280 " --> pdb=" O LEU m 266 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N TYR m 268 " --> pdb=" O TYR m 278 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N TYR m 278 " --> pdb=" O TYR m 268 " (cutoff:3.500A) Processing sheet with id=AO2, first strand: chain 'm' and resid 137 through 139 Processing sheet with id=AO3, first strand: chain 'm' and resid 154 through 158 removed outlier: 3.593A pdb=" N ASP m 204 " --> pdb=" O ASP m 158 " (cutoff:3.500A) Processing sheet with id=AO4, first strand: chain 'n' and resid 71 through 75 removed outlier: 4.043A pdb=" N ASP n 73 " --> pdb=" O ALA n 50 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N ALA n 50 " --> pdb=" O ASP n 73 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N ILE n 49 " --> pdb=" O TYR n 43 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N TYR n 43 " --> pdb=" O ILE n 49 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N THR n 51 " --> pdb=" O VAL n 41 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE n 36 " --> pdb=" O ILE n 98 " (cutoff:3.500A) Processing sheet with id=AO5, first strand: chain 'n' and resid 58 through 59 Processing sheet with id=AO6, first strand: chain 'n' and resid 86 through 87 removed outlier: 3.675A pdb=" N ILE p 166 " --> pdb=" O ASN n 173 " (cutoff:3.500A) Processing sheet with id=AO7, first strand: chain 'n' and resid 198 through 199 removed outlier: 6.622A pdb=" N VAL n 194 " --> pdb=" O ILE p 189 " (cutoff:3.500A) Processing sheet with id=AO8, first strand: chain 'o' and resid 24 through 25 removed outlier: 4.671A pdb=" N ILE o 16 " --> pdb=" O VAL o 25 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ILE o 105 " --> pdb=" O ASP o 113 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N ASP o 113 " --> pdb=" O ILE o 105 " (cutoff:3.500A) Processing sheet with id=AO9, first strand: chain 'o' and resid 40 through 42 removed outlier: 3.686A pdb=" N ILE o 71 " --> pdb=" O SER o 41 " (cutoff:3.500A) Processing sheet with id=AP1, first strand: chain 'p' and resid 71 through 75 removed outlier: 5.512A pdb=" N VAL p 72 " --> pdb=" O ILE p 52 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE p 52 " --> pdb=" O VAL p 72 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N ILE p 49 " --> pdb=" O TYR p 43 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N TYR p 43 " --> pdb=" O ILE p 49 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N THR p 51 " --> pdb=" O VAL p 41 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE p 36 " --> pdb=" O ILE p 98 " (cutoff:3.500A) Processing sheet with id=AP2, first strand: chain 'p' and resid 58 through 59 Processing sheet with id=AP3, first strand: chain 'q' and resid 96 through 104 WARNING: can't find start of bonding for strands! previous: chain 'q' and resid 96 through 104 current: chain 'q' and resid 138 through 144 No H-bonds generated for sheet with id=AP3 Processing sheet with id=AP4, first strand: chain 'q' and resid 108 through 110 removed outlier: 4.169A pdb=" N GLN q 108 " --> pdb=" O THR q 132 " (cutoff:3.500A) Processing sheet with id=AP5, first strand: chain 'q' and resid 116 through 117 Processing sheet with id=AP6, first strand: chain 'q' and resid 222 through 226 removed outlier: 3.696A pdb=" N ILE q 225 " --> pdb=" O TRP q 247 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N TRP q 247 " --> pdb=" O ILE q 225 " (cutoff:3.500A) Processing sheet with id=AP7, first strand: chain 'q' and resid 309 through 319 Processing sheet with id=AP8, first strand: chain 'r' and resid 96 through 104 WARNING: can't find start of bonding for strands! previous: chain 'r' and resid 96 through 104 current: chain 'r' and resid 138 through 144 No H-bonds generated for sheet with id=AP8 Processing sheet with id=AP9, first strand: chain 'r' and resid 108 through 110 removed outlier: 4.081A pdb=" N GLN r 108 " --> pdb=" O THR r 132 " (cutoff:3.500A) Processing sheet with id=AQ1, first strand: chain 'r' and resid 116 through 117 Processing sheet with id=AQ2, first strand: chain 'r' and resid 222 through 226 removed outlier: 3.782A pdb=" N ILE r 225 " --> pdb=" O TRP r 247 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N TRP r 247 " --> pdb=" O ILE r 225 " (cutoff:3.500A) Processing sheet with id=AQ3, first strand: chain 'r' and resid 309 through 319 Processing sheet with id=AQ4, first strand: chain 's' and resid 96 through 104 WARNING: can't find start of bonding for strands! previous: chain 's' and resid 96 through 104 current: chain 's' and resid 138 through 144 No H-bonds generated for sheet with id=AQ4 Processing sheet with id=AQ5, first strand: chain 's' and resid 108 through 110 removed outlier: 4.152A pdb=" N GLN s 108 " --> pdb=" O THR s 132 " (cutoff:3.500A) Processing sheet with id=AQ6, first strand: chain 's' and resid 116 through 117 Processing sheet with id=AQ7, first strand: chain 's' and resid 222 through 226 removed outlier: 3.762A pdb=" N ILE s 225 " --> pdb=" O TRP s 247 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N TRP s 247 " --> pdb=" O ILE s 225 " (cutoff:3.500A) Processing sheet with id=AQ8, first strand: chain 's' and resid 309 through 319 Processing sheet with id=AQ9, first strand: chain 't' and resid 137 through 138 removed outlier: 3.985A pdb=" N VAL t 138 " --> pdb=" O GLN t 102 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL t 101 " --> pdb=" O ALA t 170 " (cutoff:3.500A) Processing sheet with id=AR1, first strand: chain 't' and resid 124 through 126 removed outlier: 3.617A pdb=" N ILE t 143 " --> pdb=" O PHE t 125 " (cutoff:3.500A) Processing sheet with id=AR2, first strand: chain 't' and resid 219 through 221 removed outlier: 3.538A pdb=" N SER t 221 " --> pdb=" O CYS t 249 " (cutoff:3.500A) Processing sheet with id=AR3, first strand: chain 't' and resid 224 through 226 Processing sheet with id=AR4, first strand: chain 't' and resid 282 through 283 removed outlier: 4.304A pdb=" N VAL t 282 " --> pdb=" O THR t 307 " (cutoff:3.500A) Processing sheet with id=AR5, first strand: chain 't' and resid 373 through 378 removed outlier: 3.719A pdb=" N ASN t 316 " --> pdb=" O GLN t 377 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL t 317 " --> pdb=" O ARG t 413 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR t 415 " --> pdb=" O VAL t 317 " (cutoff:3.500A) Processing sheet with id=AR6, first strand: chain 'u' and resid 97 through 98 removed outlier: 4.353A pdb=" N GLY u 98 " --> pdb=" O THR u 176 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR u 176 " --> pdb=" O GLY u 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AR6 Processing sheet with id=AR7, first strand: chain 'u' and resid 137 through 138 removed outlier: 3.950A pdb=" N VAL u 138 " --> pdb=" O GLN u 102 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL u 101 " --> pdb=" O ALA u 170 " (cutoff:3.500A) Processing sheet with id=AR8, first strand: chain 'u' and resid 109 through 110 removed outlier: 3.848A pdb=" N ASP u 130 " --> pdb=" O ARG u 110 " (cutoff:3.500A) Processing sheet with id=AR9, first strand: chain 'u' and resid 124 through 126 Processing sheet with id=AS1, first strand: chain 'u' and resid 219 through 221 Processing sheet with id=AS2, first strand: chain 'u' and resid 224 through 226 Processing sheet with id=AS3, first strand: chain 'u' and resid 282 through 283 removed outlier: 3.717A pdb=" N VAL u 282 " --> pdb=" O THR u 307 " (cutoff:3.500A) Processing sheet with id=AS4, first strand: chain 'u' and resid 373 through 379 removed outlier: 3.636A pdb=" N ASN u 316 " --> pdb=" O GLN u 377 " (cutoff:3.500A) Processing sheet with id=AS5, first strand: chain 'u' and resid 355 through 356 Processing sheet with id=AS6, first strand: chain 'v' and resid 137 through 138 removed outlier: 3.806A pdb=" N VAL v 138 " --> pdb=" O GLN v 102 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL v 101 " --> pdb=" O ALA v 170 " (cutoff:3.500A) Processing sheet with id=AS7, first strand: chain 'v' and resid 109 through 110 removed outlier: 3.679A pdb=" N ASP v 130 " --> pdb=" O ARG v 110 " (cutoff:3.500A) Processing sheet with id=AS8, first strand: chain 'v' and resid 124 through 126 removed outlier: 3.775A pdb=" N ILE v 143 " --> pdb=" O PHE v 125 " (cutoff:3.500A) Processing sheet with id=AS9, first strand: chain 'v' and resid 219 through 221 Processing sheet with id=AT1, first strand: chain 'v' and resid 224 through 226 Processing sheet with id=AT2, first strand: chain 'v' and resid 282 through 283 removed outlier: 4.232A pdb=" N VAL v 282 " --> pdb=" O THR v 307 " (cutoff:3.500A) Processing sheet with id=AT3, first strand: chain 'v' and resid 373 through 379 removed outlier: 3.616A pdb=" N ASN v 316 " --> pdb=" O GLN v 377 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL v 315 " --> pdb=" O ARG v 413 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N THR v 415 " --> pdb=" O VAL v 315 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL v 317 " --> pdb=" O THR v 415 " (cutoff:3.500A) 2495 hydrogen bonds defined for protein. 6975 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: 39.56 Time building geometry restraints manager: 30.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.06 - 1.45: 42529 1.45 - 1.84: 55077 1.84 - 2.23: 5 2.23 - 2.62: 2 2.62 - 3.01: 1 Bond restraints: 97614 Sorted by residual: bond pdb=" CG MET o 1 " pdb=" SD MET o 1 " ideal model delta sigma weight residual 1.803 3.007 -1.204 2.50e-02 1.60e+03 2.32e+03 bond pdb=" CD2 TYR X 49 " pdb=" CE2 TYR X 49 " ideal model delta sigma weight residual 1.382 2.398 -1.016 3.00e-02 1.11e+03 1.15e+03 bond pdb=" CD1 TYR X 49 " pdb=" CE1 TYR X 49 " ideal model delta sigma weight residual 1.382 2.265 -0.883 3.00e-02 1.11e+03 8.65e+02 bond pdb=" CD1 TYR N 146 " pdb=" CE1 TYR N 146 " ideal model delta sigma weight residual 1.382 2.048 -0.666 3.00e-02 1.11e+03 4.93e+02 bond pdb=" CE2 TYR X 49 " pdb=" CZ TYR X 49 " ideal model delta sigma weight residual 1.378 1.910 -0.532 2.40e-02 1.74e+03 4.92e+02 ... (remaining 97609 not shown) Histogram of bond angle deviations from ideal: 75.34 - 91.65: 4 91.65 - 107.96: 4295 107.96 - 124.27: 126618 124.27 - 140.59: 2169 140.59 - 156.90: 3 Bond angle restraints: 133089 Sorted by residual: angle pdb=" C SER A 32 " pdb=" N ARG A 33 " pdb=" CA ARG A 33 " ideal model delta sigma weight residual 122.29 156.90 -34.61 1.65e+00 3.67e-01 4.40e+02 angle pdb=" N PRO e 221 " pdb=" CD PRO e 221 " pdb=" CG PRO e 221 " ideal model delta sigma weight residual 103.20 75.34 27.86 1.50e+00 4.44e-01 3.45e+02 angle pdb=" N PRO Z 413 " pdb=" CD PRO Z 413 " pdb=" CG PRO Z 413 " ideal model delta sigma weight residual 103.20 82.45 20.75 1.50e+00 4.44e-01 1.91e+02 angle pdb=" CG MET o 1 " pdb=" SD MET o 1 " pdb=" CE MET o 1 " ideal model delta sigma weight residual 100.90 128.77 -27.87 2.20e+00 2.07e-01 1.61e+02 angle pdb=" CB PRO e 221 " pdb=" CG PRO e 221 " pdb=" CD PRO e 221 " ideal model delta sigma weight residual 106.10 146.13 -40.03 3.20e+00 9.77e-02 1.56e+02 ... (remaining 133084 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 52678 17.98 - 35.95: 4436 35.95 - 53.93: 740 53.93 - 71.90: 125 71.90 - 89.88: 74 Dihedral angle restraints: 58053 sinusoidal: 21786 harmonic: 36267 Sorted by residual: dihedral pdb=" CA ARG G 65 " pdb=" C ARG G 65 " pdb=" N PRO G 66 " pdb=" CA PRO G 66 " ideal model delta harmonic sigma weight residual 180.00 132.10 47.90 0 5.00e+00 4.00e-02 9.18e+01 dihedral pdb=" CA ARG Q 65 " pdb=" C ARG Q 65 " pdb=" N PRO Q 66 " pdb=" CA PRO Q 66 " ideal model delta harmonic sigma weight residual 180.00 132.51 47.49 0 5.00e+00 4.00e-02 9.02e+01 dihedral pdb=" CA ARG a 65 " pdb=" C ARG a 65 " pdb=" N PRO a 66 " pdb=" CA PRO a 66 " ideal model delta harmonic sigma weight residual 180.00 133.72 46.28 0 5.00e+00 4.00e-02 8.57e+01 ... (remaining 58050 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 11434 0.050 - 0.099: 2898 0.099 - 0.149: 942 0.149 - 0.199: 67 0.199 - 0.249: 4 Chirality restraints: 15345 Sorted by residual: chirality pdb=" CB VAL E 257 " pdb=" CA VAL E 257 " pdb=" CG1 VAL E 257 " pdb=" CG2 VAL E 257 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CA ARG A 33 " pdb=" N ARG A 33 " pdb=" C ARG A 33 " pdb=" CB ARG A 33 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA GLU Y 25 " pdb=" N GLU Y 25 " pdb=" C GLU Y 25 " pdb=" CB GLU Y 25 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 15342 not shown) Planarity restraints: 17451 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN Z 412 " -0.089 5.00e-02 4.00e+02 1.19e-01 2.28e+01 pdb=" N PRO Z 413 " 0.206 5.00e-02 4.00e+02 pdb=" CA PRO Z 413 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO Z 413 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR X 49 " -0.037 2.00e-02 2.50e+03 2.85e-02 1.62e+01 pdb=" CG TYR X 49 " 0.003 2.00e-02 2.50e+03 pdb=" CD1 TYR X 49 " 0.058 2.00e-02 2.50e+03 pdb=" CD2 TYR X 49 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR X 49 " -0.027 2.00e-02 2.50e+03 pdb=" CE2 TYR X 49 " 0.024 2.00e-02 2.50e+03 pdb=" CZ TYR X 49 " -0.019 2.00e-02 2.50e+03 pdb=" OH TYR X 49 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG v 55 " 0.329 9.50e-02 1.11e+02 1.48e-01 1.37e+01 pdb=" NE ARG v 55 " -0.023 2.00e-02 2.50e+03 pdb=" CZ ARG v 55 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG v 55 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG v 55 " 0.008 2.00e-02 2.50e+03 ... (remaining 17448 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 409 2.43 - 3.05: 61821 3.05 - 3.66: 139782 3.66 - 4.28: 197855 4.28 - 4.90: 334276 Nonbonded interactions: 734143 Sorted by model distance: nonbonded pdb=" CE2 TYR X 49 " pdb=" N ARG A 33 " model vdw 1.812 3.420 nonbonded pdb=" CD2 TYR X 49 " pdb=" N ARG A 33 " model vdw 1.916 3.420 nonbonded pdb=" CZ TYR X 49 " pdb=" N ARG A 33 " model vdw 1.956 3.340 nonbonded pdb=" OE1 GLU Y 51 " pdb=" NH1 ARG v 55 " model vdw 1.987 2.520 nonbonded pdb=" OH TYR V 60 " pdb=" OD1 ASP t 80 " model vdw 1.993 2.440 ... (remaining 734138 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'k' selection = chain 'o' } ncs_group { reference = chain 'E' selection = chain 'l' selection = chain 'm' } ncs_group { reference = chain 'F' selection = chain 'n' selection = chain 'p' } ncs_group { reference = chain 'G' selection = chain 'L' selection = chain 'Q' selection = chain 'V' selection = chain 'a' selection = chain 'f' } ncs_group { reference = chain 'H' selection = chain 'M' selection = chain 'R' selection = chain 'W' selection = chain 'b' selection = chain 'g' } ncs_group { reference = chain 'I' selection = chain 'N' selection = chain 'S' selection = chain 'X' selection = chain 'c' selection = chain 'h' } ncs_group { reference = (chain 'J' and resid 14 through 417) selection = (chain 'O' and resid 14 through 417) selection = (chain 'T' and resid 14 through 417) selection = (chain 'Y' and resid 14 through 417) selection = (chain 'd' and resid 14 through 417) selection = (chain 'i' and resid 14 through 417) selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' } ncs_group { reference = chain 'K' selection = chain 'P' selection = chain 'U' selection = chain 'Z' selection = chain 'e' selection = chain 'j' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 16.820 Check model and map are aligned: 1.060 Set scattering table: 0.630 Process input model: 190.900 Find NCS groups from input model: 6.210 Set up NCS constraints: 0.880 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:2.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 223.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 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 : 0.009 1.204 97614 Z= 0.572 Angle : 0.764 40.032 133089 Z= 0.418 Chirality : 0.049 0.249 15345 Planarity : 0.006 0.148 17451 Dihedral : 13.952 89.879 34833 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.36 % Allowed : 10.12 % Favored : 89.52 % Rotamer: Outliers : 0.02 % Allowed : 0.46 % Favored : 99.52 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 3.18 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.07), residues: 12609 helix: 0.40 (0.11), residues: 2334 sheet: -0.42 (0.10), residues: 2766 loop : -2.12 (0.07), residues: 7509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP U 358 HIS 0.010 0.001 HIS Z 52 PHE 0.029 0.002 PHE Y 78 TYR 0.058 0.002 TYR X 49 ARG 0.011 0.001 ARG v 55 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25218 Ramachandran restraints generated. 12609 Oldfield, 0 Emsley, 12609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25218 Ramachandran restraints generated. 12609 Oldfield, 0 Emsley, 12609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1076 residues out of total 10284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1074 time to evaluate : 7.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 96 THR cc_start: 0.5891 (p) cc_final: 0.5644 (p) REVERT: O 128 MET cc_start: 0.4453 (mmm) cc_final: 0.4101 (mmm) REVERT: O 180 PRO cc_start: 0.4954 (Cg_endo) cc_final: 0.4562 (Cg_exo) REVERT: O 412 VAL cc_start: 0.5053 (t) cc_final: 0.4777 (p) REVERT: O 413 ARG cc_start: 0.4551 (mmm160) cc_final: 0.4120 (mmp-170) REVERT: U 459 THR cc_start: 0.7825 (m) cc_final: 0.7623 (m) REVERT: U 497 CYS cc_start: 0.5900 (m) cc_final: 0.5600 (m) REVERT: Y 85 LEU cc_start: 0.8440 (mt) cc_final: 0.7866 (mp) REVERT: Y 128 MET cc_start: 0.4995 (mmm) cc_final: 0.3987 (tpt) REVERT: c 46 GLU cc_start: 0.7022 (mm-30) cc_final: 0.6752 (mm-30) REVERT: c 111 ARG cc_start: 0.6679 (mtt180) cc_final: 0.6352 (mtm-85) REVERT: c 133 ARG cc_start: 0.6614 (mmt-90) cc_final: 0.6390 (tpp-160) REVERT: i 143 ILE cc_start: 0.7312 (tt) cc_final: 0.6981 (tp) REVERT: j 312 GLN cc_start: 0.5190 (tm-30) cc_final: 0.4709 (tp40) REVERT: A 146 MET cc_start: 0.7824 (tmm) cc_final: 0.7539 (tmm) REVERT: E 161 TYR cc_start: 0.7834 (m-10) cc_final: 0.7507 (m-10) REVERT: s 88 ILE cc_start: 0.7308 (pt) cc_final: 0.7096 (pt) REVERT: v 192 ASN cc_start: 0.6444 (p0) cc_final: 0.6222 (p0) outliers start: 2 outliers final: 1 residues processed: 1076 average time/residue: 0.8380 time to fit residues: 1562.5249 Evaluate side-chains 875 residues out of total 10284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 874 time to evaluate : 7.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 150 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1251 random chunks: chunk 1056 optimal weight: 1.9990 chunk 948 optimal weight: 7.9990 chunk 526 optimal weight: 10.0000 chunk 323 optimal weight: 5.9990 chunk 639 optimal weight: 20.0000 chunk 506 optimal weight: 4.9990 chunk 980 optimal weight: 9.9990 chunk 379 optimal weight: 20.0000 chunk 596 optimal weight: 10.0000 chunk 729 optimal weight: 9.9990 chunk 1136 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 44 GLN ** J 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 11 GLN U 29 GLN ** U 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 402 ASN V 30 ASN V 87 ASN X 150 GLN Y 108 GLN ** Y 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 377 GLN Z 478 GLN ** a 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 51 ASN ** d 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 321 GLN ** d 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 17 ASN h 116 ASN ** i 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 280 ASN ** j 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 92 GLN n 3 ASN n 53 GLN ** n 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 165 GLN o 191 ASN ** p 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 127 HIS ** p 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 228 ASN u 150 ASN ** u 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.0948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 1.207 97614 Z= 0.575 Angle : 0.705 34.749 133089 Z= 0.370 Chirality : 0.049 0.282 15345 Planarity : 0.006 0.079 17451 Dihedral : 5.856 67.074 13647 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.36 % Allowed : 9.89 % Favored : 89.75 % Rotamer: Outliers : 1.06 % Allowed : 10.40 % Favored : 88.54 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 3.18 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.07), residues: 12609 helix: 0.41 (0.11), residues: 2409 sheet: -0.49 (0.10), residues: 2688 loop : -2.20 (0.07), residues: 7512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP Y 247 HIS 0.019 0.001 HIS j 204 PHE 0.031 0.002 PHE U 275 TYR 0.057 0.002 TYR X 49 ARG 0.009 0.001 ARG F 24 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25218 Ramachandran restraints generated. 12609 Oldfield, 0 Emsley, 12609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25218 Ramachandran restraints generated. 12609 Oldfield, 0 Emsley, 12609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1049 residues out of total 10284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 940 time to evaluate : 8.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 141 ILE cc_start: 0.6542 (mm) cc_final: 0.6259 (mt) REVERT: O 143 ILE cc_start: 0.8139 (tt) cc_final: 0.7772 (tp) REVERT: O 180 PRO cc_start: 0.4796 (Cg_endo) cc_final: 0.4288 (Cg_exo) REVERT: P 455 ILE cc_start: 0.5278 (mt) cc_final: 0.5001 (mm) REVERT: Y 25 GLU cc_start: 0.6691 (OUTLIER) cc_final: 0.6352 (pt0) REVERT: Y 185 MET cc_start: 0.4797 (pmm) cc_final: 0.4592 (ptp) REVERT: Z 51 PHE cc_start: 0.6937 (OUTLIER) cc_final: 0.6334 (m-80) REVERT: c 111 ARG cc_start: 0.6888 (mtt180) cc_final: 0.6514 (mtm-85) REVERT: e 221 PRO cc_start: 0.2807 (Cg_exo) cc_final: 0.2550 (Cg_endo) REVERT: i 143 ILE cc_start: 0.7736 (tt) cc_final: 0.7531 (tp) REVERT: A 146 MET cc_start: 0.7772 (tmm) cc_final: 0.7554 (tmm) REVERT: D 90 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7844 (mp0) REVERT: E 161 TYR cc_start: 0.7735 (m-10) cc_final: 0.7490 (m-10) REVERT: o 90 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7823 (mp0) REVERT: s 177 ARG cc_start: 0.5319 (mtp-110) cc_final: 0.5007 (ttp80) REVERT: s 397 TYR cc_start: 0.6569 (t80) cc_final: 0.6076 (t80) REVERT: t 183 ARG cc_start: 0.4951 (tpt170) cc_final: 0.4424 (mmt90) REVERT: v 183 ARG cc_start: 0.4492 (tpt170) cc_final: 0.3854 (mmt90) REVERT: v 367 GLU cc_start: 0.5692 (mt-10) cc_final: 0.5431 (mt-10) outliers start: 109 outliers final: 80 residues processed: 1010 average time/residue: 0.8787 time to fit residues: 1530.5736 Evaluate side-chains 936 residues out of total 10284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 853 time to evaluate : 8.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain I residue 74 ASP Chi-restraints excluded: chain I residue 126 ASP Chi-restraints excluded: chain J residue 44 GLN Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain K residue 193 MET Chi-restraints excluded: chain L residue 14 ILE Chi-restraints excluded: chain O residue 172 VAL Chi-restraints excluded: chain O residue 380 CYS Chi-restraints excluded: chain O residue 414 VAL Chi-restraints excluded: chain P residue 124 ASP Chi-restraints excluded: chain P residue 143 ILE Chi-restraints excluded: chain P residue 256 TYR Chi-restraints excluded: chain P residue 257 VAL Chi-restraints excluded: chain S residue 18 SER Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 119 THR Chi-restraints excluded: chain T residue 128 MET Chi-restraints excluded: chain T residue 279 ASN Chi-restraints excluded: chain U residue 57 ASN Chi-restraints excluded: chain U residue 65 CYS Chi-restraints excluded: chain U residue 229 THR Chi-restraints excluded: chain V residue 72 VAL Chi-restraints excluded: chain W residue 10 THR Chi-restraints excluded: chain X residue 150 GLN Chi-restraints excluded: chain Y residue 25 GLU Chi-restraints excluded: chain Y residue 195 VAL Chi-restraints excluded: chain Y residue 225 ILE Chi-restraints excluded: chain Y residue 380 CYS Chi-restraints excluded: chain Z residue 51 PHE Chi-restraints excluded: chain Z residue 195 LEU Chi-restraints excluded: chain Z residue 474 ASN Chi-restraints excluded: chain a residue 32 ASP Chi-restraints excluded: chain a residue 99 TYR Chi-restraints excluded: chain c residue 150 GLN Chi-restraints excluded: chain d residue 351 VAL Chi-restraints excluded: chain d residue 399 MET Chi-restraints excluded: chain e residue 305 SER Chi-restraints excluded: chain e residue 367 ILE Chi-restraints excluded: chain e residue 473 LEU Chi-restraints excluded: chain g residue 10 THR Chi-restraints excluded: chain h residue 74 ASP Chi-restraints excluded: chain h residue 126 ASP Chi-restraints excluded: chain i residue 172 VAL Chi-restraints excluded: chain i residue 246 VAL Chi-restraints excluded: chain i residue 271 THR Chi-restraints excluded: chain i residue 407 ILE Chi-restraints excluded: chain j residue 78 TYR Chi-restraints excluded: chain j residue 474 ASN Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 148 ASP Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 76 MET Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 228 GLU Chi-restraints excluded: chain F residue 220 ILE Chi-restraints excluded: chain l residue 149 ASN Chi-restraints excluded: chain m residue 76 MET Chi-restraints excluded: chain m residue 149 ASN Chi-restraints excluded: chain n residue 122 ILE Chi-restraints excluded: chain n residue 220 ILE Chi-restraints excluded: chain q residue 17 THR Chi-restraints excluded: chain q residue 58 VAL Chi-restraints excluded: chain q residue 138 VAL Chi-restraints excluded: chain r residue 17 THR Chi-restraints excluded: chain r residue 138 VAL Chi-restraints excluded: chain s residue 17 THR Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain t residue 234 VAL Chi-restraints excluded: chain t residue 292 VAL Chi-restraints excluded: chain u residue 206 THR Chi-restraints excluded: chain u residue 209 ILE Chi-restraints excluded: chain u residue 271 THR Chi-restraints excluded: chain u residue 292 VAL Chi-restraints excluded: chain v residue 220 THR Chi-restraints excluded: chain v residue 234 VAL Chi-restraints excluded: chain v residue 292 VAL Chi-restraints excluded: chain v residue 398 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1251 random chunks: chunk 631 optimal weight: 9.9990 chunk 352 optimal weight: 20.0000 chunk 945 optimal weight: 6.9990 chunk 773 optimal weight: 9.9990 chunk 313 optimal weight: 9.9990 chunk 1138 optimal weight: 0.4980 chunk 1229 optimal weight: 4.9990 chunk 1013 optimal weight: 5.9990 chunk 1128 optimal weight: 0.0060 chunk 387 optimal weight: 10.0000 chunk 913 optimal weight: 10.0000 overall best weight: 3.7002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 44 GLN ** J 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 321 GLN ** O 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 253 ASN ** T 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 312 GLN X 150 GLN ** Y 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 377 GLN ** a 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 102 GLN ** d 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 201 GLN ** d 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 218 ASN ** i 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 64 HIS F 3 ASN ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 165 GLN ** p 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 316 ASN ** v 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 267 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 1.204 97614 Z= 0.530 Angle : 0.636 34.346 133089 Z= 0.332 Chirality : 0.047 0.280 15345 Planarity : 0.005 0.093 17451 Dihedral : 5.539 63.296 13647 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.36 % Allowed : 9.17 % Favored : 90.47 % Rotamer: Outliers : 1.75 % Allowed : 13.71 % Favored : 84.54 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 3.18 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.07), residues: 12609 helix: 0.70 (0.11), residues: 2394 sheet: -0.47 (0.10), residues: 2754 loop : -2.17 (0.07), residues: 7461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP K 331 HIS 0.008 0.001 HIS j 204 PHE 0.023 0.001 PHE Z 437 TYR 0.054 0.002 TYR X 49 ARG 0.009 0.000 ARG v 55 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25218 Ramachandran restraints generated. 12609 Oldfield, 0 Emsley, 12609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25218 Ramachandran restraints generated. 12609 Oldfield, 0 Emsley, 12609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1113 residues out of total 10284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 933 time to evaluate : 7.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 173 ILE cc_start: 0.6296 (OUTLIER) cc_final: 0.5688 (tt) REVERT: K 78 TYR cc_start: 0.5237 (p90) cc_final: 0.5031 (p90) REVERT: N 21 MET cc_start: 0.5935 (mmm) cc_final: 0.5658 (mmp) REVERT: O 141 ILE cc_start: 0.6592 (mm) cc_final: 0.6381 (mt) REVERT: O 143 ILE cc_start: 0.8202 (tt) cc_final: 0.7794 (tp) REVERT: O 180 PRO cc_start: 0.4810 (Cg_endo) cc_final: 0.4440 (Cg_exo) REVERT: P 455 ILE cc_start: 0.5179 (mt) cc_final: 0.4813 (mm) REVERT: P 491 MET cc_start: 0.7836 (mmm) cc_final: 0.7611 (mtp) REVERT: T 399 MET cc_start: 0.7252 (OUTLIER) cc_final: 0.7041 (ttm) REVERT: V 33 MET cc_start: 0.6955 (ptp) cc_final: 0.6592 (pmm) REVERT: Y 25 GLU cc_start: 0.6958 (OUTLIER) cc_final: 0.6544 (pt0) REVERT: Z 51 PHE cc_start: 0.6811 (OUTLIER) cc_final: 0.6165 (m-80) REVERT: c 111 ARG cc_start: 0.6938 (mtt180) cc_final: 0.6560 (mtm-85) REVERT: e 51 PHE cc_start: 0.5154 (OUTLIER) cc_final: 0.4890 (t80) REVERT: e 149 MET cc_start: 0.7571 (mmm) cc_final: 0.7026 (mmm) REVERT: e 221 PRO cc_start: 0.2623 (Cg_exo) cc_final: 0.2339 (Cg_endo) REVERT: i 180 PRO cc_start: 0.3863 (Cg_endo) cc_final: 0.3502 (Cg_exo) REVERT: j 120 ILE cc_start: 0.6133 (mp) cc_final: 0.5767 (mt) REVERT: A 146 MET cc_start: 0.7652 (tmm) cc_final: 0.7441 (tmm) REVERT: A 149 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.7211 (ptt90) REVERT: A 153 LEU cc_start: 0.5938 (OUTLIER) cc_final: 0.5545 (mp) REVERT: B 116 ILE cc_start: 0.8858 (OUTLIER) cc_final: 0.8618 (mt) REVERT: D 90 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7858 (mp0) REVERT: s 185 MET cc_start: 0.6702 (tpp) cc_final: 0.6232 (ttt) REVERT: s 397 TYR cc_start: 0.6515 (t80) cc_final: 0.6035 (t80) REVERT: t 64 ARG cc_start: 0.7189 (tmt170) cc_final: 0.6590 (tpt90) REVERT: t 183 ARG cc_start: 0.4797 (tpt170) cc_final: 0.4324 (mmt90) REVERT: v 183 ARG cc_start: 0.4385 (OUTLIER) cc_final: 0.3623 (mmt90) REVERT: v 244 TYR cc_start: 0.3568 (m-80) cc_final: 0.3303 (m-80) outliers start: 180 outliers final: 114 residues processed: 1065 average time/residue: 0.8450 time to fit residues: 1560.0503 Evaluate side-chains 987 residues out of total 10284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 863 time to evaluate : 7.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain I residue 126 ASP Chi-restraints excluded: chain J residue 44 GLN Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain J residue 173 ILE Chi-restraints excluded: chain J residue 282 VAL Chi-restraints excluded: chain K residue 170 LEU Chi-restraints excluded: chain K residue 193 MET Chi-restraints excluded: chain K residue 308 VAL Chi-restraints excluded: chain O residue 172 VAL Chi-restraints excluded: chain O residue 240 PHE Chi-restraints excluded: chain O residue 246 VAL Chi-restraints excluded: chain P residue 124 ASP Chi-restraints excluded: chain P residue 143 ILE Chi-restraints excluded: chain P residue 256 TYR Chi-restraints excluded: chain P residue 257 VAL Chi-restraints excluded: chain P residue 367 ILE Chi-restraints excluded: chain P residue 388 THR Chi-restraints excluded: chain R residue 27 ASP Chi-restraints excluded: chain R residue 41 MET Chi-restraints excluded: chain S residue 18 SER Chi-restraints excluded: chain S residue 74 ASP Chi-restraints excluded: chain T residue 19 ASP Chi-restraints excluded: chain T residue 119 THR Chi-restraints excluded: chain T residue 279 ASN Chi-restraints excluded: chain T residue 399 MET Chi-restraints excluded: chain U residue 57 ASN Chi-restraints excluded: chain U residue 65 CYS Chi-restraints excluded: chain U residue 143 ILE Chi-restraints excluded: chain U residue 229 THR Chi-restraints excluded: chain U residue 245 CYS Chi-restraints excluded: chain U residue 308 VAL Chi-restraints excluded: chain V residue 72 VAL Chi-restraints excluded: chain W residue 10 THR Chi-restraints excluded: chain X residue 151 THR Chi-restraints excluded: chain Y residue 25 GLU Chi-restraints excluded: chain Y residue 68 THR Chi-restraints excluded: chain Y residue 225 ILE Chi-restraints excluded: chain Y residue 268 ASN Chi-restraints excluded: chain Y residue 380 CYS Chi-restraints excluded: chain Z residue 51 PHE Chi-restraints excluded: chain Z residue 195 LEU Chi-restraints excluded: chain a residue 32 ASP Chi-restraints excluded: chain c residue 35 ILE Chi-restraints excluded: chain c residue 128 ILE Chi-restraints excluded: chain c residue 150 GLN Chi-restraints excluded: chain d residue 351 VAL Chi-restraints excluded: chain e residue 51 PHE Chi-restraints excluded: chain e residue 305 SER Chi-restraints excluded: chain e residue 367 ILE Chi-restraints excluded: chain e residue 473 LEU Chi-restraints excluded: chain g residue 10 THR Chi-restraints excluded: chain h residue 74 ASP Chi-restraints excluded: chain h residue 126 ASP Chi-restraints excluded: chain i residue 160 ILE Chi-restraints excluded: chain i residue 172 VAL Chi-restraints excluded: chain i residue 246 VAL Chi-restraints excluded: chain i residue 255 ASP Chi-restraints excluded: chain i residue 275 TYR Chi-restraints excluded: chain i residue 315 VAL Chi-restraints excluded: chain i residue 407 ILE Chi-restraints excluded: chain j residue 257 VAL Chi-restraints excluded: chain A residue 149 ARG Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 148 ASP Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain E residue 76 MET Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 228 GLU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain F residue 3 ASN Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 220 ILE Chi-restraints excluded: chain k residue 100 THR Chi-restraints excluded: chain l residue 48 THR Chi-restraints excluded: chain l residue 149 ASN Chi-restraints excluded: chain m residue 41 THR Chi-restraints excluded: chain m residue 76 MET Chi-restraints excluded: chain m residue 149 ASN Chi-restraints excluded: chain m residue 228 GLU Chi-restraints excluded: chain m residue 231 VAL Chi-restraints excluded: chain n residue 3 ASN Chi-restraints excluded: chain n residue 49 ILE Chi-restraints excluded: chain n residue 122 ILE Chi-restraints excluded: chain o residue 100 THR Chi-restraints excluded: chain p residue 49 ILE Chi-restraints excluded: chain q residue 17 THR Chi-restraints excluded: chain q residue 58 VAL Chi-restraints excluded: chain q residue 138 VAL Chi-restraints excluded: chain q residue 412 VAL Chi-restraints excluded: chain r residue 17 THR Chi-restraints excluded: chain r residue 119 THR Chi-restraints excluded: chain r residue 138 VAL Chi-restraints excluded: chain r residue 412 VAL Chi-restraints excluded: chain s residue 17 THR Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain s residue 119 THR Chi-restraints excluded: chain s residue 412 VAL Chi-restraints excluded: chain t residue 234 VAL Chi-restraints excluded: chain t residue 292 VAL Chi-restraints excluded: chain t residue 302 VAL Chi-restraints excluded: chain u residue 209 ILE Chi-restraints excluded: chain u residue 271 THR Chi-restraints excluded: chain u residue 292 VAL Chi-restraints excluded: chain v residue 104 THR Chi-restraints excluded: chain v residue 141 ILE Chi-restraints excluded: chain v residue 183 ARG Chi-restraints excluded: chain v residue 220 THR Chi-restraints excluded: chain v residue 234 VAL Chi-restraints excluded: chain v residue 282 VAL Chi-restraints excluded: chain v residue 292 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1251 random chunks: chunk 1124 optimal weight: 20.0000 chunk 855 optimal weight: 3.9990 chunk 590 optimal weight: 0.1980 chunk 125 optimal weight: 10.0000 chunk 543 optimal weight: 9.9990 chunk 764 optimal weight: 7.9990 chunk 1142 optimal weight: 20.0000 chunk 1209 optimal weight: 30.0000 chunk 596 optimal weight: 10.0000 chunk 1082 optimal weight: 1.9990 chunk 325 optimal weight: 9.9990 overall best weight: 4.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 44 GLN ** J 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 46 ASN ** O 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 157 ASN ** O 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 52 HIS ** P 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 288 GLN T 5 ASN T 35 ASN ** T 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 150 ASN T 228 ASN ** T 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 337 ASN ** V 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 377 GLN ** a 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 129 GLN ** d 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 340 GLN ** e 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 411 ASN E 64 HIS F 3 ASN ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 165 GLN ** t 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 192 ASN ** u 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 267 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 1.203 97614 Z= 0.548 Angle : 0.646 34.287 133089 Z= 0.337 Chirality : 0.047 0.279 15345 Planarity : 0.005 0.076 17451 Dihedral : 5.551 63.007 13647 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.35 % Allowed : 9.98 % Favored : 89.67 % Rotamer: Outliers : 2.57 % Allowed : 15.93 % Favored : 81.51 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 3.18 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.07), residues: 12609 helix: 0.66 (0.11), residues: 2412 sheet: -0.50 (0.10), residues: 2715 loop : -2.20 (0.07), residues: 7482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP i 247 HIS 0.009 0.001 HIS E 64 PHE 0.022 0.002 PHE Z 437 TYR 0.053 0.002 TYR X 49 ARG 0.005 0.000 ARG U 296 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25218 Ramachandran restraints generated. 12609 Oldfield, 0 Emsley, 12609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25218 Ramachandran restraints generated. 12609 Oldfield, 0 Emsley, 12609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1149 residues out of total 10284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 264 poor density : 885 time to evaluate : 8.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 62 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.7801 (tt) REVERT: J 173 ILE cc_start: 0.6335 (OUTLIER) cc_final: 0.5712 (tt) REVERT: K 91 GLN cc_start: 0.4320 (OUTLIER) cc_final: 0.3632 (mt0) REVERT: K 153 ILE cc_start: 0.8090 (OUTLIER) cc_final: 0.7455 (mt) REVERT: N 133 ARG cc_start: 0.6266 (mmm160) cc_final: 0.6018 (mmm160) REVERT: O 25 GLU cc_start: 0.6558 (OUTLIER) cc_final: 0.6214 (mp0) REVERT: O 141 ILE cc_start: 0.6855 (mm) cc_final: 0.6615 (mt) REVERT: O 143 ILE cc_start: 0.8100 (tt) cc_final: 0.7877 (tp) REVERT: O 180 PRO cc_start: 0.5019 (Cg_endo) cc_final: 0.4627 (Cg_exo) REVERT: P 360 ASP cc_start: 0.2091 (OUTLIER) cc_final: 0.1136 (t0) REVERT: P 455 ILE cc_start: 0.5226 (mt) cc_final: 0.4875 (mm) REVERT: T 94 LEU cc_start: 0.7092 (OUTLIER) cc_final: 0.6487 (tp) REVERT: T 399 MET cc_start: 0.7352 (ttm) cc_final: 0.7089 (ttm) REVERT: U 59 PHE cc_start: 0.6177 (OUTLIER) cc_final: 0.5101 (t80) REVERT: Y 25 GLU cc_start: 0.6957 (OUTLIER) cc_final: 0.6531 (pt0) REVERT: Y 144 LYS cc_start: 0.7117 (mmtt) cc_final: 0.6856 (mttp) REVERT: Z 51 PHE cc_start: 0.6861 (OUTLIER) cc_final: 0.6218 (m-80) REVERT: c 111 ARG cc_start: 0.7017 (mtt180) cc_final: 0.6629 (mtm-85) REVERT: d 189 GLU cc_start: 0.6030 (OUTLIER) cc_final: 0.5458 (pm20) REVERT: e 51 PHE cc_start: 0.5313 (OUTLIER) cc_final: 0.5006 (t80) REVERT: e 149 MET cc_start: 0.7629 (mmm) cc_final: 0.7101 (mmm) REVERT: e 221 PRO cc_start: 0.2636 (Cg_exo) cc_final: 0.2345 (Cg_endo) REVERT: i 167 TRP cc_start: 0.2733 (OUTLIER) cc_final: 0.1479 (p90) REVERT: i 180 PRO cc_start: 0.4204 (Cg_endo) cc_final: 0.3812 (Cg_exo) REVERT: j 120 ILE cc_start: 0.6187 (mp) cc_final: 0.5841 (mt) REVERT: A 146 MET cc_start: 0.7690 (tmm) cc_final: 0.7478 (tmm) REVERT: A 149 ARG cc_start: 0.7733 (OUTLIER) cc_final: 0.7184 (ptt90) REVERT: A 153 LEU cc_start: 0.6007 (OUTLIER) cc_final: 0.5599 (mp) REVERT: D 90 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7844 (mp0) REVERT: m 205 ARG cc_start: 0.7926 (OUTLIER) cc_final: 0.7410 (ttm110) REVERT: n 53 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.7992 (tm130) REVERT: o 90 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7924 (mp0) REVERT: r 59 MET cc_start: 0.7117 (tmm) cc_final: 0.6745 (tmm) REVERT: s 177 ARG cc_start: 0.5334 (mtp-110) cc_final: 0.5115 (ttp80) REVERT: t 32 LEU cc_start: 0.5777 (OUTLIER) cc_final: 0.5442 (mp) REVERT: t 183 ARG cc_start: 0.4825 (tpt170) cc_final: 0.4296 (mmt90) REVERT: v 183 ARG cc_start: 0.4455 (OUTLIER) cc_final: 0.3593 (mmt90) outliers start: 264 outliers final: 180 residues processed: 1088 average time/residue: 0.8684 time to fit residues: 1650.8328 Evaluate side-chains 1046 residues out of total 10284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 846 time to evaluate : 7.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 92 ASP Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain I residue 74 ASP Chi-restraints excluded: chain I residue 126 ASP Chi-restraints excluded: chain J residue 44 GLN Chi-restraints excluded: chain J residue 69 ILE Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain J residue 173 ILE Chi-restraints excluded: chain J residue 282 VAL Chi-restraints excluded: chain J residue 412 VAL Chi-restraints excluded: chain K residue 91 GLN Chi-restraints excluded: chain K residue 153 ILE Chi-restraints excluded: chain K residue 170 LEU Chi-restraints excluded: chain K residue 193 MET Chi-restraints excluded: chain K residue 308 VAL Chi-restraints excluded: chain K residue 408 VAL Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain N residue 14 VAL Chi-restraints excluded: chain O residue 25 GLU Chi-restraints excluded: chain O residue 68 THR Chi-restraints excluded: chain O residue 118 GLN Chi-restraints excluded: chain O residue 172 VAL Chi-restraints excluded: chain O residue 173 ILE Chi-restraints excluded: chain O residue 240 PHE Chi-restraints excluded: chain O residue 246 VAL Chi-restraints excluded: chain O residue 248 VAL Chi-restraints excluded: chain O residue 315 VAL Chi-restraints excluded: chain O residue 326 VAL Chi-restraints excluded: chain O residue 380 CYS Chi-restraints excluded: chain P residue 124 ASP Chi-restraints excluded: chain P residue 143 ILE Chi-restraints excluded: chain P residue 256 TYR Chi-restraints excluded: chain P residue 257 VAL Chi-restraints excluded: chain P residue 360 ASP Chi-restraints excluded: chain P residue 367 ILE Chi-restraints excluded: chain P residue 388 THR Chi-restraints excluded: chain P residue 473 LEU Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain R residue 27 ASP Chi-restraints excluded: chain R residue 41 MET Chi-restraints excluded: chain S residue 18 SER Chi-restraints excluded: chain S residue 101 THR Chi-restraints excluded: chain T residue 19 ASP Chi-restraints excluded: chain T residue 94 LEU Chi-restraints excluded: chain T residue 119 THR Chi-restraints excluded: chain T residue 128 MET Chi-restraints excluded: chain T residue 279 ASN Chi-restraints excluded: chain U residue 10 ILE Chi-restraints excluded: chain U residue 57 ASN Chi-restraints excluded: chain U residue 59 PHE Chi-restraints excluded: chain U residue 65 CYS Chi-restraints excluded: chain U residue 143 ILE Chi-restraints excluded: chain U residue 229 THR Chi-restraints excluded: chain U residue 245 CYS Chi-restraints excluded: chain U residue 308 VAL Chi-restraints excluded: chain V residue 49 VAL Chi-restraints excluded: chain V residue 72 VAL Chi-restraints excluded: chain W residue 10 THR Chi-restraints excluded: chain X residue 14 VAL Chi-restraints excluded: chain Y residue 25 GLU Chi-restraints excluded: chain Y residue 68 THR Chi-restraints excluded: chain Y residue 225 ILE Chi-restraints excluded: chain Y residue 268 ASN Chi-restraints excluded: chain Y residue 290 VAL Chi-restraints excluded: chain Y residue 380 CYS Chi-restraints excluded: chain Z residue 51 PHE Chi-restraints excluded: chain Z residue 195 LEU Chi-restraints excluded: chain a residue 32 ASP Chi-restraints excluded: chain a residue 49 VAL Chi-restraints excluded: chain c residue 14 VAL Chi-restraints excluded: chain c residue 35 ILE Chi-restraints excluded: chain c residue 57 ASP Chi-restraints excluded: chain c residue 120 LEU Chi-restraints excluded: chain c residue 128 ILE Chi-restraints excluded: chain c residue 150 GLN Chi-restraints excluded: chain d residue 14 VAL Chi-restraints excluded: chain d residue 124 ILE Chi-restraints excluded: chain d residue 189 GLU Chi-restraints excluded: chain d residue 282 VAL Chi-restraints excluded: chain d residue 319 VAL Chi-restraints excluded: chain d residue 351 VAL Chi-restraints excluded: chain d residue 399 MET Chi-restraints excluded: chain e residue 51 PHE Chi-restraints excluded: chain e residue 305 SER Chi-restraints excluded: chain e residue 367 ILE Chi-restraints excluded: chain e residue 473 LEU Chi-restraints excluded: chain f residue 27 LEU Chi-restraints excluded: chain g residue 10 THR Chi-restraints excluded: chain g residue 108 ILE Chi-restraints excluded: chain h residue 74 ASP Chi-restraints excluded: chain h residue 126 ASP Chi-restraints excluded: chain i residue 167 TRP Chi-restraints excluded: chain i residue 172 VAL Chi-restraints excluded: chain i residue 246 VAL Chi-restraints excluded: chain i residue 248 VAL Chi-restraints excluded: chain i residue 255 ASP Chi-restraints excluded: chain i residue 275 TYR Chi-restraints excluded: chain i residue 303 VAL Chi-restraints excluded: chain i residue 315 VAL Chi-restraints excluded: chain i residue 407 ILE Chi-restraints excluded: chain j residue 78 TYR Chi-restraints excluded: chain j residue 257 VAL Chi-restraints excluded: chain j residue 474 ASN Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 149 ARG Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 148 ASP Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 76 MET Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 223 ILE Chi-restraints excluded: chain E residue 228 GLU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain F residue 3 ASN Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 220 ILE Chi-restraints excluded: chain k residue 100 THR Chi-restraints excluded: chain l residue 48 THR Chi-restraints excluded: chain l residue 141 VAL Chi-restraints excluded: chain l residue 149 ASN Chi-restraints excluded: chain l residue 231 VAL Chi-restraints excluded: chain m residue 41 THR Chi-restraints excluded: chain m residue 76 MET Chi-restraints excluded: chain m residue 149 ASN Chi-restraints excluded: chain m residue 174 THR Chi-restraints excluded: chain m residue 205 ARG Chi-restraints excluded: chain m residue 228 GLU Chi-restraints excluded: chain m residue 231 VAL Chi-restraints excluded: chain m residue 257 VAL Chi-restraints excluded: chain n residue 3 ASN Chi-restraints excluded: chain n residue 49 ILE Chi-restraints excluded: chain n residue 53 GLN Chi-restraints excluded: chain n residue 122 ILE Chi-restraints excluded: chain n residue 220 ILE Chi-restraints excluded: chain o residue 100 THR Chi-restraints excluded: chain o residue 121 ASP Chi-restraints excluded: chain p residue 49 ILE Chi-restraints excluded: chain p residue 184 THR Chi-restraints excluded: chain p residue 220 ILE Chi-restraints excluded: chain q residue 17 THR Chi-restraints excluded: chain q residue 58 VAL Chi-restraints excluded: chain q residue 119 THR Chi-restraints excluded: chain q residue 138 VAL Chi-restraints excluded: chain q residue 185 MET Chi-restraints excluded: chain q residue 412 VAL Chi-restraints excluded: chain r residue 17 THR Chi-restraints excluded: chain r residue 119 THR Chi-restraints excluded: chain r residue 138 VAL Chi-restraints excluded: chain r residue 165 ILE Chi-restraints excluded: chain r residue 204 ASN Chi-restraints excluded: chain r residue 227 ASN Chi-restraints excluded: chain r residue 234 VAL Chi-restraints excluded: chain r residue 271 THR Chi-restraints excluded: chain r residue 412 VAL Chi-restraints excluded: chain s residue 17 THR Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain s residue 82 ILE Chi-restraints excluded: chain s residue 85 LEU Chi-restraints excluded: chain s residue 119 THR Chi-restraints excluded: chain s residue 412 VAL Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 234 VAL Chi-restraints excluded: chain t residue 292 VAL Chi-restraints excluded: chain t residue 302 VAL Chi-restraints excluded: chain u residue 32 LEU Chi-restraints excluded: chain u residue 141 ILE Chi-restraints excluded: chain u residue 206 THR Chi-restraints excluded: chain u residue 209 ILE Chi-restraints excluded: chain u residue 271 THR Chi-restraints excluded: chain u residue 292 VAL Chi-restraints excluded: chain v residue 96 THR Chi-restraints excluded: chain v residue 104 THR Chi-restraints excluded: chain v residue 133 ILE Chi-restraints excluded: chain v residue 141 ILE Chi-restraints excluded: chain v residue 183 ARG Chi-restraints excluded: chain v residue 220 THR Chi-restraints excluded: chain v residue 234 VAL Chi-restraints excluded: chain v residue 282 VAL Chi-restraints excluded: chain v residue 292 VAL Chi-restraints excluded: chain v residue 398 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1251 random chunks: chunk 1007 optimal weight: 20.0000 chunk 686 optimal weight: 0.7980 chunk 17 optimal weight: 7.9990 chunk 900 optimal weight: 9.9990 chunk 498 optimal weight: 30.0000 chunk 1031 optimal weight: 3.9990 chunk 835 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 617 optimal weight: 30.0000 chunk 1085 optimal weight: 30.0000 chunk 305 optimal weight: 5.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 33 GLN ** H 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 44 GLN ** J 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 157 ASN ** O 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 204 HIS ** T 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 268 ASN ** V 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 321 GLN ** a 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 228 ASN ** d 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 328 ASN ** e 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 411 ASN j 441 ASN F 3 ASN ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 165 GLN ** p 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 192 ASN ** u 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 267 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 1.207 97614 Z= 0.540 Angle : 0.635 34.183 133089 Z= 0.331 Chirality : 0.047 0.276 15345 Planarity : 0.005 0.076 17451 Dihedral : 5.495 62.087 13647 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.36 % Allowed : 9.60 % Favored : 90.04 % Rotamer: Outliers : 3.48 % Allowed : 17.15 % Favored : 79.37 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 3.18 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.07), residues: 12609 helix: 0.79 (0.11), residues: 2369 sheet: -0.56 (0.10), residues: 2689 loop : -2.18 (0.07), residues: 7551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP P 216 HIS 0.004 0.001 HIS P 18 PHE 0.021 0.002 PHE Z 437 TYR 0.052 0.002 TYR X 49 ARG 0.006 0.000 ARG U 296 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25218 Ramachandran restraints generated. 12609 Oldfield, 0 Emsley, 12609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25218 Ramachandran restraints generated. 12609 Oldfield, 0 Emsley, 12609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1248 residues out of total 10284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 358 poor density : 890 time to evaluate : 8.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 62 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.7757 (tt) REVERT: I 114 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8771 (mt) REVERT: J 173 ILE cc_start: 0.6357 (OUTLIER) cc_final: 0.5741 (tt) REVERT: J 189 GLU cc_start: 0.6060 (OUTLIER) cc_final: 0.5826 (pm20) REVERT: K 153 ILE cc_start: 0.8100 (OUTLIER) cc_final: 0.7487 (mt) REVERT: K 491 MET cc_start: 0.7339 (ttm) cc_final: 0.7122 (ttm) REVERT: O 25 GLU cc_start: 0.6664 (OUTLIER) cc_final: 0.6200 (mp0) REVERT: O 180 PRO cc_start: 0.4898 (Cg_endo) cc_final: 0.4459 (Cg_exo) REVERT: O 314 TYR cc_start: 0.5169 (OUTLIER) cc_final: 0.4225 (m-80) REVERT: P 51 PHE cc_start: 0.7065 (OUTLIER) cc_final: 0.5837 (m-80) REVERT: P 153 ILE cc_start: 0.8587 (OUTLIER) cc_final: 0.8343 (mt) REVERT: P 313 MET cc_start: 0.2711 (OUTLIER) cc_final: 0.2353 (tpp) REVERT: P 360 ASP cc_start: 0.2096 (OUTLIER) cc_final: 0.1167 (t0) REVERT: P 455 ILE cc_start: 0.5096 (mt) cc_final: 0.4832 (mm) REVERT: P 485 ASP cc_start: 0.5042 (OUTLIER) cc_final: 0.4421 (p0) REVERT: Q 92 ASP cc_start: 0.6616 (OUTLIER) cc_final: 0.6318 (p0) REVERT: T 94 LEU cc_start: 0.7191 (OUTLIER) cc_final: 0.6553 (tp) REVERT: T 189 GLU cc_start: 0.5799 (OUTLIER) cc_final: 0.5433 (pm20) REVERT: U 59 PHE cc_start: 0.6185 (OUTLIER) cc_final: 0.5121 (t80) REVERT: U 120 ILE cc_start: 0.3557 (OUTLIER) cc_final: 0.3092 (mt) REVERT: U 247 LEU cc_start: 0.5847 (OUTLIER) cc_final: 0.5631 (pp) REVERT: W 16 LEU cc_start: 0.6657 (OUTLIER) cc_final: 0.6273 (mt) REVERT: Y 25 GLU cc_start: 0.6919 (OUTLIER) cc_final: 0.6495 (pt0) REVERT: Y 141 ILE cc_start: 0.5745 (mm) cc_final: 0.5422 (mt) REVERT: Z 51 PHE cc_start: 0.6918 (OUTLIER) cc_final: 0.6245 (m-80) REVERT: a 34 MET cc_start: 0.7825 (mtp) cc_final: 0.7563 (mtp) REVERT: c 49 TYR cc_start: 0.8612 (OUTLIER) cc_final: 0.7492 (p90) REVERT: c 111 ARG cc_start: 0.7071 (mtt180) cc_final: 0.6551 (mtm-85) REVERT: d 189 GLU cc_start: 0.6056 (OUTLIER) cc_final: 0.5497 (pm20) REVERT: e 51 PHE cc_start: 0.5340 (OUTLIER) cc_final: 0.5022 (t80) REVERT: e 120 ILE cc_start: 0.3174 (OUTLIER) cc_final: 0.2710 (mt) REVERT: e 149 MET cc_start: 0.7633 (mmm) cc_final: 0.7157 (mmm) REVERT: e 153 ILE cc_start: 0.7966 (OUTLIER) cc_final: 0.7228 (mt) REVERT: e 221 PRO cc_start: 0.1994 (Cg_exo) cc_final: 0.1682 (Cg_endo) REVERT: h 105 THR cc_start: 0.7684 (OUTLIER) cc_final: 0.7159 (m) REVERT: i 167 TRP cc_start: 0.2859 (OUTLIER) cc_final: 0.1552 (p90) REVERT: i 180 PRO cc_start: 0.4107 (Cg_endo) cc_final: 0.3731 (Cg_exo) REVERT: i 194 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.7623 (ttt-90) REVERT: j 120 ILE cc_start: 0.6194 (mp) cc_final: 0.5848 (mt) REVERT: j 285 ILE cc_start: 0.5078 (OUTLIER) cc_final: 0.4858 (mm) REVERT: j 313 MET cc_start: 0.2827 (tmm) cc_final: 0.2461 (tmm) REVERT: A 146 MET cc_start: 0.7735 (tmm) cc_final: 0.7495 (tmm) REVERT: A 149 ARG cc_start: 0.7766 (OUTLIER) cc_final: 0.7198 (ptt90) REVERT: A 153 LEU cc_start: 0.6037 (OUTLIER) cc_final: 0.5609 (mp) REVERT: D 90 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7844 (mp0) REVERT: E 186 MET cc_start: 0.7985 (OUTLIER) cc_final: 0.7669 (mpp) REVERT: l 186 MET cc_start: 0.8032 (OUTLIER) cc_final: 0.7654 (mpp) REVERT: m 205 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.7408 (ttm110) REVERT: n 53 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.7972 (tm130) REVERT: o 90 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7863 (mp0) REVERT: s 397 TYR cc_start: 0.6555 (t80) cc_final: 0.6045 (t80) REVERT: t 32 LEU cc_start: 0.5702 (OUTLIER) cc_final: 0.5369 (mp) REVERT: t 59 MET cc_start: 0.7626 (tmm) cc_final: 0.7417 (tmm) REVERT: t 64 ARG cc_start: 0.7172 (tmt170) cc_final: 0.6909 (tpt90) REVERT: t 183 ARG cc_start: 0.4865 (tpt170) cc_final: 0.4324 (mmt90) REVERT: v 64 ARG cc_start: 0.7110 (tmt170) cc_final: 0.6810 (tpt90) REVERT: v 183 ARG cc_start: 0.4390 (OUTLIER) cc_final: 0.3551 (mmt90) outliers start: 358 outliers final: 234 residues processed: 1174 average time/residue: 0.8341 time to fit residues: 1721.4301 Evaluate side-chains 1121 residues out of total 10284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 273 poor density : 848 time to evaluate : 7.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 92 ASP Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain I residue 74 ASP Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain I residue 126 ASP Chi-restraints excluded: chain I residue 138 THR Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 69 ILE Chi-restraints excluded: chain J residue 82 ILE Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain J residue 173 ILE Chi-restraints excluded: chain J residue 189 GLU Chi-restraints excluded: chain J residue 209 ILE Chi-restraints excluded: chain J residue 229 THR Chi-restraints excluded: chain J residue 412 VAL Chi-restraints excluded: chain K residue 153 ILE Chi-restraints excluded: chain K residue 170 LEU Chi-restraints excluded: chain K residue 193 MET Chi-restraints excluded: chain K residue 270 THR Chi-restraints excluded: chain K residue 308 VAL Chi-restraints excluded: chain K residue 408 VAL Chi-restraints excluded: chain M residue 46 ASN Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain N residue 13 ILE Chi-restraints excluded: chain N residue 14 VAL Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain O residue 25 GLU Chi-restraints excluded: chain O residue 68 THR Chi-restraints excluded: chain O residue 113 THR Chi-restraints excluded: chain O residue 118 GLN Chi-restraints excluded: chain O residue 119 THR Chi-restraints excluded: chain O residue 172 VAL Chi-restraints excluded: chain O residue 173 ILE Chi-restraints excluded: chain O residue 234 VAL Chi-restraints excluded: chain O residue 240 PHE Chi-restraints excluded: chain O residue 246 VAL Chi-restraints excluded: chain O residue 248 VAL Chi-restraints excluded: chain O residue 314 TYR Chi-restraints excluded: chain O residue 315 VAL Chi-restraints excluded: chain O residue 326 VAL Chi-restraints excluded: chain O residue 380 CYS Chi-restraints excluded: chain P residue 51 PHE Chi-restraints excluded: chain P residue 124 ASP Chi-restraints excluded: chain P residue 143 ILE Chi-restraints excluded: chain P residue 153 ILE Chi-restraints excluded: chain P residue 166 LEU Chi-restraints excluded: chain P residue 171 MET Chi-restraints excluded: chain P residue 256 TYR Chi-restraints excluded: chain P residue 257 VAL Chi-restraints excluded: chain P residue 313 MET Chi-restraints excluded: chain P residue 360 ASP Chi-restraints excluded: chain P residue 367 ILE Chi-restraints excluded: chain P residue 388 THR Chi-restraints excluded: chain P residue 473 LEU Chi-restraints excluded: chain P residue 485 ASP Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain Q residue 92 ASP Chi-restraints excluded: chain R residue 27 ASP Chi-restraints excluded: chain R residue 41 MET Chi-restraints excluded: chain S residue 18 SER Chi-restraints excluded: chain S residue 74 ASP Chi-restraints excluded: chain S residue 101 THR Chi-restraints excluded: chain T residue 19 ASP Chi-restraints excluded: chain T residue 69 ILE Chi-restraints excluded: chain T residue 94 LEU Chi-restraints excluded: chain T residue 119 THR Chi-restraints excluded: chain T residue 185 MET Chi-restraints excluded: chain T residue 189 GLU Chi-restraints excluded: chain T residue 279 ASN Chi-restraints excluded: chain T residue 318 THR Chi-restraints excluded: chain T residue 394 THR Chi-restraints excluded: chain U residue 57 ASN Chi-restraints excluded: chain U residue 59 PHE Chi-restraints excluded: chain U residue 65 CYS Chi-restraints excluded: chain U residue 120 ILE Chi-restraints excluded: chain U residue 143 ILE Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 229 THR Chi-restraints excluded: chain U residue 245 CYS Chi-restraints excluded: chain U residue 247 LEU Chi-restraints excluded: chain U residue 308 VAL Chi-restraints excluded: chain U residue 361 SER Chi-restraints excluded: chain U residue 502 ILE Chi-restraints excluded: chain V residue 49 VAL Chi-restraints excluded: chain V residue 72 VAL Chi-restraints excluded: chain W residue 8 THR Chi-restraints excluded: chain W residue 10 THR Chi-restraints excluded: chain W residue 16 LEU Chi-restraints excluded: chain W residue 94 ILE Chi-restraints excluded: chain X residue 14 VAL Chi-restraints excluded: chain Y residue 25 GLU Chi-restraints excluded: chain Y residue 68 THR Chi-restraints excluded: chain Y residue 113 THR Chi-restraints excluded: chain Y residue 195 VAL Chi-restraints excluded: chain Y residue 225 ILE Chi-restraints excluded: chain Y residue 268 ASN Chi-restraints excluded: chain Y residue 290 VAL Chi-restraints excluded: chain Y residue 380 CYS Chi-restraints excluded: chain Z residue 51 PHE Chi-restraints excluded: chain Z residue 195 LEU Chi-restraints excluded: chain Z residue 230 VAL Chi-restraints excluded: chain Z residue 474 ASN Chi-restraints excluded: chain Z residue 499 VAL Chi-restraints excluded: chain a residue 32 ASP Chi-restraints excluded: chain a residue 49 VAL Chi-restraints excluded: chain c residue 14 VAL Chi-restraints excluded: chain c residue 35 ILE Chi-restraints excluded: chain c residue 49 TYR Chi-restraints excluded: chain c residue 57 ASP Chi-restraints excluded: chain c residue 120 LEU Chi-restraints excluded: chain c residue 128 ILE Chi-restraints excluded: chain c residue 150 GLN Chi-restraints excluded: chain d residue 14 VAL Chi-restraints excluded: chain d residue 124 ILE Chi-restraints excluded: chain d residue 189 GLU Chi-restraints excluded: chain d residue 227 ASN Chi-restraints excluded: chain d residue 275 TYR Chi-restraints excluded: chain d residue 282 VAL Chi-restraints excluded: chain d residue 319 VAL Chi-restraints excluded: chain d residue 351 VAL Chi-restraints excluded: chain d residue 394 THR Chi-restraints excluded: chain d residue 399 MET Chi-restraints excluded: chain d residue 417 VAL Chi-restraints excluded: chain e residue 51 PHE Chi-restraints excluded: chain e residue 120 ILE Chi-restraints excluded: chain e residue 153 ILE Chi-restraints excluded: chain e residue 180 VAL Chi-restraints excluded: chain e residue 247 LEU Chi-restraints excluded: chain e residue 305 SER Chi-restraints excluded: chain e residue 318 VAL Chi-restraints excluded: chain e residue 367 ILE Chi-restraints excluded: chain e residue 386 LEU Chi-restraints excluded: chain e residue 473 LEU Chi-restraints excluded: chain e residue 502 ILE Chi-restraints excluded: chain f residue 27 LEU Chi-restraints excluded: chain g residue 10 THR Chi-restraints excluded: chain g residue 108 ILE Chi-restraints excluded: chain h residue 74 ASP Chi-restraints excluded: chain h residue 105 THR Chi-restraints excluded: chain h residue 126 ASP Chi-restraints excluded: chain i residue 167 TRP Chi-restraints excluded: chain i residue 172 VAL Chi-restraints excluded: chain i residue 194 ARG Chi-restraints excluded: chain i residue 246 VAL Chi-restraints excluded: chain i residue 248 VAL Chi-restraints excluded: chain i residue 255 ASP Chi-restraints excluded: chain i residue 271 THR Chi-restraints excluded: chain i residue 275 TYR Chi-restraints excluded: chain i residue 303 VAL Chi-restraints excluded: chain i residue 315 VAL Chi-restraints excluded: chain i residue 407 ILE Chi-restraints excluded: chain j residue 185 VAL Chi-restraints excluded: chain j residue 257 VAL Chi-restraints excluded: chain j residue 285 ILE Chi-restraints excluded: chain j residue 367 ILE Chi-restraints excluded: chain j residue 494 CYS Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 149 ARG Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 148 ASP Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 76 MET Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 186 MET Chi-restraints excluded: chain E residue 223 ILE Chi-restraints excluded: chain E residue 228 GLU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain F residue 3 ASN Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 220 ILE Chi-restraints excluded: chain k residue 41 SER Chi-restraints excluded: chain k residue 100 THR Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 48 THR Chi-restraints excluded: chain l residue 149 ASN Chi-restraints excluded: chain l residue 186 MET Chi-restraints excluded: chain l residue 223 ILE Chi-restraints excluded: chain l residue 231 VAL Chi-restraints excluded: chain l residue 257 VAL Chi-restraints excluded: chain m residue 41 THR Chi-restraints excluded: chain m residue 48 THR Chi-restraints excluded: chain m residue 76 MET Chi-restraints excluded: chain m residue 149 ASN Chi-restraints excluded: chain m residue 174 THR Chi-restraints excluded: chain m residue 205 ARG Chi-restraints excluded: chain m residue 228 GLU Chi-restraints excluded: chain m residue 231 VAL Chi-restraints excluded: chain m residue 262 VAL Chi-restraints excluded: chain n residue 3 ASN Chi-restraints excluded: chain n residue 49 ILE Chi-restraints excluded: chain n residue 53 GLN Chi-restraints excluded: chain n residue 122 ILE Chi-restraints excluded: chain n residue 220 ILE Chi-restraints excluded: chain o residue 100 THR Chi-restraints excluded: chain o residue 121 ASP Chi-restraints excluded: chain p residue 49 ILE Chi-restraints excluded: chain p residue 59 VAL Chi-restraints excluded: chain p residue 122 ILE Chi-restraints excluded: chain p residue 184 THR Chi-restraints excluded: chain p residue 220 ILE Chi-restraints excluded: chain q residue 17 THR Chi-restraints excluded: chain q residue 58 VAL Chi-restraints excluded: chain q residue 73 VAL Chi-restraints excluded: chain q residue 109 THR Chi-restraints excluded: chain q residue 119 THR Chi-restraints excluded: chain q residue 138 VAL Chi-restraints excluded: chain q residue 267 HIS Chi-restraints excluded: chain q residue 303 VAL Chi-restraints excluded: chain q residue 306 THR Chi-restraints excluded: chain q residue 412 VAL Chi-restraints excluded: chain r residue 17 THR Chi-restraints excluded: chain r residue 109 THR Chi-restraints excluded: chain r residue 119 THR Chi-restraints excluded: chain r residue 138 VAL Chi-restraints excluded: chain r residue 165 ILE Chi-restraints excluded: chain r residue 204 ASN Chi-restraints excluded: chain r residue 227 ASN Chi-restraints excluded: chain r residue 271 THR Chi-restraints excluded: chain s residue 17 THR Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain s residue 82 ILE Chi-restraints excluded: chain s residue 85 LEU Chi-restraints excluded: chain s residue 86 MET Chi-restraints excluded: chain s residue 119 THR Chi-restraints excluded: chain s residue 412 VAL Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 234 VAL Chi-restraints excluded: chain t residue 292 VAL Chi-restraints excluded: chain t residue 302 VAL Chi-restraints excluded: chain u residue 32 LEU Chi-restraints excluded: chain u residue 104 THR Chi-restraints excluded: chain u residue 131 VAL Chi-restraints excluded: chain u residue 141 ILE Chi-restraints excluded: chain u residue 206 THR Chi-restraints excluded: chain u residue 209 ILE Chi-restraints excluded: chain u residue 271 THR Chi-restraints excluded: chain u residue 292 VAL Chi-restraints excluded: chain v residue 42 THR Chi-restraints excluded: chain v residue 104 THR Chi-restraints excluded: chain v residue 119 THR Chi-restraints excluded: chain v residue 133 ILE Chi-restraints excluded: chain v residue 141 ILE Chi-restraints excluded: chain v residue 183 ARG Chi-restraints excluded: chain v residue 201 GLN Chi-restraints excluded: chain v residue 220 THR Chi-restraints excluded: chain v residue 234 VAL Chi-restraints excluded: chain v residue 282 VAL Chi-restraints excluded: chain v residue 292 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1251 random chunks: chunk 406 optimal weight: 9.9990 chunk 1088 optimal weight: 9.9990 chunk 239 optimal weight: 30.0000 chunk 709 optimal weight: 10.0000 chunk 298 optimal weight: 7.9990 chunk 1210 optimal weight: 9.9990 chunk 1004 optimal weight: 9.9990 chunk 560 optimal weight: 7.9990 chunk 100 optimal weight: 20.0000 chunk 400 optimal weight: 5.9990 chunk 635 optimal weight: 10.0000 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 62 HIS J 44 GLN J 236 ASN ** J 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 157 ASN ** O 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 377 GLN V 30 ASN V 35 ASN ** X 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 257 GLN ** Y 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 236 ASN ** e 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 59 GLN ** g 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 411 ASN j 52 HIS F 3 ASN l 37 GLN o 165 GLN ** p 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 184 GLN ** u 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 218 ASN ** u 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 1.212 97614 Z= 0.627 Angle : 0.752 34.695 133089 Z= 0.396 Chirality : 0.051 0.294 15345 Planarity : 0.006 0.085 17451 Dihedral : 6.155 69.423 13647 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.36 % Allowed : 11.74 % Favored : 87.90 % Rotamer: Outliers : 4.53 % Allowed : 17.80 % Favored : 77.66 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 3.18 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.07), residues: 12609 helix: 0.26 (0.11), residues: 2397 sheet: -0.76 (0.10), residues: 2619 loop : -2.38 (0.07), residues: 7593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP t 167 HIS 0.009 0.001 HIS j 204 PHE 0.025 0.002 PHE P 59 TYR 0.054 0.002 TYR X 49 ARG 0.012 0.001 ARG T 177 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25218 Ramachandran restraints generated. 12609 Oldfield, 0 Emsley, 12609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25218 Ramachandran restraints generated. 12609 Oldfield, 0 Emsley, 12609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1323 residues out of total 10284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 466 poor density : 857 time to evaluate : 7.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 65 ARG cc_start: 0.4702 (OUTLIER) cc_final: 0.4403 (ppt170) REVERT: I 62 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.7773 (tt) REVERT: I 114 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8775 (mt) REVERT: J 173 ILE cc_start: 0.6476 (OUTLIER) cc_final: 0.5816 (tt) REVERT: J 189 GLU cc_start: 0.6376 (OUTLIER) cc_final: 0.6072 (pm20) REVERT: K 91 GLN cc_start: 0.3738 (OUTLIER) cc_final: 0.3080 (mt0) REVERT: K 138 ILE cc_start: 0.6467 (OUTLIER) cc_final: 0.6231 (tp) REVERT: K 153 ILE cc_start: 0.8302 (OUTLIER) cc_final: 0.7468 (mt) REVERT: O 25 GLU cc_start: 0.6548 (OUTLIER) cc_final: 0.6099 (mp0) REVERT: O 118 GLN cc_start: 0.6543 (OUTLIER) cc_final: 0.6050 (pt0) REVERT: O 180 PRO cc_start: 0.4632 (Cg_endo) cc_final: 0.4024 (Cg_exo) REVERT: O 314 TYR cc_start: 0.5602 (OUTLIER) cc_final: 0.4594 (m-80) REVERT: P 51 PHE cc_start: 0.7003 (OUTLIER) cc_final: 0.5904 (m-80) REVERT: P 78 TYR cc_start: 0.5529 (p90) cc_final: 0.5260 (p90) REVERT: P 264 PRO cc_start: 0.6803 (Cg_exo) cc_final: 0.6503 (Cg_endo) REVERT: P 313 MET cc_start: 0.2569 (OUTLIER) cc_final: 0.2313 (tpp) REVERT: P 455 ILE cc_start: 0.5232 (mt) cc_final: 0.4987 (mm) REVERT: Q 92 ASP cc_start: 0.6911 (OUTLIER) cc_final: 0.6639 (p0) REVERT: S 89 PHE cc_start: 0.5972 (OUTLIER) cc_final: 0.5247 (p90) REVERT: T 189 GLU cc_start: 0.6226 (OUTLIER) cc_final: 0.5817 (pm20) REVERT: U 59 PHE cc_start: 0.6597 (OUTLIER) cc_final: 0.5333 (t80) REVERT: U 153 ILE cc_start: 0.8266 (OUTLIER) cc_final: 0.7644 (mt) REVERT: W 16 LEU cc_start: 0.6697 (OUTLIER) cc_final: 0.6265 (mt) REVERT: Y 25 GLU cc_start: 0.6862 (OUTLIER) cc_final: 0.6438 (pt0) REVERT: Y 141 ILE cc_start: 0.5863 (mm) cc_final: 0.5623 (mt) REVERT: Z 51 PHE cc_start: 0.6905 (OUTLIER) cc_final: 0.6340 (m-80) REVERT: Z 153 ILE cc_start: 0.8376 (OUTLIER) cc_final: 0.8174 (mt) REVERT: Z 386 LEU cc_start: 0.3408 (OUTLIER) cc_final: 0.2702 (pp) REVERT: a 34 MET cc_start: 0.7783 (mtp) cc_final: 0.7512 (mtp) REVERT: c 49 TYR cc_start: 0.8740 (OUTLIER) cc_final: 0.7854 (p90) REVERT: c 111 ARG cc_start: 0.7088 (mtt180) cc_final: 0.6536 (mtm-85) REVERT: c 133 ARG cc_start: 0.6439 (mmt180) cc_final: 0.5426 (mtp85) REVERT: d 167 TRP cc_start: 0.6223 (m100) cc_final: 0.5963 (m-90) REVERT: d 189 GLU cc_start: 0.6387 (OUTLIER) cc_final: 0.5839 (pm20) REVERT: e 51 PHE cc_start: 0.5940 (OUTLIER) cc_final: 0.5462 (t80) REVERT: e 120 ILE cc_start: 0.3196 (OUTLIER) cc_final: 0.2772 (mt) REVERT: e 153 ILE cc_start: 0.8085 (OUTLIER) cc_final: 0.7311 (mt) REVERT: e 491 MET cc_start: 0.6988 (tpp) cc_final: 0.6250 (tpp) REVERT: h 133 ARG cc_start: 0.5595 (OUTLIER) cc_final: 0.4816 (mmt180) REVERT: i 167 TRP cc_start: 0.2692 (OUTLIER) cc_final: 0.1335 (p90) REVERT: i 180 PRO cc_start: 0.4375 (Cg_endo) cc_final: 0.4066 (Cg_exo) REVERT: i 194 ARG cc_start: 0.7955 (OUTLIER) cc_final: 0.7744 (ttt-90) REVERT: j 120 ILE cc_start: 0.6383 (mp) cc_final: 0.6098 (mt) REVERT: j 153 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.8181 (mt) REVERT: j 285 ILE cc_start: 0.5100 (OUTLIER) cc_final: 0.4890 (mm) REVERT: j 313 MET cc_start: 0.2827 (tmm) cc_final: 0.2524 (tmm) REVERT: A 146 MET cc_start: 0.7805 (tmm) cc_final: 0.7581 (tmm) REVERT: A 153 LEU cc_start: 0.6230 (OUTLIER) cc_final: 0.5699 (mp) REVERT: A 165 PHE cc_start: 0.7124 (m-10) cc_final: 0.6883 (m-10) REVERT: D 72 ILE cc_start: 0.8152 (OUTLIER) cc_final: 0.7830 (mp) REVERT: D 90 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.8002 (mp0) REVERT: E 186 MET cc_start: 0.7983 (OUTLIER) cc_final: 0.7715 (mpp) REVERT: k 72 ILE cc_start: 0.8206 (OUTLIER) cc_final: 0.7822 (mp) REVERT: l 186 MET cc_start: 0.8008 (OUTLIER) cc_final: 0.7706 (mpp) REVERT: l 205 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7639 (ptm160) REVERT: m 112 ASP cc_start: 0.7248 (OUTLIER) cc_final: 0.6986 (p0) REVERT: m 186 MET cc_start: 0.7956 (OUTLIER) cc_final: 0.7720 (mpp) REVERT: m 205 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7369 (ttm110) REVERT: n 53 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.7972 (tm130) REVERT: o 72 ILE cc_start: 0.8265 (OUTLIER) cc_final: 0.7970 (mp) REVERT: q 59 MET cc_start: 0.7091 (tmm) cc_final: 0.6887 (tmm) REVERT: q 102 GLN cc_start: 0.7678 (tp-100) cc_final: 0.7447 (tp-100) REVERT: t 32 LEU cc_start: 0.5575 (OUTLIER) cc_final: 0.5240 (mp) REVERT: v 183 ARG cc_start: 0.4599 (tpt170) cc_final: 0.3860 (mmt90) REVERT: v 267 HIS cc_start: 0.4457 (OUTLIER) cc_final: 0.3753 (t70) outliers start: 466 outliers final: 313 residues processed: 1239 average time/residue: 0.8183 time to fit residues: 1775.1464 Evaluate side-chains 1187 residues out of total 10284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 360 poor density : 827 time to evaluate : 7.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 65 ARG Chi-restraints excluded: chain G residue 73 PHE Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 92 ASP Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 35 ILE Chi-restraints excluded: chain I residue 49 TYR Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain I residue 74 ASP Chi-restraints excluded: chain I residue 75 ASP Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain I residue 126 ASP Chi-restraints excluded: chain I residue 138 THR Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 44 GLN Chi-restraints excluded: chain J residue 69 ILE Chi-restraints excluded: chain J residue 82 ILE Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain J residue 173 ILE Chi-restraints excluded: chain J residue 189 GLU Chi-restraints excluded: chain J residue 209 ILE Chi-restraints excluded: chain J residue 282 VAL Chi-restraints excluded: chain J residue 319 VAL Chi-restraints excluded: chain J residue 412 VAL Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 91 GLN Chi-restraints excluded: chain K residue 138 ILE Chi-restraints excluded: chain K residue 153 ILE Chi-restraints excluded: chain K residue 170 LEU Chi-restraints excluded: chain K residue 193 MET Chi-restraints excluded: chain K residue 247 LEU Chi-restraints excluded: chain K residue 270 THR Chi-restraints excluded: chain K residue 308 VAL Chi-restraints excluded: chain K residue 408 VAL Chi-restraints excluded: chain K residue 469 VAL Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 41 MET Chi-restraints excluded: chain M residue 46 ASN Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain N residue 14 VAL Chi-restraints excluded: chain N residue 120 LEU Chi-restraints excluded: chain O residue 25 GLU Chi-restraints excluded: chain O residue 42 THR Chi-restraints excluded: chain O residue 68 THR Chi-restraints excluded: chain O residue 113 THR Chi-restraints excluded: chain O residue 118 GLN Chi-restraints excluded: chain O residue 119 THR Chi-restraints excluded: chain O residue 131 VAL Chi-restraints excluded: chain O residue 172 VAL Chi-restraints excluded: chain O residue 234 VAL Chi-restraints excluded: chain O residue 240 PHE Chi-restraints excluded: chain O residue 246 VAL Chi-restraints excluded: chain O residue 248 VAL Chi-restraints excluded: chain O residue 314 TYR Chi-restraints excluded: chain O residue 315 VAL Chi-restraints excluded: chain O residue 326 VAL Chi-restraints excluded: chain O residue 380 CYS Chi-restraints excluded: chain P residue 51 PHE Chi-restraints excluded: chain P residue 124 ASP Chi-restraints excluded: chain P residue 143 ILE Chi-restraints excluded: chain P residue 166 LEU Chi-restraints excluded: chain P residue 171 MET Chi-restraints excluded: chain P residue 185 VAL Chi-restraints excluded: chain P residue 256 TYR Chi-restraints excluded: chain P residue 257 VAL Chi-restraints excluded: chain P residue 313 MET Chi-restraints excluded: chain P residue 367 ILE Chi-restraints excluded: chain P residue 388 THR Chi-restraints excluded: chain P residue 473 LEU Chi-restraints excluded: chain P residue 498 ASP Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain Q residue 92 ASP Chi-restraints excluded: chain R residue 27 ASP Chi-restraints excluded: chain R residue 41 MET Chi-restraints excluded: chain S residue 18 SER Chi-restraints excluded: chain S residue 74 ASP Chi-restraints excluded: chain S residue 89 PHE Chi-restraints excluded: chain S residue 101 THR Chi-restraints excluded: chain T residue 19 ASP Chi-restraints excluded: chain T residue 69 ILE Chi-restraints excluded: chain T residue 119 THR Chi-restraints excluded: chain T residue 128 MET Chi-restraints excluded: chain T residue 185 MET Chi-restraints excluded: chain T residue 189 GLU Chi-restraints excluded: chain T residue 279 ASN Chi-restraints excluded: chain T residue 318 THR Chi-restraints excluded: chain T residue 394 THR Chi-restraints excluded: chain T residue 414 VAL Chi-restraints excluded: chain U residue 10 ILE Chi-restraints excluded: chain U residue 50 VAL Chi-restraints excluded: chain U residue 57 ASN Chi-restraints excluded: chain U residue 59 PHE Chi-restraints excluded: chain U residue 65 CYS Chi-restraints excluded: chain U residue 143 ILE Chi-restraints excluded: chain U residue 153 ILE Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 229 THR Chi-restraints excluded: chain U residue 245 CYS Chi-restraints excluded: chain U residue 308 VAL Chi-restraints excluded: chain U residue 361 SER Chi-restraints excluded: chain U residue 400 LEU Chi-restraints excluded: chain U residue 483 MET Chi-restraints excluded: chain U residue 497 CYS Chi-restraints excluded: chain U residue 502 ILE Chi-restraints excluded: chain V residue 49 VAL Chi-restraints excluded: chain V residue 72 VAL Chi-restraints excluded: chain W residue 8 THR Chi-restraints excluded: chain W residue 10 THR Chi-restraints excluded: chain W residue 16 LEU Chi-restraints excluded: chain W residue 94 ILE Chi-restraints excluded: chain X residue 14 VAL Chi-restraints excluded: chain X residue 120 LEU Chi-restraints excluded: chain Y residue 25 GLU Chi-restraints excluded: chain Y residue 68 THR Chi-restraints excluded: chain Y residue 111 ILE Chi-restraints excluded: chain Y residue 113 THR Chi-restraints excluded: chain Y residue 172 VAL Chi-restraints excluded: chain Y residue 195 VAL Chi-restraints excluded: chain Y residue 225 ILE Chi-restraints excluded: chain Y residue 248 VAL Chi-restraints excluded: chain Y residue 268 ASN Chi-restraints excluded: chain Y residue 290 VAL Chi-restraints excluded: chain Y residue 307 THR Chi-restraints excluded: chain Y residue 380 CYS Chi-restraints excluded: chain Z residue 51 PHE Chi-restraints excluded: chain Z residue 120 ILE Chi-restraints excluded: chain Z residue 153 ILE Chi-restraints excluded: chain Z residue 180 VAL Chi-restraints excluded: chain Z residue 195 LEU Chi-restraints excluded: chain Z residue 230 VAL Chi-restraints excluded: chain Z residue 337 THR Chi-restraints excluded: chain Z residue 353 GLU Chi-restraints excluded: chain Z residue 367 ILE Chi-restraints excluded: chain Z residue 386 LEU Chi-restraints excluded: chain Z residue 474 ASN Chi-restraints excluded: chain a residue 32 ASP Chi-restraints excluded: chain a residue 49 VAL Chi-restraints excluded: chain b residue 10 THR Chi-restraints excluded: chain c residue 14 VAL Chi-restraints excluded: chain c residue 35 ILE Chi-restraints excluded: chain c residue 49 TYR Chi-restraints excluded: chain c residue 92 LEU Chi-restraints excluded: chain c residue 120 LEU Chi-restraints excluded: chain c residue 128 ILE Chi-restraints excluded: chain c residue 150 GLN Chi-restraints excluded: chain d residue 10 THR Chi-restraints excluded: chain d residue 14 VAL Chi-restraints excluded: chain d residue 104 THR Chi-restraints excluded: chain d residue 124 ILE Chi-restraints excluded: chain d residue 189 GLU Chi-restraints excluded: chain d residue 227 ASN Chi-restraints excluded: chain d residue 275 TYR Chi-restraints excluded: chain d residue 282 VAL Chi-restraints excluded: chain d residue 319 VAL Chi-restraints excluded: chain d residue 351 VAL Chi-restraints excluded: chain d residue 394 THR Chi-restraints excluded: chain d residue 399 MET Chi-restraints excluded: chain d residue 417 VAL Chi-restraints excluded: chain e residue 10 ILE Chi-restraints excluded: chain e residue 51 PHE Chi-restraints excluded: chain e residue 120 ILE Chi-restraints excluded: chain e residue 153 ILE Chi-restraints excluded: chain e residue 180 VAL Chi-restraints excluded: chain e residue 247 LEU Chi-restraints excluded: chain e residue 285 ILE Chi-restraints excluded: chain e residue 305 SER Chi-restraints excluded: chain e residue 318 VAL Chi-restraints excluded: chain e residue 367 ILE Chi-restraints excluded: chain e residue 386 LEU Chi-restraints excluded: chain e residue 473 LEU Chi-restraints excluded: chain e residue 502 ILE Chi-restraints excluded: chain f residue 27 LEU Chi-restraints excluded: chain g residue 10 THR Chi-restraints excluded: chain g residue 98 VAL Chi-restraints excluded: chain g residue 108 ILE Chi-restraints excluded: chain h residue 74 ASP Chi-restraints excluded: chain h residue 105 THR Chi-restraints excluded: chain h residue 133 ARG Chi-restraints excluded: chain i residue 138 VAL Chi-restraints excluded: chain i residue 167 TRP Chi-restraints excluded: chain i residue 172 VAL Chi-restraints excluded: chain i residue 194 ARG Chi-restraints excluded: chain i residue 238 VAL Chi-restraints excluded: chain i residue 246 VAL Chi-restraints excluded: chain i residue 248 VAL Chi-restraints excluded: chain i residue 255 ASP Chi-restraints excluded: chain i residue 271 THR Chi-restraints excluded: chain i residue 275 TYR Chi-restraints excluded: chain i residue 303 VAL Chi-restraints excluded: chain i residue 315 VAL Chi-restraints excluded: chain i residue 407 ILE Chi-restraints excluded: chain j residue 78 TYR Chi-restraints excluded: chain j residue 153 ILE Chi-restraints excluded: chain j residue 185 VAL Chi-restraints excluded: chain j residue 257 VAL Chi-restraints excluded: chain j residue 285 ILE Chi-restraints excluded: chain j residue 367 ILE Chi-restraints excluded: chain j residue 494 CYS Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 149 ARG Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 148 ASP Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain E residue 41 THR Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 76 MET Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 186 MET Chi-restraints excluded: chain E residue 223 ILE Chi-restraints excluded: chain E residue 228 GLU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain F residue 3 ASN Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain F residue 220 ILE Chi-restraints excluded: chain k residue 13 THR Chi-restraints excluded: chain k residue 41 SER Chi-restraints excluded: chain k residue 72 ILE Chi-restraints excluded: chain k residue 100 THR Chi-restraints excluded: chain k residue 182 ILE Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 48 THR Chi-restraints excluded: chain l residue 139 THR Chi-restraints excluded: chain l residue 141 VAL Chi-restraints excluded: chain l residue 149 ASN Chi-restraints excluded: chain l residue 156 ILE Chi-restraints excluded: chain l residue 186 MET Chi-restraints excluded: chain l residue 205 ARG Chi-restraints excluded: chain l residue 223 ILE Chi-restraints excluded: chain l residue 231 VAL Chi-restraints excluded: chain l residue 257 VAL Chi-restraints excluded: chain l residue 264 THR Chi-restraints excluded: chain m residue 41 THR Chi-restraints excluded: chain m residue 48 THR Chi-restraints excluded: chain m residue 76 MET Chi-restraints excluded: chain m residue 112 ASP Chi-restraints excluded: chain m residue 139 THR Chi-restraints excluded: chain m residue 149 ASN Chi-restraints excluded: chain m residue 174 THR Chi-restraints excluded: chain m residue 186 MET Chi-restraints excluded: chain m residue 205 ARG Chi-restraints excluded: chain m residue 228 GLU Chi-restraints excluded: chain m residue 231 VAL Chi-restraints excluded: chain m residue 257 VAL Chi-restraints excluded: chain m residue 262 VAL Chi-restraints excluded: chain n residue 3 ASN Chi-restraints excluded: chain n residue 49 ILE Chi-restraints excluded: chain n residue 53 GLN Chi-restraints excluded: chain n residue 99 TYR Chi-restraints excluded: chain n residue 109 LEU Chi-restraints excluded: chain n residue 122 ILE Chi-restraints excluded: chain n residue 220 ILE Chi-restraints excluded: chain o residue 72 ILE Chi-restraints excluded: chain o residue 100 THR Chi-restraints excluded: chain o residue 121 ASP Chi-restraints excluded: chain o residue 182 ILE Chi-restraints excluded: chain p residue 49 ILE Chi-restraints excluded: chain p residue 59 VAL Chi-restraints excluded: chain p residue 122 ILE Chi-restraints excluded: chain p residue 164 ASP Chi-restraints excluded: chain p residue 184 THR Chi-restraints excluded: chain p residue 220 ILE Chi-restraints excluded: chain q residue 17 THR Chi-restraints excluded: chain q residue 58 VAL Chi-restraints excluded: chain q residue 73 VAL Chi-restraints excluded: chain q residue 88 ILE Chi-restraints excluded: chain q residue 109 THR Chi-restraints excluded: chain q residue 119 THR Chi-restraints excluded: chain q residue 138 VAL Chi-restraints excluded: chain q residue 165 ILE Chi-restraints excluded: chain q residue 216 VAL Chi-restraints excluded: chain q residue 267 HIS Chi-restraints excluded: chain q residue 303 VAL Chi-restraints excluded: chain q residue 306 THR Chi-restraints excluded: chain q residue 412 VAL Chi-restraints excluded: chain r residue 17 THR Chi-restraints excluded: chain r residue 82 ILE Chi-restraints excluded: chain r residue 109 THR Chi-restraints excluded: chain r residue 119 THR Chi-restraints excluded: chain r residue 138 VAL Chi-restraints excluded: chain r residue 165 ILE Chi-restraints excluded: chain r residue 204 ASN Chi-restraints excluded: chain r residue 216 VAL Chi-restraints excluded: chain r residue 227 ASN Chi-restraints excluded: chain r residue 234 VAL Chi-restraints excluded: chain r residue 267 HIS Chi-restraints excluded: chain r residue 271 THR Chi-restraints excluded: chain r residue 306 THR Chi-restraints excluded: chain r residue 412 VAL Chi-restraints excluded: chain s residue 17 THR Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain s residue 82 ILE Chi-restraints excluded: chain s residue 85 LEU Chi-restraints excluded: chain s residue 86 MET Chi-restraints excluded: chain s residue 119 THR Chi-restraints excluded: chain s residue 128 MET Chi-restraints excluded: chain s residue 133 ILE Chi-restraints excluded: chain s residue 165 ILE Chi-restraints excluded: chain s residue 271 THR Chi-restraints excluded: chain s residue 282 VAL Chi-restraints excluded: chain s residue 303 VAL Chi-restraints excluded: chain s residue 306 THR Chi-restraints excluded: chain s residue 412 VAL Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 119 THR Chi-restraints excluded: chain t residue 234 VAL Chi-restraints excluded: chain t residue 282 VAL Chi-restraints excluded: chain t residue 292 VAL Chi-restraints excluded: chain t residue 302 VAL Chi-restraints excluded: chain u residue 32 LEU Chi-restraints excluded: chain u residue 104 THR Chi-restraints excluded: chain u residue 119 THR Chi-restraints excluded: chain u residue 131 VAL Chi-restraints excluded: chain u residue 141 ILE Chi-restraints excluded: chain u residue 206 THR Chi-restraints excluded: chain u residue 209 ILE Chi-restraints excluded: chain u residue 226 GLU Chi-restraints excluded: chain u residue 234 VAL Chi-restraints excluded: chain u residue 271 THR Chi-restraints excluded: chain u residue 292 VAL Chi-restraints excluded: chain v residue 42 THR Chi-restraints excluded: chain v residue 96 THR Chi-restraints excluded: chain v residue 104 THR Chi-restraints excluded: chain v residue 141 ILE Chi-restraints excluded: chain v residue 201 GLN Chi-restraints excluded: chain v residue 220 THR Chi-restraints excluded: chain v residue 226 GLU Chi-restraints excluded: chain v residue 234 VAL Chi-restraints excluded: chain v residue 267 HIS Chi-restraints excluded: chain v residue 282 VAL Chi-restraints excluded: chain v residue 292 VAL Chi-restraints excluded: chain v residue 368 ILE Chi-restraints excluded: chain v residue 398 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1251 random chunks: chunk 1166 optimal weight: 0.8980 chunk 136 optimal weight: 0.9980 chunk 689 optimal weight: 10.0000 chunk 883 optimal weight: 2.9990 chunk 684 optimal weight: 2.9990 chunk 1018 optimal weight: 0.9980 chunk 675 optimal weight: 40.0000 chunk 1205 optimal weight: 20.0000 chunk 754 optimal weight: 5.9990 chunk 735 optimal weight: 6.9990 chunk 556 optimal weight: 10.0000 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 33 GLN ** O 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 157 ASN ** T 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 377 GLN U 11 GLN U 29 GLN ** V 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 321 GLN Z 19 ASN ** a 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 268 ASN e 402 ASN ** e 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 411 ASN F 3 ASN ** n 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 165 GLN ** p 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 1.206 97614 Z= 0.515 Angle : 0.620 33.504 133089 Z= 0.322 Chirality : 0.046 0.275 15345 Planarity : 0.005 0.083 17451 Dihedral : 5.428 59.602 13647 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.35 % Allowed : 8.04 % Favored : 91.61 % Rotamer: Outliers : 2.72 % Allowed : 20.18 % Favored : 77.10 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 3.18 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.07), residues: 12609 helix: 0.79 (0.11), residues: 2391 sheet: -0.56 (0.10), residues: 2577 loop : -2.19 (0.07), residues: 7641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP t 167 HIS 0.007 0.001 HIS j 204 PHE 0.020 0.001 PHE Z 437 TYR 0.049 0.001 TYR X 49 ARG 0.007 0.000 ARG U 296 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25218 Ramachandran restraints generated. 12609 Oldfield, 0 Emsley, 12609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25218 Ramachandran restraints generated. 12609 Oldfield, 0 Emsley, 12609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1188 residues out of total 10284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 280 poor density : 908 time to evaluate : 8.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 65 ARG cc_start: 0.4156 (OUTLIER) cc_final: 0.3933 (ppt170) REVERT: J 69 ILE cc_start: 0.7551 (OUTLIER) cc_final: 0.7122 (tt) REVERT: J 173 ILE cc_start: 0.6321 (OUTLIER) cc_final: 0.5778 (tt) REVERT: J 189 GLU cc_start: 0.5912 (OUTLIER) cc_final: 0.5644 (pm20) REVERT: K 91 GLN cc_start: 0.4056 (OUTLIER) cc_final: 0.3427 (mt0) REVERT: K 153 ILE cc_start: 0.8182 (OUTLIER) cc_final: 0.7566 (mt) REVERT: K 189 ASP cc_start: 0.5277 (OUTLIER) cc_final: 0.4786 (p0) REVERT: O 25 GLU cc_start: 0.6627 (OUTLIER) cc_final: 0.6169 (mp0) REVERT: O 147 GLU cc_start: 0.5004 (OUTLIER) cc_final: 0.4717 (mt-10) REVERT: O 180 PRO cc_start: 0.4653 (Cg_endo) cc_final: 0.4236 (Cg_exo) REVERT: O 300 LYS cc_start: 0.5069 (OUTLIER) cc_final: 0.4784 (pttm) REVERT: O 314 TYR cc_start: 0.5071 (OUTLIER) cc_final: 0.4617 (m-80) REVERT: O 413 ARG cc_start: 0.5253 (mmm160) cc_final: 0.4979 (mmp-170) REVERT: P 51 PHE cc_start: 0.7122 (OUTLIER) cc_final: 0.5883 (m-80) REVERT: P 78 TYR cc_start: 0.5394 (p90) cc_final: 0.5155 (p90) REVERT: P 264 PRO cc_start: 0.6580 (Cg_exo) cc_final: 0.6343 (Cg_endo) REVERT: P 485 ASP cc_start: 0.5896 (OUTLIER) cc_final: 0.4775 (p0) REVERT: Q 92 ASP cc_start: 0.6558 (OUTLIER) cc_final: 0.6277 (p0) REVERT: S 89 PHE cc_start: 0.5670 (OUTLIER) cc_final: 0.5144 (p90) REVERT: T 189 GLU cc_start: 0.5773 (OUTLIER) cc_final: 0.5390 (pm20) REVERT: T 241 THR cc_start: 0.5988 (OUTLIER) cc_final: 0.5476 (m) REVERT: U 59 PHE cc_start: 0.6302 (OUTLIER) cc_final: 0.5256 (t80) REVERT: U 120 ILE cc_start: 0.3262 (OUTLIER) cc_final: 0.2821 (mp) REVERT: W 16 LEU cc_start: 0.6640 (OUTLIER) cc_final: 0.6256 (mt) REVERT: X 120 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8679 (tp) REVERT: Y 25 GLU cc_start: 0.6865 (OUTLIER) cc_final: 0.6244 (pt0) REVERT: Y 141 ILE cc_start: 0.5808 (mm) cc_final: 0.5548 (mt) REVERT: Z 51 PHE cc_start: 0.6846 (OUTLIER) cc_final: 0.6248 (m-80) REVERT: Z 386 LEU cc_start: 0.3497 (OUTLIER) cc_final: 0.2786 (pp) REVERT: c 49 TYR cc_start: 0.8552 (OUTLIER) cc_final: 0.7529 (p90) REVERT: c 111 ARG cc_start: 0.7036 (mtt180) cc_final: 0.6523 (mtm-85) REVERT: c 133 ARG cc_start: 0.6275 (mmt180) cc_final: 0.5374 (mtp85) REVERT: d 189 GLU cc_start: 0.5929 (OUTLIER) cc_final: 0.5429 (pm20) REVERT: e 51 PHE cc_start: 0.5701 (OUTLIER) cc_final: 0.5122 (t80) REVERT: e 120 ILE cc_start: 0.3198 (OUTLIER) cc_final: 0.2716 (mt) REVERT: e 169 TYR cc_start: 0.6753 (t80) cc_final: 0.6162 (t80) REVERT: e 473 LEU cc_start: 0.6478 (OUTLIER) cc_final: 0.6213 (mm) REVERT: e 491 MET cc_start: 0.7072 (tpp) cc_final: 0.6450 (tpp) REVERT: h 105 THR cc_start: 0.7610 (OUTLIER) cc_final: 0.7132 (m) REVERT: i 167 TRP cc_start: 0.2793 (OUTLIER) cc_final: 0.1565 (p90) REVERT: i 180 PRO cc_start: 0.4625 (Cg_endo) cc_final: 0.4243 (Cg_exo) REVERT: i 194 ARG cc_start: 0.7960 (OUTLIER) cc_final: 0.7658 (ttt-90) REVERT: j 120 ILE cc_start: 0.6182 (mp) cc_final: 0.5857 (mt) REVERT: A 153 LEU cc_start: 0.6171 (OUTLIER) cc_final: 0.5674 (mp) REVERT: D 90 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7902 (mp0) REVERT: E 186 MET cc_start: 0.7958 (OUTLIER) cc_final: 0.7650 (mpp) REVERT: l 186 MET cc_start: 0.7977 (OUTLIER) cc_final: 0.7605 (mpp) REVERT: m 112 ASP cc_start: 0.7129 (OUTLIER) cc_final: 0.6812 (p0) REVERT: m 186 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.7625 (mpp) REVERT: n 53 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.7987 (tm130) REVERT: o 90 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7893 (mp0) REVERT: q 234 VAL cc_start: 0.5487 (OUTLIER) cc_final: 0.5202 (t) REVERT: r 59 MET cc_start: 0.7165 (tmm) cc_final: 0.6797 (tmm) REVERT: s 128 MET cc_start: 0.6282 (mtp) cc_final: 0.5992 (mtp) REVERT: s 185 MET cc_start: 0.6476 (tpp) cc_final: 0.5988 (ttt) REVERT: t 32 LEU cc_start: 0.5513 (OUTLIER) cc_final: 0.5189 (mp) REVERT: t 64 ARG cc_start: 0.7097 (tmt170) cc_final: 0.6841 (tpt90) REVERT: t 183 ARG cc_start: 0.4805 (tpt170) cc_final: 0.4250 (mmt90) REVERT: v 64 ARG cc_start: 0.7207 (tmt170) cc_final: 0.6912 (tpt90) REVERT: v 183 ARG cc_start: 0.4246 (OUTLIER) cc_final: 0.3510 (mmt90) outliers start: 280 outliers final: 194 residues processed: 1128 average time/residue: 0.8368 time to fit residues: 1642.2523 Evaluate side-chains 1098 residues out of total 10284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 862 time to evaluate : 7.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 65 ARG Chi-restraints excluded: chain G residue 92 ASP Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 49 TYR Chi-restraints excluded: chain I residue 74 ASP Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain I residue 126 ASP Chi-restraints excluded: chain J residue 69 ILE Chi-restraints excluded: chain J residue 82 ILE Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain J residue 141 ILE Chi-restraints excluded: chain J residue 173 ILE Chi-restraints excluded: chain J residue 189 GLU Chi-restraints excluded: chain J residue 209 ILE Chi-restraints excluded: chain J residue 282 VAL Chi-restraints excluded: chain J residue 318 THR Chi-restraints excluded: chain J residue 414 VAL Chi-restraints excluded: chain K residue 91 GLN Chi-restraints excluded: chain K residue 153 ILE Chi-restraints excluded: chain K residue 170 LEU Chi-restraints excluded: chain K residue 189 ASP Chi-restraints excluded: chain K residue 193 MET Chi-restraints excluded: chain K residue 308 VAL Chi-restraints excluded: chain K residue 359 ILE Chi-restraints excluded: chain K residue 408 VAL Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 46 ASN Chi-restraints excluded: chain N residue 14 VAL Chi-restraints excluded: chain O residue 25 GLU Chi-restraints excluded: chain O residue 113 THR Chi-restraints excluded: chain O residue 118 GLN Chi-restraints excluded: chain O residue 119 THR Chi-restraints excluded: chain O residue 147 GLU Chi-restraints excluded: chain O residue 172 VAL Chi-restraints excluded: chain O residue 234 VAL Chi-restraints excluded: chain O residue 240 PHE Chi-restraints excluded: chain O residue 246 VAL Chi-restraints excluded: chain O residue 300 LYS Chi-restraints excluded: chain O residue 314 TYR Chi-restraints excluded: chain O residue 315 VAL Chi-restraints excluded: chain O residue 326 VAL Chi-restraints excluded: chain O residue 380 CYS Chi-restraints excluded: chain O residue 412 VAL Chi-restraints excluded: chain P residue 51 PHE Chi-restraints excluded: chain P residue 143 ILE Chi-restraints excluded: chain P residue 171 MET Chi-restraints excluded: chain P residue 209 THR Chi-restraints excluded: chain P residue 256 TYR Chi-restraints excluded: chain P residue 367 ILE Chi-restraints excluded: chain P residue 388 THR Chi-restraints excluded: chain P residue 473 LEU Chi-restraints excluded: chain P residue 485 ASP Chi-restraints excluded: chain Q residue 32 ASP Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain Q residue 92 ASP Chi-restraints excluded: chain R residue 27 ASP Chi-restraints excluded: chain S residue 74 ASP Chi-restraints excluded: chain S residue 89 PHE Chi-restraints excluded: chain S residue 101 THR Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 19 ASP Chi-restraints excluded: chain T residue 69 ILE Chi-restraints excluded: chain T residue 119 THR Chi-restraints excluded: chain T residue 189 GLU Chi-restraints excluded: chain T residue 241 THR Chi-restraints excluded: chain T residue 279 ASN Chi-restraints excluded: chain T residue 394 THR Chi-restraints excluded: chain T residue 414 VAL Chi-restraints excluded: chain U residue 10 ILE Chi-restraints excluded: chain U residue 57 ASN Chi-restraints excluded: chain U residue 59 PHE Chi-restraints excluded: chain U residue 120 ILE Chi-restraints excluded: chain U residue 143 ILE Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 229 THR Chi-restraints excluded: chain U residue 245 CYS Chi-restraints excluded: chain U residue 308 VAL Chi-restraints excluded: chain U residue 497 CYS Chi-restraints excluded: chain V residue 49 VAL Chi-restraints excluded: chain V residue 72 VAL Chi-restraints excluded: chain W residue 16 LEU Chi-restraints excluded: chain X residue 120 LEU Chi-restraints excluded: chain Y residue 25 GLU Chi-restraints excluded: chain Y residue 111 ILE Chi-restraints excluded: chain Y residue 113 THR Chi-restraints excluded: chain Y residue 225 ILE Chi-restraints excluded: chain Y residue 290 VAL Chi-restraints excluded: chain Y residue 307 THR Chi-restraints excluded: chain Y residue 380 CYS Chi-restraints excluded: chain Z residue 19 ASN Chi-restraints excluded: chain Z residue 51 PHE Chi-restraints excluded: chain Z residue 195 LEU Chi-restraints excluded: chain Z residue 386 LEU Chi-restraints excluded: chain Z residue 499 VAL Chi-restraints excluded: chain a residue 32 ASP Chi-restraints excluded: chain b residue 10 THR Chi-restraints excluded: chain c residue 14 VAL Chi-restraints excluded: chain c residue 49 TYR Chi-restraints excluded: chain c residue 92 LEU Chi-restraints excluded: chain c residue 150 GLN Chi-restraints excluded: chain d residue 10 THR Chi-restraints excluded: chain d residue 13 ILE Chi-restraints excluded: chain d residue 124 ILE Chi-restraints excluded: chain d residue 157 ASN Chi-restraints excluded: chain d residue 173 ILE Chi-restraints excluded: chain d residue 189 GLU Chi-restraints excluded: chain d residue 275 TYR Chi-restraints excluded: chain d residue 351 VAL Chi-restraints excluded: chain d residue 394 THR Chi-restraints excluded: chain d residue 399 MET Chi-restraints excluded: chain e residue 10 ILE Chi-restraints excluded: chain e residue 51 PHE Chi-restraints excluded: chain e residue 120 ILE Chi-restraints excluded: chain e residue 180 VAL Chi-restraints excluded: chain e residue 246 LYS Chi-restraints excluded: chain e residue 247 LEU Chi-restraints excluded: chain e residue 367 ILE Chi-restraints excluded: chain e residue 386 LEU Chi-restraints excluded: chain e residue 473 LEU Chi-restraints excluded: chain f residue 27 LEU Chi-restraints excluded: chain g residue 108 ILE Chi-restraints excluded: chain h residue 30 ASP Chi-restraints excluded: chain h residue 74 ASP Chi-restraints excluded: chain h residue 105 THR Chi-restraints excluded: chain h residue 126 ASP Chi-restraints excluded: chain i residue 167 TRP Chi-restraints excluded: chain i residue 172 VAL Chi-restraints excluded: chain i residue 179 ASP Chi-restraints excluded: chain i residue 194 ARG Chi-restraints excluded: chain i residue 238 VAL Chi-restraints excluded: chain i residue 246 VAL Chi-restraints excluded: chain i residue 255 ASP Chi-restraints excluded: chain i residue 275 TYR Chi-restraints excluded: chain i residue 303 VAL Chi-restraints excluded: chain i residue 318 THR Chi-restraints excluded: chain j residue 257 VAL Chi-restraints excluded: chain j residue 494 CYS Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 148 ASP Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 76 MET Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 186 MET Chi-restraints excluded: chain E residue 223 ILE Chi-restraints excluded: chain E residue 228 GLU Chi-restraints excluded: chain F residue 3 ASN Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 220 ILE Chi-restraints excluded: chain k residue 100 THR Chi-restraints excluded: chain l residue 48 THR Chi-restraints excluded: chain l residue 139 THR Chi-restraints excluded: chain l residue 149 ASN Chi-restraints excluded: chain l residue 186 MET Chi-restraints excluded: chain m residue 76 MET Chi-restraints excluded: chain m residue 112 ASP Chi-restraints excluded: chain m residue 139 THR Chi-restraints excluded: chain m residue 149 ASN Chi-restraints excluded: chain m residue 186 MET Chi-restraints excluded: chain m residue 228 GLU Chi-restraints excluded: chain m residue 262 VAL Chi-restraints excluded: chain n residue 3 ASN Chi-restraints excluded: chain n residue 49 ILE Chi-restraints excluded: chain n residue 53 GLN Chi-restraints excluded: chain o residue 100 THR Chi-restraints excluded: chain p residue 3 ASN Chi-restraints excluded: chain p residue 49 ILE Chi-restraints excluded: chain p residue 110 GLU Chi-restraints excluded: chain p residue 164 ASP Chi-restraints excluded: chain q residue 17 THR Chi-restraints excluded: chain q residue 73 VAL Chi-restraints excluded: chain q residue 119 THR Chi-restraints excluded: chain q residue 234 VAL Chi-restraints excluded: chain q residue 267 HIS Chi-restraints excluded: chain q residue 303 VAL Chi-restraints excluded: chain q residue 412 VAL Chi-restraints excluded: chain r residue 17 THR Chi-restraints excluded: chain r residue 82 ILE Chi-restraints excluded: chain r residue 119 THR Chi-restraints excluded: chain r residue 165 ILE Chi-restraints excluded: chain r residue 204 ASN Chi-restraints excluded: chain r residue 227 ASN Chi-restraints excluded: chain r residue 267 HIS Chi-restraints excluded: chain r residue 271 THR Chi-restraints excluded: chain r residue 412 VAL Chi-restraints excluded: chain s residue 17 THR Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain s residue 82 ILE Chi-restraints excluded: chain s residue 86 MET Chi-restraints excluded: chain s residue 119 THR Chi-restraints excluded: chain s residue 165 ILE Chi-restraints excluded: chain s residue 303 VAL Chi-restraints excluded: chain s residue 412 VAL Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 111 ILE Chi-restraints excluded: chain t residue 119 THR Chi-restraints excluded: chain t residue 172 VAL Chi-restraints excluded: chain t residue 234 VAL Chi-restraints excluded: chain t residue 250 VAL Chi-restraints excluded: chain t residue 282 VAL Chi-restraints excluded: chain t residue 292 VAL Chi-restraints excluded: chain t residue 302 VAL Chi-restraints excluded: chain u residue 32 LEU Chi-restraints excluded: chain u residue 96 THR Chi-restraints excluded: chain u residue 104 THR Chi-restraints excluded: chain u residue 119 THR Chi-restraints excluded: chain u residue 141 ILE Chi-restraints excluded: chain u residue 206 THR Chi-restraints excluded: chain u residue 234 VAL Chi-restraints excluded: chain u residue 271 THR Chi-restraints excluded: chain u residue 292 VAL Chi-restraints excluded: chain u residue 307 THR Chi-restraints excluded: chain v residue 42 THR Chi-restraints excluded: chain v residue 96 THR Chi-restraints excluded: chain v residue 119 THR Chi-restraints excluded: chain v residue 141 ILE Chi-restraints excluded: chain v residue 183 ARG Chi-restraints excluded: chain v residue 220 THR Chi-restraints excluded: chain v residue 226 GLU Chi-restraints excluded: chain v residue 234 VAL Chi-restraints excluded: chain v residue 282 VAL Chi-restraints excluded: chain v residue 292 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1251 random chunks: chunk 745 optimal weight: 20.0000 chunk 481 optimal weight: 40.0000 chunk 720 optimal weight: 6.9990 chunk 363 optimal weight: 20.0000 chunk 236 optimal weight: 6.9990 chunk 233 optimal weight: 5.9990 chunk 766 optimal weight: 5.9990 chunk 821 optimal weight: 9.9990 chunk 596 optimal weight: 9.9990 chunk 112 optimal weight: 9.9990 chunk 947 optimal weight: 4.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 44 GLN ** J 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 377 GLN V 35 ASN ** X 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 411 ASN Z 19 ASN ** a 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 411 ASN F 3 ASN o 165 GLN ** q 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 321 GLN ** v 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 1.210 97614 Z= 0.574 Angle : 0.686 33.852 133089 Z= 0.357 Chirality : 0.048 0.269 15345 Planarity : 0.006 0.082 17451 Dihedral : 5.718 63.682 13647 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.34 % Allowed : 10.93 % Favored : 88.73 % Rotamer: Outliers : 3.74 % Allowed : 19.83 % Favored : 76.43 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 3.18 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.07), residues: 12609 helix: 0.60 (0.11), residues: 2397 sheet: -0.71 (0.10), residues: 2574 loop : -2.26 (0.07), residues: 7638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP t 167 HIS 0.008 0.001 HIS Z 18 PHE 0.023 0.002 PHE j 437 TYR 0.050 0.002 TYR X 49 ARG 0.007 0.001 ARG u 55 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25218 Ramachandran restraints generated. 12609 Oldfield, 0 Emsley, 12609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25218 Ramachandran restraints generated. 12609 Oldfield, 0 Emsley, 12609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1240 residues out of total 10284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 385 poor density : 855 time to evaluate : 8.191 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 65 ARG cc_start: 0.4377 (OUTLIER) cc_final: 0.4097 (ppt170) REVERT: I 62 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.7783 (tt) REVERT: J 173 ILE cc_start: 0.6497 (OUTLIER) cc_final: 0.5931 (tt) REVERT: J 189 GLU cc_start: 0.6173 (OUTLIER) cc_final: 0.5893 (pm20) REVERT: K 91 GLN cc_start: 0.3705 (OUTLIER) cc_final: 0.3098 (mt0) REVERT: K 153 ILE cc_start: 0.8292 (OUTLIER) cc_final: 0.7544 (mt) REVERT: K 189 ASP cc_start: 0.5579 (OUTLIER) cc_final: 0.5110 (p0) REVERT: O 25 GLU cc_start: 0.6655 (OUTLIER) cc_final: 0.6181 (mp0) REVERT: O 177 ARG cc_start: 0.6519 (ttm170) cc_final: 0.6249 (ttt90) REVERT: O 180 PRO cc_start: 0.4916 (Cg_endo) cc_final: 0.4476 (Cg_exo) REVERT: O 300 LYS cc_start: 0.5185 (OUTLIER) cc_final: 0.4940 (pttm) REVERT: O 314 TYR cc_start: 0.5172 (OUTLIER) cc_final: 0.4640 (m-80) REVERT: P 51 PHE cc_start: 0.6911 (OUTLIER) cc_final: 0.5726 (m-80) REVERT: P 78 TYR cc_start: 0.5297 (p90) cc_final: 0.5032 (p90) REVERT: P 485 ASP cc_start: 0.5781 (OUTLIER) cc_final: 0.4747 (p0) REVERT: Q 92 ASP cc_start: 0.6745 (OUTLIER) cc_final: 0.6534 (p0) REVERT: R 79 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7456 (mp) REVERT: S 89 PHE cc_start: 0.5871 (OUTLIER) cc_final: 0.5154 (p90) REVERT: T 189 GLU cc_start: 0.6012 (OUTLIER) cc_final: 0.5625 (pm20) REVERT: T 241 THR cc_start: 0.6185 (OUTLIER) cc_final: 0.5628 (m) REVERT: U 59 PHE cc_start: 0.6545 (OUTLIER) cc_final: 0.5311 (t80) REVERT: U 120 ILE cc_start: 0.3515 (OUTLIER) cc_final: 0.2841 (mp) REVERT: W 16 LEU cc_start: 0.6677 (OUTLIER) cc_final: 0.6248 (mt) REVERT: Y 25 GLU cc_start: 0.6889 (OUTLIER) cc_final: 0.6464 (pt0) REVERT: Y 128 MET cc_start: 0.5030 (mmm) cc_final: 0.4150 (tpt) REVERT: Y 141 ILE cc_start: 0.5922 (mm) cc_final: 0.5645 (mt) REVERT: Z 51 PHE cc_start: 0.6815 (OUTLIER) cc_final: 0.6260 (m-80) REVERT: Z 386 LEU cc_start: 0.3524 (OUTLIER) cc_final: 0.2600 (pp) REVERT: c 49 TYR cc_start: 0.8706 (OUTLIER) cc_final: 0.7803 (p90) REVERT: c 111 ARG cc_start: 0.7148 (mtt180) cc_final: 0.6622 (mtm-85) REVERT: c 133 ARG cc_start: 0.6409 (mmt180) cc_final: 0.5618 (mmm160) REVERT: d 167 TRP cc_start: 0.6410 (m100) cc_final: 0.6062 (m-90) REVERT: d 189 GLU cc_start: 0.6269 (OUTLIER) cc_final: 0.5714 (pm20) REVERT: e 51 PHE cc_start: 0.5966 (OUTLIER) cc_final: 0.5441 (t80) REVERT: e 120 ILE cc_start: 0.3113 (OUTLIER) cc_final: 0.2684 (mt) REVERT: e 149 MET cc_start: 0.7953 (mmp) cc_final: 0.7278 (mmm) REVERT: e 153 ILE cc_start: 0.8058 (OUTLIER) cc_final: 0.7365 (mt) REVERT: e 169 TYR cc_start: 0.6775 (t80) cc_final: 0.6290 (t80) REVERT: e 473 LEU cc_start: 0.6546 (OUTLIER) cc_final: 0.6297 (mm) REVERT: e 491 MET cc_start: 0.7054 (tpp) cc_final: 0.6386 (tpp) REVERT: h 133 ARG cc_start: 0.5570 (OUTLIER) cc_final: 0.4784 (mmt180) REVERT: i 167 TRP cc_start: 0.2737 (OUTLIER) cc_final: 0.1454 (p90) REVERT: i 180 PRO cc_start: 0.4819 (Cg_endo) cc_final: 0.4378 (Cg_exo) REVERT: i 183 ARG cc_start: 0.5690 (OUTLIER) cc_final: 0.4682 (tpp-160) REVERT: i 194 ARG cc_start: 0.8004 (OUTLIER) cc_final: 0.7694 (ttt-90) REVERT: j 120 ILE cc_start: 0.6340 (mp) cc_final: 0.6032 (mt) REVERT: j 285 ILE cc_start: 0.5232 (OUTLIER) cc_final: 0.5017 (mm) REVERT: A 149 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.7294 (ptt90) REVERT: A 153 LEU cc_start: 0.6215 (OUTLIER) cc_final: 0.5690 (mp) REVERT: D 72 ILE cc_start: 0.8091 (OUTLIER) cc_final: 0.7751 (mp) REVERT: D 90 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7955 (mp0) REVERT: E 186 MET cc_start: 0.7903 (OUTLIER) cc_final: 0.7628 (mpp) REVERT: l 186 MET cc_start: 0.8004 (OUTLIER) cc_final: 0.7679 (mpp) REVERT: m 112 ASP cc_start: 0.7253 (OUTLIER) cc_final: 0.6918 (p0) REVERT: m 186 MET cc_start: 0.7967 (OUTLIER) cc_final: 0.7734 (mpp) REVERT: n 53 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.7935 (tm130) REVERT: n 110 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7062 (tm-30) REVERT: o 90 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7846 (mp0) REVERT: q 234 VAL cc_start: 0.5574 (OUTLIER) cc_final: 0.5280 (t) REVERT: r 59 MET cc_start: 0.7095 (tmm) cc_final: 0.6773 (tmm) REVERT: t 32 LEU cc_start: 0.5537 (OUTLIER) cc_final: 0.5209 (mp) REVERT: t 64 ARG cc_start: 0.7244 (tmt170) cc_final: 0.7012 (tpt90) REVERT: v 151 ILE cc_start: 0.7083 (OUTLIER) cc_final: 0.6854 (tt) REVERT: v 183 ARG cc_start: 0.4523 (OUTLIER) cc_final: 0.3599 (mmt90) outliers start: 385 outliers final: 279 residues processed: 1170 average time/residue: 0.8276 time to fit residues: 1692.7679 Evaluate side-chains 1167 residues out of total 10284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 327 poor density : 840 time to evaluate : 8.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 65 ARG Chi-restraints excluded: chain G residue 73 PHE Chi-restraints excluded: chain G residue 92 ASP Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 35 ILE Chi-restraints excluded: chain I residue 49 TYR Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain I residue 74 ASP Chi-restraints excluded: chain I residue 75 ASP Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain I residue 126 ASP Chi-restraints excluded: chain I residue 138 THR Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 69 ILE Chi-restraints excluded: chain J residue 82 ILE Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain J residue 173 ILE Chi-restraints excluded: chain J residue 189 GLU Chi-restraints excluded: chain J residue 209 ILE Chi-restraints excluded: chain J residue 282 VAL Chi-restraints excluded: chain J residue 318 THR Chi-restraints excluded: chain J residue 319 VAL Chi-restraints excluded: chain J residue 412 VAL Chi-restraints excluded: chain J residue 414 VAL Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 91 GLN Chi-restraints excluded: chain K residue 153 ILE Chi-restraints excluded: chain K residue 170 LEU Chi-restraints excluded: chain K residue 189 ASP Chi-restraints excluded: chain K residue 193 MET Chi-restraints excluded: chain K residue 247 LEU Chi-restraints excluded: chain K residue 308 VAL Chi-restraints excluded: chain K residue 359 ILE Chi-restraints excluded: chain K residue 408 VAL Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 41 MET Chi-restraints excluded: chain M residue 46 ASN Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain N residue 14 VAL Chi-restraints excluded: chain N residue 25 LEU Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain O residue 25 GLU Chi-restraints excluded: chain O residue 113 THR Chi-restraints excluded: chain O residue 118 GLN Chi-restraints excluded: chain O residue 119 THR Chi-restraints excluded: chain O residue 131 VAL Chi-restraints excluded: chain O residue 172 VAL Chi-restraints excluded: chain O residue 200 ILE Chi-restraints excluded: chain O residue 234 VAL Chi-restraints excluded: chain O residue 240 PHE Chi-restraints excluded: chain O residue 246 VAL Chi-restraints excluded: chain O residue 248 VAL Chi-restraints excluded: chain O residue 300 LYS Chi-restraints excluded: chain O residue 314 TYR Chi-restraints excluded: chain O residue 315 VAL Chi-restraints excluded: chain O residue 380 CYS Chi-restraints excluded: chain P residue 51 PHE Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 166 LEU Chi-restraints excluded: chain P residue 171 MET Chi-restraints excluded: chain P residue 185 VAL Chi-restraints excluded: chain P residue 209 THR Chi-restraints excluded: chain P residue 256 TYR Chi-restraints excluded: chain P residue 367 ILE Chi-restraints excluded: chain P residue 388 THR Chi-restraints excluded: chain P residue 454 TYR Chi-restraints excluded: chain P residue 485 ASP Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain Q residue 92 ASP Chi-restraints excluded: chain R residue 27 ASP Chi-restraints excluded: chain R residue 41 MET Chi-restraints excluded: chain R residue 79 LEU Chi-restraints excluded: chain S residue 74 ASP Chi-restraints excluded: chain S residue 89 PHE Chi-restraints excluded: chain S residue 101 THR Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 69 ILE Chi-restraints excluded: chain T residue 119 THR Chi-restraints excluded: chain T residue 128 MET Chi-restraints excluded: chain T residue 165 ILE Chi-restraints excluded: chain T residue 189 GLU Chi-restraints excluded: chain T residue 219 VAL Chi-restraints excluded: chain T residue 241 THR Chi-restraints excluded: chain T residue 279 ASN Chi-restraints excluded: chain T residue 394 THR Chi-restraints excluded: chain T residue 414 VAL Chi-restraints excluded: chain U residue 10 ILE Chi-restraints excluded: chain U residue 50 VAL Chi-restraints excluded: chain U residue 57 ASN Chi-restraints excluded: chain U residue 59 PHE Chi-restraints excluded: chain U residue 65 CYS Chi-restraints excluded: chain U residue 120 ILE Chi-restraints excluded: chain U residue 143 ILE Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 229 THR Chi-restraints excluded: chain U residue 245 CYS Chi-restraints excluded: chain U residue 308 VAL Chi-restraints excluded: chain U residue 361 SER Chi-restraints excluded: chain U residue 497 CYS Chi-restraints excluded: chain U residue 502 ILE Chi-restraints excluded: chain V residue 49 VAL Chi-restraints excluded: chain V residue 72 VAL Chi-restraints excluded: chain W residue 8 THR Chi-restraints excluded: chain W residue 16 LEU Chi-restraints excluded: chain W residue 94 ILE Chi-restraints excluded: chain X residue 14 VAL Chi-restraints excluded: chain Y residue 25 GLU Chi-restraints excluded: chain Y residue 111 ILE Chi-restraints excluded: chain Y residue 113 THR Chi-restraints excluded: chain Y residue 172 VAL Chi-restraints excluded: chain Y residue 225 ILE Chi-restraints excluded: chain Y residue 290 VAL Chi-restraints excluded: chain Y residue 307 THR Chi-restraints excluded: chain Y residue 380 CYS Chi-restraints excluded: chain Z residue 51 PHE Chi-restraints excluded: chain Z residue 120 ILE Chi-restraints excluded: chain Z residue 180 VAL Chi-restraints excluded: chain Z residue 195 LEU Chi-restraints excluded: chain Z residue 386 LEU Chi-restraints excluded: chain Z residue 499 VAL Chi-restraints excluded: chain a residue 32 ASP Chi-restraints excluded: chain a residue 49 VAL Chi-restraints excluded: chain b residue 10 THR Chi-restraints excluded: chain c residue 14 VAL Chi-restraints excluded: chain c residue 35 ILE Chi-restraints excluded: chain c residue 49 TYR Chi-restraints excluded: chain c residue 92 LEU Chi-restraints excluded: chain c residue 120 LEU Chi-restraints excluded: chain c residue 150 GLN Chi-restraints excluded: chain d residue 10 THR Chi-restraints excluded: chain d residue 13 ILE Chi-restraints excluded: chain d residue 14 VAL Chi-restraints excluded: chain d residue 119 THR Chi-restraints excluded: chain d residue 124 ILE Chi-restraints excluded: chain d residue 157 ASN Chi-restraints excluded: chain d residue 173 ILE Chi-restraints excluded: chain d residue 189 GLU Chi-restraints excluded: chain d residue 227 ASN Chi-restraints excluded: chain d residue 275 TYR Chi-restraints excluded: chain d residue 351 VAL Chi-restraints excluded: chain d residue 394 THR Chi-restraints excluded: chain d residue 399 MET Chi-restraints excluded: chain d residue 417 VAL Chi-restraints excluded: chain e residue 10 ILE Chi-restraints excluded: chain e residue 51 PHE Chi-restraints excluded: chain e residue 120 ILE Chi-restraints excluded: chain e residue 153 ILE Chi-restraints excluded: chain e residue 180 VAL Chi-restraints excluded: chain e residue 246 LYS Chi-restraints excluded: chain e residue 247 LEU Chi-restraints excluded: chain e residue 285 ILE Chi-restraints excluded: chain e residue 305 SER Chi-restraints excluded: chain e residue 367 ILE Chi-restraints excluded: chain e residue 386 LEU Chi-restraints excluded: chain e residue 473 LEU Chi-restraints excluded: chain f residue 27 LEU Chi-restraints excluded: chain g residue 108 ILE Chi-restraints excluded: chain h residue 30 ASP Chi-restraints excluded: chain h residue 74 ASP Chi-restraints excluded: chain h residue 105 THR Chi-restraints excluded: chain h residue 126 ASP Chi-restraints excluded: chain h residue 133 ARG Chi-restraints excluded: chain i residue 138 VAL Chi-restraints excluded: chain i residue 167 TRP Chi-restraints excluded: chain i residue 172 VAL Chi-restraints excluded: chain i residue 179 ASP Chi-restraints excluded: chain i residue 183 ARG Chi-restraints excluded: chain i residue 194 ARG Chi-restraints excluded: chain i residue 238 VAL Chi-restraints excluded: chain i residue 246 VAL Chi-restraints excluded: chain i residue 255 ASP Chi-restraints excluded: chain i residue 275 TYR Chi-restraints excluded: chain i residue 303 VAL Chi-restraints excluded: chain i residue 318 THR Chi-restraints excluded: chain j residue 257 VAL Chi-restraints excluded: chain j residue 285 ILE Chi-restraints excluded: chain j residue 367 ILE Chi-restraints excluded: chain j residue 488 VAL Chi-restraints excluded: chain j residue 494 CYS Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 149 ARG Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 148 ASP Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain E residue 41 THR Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 76 MET Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 186 MET Chi-restraints excluded: chain E residue 223 ILE Chi-restraints excluded: chain E residue 228 GLU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain F residue 3 ASN Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 212 ASP Chi-restraints excluded: chain F residue 220 ILE Chi-restraints excluded: chain k residue 65 ASP Chi-restraints excluded: chain k residue 100 THR Chi-restraints excluded: chain l residue 48 THR Chi-restraints excluded: chain l residue 139 THR Chi-restraints excluded: chain l residue 141 VAL Chi-restraints excluded: chain l residue 149 ASN Chi-restraints excluded: chain l residue 157 CYS Chi-restraints excluded: chain l residue 159 THR Chi-restraints excluded: chain l residue 186 MET Chi-restraints excluded: chain l residue 264 THR Chi-restraints excluded: chain m residue 48 THR Chi-restraints excluded: chain m residue 76 MET Chi-restraints excluded: chain m residue 79 VAL Chi-restraints excluded: chain m residue 112 ASP Chi-restraints excluded: chain m residue 139 THR Chi-restraints excluded: chain m residue 149 ASN Chi-restraints excluded: chain m residue 174 THR Chi-restraints excluded: chain m residue 186 MET Chi-restraints excluded: chain m residue 228 GLU Chi-restraints excluded: chain m residue 231 VAL Chi-restraints excluded: chain m residue 257 VAL Chi-restraints excluded: chain m residue 262 VAL Chi-restraints excluded: chain n residue 3 ASN Chi-restraints excluded: chain n residue 49 ILE Chi-restraints excluded: chain n residue 53 GLN Chi-restraints excluded: chain n residue 109 LEU Chi-restraints excluded: chain n residue 110 GLU Chi-restraints excluded: chain n residue 164 ASP Chi-restraints excluded: chain n residue 209 ASN Chi-restraints excluded: chain n residue 220 ILE Chi-restraints excluded: chain o residue 100 THR Chi-restraints excluded: chain p residue 3 ASN Chi-restraints excluded: chain p residue 49 ILE Chi-restraints excluded: chain p residue 59 VAL Chi-restraints excluded: chain p residue 143 GLU Chi-restraints excluded: chain p residue 164 ASP Chi-restraints excluded: chain p residue 220 ILE Chi-restraints excluded: chain q residue 17 THR Chi-restraints excluded: chain q residue 73 VAL Chi-restraints excluded: chain q residue 88 ILE Chi-restraints excluded: chain q residue 109 THR Chi-restraints excluded: chain q residue 119 THR Chi-restraints excluded: chain q residue 138 VAL Chi-restraints excluded: chain q residue 165 ILE Chi-restraints excluded: chain q residue 229 THR Chi-restraints excluded: chain q residue 234 VAL Chi-restraints excluded: chain q residue 267 HIS Chi-restraints excluded: chain q residue 303 VAL Chi-restraints excluded: chain q residue 412 VAL Chi-restraints excluded: chain r residue 17 THR Chi-restraints excluded: chain r residue 82 ILE Chi-restraints excluded: chain r residue 109 THR Chi-restraints excluded: chain r residue 119 THR Chi-restraints excluded: chain r residue 138 VAL Chi-restraints excluded: chain r residue 165 ILE Chi-restraints excluded: chain r residue 204 ASN Chi-restraints excluded: chain r residue 227 ASN Chi-restraints excluded: chain r residue 234 VAL Chi-restraints excluded: chain r residue 250 VAL Chi-restraints excluded: chain r residue 267 HIS Chi-restraints excluded: chain r residue 271 THR Chi-restraints excluded: chain r residue 303 VAL Chi-restraints excluded: chain r residue 412 VAL Chi-restraints excluded: chain s residue 17 THR Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain s residue 82 ILE Chi-restraints excluded: chain s residue 85 LEU Chi-restraints excluded: chain s residue 86 MET Chi-restraints excluded: chain s residue 119 THR Chi-restraints excluded: chain s residue 133 ILE Chi-restraints excluded: chain s residue 165 ILE Chi-restraints excluded: chain s residue 271 THR Chi-restraints excluded: chain s residue 282 VAL Chi-restraints excluded: chain s residue 303 VAL Chi-restraints excluded: chain s residue 412 VAL Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 111 ILE Chi-restraints excluded: chain t residue 119 THR Chi-restraints excluded: chain t residue 172 VAL Chi-restraints excluded: chain t residue 234 VAL Chi-restraints excluded: chain t residue 282 VAL Chi-restraints excluded: chain t residue 292 VAL Chi-restraints excluded: chain t residue 302 VAL Chi-restraints excluded: chain u residue 32 LEU Chi-restraints excluded: chain u residue 104 THR Chi-restraints excluded: chain u residue 119 THR Chi-restraints excluded: chain u residue 131 VAL Chi-restraints excluded: chain u residue 141 ILE Chi-restraints excluded: chain u residue 151 ILE Chi-restraints excluded: chain u residue 206 THR Chi-restraints excluded: chain u residue 209 ILE Chi-restraints excluded: chain u residue 226 GLU Chi-restraints excluded: chain u residue 234 VAL Chi-restraints excluded: chain u residue 246 VAL Chi-restraints excluded: chain u residue 271 THR Chi-restraints excluded: chain u residue 292 VAL Chi-restraints excluded: chain u residue 307 THR Chi-restraints excluded: chain u residue 321 GLN Chi-restraints excluded: chain v residue 42 THR Chi-restraints excluded: chain v residue 96 THR Chi-restraints excluded: chain v residue 104 THR Chi-restraints excluded: chain v residue 119 THR Chi-restraints excluded: chain v residue 133 ILE Chi-restraints excluded: chain v residue 141 ILE Chi-restraints excluded: chain v residue 151 ILE Chi-restraints excluded: chain v residue 183 ARG Chi-restraints excluded: chain v residue 220 THR Chi-restraints excluded: chain v residue 226 GLU Chi-restraints excluded: chain v residue 234 VAL Chi-restraints excluded: chain v residue 282 VAL Chi-restraints excluded: chain v residue 292 VAL Chi-restraints excluded: chain v residue 368 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1251 random chunks: chunk 1096 optimal weight: 10.0000 chunk 1155 optimal weight: 3.9990 chunk 1053 optimal weight: 0.0770 chunk 1123 optimal weight: 6.9990 chunk 1154 optimal weight: 30.0000 chunk 676 optimal weight: 30.0000 chunk 489 optimal weight: 20.0000 chunk 882 optimal weight: 7.9990 chunk 344 optimal weight: 5.9990 chunk 1015 optimal weight: 7.9990 chunk 1062 optimal weight: 20.0000 overall best weight: 5.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 44 GLN ** J 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 131 GLN ** a 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 108 GLN ** e 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 411 ASN F 3 ASN o 165 GLN ** p 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 268 ASN ** t 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 321 GLN ** v 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 1.209 97614 Z= 0.549 Angle : 0.665 33.809 133089 Z= 0.345 Chirality : 0.047 0.258 15345 Planarity : 0.005 0.081 17451 Dihedral : 5.647 62.481 13647 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.35 % Allowed : 9.72 % Favored : 89.94 % Rotamer: Outliers : 3.69 % Allowed : 19.97 % Favored : 76.34 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 3.18 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.07), residues: 12609 helix: 0.64 (0.11), residues: 2400 sheet: -0.72 (0.10), residues: 2667 loop : -2.27 (0.07), residues: 7542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP u 167 HIS 0.005 0.001 HIS j 204 PHE 0.021 0.002 PHE j 437 TYR 0.050 0.002 TYR X 49 ARG 0.012 0.000 ARG O 413 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25218 Ramachandran restraints generated. 12609 Oldfield, 0 Emsley, 12609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25218 Ramachandran restraints generated. 12609 Oldfield, 0 Emsley, 12609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1242 residues out of total 10284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 379 poor density : 863 time to evaluate : 8.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 65 ARG cc_start: 0.4310 (OUTLIER) cc_final: 0.4051 (ppt170) REVERT: I 62 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.7792 (tt) REVERT: J 173 ILE cc_start: 0.6450 (OUTLIER) cc_final: 0.5813 (tt) REVERT: J 189 GLU cc_start: 0.6085 (OUTLIER) cc_final: 0.5778 (pm20) REVERT: K 91 GLN cc_start: 0.3896 (OUTLIER) cc_final: 0.3317 (mt0) REVERT: K 153 ILE cc_start: 0.8273 (OUTLIER) cc_final: 0.7552 (mt) REVERT: K 189 ASP cc_start: 0.5577 (OUTLIER) cc_final: 0.5097 (p0) REVERT: K 231 GLU cc_start: 0.5549 (mp0) cc_final: 0.5266 (mp0) REVERT: O 25 GLU cc_start: 0.6636 (OUTLIER) cc_final: 0.6171 (mp0) REVERT: O 180 PRO cc_start: 0.4837 (Cg_endo) cc_final: 0.4413 (Cg_exo) REVERT: O 300 LYS cc_start: 0.5206 (OUTLIER) cc_final: 0.4959 (pttm) REVERT: O 314 TYR cc_start: 0.5107 (OUTLIER) cc_final: 0.4574 (m-80) REVERT: P 51 PHE cc_start: 0.6882 (OUTLIER) cc_final: 0.5703 (m-80) REVERT: P 78 TYR cc_start: 0.5251 (p90) cc_final: 0.4987 (p90) REVERT: P 298 ASP cc_start: 0.6367 (p0) cc_final: 0.6073 (p0) REVERT: P 485 ASP cc_start: 0.5600 (OUTLIER) cc_final: 0.4696 (p0) REVERT: Q 92 ASP cc_start: 0.6707 (OUTLIER) cc_final: 0.6428 (p0) REVERT: R 79 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7501 (mp) REVERT: S 89 PHE cc_start: 0.5727 (OUTLIER) cc_final: 0.5196 (p90) REVERT: T 189 GLU cc_start: 0.5972 (OUTLIER) cc_final: 0.5571 (pm20) REVERT: T 241 THR cc_start: 0.6094 (OUTLIER) cc_final: 0.5555 (m) REVERT: U 59 PHE cc_start: 0.6556 (OUTLIER) cc_final: 0.5355 (t80) REVERT: U 120 ILE cc_start: 0.3446 (OUTLIER) cc_final: 0.2816 (mp) REVERT: W 16 LEU cc_start: 0.6668 (OUTLIER) cc_final: 0.6237 (mt) REVERT: Y 25 GLU cc_start: 0.6878 (OUTLIER) cc_final: 0.6435 (pt0) REVERT: Y 128 MET cc_start: 0.5166 (mmm) cc_final: 0.4346 (mmm) REVERT: Y 141 ILE cc_start: 0.5874 (mm) cc_final: 0.5620 (mt) REVERT: Z 51 PHE cc_start: 0.6852 (OUTLIER) cc_final: 0.6326 (m-80) REVERT: Z 386 LEU cc_start: 0.3365 (OUTLIER) cc_final: 0.2322 (pp) REVERT: c 49 TYR cc_start: 0.8670 (OUTLIER) cc_final: 0.7770 (p90) REVERT: c 111 ARG cc_start: 0.7131 (mtt180) cc_final: 0.6608 (mtm-85) REVERT: c 133 ARG cc_start: 0.6399 (mmt180) cc_final: 0.5596 (mmm160) REVERT: d 167 TRP cc_start: 0.6422 (m100) cc_final: 0.6094 (m-90) REVERT: d 189 GLU cc_start: 0.6194 (OUTLIER) cc_final: 0.5654 (pm20) REVERT: e 51 PHE cc_start: 0.5990 (OUTLIER) cc_final: 0.5382 (t80) REVERT: e 120 ILE cc_start: 0.3063 (OUTLIER) cc_final: 0.2576 (mt) REVERT: e 149 MET cc_start: 0.7911 (mmp) cc_final: 0.7294 (mmm) REVERT: e 153 ILE cc_start: 0.8076 (OUTLIER) cc_final: 0.7372 (mt) REVERT: e 169 TYR cc_start: 0.6712 (t80) cc_final: 0.6196 (t80) REVERT: e 473 LEU cc_start: 0.6544 (OUTLIER) cc_final: 0.6321 (mm) REVERT: e 491 MET cc_start: 0.7069 (tpp) cc_final: 0.6430 (tpp) REVERT: h 105 THR cc_start: 0.7563 (OUTLIER) cc_final: 0.7113 (m) REVERT: i 167 TRP cc_start: 0.2817 (OUTLIER) cc_final: 0.1517 (p90) REVERT: i 177 ARG cc_start: 0.5853 (mmt180) cc_final: 0.5264 (mmm-85) REVERT: i 180 PRO cc_start: 0.4538 (Cg_endo) cc_final: 0.4215 (Cg_exo) REVERT: i 183 ARG cc_start: 0.5623 (OUTLIER) cc_final: 0.4644 (tpp-160) REVERT: i 194 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.7689 (ttt-90) REVERT: j 120 ILE cc_start: 0.6311 (mp) cc_final: 0.6014 (mt) REVERT: j 139 SER cc_start: 0.5881 (m) cc_final: 0.5445 (t) REVERT: j 153 ILE cc_start: 0.8490 (OUTLIER) cc_final: 0.8149 (mt) REVERT: j 312 GLN cc_start: 0.4859 (pt0) cc_final: 0.4523 (mt0) REVERT: A 149 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.7312 (ptt90) REVERT: A 153 LEU cc_start: 0.6233 (OUTLIER) cc_final: 0.5714 (mp) REVERT: D 72 ILE cc_start: 0.8092 (OUTLIER) cc_final: 0.7778 (mp) REVERT: D 90 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7926 (mp0) REVERT: E 186 MET cc_start: 0.7998 (OUTLIER) cc_final: 0.7731 (mpp) REVERT: l 186 MET cc_start: 0.8047 (OUTLIER) cc_final: 0.7690 (mpp) REVERT: l 205 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.7576 (ptm160) REVERT: m 112 ASP cc_start: 0.7219 (OUTLIER) cc_final: 0.6881 (p0) REVERT: m 186 MET cc_start: 0.7962 (OUTLIER) cc_final: 0.7711 (mpp) REVERT: n 53 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.7963 (tm130) REVERT: n 110 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7060 (tm-30) REVERT: o 90 GLU cc_start: 0.8293 (mt-10) cc_final: 0.7881 (mp0) REVERT: q 234 VAL cc_start: 0.5551 (OUTLIER) cc_final: 0.5263 (t) REVERT: r 59 MET cc_start: 0.7283 (tmm) cc_final: 0.7005 (tmm) REVERT: s 397 TYR cc_start: 0.6437 (t80) cc_final: 0.6136 (t80) REVERT: t 32 LEU cc_start: 0.5527 (OUTLIER) cc_final: 0.5213 (mp) REVERT: t 64 ARG cc_start: 0.7222 (tmt170) cc_final: 0.7011 (tpt90) REVERT: t 183 ARG cc_start: 0.5013 (tpt170) cc_final: 0.4321 (mmt90) REVERT: v 64 ARG cc_start: 0.7259 (tmt170) cc_final: 0.6969 (tpt90) REVERT: v 151 ILE cc_start: 0.7054 (OUTLIER) cc_final: 0.6814 (tt) REVERT: v 183 ARG cc_start: 0.4397 (OUTLIER) cc_final: 0.3521 (mmt90) outliers start: 379 outliers final: 303 residues processed: 1169 average time/residue: 0.9140 time to fit residues: 1882.0028 Evaluate side-chains 1198 residues out of total 10284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 352 poor density : 846 time to evaluate : 7.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 65 ARG Chi-restraints excluded: chain G residue 73 PHE Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 92 ASP Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 35 ILE Chi-restraints excluded: chain I residue 49 TYR Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain I residue 74 ASP Chi-restraints excluded: chain I residue 75 ASP Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain I residue 126 ASP Chi-restraints excluded: chain I residue 138 THR Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 44 GLN Chi-restraints excluded: chain J residue 69 ILE Chi-restraints excluded: chain J residue 82 ILE Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain J residue 173 ILE Chi-restraints excluded: chain J residue 189 GLU Chi-restraints excluded: chain J residue 209 ILE Chi-restraints excluded: chain J residue 282 VAL Chi-restraints excluded: chain J residue 318 THR Chi-restraints excluded: chain J residue 412 VAL Chi-restraints excluded: chain J residue 414 VAL Chi-restraints excluded: chain K residue 91 GLN Chi-restraints excluded: chain K residue 153 ILE Chi-restraints excluded: chain K residue 170 LEU Chi-restraints excluded: chain K residue 189 ASP Chi-restraints excluded: chain K residue 193 MET Chi-restraints excluded: chain K residue 247 LEU Chi-restraints excluded: chain K residue 270 THR Chi-restraints excluded: chain K residue 308 VAL Chi-restraints excluded: chain K residue 359 ILE Chi-restraints excluded: chain K residue 408 VAL Chi-restraints excluded: chain K residue 469 VAL Chi-restraints excluded: chain L residue 14 ILE Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 41 MET Chi-restraints excluded: chain M residue 46 ASN Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain N residue 14 VAL Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain O residue 25 GLU Chi-restraints excluded: chain O residue 42 THR Chi-restraints excluded: chain O residue 113 THR Chi-restraints excluded: chain O residue 118 GLN Chi-restraints excluded: chain O residue 119 THR Chi-restraints excluded: chain O residue 131 VAL Chi-restraints excluded: chain O residue 172 VAL Chi-restraints excluded: chain O residue 200 ILE Chi-restraints excluded: chain O residue 234 VAL Chi-restraints excluded: chain O residue 240 PHE Chi-restraints excluded: chain O residue 246 VAL Chi-restraints excluded: chain O residue 248 VAL Chi-restraints excluded: chain O residue 300 LYS Chi-restraints excluded: chain O residue 314 TYR Chi-restraints excluded: chain O residue 315 VAL Chi-restraints excluded: chain O residue 380 CYS Chi-restraints excluded: chain P residue 51 PHE Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 166 LEU Chi-restraints excluded: chain P residue 171 MET Chi-restraints excluded: chain P residue 185 VAL Chi-restraints excluded: chain P residue 209 THR Chi-restraints excluded: chain P residue 256 TYR Chi-restraints excluded: chain P residue 367 ILE Chi-restraints excluded: chain P residue 388 THR Chi-restraints excluded: chain P residue 454 TYR Chi-restraints excluded: chain P residue 485 ASP Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain Q residue 92 ASP Chi-restraints excluded: chain R residue 27 ASP Chi-restraints excluded: chain R residue 41 MET Chi-restraints excluded: chain R residue 79 LEU Chi-restraints excluded: chain S residue 74 ASP Chi-restraints excluded: chain S residue 89 PHE Chi-restraints excluded: chain S residue 101 THR Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 69 ILE Chi-restraints excluded: chain T residue 119 THR Chi-restraints excluded: chain T residue 128 MET Chi-restraints excluded: chain T residue 189 GLU Chi-restraints excluded: chain T residue 219 VAL Chi-restraints excluded: chain T residue 241 THR Chi-restraints excluded: chain T residue 279 ASN Chi-restraints excluded: chain T residue 394 THR Chi-restraints excluded: chain T residue 408 SER Chi-restraints excluded: chain T residue 414 VAL Chi-restraints excluded: chain U residue 10 ILE Chi-restraints excluded: chain U residue 57 ASN Chi-restraints excluded: chain U residue 59 PHE Chi-restraints excluded: chain U residue 65 CYS Chi-restraints excluded: chain U residue 120 ILE Chi-restraints excluded: chain U residue 143 ILE Chi-restraints excluded: chain U residue 170 LEU Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 219 VAL Chi-restraints excluded: chain U residue 229 THR Chi-restraints excluded: chain U residue 245 CYS Chi-restraints excluded: chain U residue 308 VAL Chi-restraints excluded: chain U residue 361 SER Chi-restraints excluded: chain U residue 497 CYS Chi-restraints excluded: chain V residue 49 VAL Chi-restraints excluded: chain V residue 72 VAL Chi-restraints excluded: chain W residue 8 THR Chi-restraints excluded: chain W residue 16 LEU Chi-restraints excluded: chain W residue 94 ILE Chi-restraints excluded: chain X residue 14 VAL Chi-restraints excluded: chain Y residue 25 GLU Chi-restraints excluded: chain Y residue 68 THR Chi-restraints excluded: chain Y residue 111 ILE Chi-restraints excluded: chain Y residue 113 THR Chi-restraints excluded: chain Y residue 172 VAL Chi-restraints excluded: chain Y residue 207 MET Chi-restraints excluded: chain Y residue 225 ILE Chi-restraints excluded: chain Y residue 234 VAL Chi-restraints excluded: chain Y residue 290 VAL Chi-restraints excluded: chain Y residue 307 THR Chi-restraints excluded: chain Y residue 380 CYS Chi-restraints excluded: chain Z residue 51 PHE Chi-restraints excluded: chain Z residue 120 ILE Chi-restraints excluded: chain Z residue 180 VAL Chi-restraints excluded: chain Z residue 195 LEU Chi-restraints excluded: chain Z residue 337 THR Chi-restraints excluded: chain Z residue 386 LEU Chi-restraints excluded: chain Z residue 499 VAL Chi-restraints excluded: chain a residue 32 ASP Chi-restraints excluded: chain a residue 49 VAL Chi-restraints excluded: chain b residue 10 THR Chi-restraints excluded: chain c residue 14 VAL Chi-restraints excluded: chain c residue 35 ILE Chi-restraints excluded: chain c residue 49 TYR Chi-restraints excluded: chain c residue 92 LEU Chi-restraints excluded: chain c residue 120 LEU Chi-restraints excluded: chain c residue 150 GLN Chi-restraints excluded: chain d residue 10 THR Chi-restraints excluded: chain d residue 13 ILE Chi-restraints excluded: chain d residue 14 VAL Chi-restraints excluded: chain d residue 119 THR Chi-restraints excluded: chain d residue 124 ILE Chi-restraints excluded: chain d residue 157 ASN Chi-restraints excluded: chain d residue 173 ILE Chi-restraints excluded: chain d residue 189 GLU Chi-restraints excluded: chain d residue 227 ASN Chi-restraints excluded: chain d residue 275 TYR Chi-restraints excluded: chain d residue 282 VAL Chi-restraints excluded: chain d residue 319 VAL Chi-restraints excluded: chain d residue 351 VAL Chi-restraints excluded: chain d residue 394 THR Chi-restraints excluded: chain d residue 399 MET Chi-restraints excluded: chain e residue 10 ILE Chi-restraints excluded: chain e residue 51 PHE Chi-restraints excluded: chain e residue 120 ILE Chi-restraints excluded: chain e residue 153 ILE Chi-restraints excluded: chain e residue 180 VAL Chi-restraints excluded: chain e residue 246 LYS Chi-restraints excluded: chain e residue 247 LEU Chi-restraints excluded: chain e residue 367 ILE Chi-restraints excluded: chain e residue 386 LEU Chi-restraints excluded: chain e residue 473 LEU Chi-restraints excluded: chain f residue 27 LEU Chi-restraints excluded: chain g residue 98 VAL Chi-restraints excluded: chain g residue 108 ILE Chi-restraints excluded: chain h residue 30 ASP Chi-restraints excluded: chain h residue 74 ASP Chi-restraints excluded: chain h residue 105 THR Chi-restraints excluded: chain h residue 126 ASP Chi-restraints excluded: chain i residue 12 VAL Chi-restraints excluded: chain i residue 138 VAL Chi-restraints excluded: chain i residue 167 TRP Chi-restraints excluded: chain i residue 172 VAL Chi-restraints excluded: chain i residue 179 ASP Chi-restraints excluded: chain i residue 183 ARG Chi-restraints excluded: chain i residue 194 ARG Chi-restraints excluded: chain i residue 238 VAL Chi-restraints excluded: chain i residue 246 VAL Chi-restraints excluded: chain i residue 248 VAL Chi-restraints excluded: chain i residue 255 ASP Chi-restraints excluded: chain i residue 275 TYR Chi-restraints excluded: chain i residue 303 VAL Chi-restraints excluded: chain i residue 318 THR Chi-restraints excluded: chain i residue 381 VAL Chi-restraints excluded: chain j residue 78 TYR Chi-restraints excluded: chain j residue 153 ILE Chi-restraints excluded: chain j residue 247 LEU Chi-restraints excluded: chain j residue 257 VAL Chi-restraints excluded: chain j residue 367 ILE Chi-restraints excluded: chain j residue 488 VAL Chi-restraints excluded: chain j residue 494 CYS Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 149 ARG Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 148 ASP Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain E residue 41 THR Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 76 MET Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 186 MET Chi-restraints excluded: chain E residue 223 ILE Chi-restraints excluded: chain E residue 228 GLU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain F residue 3 ASN Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain F residue 212 ASP Chi-restraints excluded: chain F residue 220 ILE Chi-restraints excluded: chain k residue 13 THR Chi-restraints excluded: chain k residue 65 ASP Chi-restraints excluded: chain k residue 100 THR Chi-restraints excluded: chain l residue 48 THR Chi-restraints excluded: chain l residue 139 THR Chi-restraints excluded: chain l residue 141 VAL Chi-restraints excluded: chain l residue 149 ASN Chi-restraints excluded: chain l residue 157 CYS Chi-restraints excluded: chain l residue 159 THR Chi-restraints excluded: chain l residue 186 MET Chi-restraints excluded: chain l residue 205 ARG Chi-restraints excluded: chain l residue 214 VAL Chi-restraints excluded: chain l residue 223 ILE Chi-restraints excluded: chain l residue 231 VAL Chi-restraints excluded: chain l residue 257 VAL Chi-restraints excluded: chain l residue 264 THR Chi-restraints excluded: chain m residue 48 THR Chi-restraints excluded: chain m residue 76 MET Chi-restraints excluded: chain m residue 79 VAL Chi-restraints excluded: chain m residue 112 ASP Chi-restraints excluded: chain m residue 139 THR Chi-restraints excluded: chain m residue 149 ASN Chi-restraints excluded: chain m residue 174 THR Chi-restraints excluded: chain m residue 186 MET Chi-restraints excluded: chain m residue 228 GLU Chi-restraints excluded: chain m residue 257 VAL Chi-restraints excluded: chain m residue 262 VAL Chi-restraints excluded: chain n residue 3 ASN Chi-restraints excluded: chain n residue 49 ILE Chi-restraints excluded: chain n residue 53 GLN Chi-restraints excluded: chain n residue 109 LEU Chi-restraints excluded: chain n residue 110 GLU Chi-restraints excluded: chain n residue 164 ASP Chi-restraints excluded: chain n residue 209 ASN Chi-restraints excluded: chain o residue 100 THR Chi-restraints excluded: chain p residue 3 ASN Chi-restraints excluded: chain p residue 49 ILE Chi-restraints excluded: chain p residue 59 VAL Chi-restraints excluded: chain p residue 110 GLU Chi-restraints excluded: chain p residue 143 GLU Chi-restraints excluded: chain p residue 164 ASP Chi-restraints excluded: chain p residue 220 ILE Chi-restraints excluded: chain q residue 17 THR Chi-restraints excluded: chain q residue 73 VAL Chi-restraints excluded: chain q residue 88 ILE Chi-restraints excluded: chain q residue 109 THR Chi-restraints excluded: chain q residue 119 THR Chi-restraints excluded: chain q residue 138 VAL Chi-restraints excluded: chain q residue 165 ILE Chi-restraints excluded: chain q residue 229 THR Chi-restraints excluded: chain q residue 234 VAL Chi-restraints excluded: chain q residue 267 HIS Chi-restraints excluded: chain q residue 303 VAL Chi-restraints excluded: chain q residue 412 VAL Chi-restraints excluded: chain r residue 17 THR Chi-restraints excluded: chain r residue 20 VAL Chi-restraints excluded: chain r residue 82 ILE Chi-restraints excluded: chain r residue 88 ILE Chi-restraints excluded: chain r residue 109 THR Chi-restraints excluded: chain r residue 119 THR Chi-restraints excluded: chain r residue 138 VAL Chi-restraints excluded: chain r residue 165 ILE Chi-restraints excluded: chain r residue 204 ASN Chi-restraints excluded: chain r residue 227 ASN Chi-restraints excluded: chain r residue 234 VAL Chi-restraints excluded: chain r residue 267 HIS Chi-restraints excluded: chain r residue 271 THR Chi-restraints excluded: chain r residue 303 VAL Chi-restraints excluded: chain r residue 412 VAL Chi-restraints excluded: chain s residue 17 THR Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain s residue 73 VAL Chi-restraints excluded: chain s residue 82 ILE Chi-restraints excluded: chain s residue 85 LEU Chi-restraints excluded: chain s residue 86 MET Chi-restraints excluded: chain s residue 119 THR Chi-restraints excluded: chain s residue 133 ILE Chi-restraints excluded: chain s residue 165 ILE Chi-restraints excluded: chain s residue 271 THR Chi-restraints excluded: chain s residue 282 VAL Chi-restraints excluded: chain s residue 303 VAL Chi-restraints excluded: chain s residue 412 VAL Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 111 ILE Chi-restraints excluded: chain t residue 119 THR Chi-restraints excluded: chain t residue 131 VAL Chi-restraints excluded: chain t residue 172 VAL Chi-restraints excluded: chain t residue 234 VAL Chi-restraints excluded: chain t residue 282 VAL Chi-restraints excluded: chain t residue 292 VAL Chi-restraints excluded: chain t residue 302 VAL Chi-restraints excluded: chain u residue 32 LEU Chi-restraints excluded: chain u residue 72 ASN Chi-restraints excluded: chain u residue 96 THR Chi-restraints excluded: chain u residue 104 THR Chi-restraints excluded: chain u residue 119 THR Chi-restraints excluded: chain u residue 131 VAL Chi-restraints excluded: chain u residue 141 ILE Chi-restraints excluded: chain u residue 151 ILE Chi-restraints excluded: chain u residue 206 THR Chi-restraints excluded: chain u residue 234 VAL Chi-restraints excluded: chain u residue 246 VAL Chi-restraints excluded: chain u residue 271 THR Chi-restraints excluded: chain u residue 292 VAL Chi-restraints excluded: chain u residue 307 THR Chi-restraints excluded: chain u residue 321 GLN Chi-restraints excluded: chain v residue 42 THR Chi-restraints excluded: chain v residue 96 THR Chi-restraints excluded: chain v residue 104 THR Chi-restraints excluded: chain v residue 119 THR Chi-restraints excluded: chain v residue 133 ILE Chi-restraints excluded: chain v residue 141 ILE Chi-restraints excluded: chain v residue 151 ILE Chi-restraints excluded: chain v residue 183 ARG Chi-restraints excluded: chain v residue 220 THR Chi-restraints excluded: chain v residue 226 GLU Chi-restraints excluded: chain v residue 234 VAL Chi-restraints excluded: chain v residue 282 VAL Chi-restraints excluded: chain v residue 292 VAL Chi-restraints excluded: chain v residue 368 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1251 random chunks: chunk 1119 optimal weight: 5.9990 chunk 737 optimal weight: 6.9990 chunk 1188 optimal weight: 9.9990 chunk 725 optimal weight: 30.0000 chunk 563 optimal weight: 6.9990 chunk 825 optimal weight: 20.0000 chunk 1246 optimal weight: 20.0000 chunk 1147 optimal weight: 0.3980 chunk 992 optimal weight: 9.9990 chunk 103 optimal weight: 20.0000 chunk 766 optimal weight: 4.9990 overall best weight: 5.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 44 GLN ** J 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 11 GLN Z 29 GLN ** a 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 411 ASN ** j 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 3 ASN o 165 GLN ** q 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 1.196 97614 Z= 0.551 Angle : 0.668 33.851 133089 Z= 0.346 Chirality : 0.048 0.255 15345 Planarity : 0.005 0.087 17451 Dihedral : 5.643 62.462 13647 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.37 % Allowed : 10.41 % Favored : 89.21 % Rotamer: Outliers : 3.68 % Allowed : 20.21 % Favored : 76.12 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 3.18 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.07), residues: 12609 helix: 0.58 (0.11), residues: 2421 sheet: -0.72 (0.10), residues: 2637 loop : -2.28 (0.07), residues: 7551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP t 167 HIS 0.005 0.001 HIS j 204 PHE 0.036 0.002 PHE T 78 TYR 0.050 0.002 TYR X 49 ARG 0.009 0.000 ARG O 413 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25218 Ramachandran restraints generated. 12609 Oldfield, 0 Emsley, 12609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25218 Ramachandran restraints generated. 12609 Oldfield, 0 Emsley, 12609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1233 residues out of total 10284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 378 poor density : 855 time to evaluate : 8.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 65 ARG cc_start: 0.4283 (OUTLIER) cc_final: 0.4025 (ppt170) REVERT: I 62 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.7793 (tt) REVERT: J 173 ILE cc_start: 0.6618 (OUTLIER) cc_final: 0.5975 (tt) REVERT: J 189 GLU cc_start: 0.6098 (OUTLIER) cc_final: 0.5793 (pm20) REVERT: K 91 GLN cc_start: 0.3919 (OUTLIER) cc_final: 0.3337 (mt0) REVERT: K 153 ILE cc_start: 0.8289 (OUTLIER) cc_final: 0.7551 (mt) REVERT: K 189 ASP cc_start: 0.5591 (OUTLIER) cc_final: 0.5151 (p0) REVERT: K 231 GLU cc_start: 0.5405 (mp0) cc_final: 0.5133 (mp0) REVERT: O 25 GLU cc_start: 0.6626 (OUTLIER) cc_final: 0.6170 (mp0) REVERT: O 180 PRO cc_start: 0.4812 (Cg_endo) cc_final: 0.4339 (Cg_exo) REVERT: O 300 LYS cc_start: 0.5208 (OUTLIER) cc_final: 0.4964 (pttm) REVERT: O 314 TYR cc_start: 0.5110 (OUTLIER) cc_final: 0.4598 (m-80) REVERT: P 51 PHE cc_start: 0.6892 (OUTLIER) cc_final: 0.5716 (m-80) REVERT: P 78 TYR cc_start: 0.5450 (p90) cc_final: 0.5190 (p90) REVERT: P 298 ASP cc_start: 0.6419 (p0) cc_final: 0.6137 (p0) REVERT: P 485 ASP cc_start: 0.5427 (OUTLIER) cc_final: 0.4521 (p0) REVERT: Q 92 ASP cc_start: 0.6701 (OUTLIER) cc_final: 0.6496 (p0) REVERT: R 79 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7500 (mp) REVERT: S 89 PHE cc_start: 0.5984 (OUTLIER) cc_final: 0.5292 (p90) REVERT: T 185 MET cc_start: 0.6238 (OUTLIER) cc_final: 0.5830 (ptt) REVERT: T 189 GLU cc_start: 0.5990 (OUTLIER) cc_final: 0.5583 (pm20) REVERT: T 241 THR cc_start: 0.6109 (OUTLIER) cc_final: 0.5583 (m) REVERT: U 59 PHE cc_start: 0.6563 (OUTLIER) cc_final: 0.5340 (t80) REVERT: U 120 ILE cc_start: 0.3583 (OUTLIER) cc_final: 0.2909 (mp) REVERT: W 16 LEU cc_start: 0.6678 (OUTLIER) cc_final: 0.6256 (mt) REVERT: Y 25 GLU cc_start: 0.6859 (OUTLIER) cc_final: 0.6427 (pt0) REVERT: Y 128 MET cc_start: 0.5117 (mmm) cc_final: 0.4265 (mmm) REVERT: Y 141 ILE cc_start: 0.5875 (mm) cc_final: 0.5633 (mt) REVERT: Y 177 ARG cc_start: 0.5747 (mmt90) cc_final: 0.5441 (mmt90) REVERT: Z 51 PHE cc_start: 0.6897 (OUTLIER) cc_final: 0.6398 (m-80) REVERT: Z 386 LEU cc_start: 0.3381 (OUTLIER) cc_final: 0.2351 (pp) REVERT: c 49 TYR cc_start: 0.8679 (OUTLIER) cc_final: 0.7775 (p90) REVERT: c 111 ARG cc_start: 0.7136 (mtt180) cc_final: 0.6612 (mtm-85) REVERT: c 133 ARG cc_start: 0.6440 (mmt180) cc_final: 0.5654 (mmm160) REVERT: d 167 TRP cc_start: 0.6403 (m100) cc_final: 0.6095 (m-90) REVERT: d 189 GLU cc_start: 0.6124 (OUTLIER) cc_final: 0.5632 (pm20) REVERT: e 51 PHE cc_start: 0.6022 (OUTLIER) cc_final: 0.5474 (t80) REVERT: e 120 ILE cc_start: 0.3079 (OUTLIER) cc_final: 0.2596 (mt) REVERT: e 149 MET cc_start: 0.7959 (mmp) cc_final: 0.7234 (mmm) REVERT: e 153 ILE cc_start: 0.8096 (OUTLIER) cc_final: 0.7399 (mt) REVERT: e 169 TYR cc_start: 0.6688 (t80) cc_final: 0.6124 (t80) REVERT: e 436 ARG cc_start: 0.5049 (ptp-170) cc_final: 0.4846 (ttp-170) REVERT: e 473 LEU cc_start: 0.6744 (OUTLIER) cc_final: 0.6510 (mm) REVERT: e 491 MET cc_start: 0.7077 (tpp) cc_final: 0.6459 (tpp) REVERT: h 105 THR cc_start: 0.7582 (OUTLIER) cc_final: 0.7141 (m) REVERT: i 167 TRP cc_start: 0.2950 (OUTLIER) cc_final: 0.1691 (p90) REVERT: i 180 PRO cc_start: 0.4706 (Cg_endo) cc_final: 0.4339 (Cg_exo) REVERT: i 183 ARG cc_start: 0.5614 (OUTLIER) cc_final: 0.4644 (tpp-160) REVERT: i 194 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.7691 (ttt-90) REVERT: j 120 ILE cc_start: 0.6356 (mp) cc_final: 0.6062 (mt) REVERT: j 139 SER cc_start: 0.5923 (m) cc_final: 0.5572 (t) REVERT: j 153 ILE cc_start: 0.8493 (OUTLIER) cc_final: 0.8158 (mt) REVERT: A 149 ARG cc_start: 0.7879 (OUTLIER) cc_final: 0.7352 (ptt90) REVERT: A 153 LEU cc_start: 0.6249 (OUTLIER) cc_final: 0.5723 (mp) REVERT: D 72 ILE cc_start: 0.8088 (OUTLIER) cc_final: 0.7764 (mp) REVERT: D 90 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7921 (mp0) REVERT: E 186 MET cc_start: 0.7998 (OUTLIER) cc_final: 0.7723 (mpp) REVERT: k 72 ILE cc_start: 0.8193 (OUTLIER) cc_final: 0.7755 (mp) REVERT: l 186 MET cc_start: 0.8005 (OUTLIER) cc_final: 0.7659 (mpp) REVERT: l 205 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.7581 (ptm160) REVERT: m 112 ASP cc_start: 0.7231 (OUTLIER) cc_final: 0.6901 (p0) REVERT: m 186 MET cc_start: 0.7959 (OUTLIER) cc_final: 0.7704 (mpp) REVERT: n 53 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.7962 (tm130) REVERT: n 110 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7060 (tm-30) REVERT: o 1 MET cc_start: 0.6545 (ppp) cc_final: 0.6324 (ppp) REVERT: o 90 GLU cc_start: 0.8295 (mt-10) cc_final: 0.7886 (mp0) REVERT: q 234 VAL cc_start: 0.5558 (OUTLIER) cc_final: 0.5264 (t) REVERT: t 32 LEU cc_start: 0.5531 (OUTLIER) cc_final: 0.5208 (mp) REVERT: t 64 ARG cc_start: 0.7205 (tmt170) cc_final: 0.6988 (tpt90) REVERT: t 183 ARG cc_start: 0.5049 (tpt170) cc_final: 0.4462 (mmt90) REVERT: u 64 ARG cc_start: 0.7147 (tmt170) cc_final: 0.6151 (tmt170) REVERT: v 151 ILE cc_start: 0.7060 (OUTLIER) cc_final: 0.6819 (tt) REVERT: v 183 ARG cc_start: 0.4412 (OUTLIER) cc_final: 0.3509 (mmt90) outliers start: 378 outliers final: 315 residues processed: 1163 average time/residue: 0.8227 time to fit residues: 1674.1812 Evaluate side-chains 1205 residues out of total 10284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 366 poor density : 839 time to evaluate : 7.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 65 ARG Chi-restraints excluded: chain G residue 73 PHE Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 92 ASP Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 35 ILE Chi-restraints excluded: chain I residue 49 TYR Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain I residue 74 ASP Chi-restraints excluded: chain I residue 75 ASP Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain I residue 126 ASP Chi-restraints excluded: chain I residue 138 THR Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 44 GLN Chi-restraints excluded: chain J residue 69 ILE Chi-restraints excluded: chain J residue 82 ILE Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain J residue 173 ILE Chi-restraints excluded: chain J residue 189 GLU Chi-restraints excluded: chain J residue 209 ILE Chi-restraints excluded: chain J residue 282 VAL Chi-restraints excluded: chain J residue 318 THR Chi-restraints excluded: chain J residue 412 VAL Chi-restraints excluded: chain J residue 414 VAL Chi-restraints excluded: chain K residue 91 GLN Chi-restraints excluded: chain K residue 153 ILE Chi-restraints excluded: chain K residue 170 LEU Chi-restraints excluded: chain K residue 189 ASP Chi-restraints excluded: chain K residue 193 MET Chi-restraints excluded: chain K residue 247 LEU Chi-restraints excluded: chain K residue 270 THR Chi-restraints excluded: chain K residue 308 VAL Chi-restraints excluded: chain K residue 359 ILE Chi-restraints excluded: chain K residue 408 VAL Chi-restraints excluded: chain K residue 469 VAL Chi-restraints excluded: chain L residue 14 ILE Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 41 MET Chi-restraints excluded: chain M residue 46 ASN Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain N residue 13 ILE Chi-restraints excluded: chain N residue 14 VAL Chi-restraints excluded: chain N residue 25 LEU Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain O residue 25 GLU Chi-restraints excluded: chain O residue 42 THR Chi-restraints excluded: chain O residue 113 THR Chi-restraints excluded: chain O residue 118 GLN Chi-restraints excluded: chain O residue 119 THR Chi-restraints excluded: chain O residue 131 VAL Chi-restraints excluded: chain O residue 172 VAL Chi-restraints excluded: chain O residue 200 ILE Chi-restraints excluded: chain O residue 240 PHE Chi-restraints excluded: chain O residue 246 VAL Chi-restraints excluded: chain O residue 248 VAL Chi-restraints excluded: chain O residue 300 LYS Chi-restraints excluded: chain O residue 314 TYR Chi-restraints excluded: chain O residue 315 VAL Chi-restraints excluded: chain O residue 380 CYS Chi-restraints excluded: chain P residue 51 PHE Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 166 LEU Chi-restraints excluded: chain P residue 171 MET Chi-restraints excluded: chain P residue 185 VAL Chi-restraints excluded: chain P residue 209 THR Chi-restraints excluded: chain P residue 256 TYR Chi-restraints excluded: chain P residue 367 ILE Chi-restraints excluded: chain P residue 388 THR Chi-restraints excluded: chain P residue 485 ASP Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain Q residue 92 ASP Chi-restraints excluded: chain R residue 27 ASP Chi-restraints excluded: chain R residue 41 MET Chi-restraints excluded: chain R residue 79 LEU Chi-restraints excluded: chain S residue 74 ASP Chi-restraints excluded: chain S residue 89 PHE Chi-restraints excluded: chain S residue 101 THR Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 69 ILE Chi-restraints excluded: chain T residue 119 THR Chi-restraints excluded: chain T residue 128 MET Chi-restraints excluded: chain T residue 165 ILE Chi-restraints excluded: chain T residue 185 MET Chi-restraints excluded: chain T residue 189 GLU Chi-restraints excluded: chain T residue 219 VAL Chi-restraints excluded: chain T residue 241 THR Chi-restraints excluded: chain T residue 279 ASN Chi-restraints excluded: chain T residue 317 VAL Chi-restraints excluded: chain T residue 394 THR Chi-restraints excluded: chain T residue 408 SER Chi-restraints excluded: chain T residue 414 VAL Chi-restraints excluded: chain U residue 10 ILE Chi-restraints excluded: chain U residue 50 VAL Chi-restraints excluded: chain U residue 57 ASN Chi-restraints excluded: chain U residue 59 PHE Chi-restraints excluded: chain U residue 65 CYS Chi-restraints excluded: chain U residue 120 ILE Chi-restraints excluded: chain U residue 143 ILE Chi-restraints excluded: chain U residue 170 LEU Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 219 VAL Chi-restraints excluded: chain U residue 229 THR Chi-restraints excluded: chain U residue 245 CYS Chi-restraints excluded: chain U residue 308 VAL Chi-restraints excluded: chain U residue 361 SER Chi-restraints excluded: chain U residue 497 CYS Chi-restraints excluded: chain U residue 502 ILE Chi-restraints excluded: chain V residue 49 VAL Chi-restraints excluded: chain V residue 72 VAL Chi-restraints excluded: chain W residue 8 THR Chi-restraints excluded: chain W residue 16 LEU Chi-restraints excluded: chain W residue 94 ILE Chi-restraints excluded: chain X residue 14 VAL Chi-restraints excluded: chain Y residue 25 GLU Chi-restraints excluded: chain Y residue 68 THR Chi-restraints excluded: chain Y residue 111 ILE Chi-restraints excluded: chain Y residue 113 THR Chi-restraints excluded: chain Y residue 172 VAL Chi-restraints excluded: chain Y residue 207 MET Chi-restraints excluded: chain Y residue 225 ILE Chi-restraints excluded: chain Y residue 234 VAL Chi-restraints excluded: chain Y residue 290 VAL Chi-restraints excluded: chain Y residue 307 THR Chi-restraints excluded: chain Y residue 380 CYS Chi-restraints excluded: chain Z residue 51 PHE Chi-restraints excluded: chain Z residue 120 ILE Chi-restraints excluded: chain Z residue 180 VAL Chi-restraints excluded: chain Z residue 195 LEU Chi-restraints excluded: chain Z residue 337 THR Chi-restraints excluded: chain Z residue 386 LEU Chi-restraints excluded: chain Z residue 499 VAL Chi-restraints excluded: chain a residue 32 ASP Chi-restraints excluded: chain a residue 49 VAL Chi-restraints excluded: chain b residue 10 THR Chi-restraints excluded: chain c residue 14 VAL Chi-restraints excluded: chain c residue 35 ILE Chi-restraints excluded: chain c residue 49 TYR Chi-restraints excluded: chain c residue 92 LEU Chi-restraints excluded: chain c residue 120 LEU Chi-restraints excluded: chain c residue 150 GLN Chi-restraints excluded: chain d residue 10 THR Chi-restraints excluded: chain d residue 13 ILE Chi-restraints excluded: chain d residue 14 VAL Chi-restraints excluded: chain d residue 119 THR Chi-restraints excluded: chain d residue 124 ILE Chi-restraints excluded: chain d residue 151 ILE Chi-restraints excluded: chain d residue 157 ASN Chi-restraints excluded: chain d residue 173 ILE Chi-restraints excluded: chain d residue 189 GLU Chi-restraints excluded: chain d residue 227 ASN Chi-restraints excluded: chain d residue 275 TYR Chi-restraints excluded: chain d residue 319 VAL Chi-restraints excluded: chain d residue 351 VAL Chi-restraints excluded: chain d residue 394 THR Chi-restraints excluded: chain d residue 399 MET Chi-restraints excluded: chain e residue 10 ILE Chi-restraints excluded: chain e residue 51 PHE Chi-restraints excluded: chain e residue 120 ILE Chi-restraints excluded: chain e residue 153 ILE Chi-restraints excluded: chain e residue 180 VAL Chi-restraints excluded: chain e residue 246 LYS Chi-restraints excluded: chain e residue 247 LEU Chi-restraints excluded: chain e residue 285 ILE Chi-restraints excluded: chain e residue 367 ILE Chi-restraints excluded: chain e residue 386 LEU Chi-restraints excluded: chain e residue 473 LEU Chi-restraints excluded: chain e residue 502 ILE Chi-restraints excluded: chain f residue 27 LEU Chi-restraints excluded: chain g residue 98 VAL Chi-restraints excluded: chain g residue 108 ILE Chi-restraints excluded: chain h residue 30 ASP Chi-restraints excluded: chain h residue 74 ASP Chi-restraints excluded: chain h residue 105 THR Chi-restraints excluded: chain h residue 126 ASP Chi-restraints excluded: chain i residue 12 VAL Chi-restraints excluded: chain i residue 138 VAL Chi-restraints excluded: chain i residue 167 TRP Chi-restraints excluded: chain i residue 172 VAL Chi-restraints excluded: chain i residue 179 ASP Chi-restraints excluded: chain i residue 183 ARG Chi-restraints excluded: chain i residue 194 ARG Chi-restraints excluded: chain i residue 238 VAL Chi-restraints excluded: chain i residue 246 VAL Chi-restraints excluded: chain i residue 248 VAL Chi-restraints excluded: chain i residue 255 ASP Chi-restraints excluded: chain i residue 275 TYR Chi-restraints excluded: chain i residue 303 VAL Chi-restraints excluded: chain i residue 318 THR Chi-restraints excluded: chain i residue 381 VAL Chi-restraints excluded: chain j residue 78 TYR Chi-restraints excluded: chain j residue 153 ILE Chi-restraints excluded: chain j residue 247 LEU Chi-restraints excluded: chain j residue 257 VAL Chi-restraints excluded: chain j residue 367 ILE Chi-restraints excluded: chain j residue 488 VAL Chi-restraints excluded: chain j residue 494 CYS Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 149 ARG Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 148 ASP Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain E residue 41 THR Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 76 MET Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 186 MET Chi-restraints excluded: chain E residue 223 ILE Chi-restraints excluded: chain E residue 228 GLU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain F residue 3 ASN Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain F residue 212 ASP Chi-restraints excluded: chain F residue 220 ILE Chi-restraints excluded: chain k residue 13 THR Chi-restraints excluded: chain k residue 65 ASP Chi-restraints excluded: chain k residue 72 ILE Chi-restraints excluded: chain k residue 100 THR Chi-restraints excluded: chain l residue 48 THR Chi-restraints excluded: chain l residue 139 THR Chi-restraints excluded: chain l residue 141 VAL Chi-restraints excluded: chain l residue 149 ASN Chi-restraints excluded: chain l residue 157 CYS Chi-restraints excluded: chain l residue 159 THR Chi-restraints excluded: chain l residue 186 MET Chi-restraints excluded: chain l residue 205 ARG Chi-restraints excluded: chain l residue 214 VAL Chi-restraints excluded: chain l residue 223 ILE Chi-restraints excluded: chain l residue 231 VAL Chi-restraints excluded: chain l residue 257 VAL Chi-restraints excluded: chain l residue 264 THR Chi-restraints excluded: chain m residue 48 THR Chi-restraints excluded: chain m residue 76 MET Chi-restraints excluded: chain m residue 79 VAL Chi-restraints excluded: chain m residue 112 ASP Chi-restraints excluded: chain m residue 139 THR Chi-restraints excluded: chain m residue 149 ASN Chi-restraints excluded: chain m residue 174 THR Chi-restraints excluded: chain m residue 186 MET Chi-restraints excluded: chain m residue 228 GLU Chi-restraints excluded: chain m residue 231 VAL Chi-restraints excluded: chain m residue 257 VAL Chi-restraints excluded: chain m residue 262 VAL Chi-restraints excluded: chain n residue 3 ASN Chi-restraints excluded: chain n residue 49 ILE Chi-restraints excluded: chain n residue 53 GLN Chi-restraints excluded: chain n residue 109 LEU Chi-restraints excluded: chain n residue 110 GLU Chi-restraints excluded: chain n residue 164 ASP Chi-restraints excluded: chain n residue 209 ASN Chi-restraints excluded: chain n residue 220 ILE Chi-restraints excluded: chain o residue 100 THR Chi-restraints excluded: chain o residue 182 ILE Chi-restraints excluded: chain p residue 3 ASN Chi-restraints excluded: chain p residue 49 ILE Chi-restraints excluded: chain p residue 59 VAL Chi-restraints excluded: chain p residue 110 GLU Chi-restraints excluded: chain p residue 143 GLU Chi-restraints excluded: chain p residue 164 ASP Chi-restraints excluded: chain p residue 220 ILE Chi-restraints excluded: chain q residue 17 THR Chi-restraints excluded: chain q residue 73 VAL Chi-restraints excluded: chain q residue 88 ILE Chi-restraints excluded: chain q residue 109 THR Chi-restraints excluded: chain q residue 119 THR Chi-restraints excluded: chain q residue 138 VAL Chi-restraints excluded: chain q residue 165 ILE Chi-restraints excluded: chain q residue 229 THR Chi-restraints excluded: chain q residue 234 VAL Chi-restraints excluded: chain q residue 267 HIS Chi-restraints excluded: chain q residue 303 VAL Chi-restraints excluded: chain q residue 412 VAL Chi-restraints excluded: chain r residue 17 THR Chi-restraints excluded: chain r residue 20 VAL Chi-restraints excluded: chain r residue 82 ILE Chi-restraints excluded: chain r residue 88 ILE Chi-restraints excluded: chain r residue 109 THR Chi-restraints excluded: chain r residue 119 THR Chi-restraints excluded: chain r residue 138 VAL Chi-restraints excluded: chain r residue 165 ILE Chi-restraints excluded: chain r residue 204 ASN Chi-restraints excluded: chain r residue 227 ASN Chi-restraints excluded: chain r residue 234 VAL Chi-restraints excluded: chain r residue 250 VAL Chi-restraints excluded: chain r residue 267 HIS Chi-restraints excluded: chain r residue 271 THR Chi-restraints excluded: chain r residue 303 VAL Chi-restraints excluded: chain r residue 412 VAL Chi-restraints excluded: chain s residue 17 THR Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain s residue 73 VAL Chi-restraints excluded: chain s residue 82 ILE Chi-restraints excluded: chain s residue 85 LEU Chi-restraints excluded: chain s residue 86 MET Chi-restraints excluded: chain s residue 119 THR Chi-restraints excluded: chain s residue 133 ILE Chi-restraints excluded: chain s residue 165 ILE Chi-restraints excluded: chain s residue 271 THR Chi-restraints excluded: chain s residue 282 VAL Chi-restraints excluded: chain s residue 303 VAL Chi-restraints excluded: chain s residue 306 THR Chi-restraints excluded: chain s residue 412 VAL Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 111 ILE Chi-restraints excluded: chain t residue 119 THR Chi-restraints excluded: chain t residue 131 VAL Chi-restraints excluded: chain t residue 172 VAL Chi-restraints excluded: chain t residue 234 VAL Chi-restraints excluded: chain t residue 282 VAL Chi-restraints excluded: chain t residue 292 VAL Chi-restraints excluded: chain t residue 302 VAL Chi-restraints excluded: chain u residue 32 LEU Chi-restraints excluded: chain u residue 72 ASN Chi-restraints excluded: chain u residue 96 THR Chi-restraints excluded: chain u residue 104 THR Chi-restraints excluded: chain u residue 119 THR Chi-restraints excluded: chain u residue 131 VAL Chi-restraints excluded: chain u residue 141 ILE Chi-restraints excluded: chain u residue 151 ILE Chi-restraints excluded: chain u residue 206 THR Chi-restraints excluded: chain u residue 226 GLU Chi-restraints excluded: chain u residue 234 VAL Chi-restraints excluded: chain u residue 246 VAL Chi-restraints excluded: chain u residue 271 THR Chi-restraints excluded: chain u residue 292 VAL Chi-restraints excluded: chain u residue 307 THR Chi-restraints excluded: chain v residue 42 THR Chi-restraints excluded: chain v residue 96 THR Chi-restraints excluded: chain v residue 104 THR Chi-restraints excluded: chain v residue 119 THR Chi-restraints excluded: chain v residue 151 ILE Chi-restraints excluded: chain v residue 183 ARG Chi-restraints excluded: chain v residue 220 THR Chi-restraints excluded: chain v residue 226 GLU Chi-restraints excluded: chain v residue 234 VAL Chi-restraints excluded: chain v residue 282 VAL Chi-restraints excluded: chain v residue 292 VAL Chi-restraints excluded: chain v residue 368 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1251 random chunks: chunk 608 optimal weight: 20.0000 chunk 788 optimal weight: 10.0000 chunk 1057 optimal weight: 9.9990 chunk 304 optimal weight: 20.0000 chunk 915 optimal weight: 0.5980 chunk 146 optimal weight: 9.9990 chunk 275 optimal weight: 8.9990 chunk 994 optimal weight: 9.9990 chunk 416 optimal weight: 0.9990 chunk 1020 optimal weight: 5.9990 chunk 125 optimal weight: 10.0000 overall best weight: 5.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 411 ASN ** j 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 3 ASN o 165 GLN ** q 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 157 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 = 0.3830 r_free = 0.3830 target = 0.113010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.097710 restraints weight = 271909.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.097665 restraints weight = 227549.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.098383 restraints weight = 163487.730| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 1.202 97614 Z= 0.554 Angle : 0.674 33.869 133089 Z= 0.349 Chirality : 0.048 0.251 15345 Planarity : 0.005 0.086 17451 Dihedral : 5.667 62.747 13647 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.36 % Allowed : 10.22 % Favored : 89.41 % Rotamer: Outliers : 3.78 % Allowed : 20.36 % Favored : 75.86 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 3.18 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.07), residues: 12609 helix: 0.57 (0.11), residues: 2421 sheet: -0.73 (0.10), residues: 2637 loop : -2.29 (0.07), residues: 7551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP u 167 HIS 0.006 0.001 HIS j 204 PHE 0.040 0.002 PHE o 153 TYR 0.050 0.002 TYR X 49 ARG 0.007 0.001 ARG U 296 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24036.43 seconds wall clock time: 421 minutes 49.21 seconds (25309.21 seconds total)