Starting phenix.real_space_refine on Sat Feb 17 18:54:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fvh_29487/02_2024/8fvh_29487.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fvh_29487/02_2024/8fvh_29487.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fvh_29487/02_2024/8fvh_29487.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fvh_29487/02_2024/8fvh_29487.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fvh_29487/02_2024/8fvh_29487.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fvh_29487/02_2024/8fvh_29487.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 234 5.16 5 C 44712 2.51 5 N 12018 2.21 5 O 13428 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 64": "OE1" <-> "OE2" Residue "E ASP 109": "OD1" <-> "OD2" Residue "F GLU 26": "OE1" <-> "OE2" Residue "F PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 3": "OD1" <-> "OD2" Residue "M GLU 31": "OE1" <-> "OE2" Residue "M ASP 65": "OD1" <-> "OD2" Residue "M GLU 84": "OE1" <-> "OE2" Residue "M TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 144": "OE1" <-> "OE2" Residue "M PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 170": "OE1" <-> "OE2" Residue "M ASP 177": "OD1" <-> "OD2" Residue "P PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 157": "OD1" <-> "OD2" Residue "P TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 170": "OE1" <-> "OE2" Residue "S GLU 23": "OE1" <-> "OE2" Residue "S ASP 29": "OD1" <-> "OD2" Residue "S PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 31": "OE1" <-> "OE2" Residue "S PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 98": "OE1" <-> "OE2" Residue "S ASP 146": "OD1" <-> "OD2" Residue "S GLU 151": "OE1" <-> "OE2" Residue "S TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 23": "OE1" <-> "OE2" Residue "V PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 31": "OE1" <-> "OE2" Residue "V PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 65": "OD1" <-> "OD2" Residue "V TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 141": "OE1" <-> "OE2" Residue "V PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 170": "OE1" <-> "OE2" Residue "V ASP 177": "OD1" <-> "OD2" Residue "Y GLU 5": "OE1" <-> "OE2" Residue "Y GLU 23": "OE1" <-> "OE2" Residue "Y PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 31": "OE1" <-> "OE2" Residue "Y PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 107": "OD1" <-> "OD2" Residue "Y PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 170": "OE1" <-> "OE2" Residue "b GLU 23": "OE1" <-> "OE2" Residue "b PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 98": "OE1" <-> "OE2" Residue "b PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 170": "OE1" <-> "OE2" Residue "N GLU 36": "OE1" <-> "OE2" Residue "N ASP 42": "OD1" <-> "OD2" Residue "N PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 18": "OD1" <-> "OD2" Residue "T ASP 42": "OD1" <-> "OD2" Residue "T GLU 54": "OE1" <-> "OE2" Residue "W ASP 18": "OD1" <-> "OD2" Residue "W ASP 42": "OD1" <-> "OD2" Residue "W GLU 97": "OE1" <-> "OE2" Residue "W TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 24": "OD1" <-> "OD2" Residue "Z ASP 40": "OD1" <-> "OD2" Residue "Z ASP 42": "OD1" <-> "OD2" Residue "c GLU 36": "OE1" <-> "OE2" Residue "G ASP 5": "OD1" <-> "OD2" Residue "G GLU 36": "OE1" <-> "OE2" Residue "G TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 18": "OD1" <-> "OD2" Residue "H ASP 24": "OD1" <-> "OD2" Residue "H TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 5": "OD1" <-> "OD2" Residue "I GLU 6": "OE1" <-> "OE2" Residue "I ASP 24": "OD1" <-> "OD2" Residue "I PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 18": "OD1" <-> "OD2" Residue "J GLU 97": "OE1" <-> "OE2" Residue "K ASP 24": "OD1" <-> "OD2" Residue "L ASP 24": "OD1" <-> "OD2" Residue "O ASP 144": "OD1" <-> "OD2" Residue "O PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 291": "OE1" <-> "OE2" Residue "O GLU 346": "OE1" <-> "OE2" Residue "O ASP 489": "OD1" <-> "OD2" Residue "O GLU 501": "OE1" <-> "OE2" Residue "R ASP 312": "OD1" <-> "OD2" Residue "R GLU 401": "OE1" <-> "OE2" Residue "R GLU 404": "OE1" <-> "OE2" Residue "R GLU 416": "OE1" <-> "OE2" Residue "U PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 240": "OE1" <-> "OE2" Residue "U GLU 320": "OE1" <-> "OE2" Residue "U GLU 346": "OE1" <-> "OE2" Residue "U TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 321": "OE1" <-> "OE2" Residue "X GLU 402": "OE1" <-> "OE2" Residue "X TYR 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 133": "OD1" <-> "OD2" Residue "a PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 232": "OD1" <-> "OD2" Residue "a PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 349": "OE1" <-> "OE2" Residue "a GLU 401": "OE1" <-> "OE2" Residue "a GLU 402": "OE1" <-> "OE2" Residue "a GLU 433": "OE1" <-> "OE2" Residue "a ASP 479": "OD1" <-> "OD2" Residue "a ASP 490": "OD1" <-> "OD2" Residue "a GLU 501": "OE1" <-> "OE2" Residue "d GLU 132": "OE1" <-> "OE2" Residue "d GLU 236": "OE1" <-> "OE2" Residue "d GLU 416": "OE1" <-> "OE2" Residue "d GLU 427": "OE1" <-> "OE2" Residue "d GLU 471": "OE1" <-> "OE2" Residue "e TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 285": "OE1" <-> "OE2" Residue "e GLU 291": "OE1" <-> "OE2" Residue "e ASP 489": "OD1" <-> "OD2" Residue "e GLU 505": "OE1" <-> "OE2" Residue "f GLU 321": "OE1" <-> "OE2" Residue "f GLU 402": "OE1" <-> "OE2" Residue "f GLU 404": "OE1" <-> "OE2" Residue "f GLU 427": "OE1" <-> "OE2" Residue "f GLU 519": "OE1" <-> "OE2" Residue "g TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 160": "OD1" <-> "OD2" Residue "g GLU 162": "OE1" <-> "OE2" Residue "g PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 191": "OD1" <-> "OD2" Residue "g TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 320": "OE1" <-> "OE2" Residue "g GLU 321": "OE1" <-> "OE2" Residue "g ASP 345": "OD1" <-> "OD2" Residue "g GLU 346": "OE1" <-> "OE2" Residue "g GLU 402": "OE1" <-> "OE2" Residue "g GLU 449": "OE1" <-> "OE2" Residue "g ASP 489": "OD1" <-> "OD2" Residue "g GLU 501": "OE1" <-> "OE2" Residue "h PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 189": "OE1" <-> "OE2" Residue "h TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 321": "OE1" <-> "OE2" Residue "h GLU 416": "OE1" <-> "OE2" Residue "i ASP 144": "OD1" <-> "OD2" Residue "i PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 236": "OE1" <-> "OE2" Residue "j ASP 312": "OD1" <-> "OD2" Residue "j GLU 321": "OE1" <-> "OE2" Residue "j GLU 346": "OE1" <-> "OE2" Residue "j GLU 416": "OE1" <-> "OE2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 70392 Number of models: 1 Model: "" Number of chains: 36 Chain: "C" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1003 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "A" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1003 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "B" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1003 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "D" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1003 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "E" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1003 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "F" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1003 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "M" Number of atoms: 1489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1489 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 7, 'TRANS': 174} Chain: "P" Number of atoms: 1489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1489 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 7, 'TRANS': 174} Chain: "S" Number of atoms: 1489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1489 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 7, 'TRANS': 174} Chain: "V" Number of atoms: 1489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1489 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 7, 'TRANS': 174} Chain: "Y" Number of atoms: 1489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1489 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 7, 'TRANS': 174} Chain: "b" Number of atoms: 1489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1489 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 7, 'TRANS': 174} Chain: "N" Number of atoms: 1194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1194 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 146} Chain: "Q" Number of atoms: 1194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1194 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 146} Chain: "T" Number of atoms: 1194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1194 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 146} Chain: "W" Number of atoms: 1194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1194 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 146} Chain: "Z" Number of atoms: 1194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1194 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 146} Chain: "c" Number of atoms: 1194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1194 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 146} Chain: "G" Number of atoms: 1194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1194 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 146} Chain: "H" Number of atoms: 1194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1194 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 146} Chain: "I" Number of atoms: 1194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1194 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 146} Chain: "J" Number of atoms: 1194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1194 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 146} Chain: "K" Number of atoms: 1194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1194 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 146} Chain: "L" Number of atoms: 1194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1194 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 146} Chain: "O" Number of atoms: 3426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3426 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 22, 'TRANS': 410} Chain: "R" Number of atoms: 3426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3426 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 22, 'TRANS': 410} Chain: "U" Number of atoms: 3426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3426 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 22, 'TRANS': 410} Chain: "X" Number of atoms: 3426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3426 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 22, 'TRANS': 410} Chain: "a" Number of atoms: 3426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3426 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 22, 'TRANS': 410} Chain: "d" Number of atoms: 3426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3426 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 22, 'TRANS': 410} Chain: "e" Number of atoms: 3426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3426 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 22, 'TRANS': 410} Chain: "f" Number of atoms: 3426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3426 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 22, 'TRANS': 410} Chain: "g" Number of atoms: 3426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3426 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 22, 'TRANS': 410} Chain: "h" Number of atoms: 3426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3426 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 22, 'TRANS': 410} Chain: "i" Number of atoms: 3426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3426 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 22, 'TRANS': 410} Chain: "j" Number of atoms: 3426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3426 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 22, 'TRANS': 410} Time building chain proxies: 27.68, per 1000 atoms: 0.39 Number of scatterers: 70392 At special positions: 0 Unit cell: (166.88, 166.88, 285.6, 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 234 16.00 O 13428 8.00 N 12018 7.00 C 44712 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: 21.13 Conformation dependent library (CDL) restraints added in 10.2 seconds 17628 Ramachandran restraints generated. 8814 Oldfield, 0 Emsley, 8814 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16488 Finding SS restraints... Secondary structure from input PDB file: 306 helices and 65 sheets defined 47.4% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.92 Creating SS restraints... Processing helix chain 'C' and resid 6 through 12 removed outlier: 3.926A pdb=" N MET C 10 " --> pdb=" O ASN C 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 12 removed outlier: 3.552A pdb=" N MET A 10 " --> pdb=" O ASN A 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 16 removed outlier: 4.071A pdb=" N MET B 10 " --> pdb=" O ASN B 6 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY B 13 " --> pdb=" O ARG B 9 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N VAL B 14 " --> pdb=" O MET B 10 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE B 15 " --> pdb=" O ALA B 11 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLY B 16 " --> pdb=" O PHE B 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 12 removed outlier: 3.971A pdb=" N MET D 10 " --> pdb=" O ASN D 6 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 12 removed outlier: 4.351A pdb=" N MET E 10 " --> pdb=" O ASN E 6 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 12 removed outlier: 3.926A pdb=" N MET F 10 " --> pdb=" O ASN F 6 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 26 Processing helix chain 'M' and resid 104 through 118 Processing helix chain 'M' and resid 118 through 127 removed outlier: 4.160A pdb=" N GLU M 127 " --> pdb=" O GLU M 123 " (cutoff:3.500A) Processing helix chain 'P' and resid 3 through 26 removed outlier: 3.943A pdb=" N GLU P 23 " --> pdb=" O THR P 19 " (cutoff:3.500A) Processing helix chain 'P' and resid 104 through 118 Processing helix chain 'P' and resid 118 through 127 removed outlier: 4.301A pdb=" N GLU P 127 " --> pdb=" O GLU P 123 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 26 removed outlier: 3.526A pdb=" N LEU S 6 " --> pdb=" O PHE S 2 " (cutoff:3.500A) Processing helix chain 'S' and resid 104 through 117 Processing helix chain 'S' and resid 118 through 127 removed outlier: 4.142A pdb=" N GLU S 127 " --> pdb=" O GLU S 123 " (cutoff:3.500A) Processing helix chain 'V' and resid 2 through 26 removed outlier: 3.560A pdb=" N LEU V 6 " --> pdb=" O PHE V 2 " (cutoff:3.500A) Processing helix chain 'V' and resid 104 through 118 Processing helix chain 'V' and resid 118 through 127 removed outlier: 4.193A pdb=" N GLU V 127 " --> pdb=" O GLU V 123 " (cutoff:3.500A) Processing helix chain 'Y' and resid 2 through 26 Processing helix chain 'Y' and resid 104 through 118 Processing helix chain 'Y' and resid 118 through 127 removed outlier: 4.147A pdb=" N GLU Y 127 " --> pdb=" O GLU Y 123 " (cutoff:3.500A) Processing helix chain 'b' and resid 2 through 26 removed outlier: 3.593A pdb=" N LEU b 6 " --> pdb=" O PHE b 2 " (cutoff:3.500A) Processing helix chain 'b' and resid 104 through 118 Processing helix chain 'b' and resid 118 through 127 removed outlier: 4.091A pdb=" N GLU b 127 " --> pdb=" O GLU b 123 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 13 Processing helix chain 'N' and resid 14 through 17 Processing helix chain 'N' and resid 23 through 38 removed outlier: 4.362A pdb=" N GLU N 36 " --> pdb=" O ASP N 32 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N PHE N 37 " --> pdb=" O ILE N 33 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE N 38 " --> pdb=" O ALA N 34 " (cutoff:3.500A) Processing helix chain 'N' and resid 50 through 74 removed outlier: 4.064A pdb=" N GLU N 54 " --> pdb=" O GLY N 50 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLN N 71 " --> pdb=" O LEU N 67 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL N 72 " --> pdb=" O SER N 68 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N GLN N 73 " --> pdb=" O THR N 69 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLY N 74 " --> pdb=" O MET N 70 " (cutoff:3.500A) Processing helix chain 'N' and resid 109 through 116 Processing helix chain 'N' and resid 118 through 132 Processing helix chain 'N' and resid 142 through 147 removed outlier: 3.638A pdb=" N ARG N 145 " --> pdb=" O PRO N 142 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE N 147 " --> pdb=" O ARG N 144 " (cutoff:3.500A) Processing helix chain 'Q' and resid 5 through 13 Processing helix chain 'Q' and resid 14 through 17 Processing helix chain 'Q' and resid 23 through 38 removed outlier: 4.125A pdb=" N GLU Q 36 " --> pdb=" O ASP Q 32 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N PHE Q 37 " --> pdb=" O ILE Q 33 " (cutoff:3.500A) Processing helix chain 'Q' and resid 50 through 73 removed outlier: 3.670A pdb=" N GLN Q 71 " --> pdb=" O LEU Q 67 " (cutoff:3.500A) Processing helix chain 'Q' and resid 109 through 116 Processing helix chain 'Q' and resid 118 through 132 Processing helix chain 'Q' and resid 142 through 147 removed outlier: 3.880A pdb=" N GLY Q 146 " --> pdb=" O GLU Q 143 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE Q 147 " --> pdb=" O ARG Q 144 " (cutoff:3.500A) Processing helix chain 'T' and resid 5 through 13 Processing helix chain 'T' and resid 14 through 17 Processing helix chain 'T' and resid 23 through 38 removed outlier: 4.385A pdb=" N GLU T 36 " --> pdb=" O ASP T 32 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N PHE T 37 " --> pdb=" O ILE T 33 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE T 38 " --> pdb=" O ALA T 34 " (cutoff:3.500A) Processing helix chain 'T' and resid 50 through 73 removed outlier: 4.190A pdb=" N GLN T 71 " --> pdb=" O LEU T 67 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL T 72 " --> pdb=" O SER T 68 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLN T 73 " --> pdb=" O THR T 69 " (cutoff:3.500A) Processing helix chain 'T' and resid 109 through 116 Processing helix chain 'T' and resid 118 through 132 Processing helix chain 'T' and resid 142 through 147 removed outlier: 3.740A pdb=" N ARG T 145 " --> pdb=" O PRO T 142 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE T 147 " --> pdb=" O ARG T 144 " (cutoff:3.500A) Processing helix chain 'W' and resid 5 through 13 Processing helix chain 'W' and resid 14 through 17 Processing helix chain 'W' and resid 23 through 38 removed outlier: 4.043A pdb=" N GLU W 36 " --> pdb=" O ASP W 32 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N PHE W 37 " --> pdb=" O ILE W 33 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE W 38 " --> pdb=" O ALA W 34 " (cutoff:3.500A) Processing helix chain 'W' and resid 50 through 74 removed outlier: 4.104A pdb=" N GLU W 54 " --> pdb=" O GLY W 50 " (cutoff:3.500A) Processing helix chain 'W' and resid 109 through 116 Processing helix chain 'W' and resid 118 through 132 Processing helix chain 'W' and resid 142 through 147 removed outlier: 3.512A pdb=" N ARG W 145 " --> pdb=" O PRO W 142 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLY W 146 " --> pdb=" O GLU W 143 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N PHE W 147 " --> pdb=" O ARG W 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 142 through 147' Processing helix chain 'Z' and resid 5 through 13 Processing helix chain 'Z' and resid 14 through 17 Processing helix chain 'Z' and resid 23 through 38 removed outlier: 4.342A pdb=" N GLU Z 36 " --> pdb=" O ASP Z 32 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N PHE Z 37 " --> pdb=" O ILE Z 33 " (cutoff:3.500A) Processing helix chain 'Z' and resid 50 through 74 removed outlier: 4.165A pdb=" N GLN Z 71 " --> pdb=" O LEU Z 67 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N VAL Z 72 " --> pdb=" O SER Z 68 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N GLN Z 73 " --> pdb=" O THR Z 69 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLY Z 74 " --> pdb=" O MET Z 70 " (cutoff:3.500A) Processing helix chain 'Z' and resid 109 through 116 Processing helix chain 'Z' and resid 118 through 132 Processing helix chain 'Z' and resid 142 through 147 removed outlier: 3.744A pdb=" N ARG Z 145 " --> pdb=" O PRO Z 142 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY Z 146 " --> pdb=" O GLU Z 143 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE Z 147 " --> pdb=" O ARG Z 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 142 through 147' Processing helix chain 'c' and resid 5 through 13 Processing helix chain 'c' and resid 14 through 17 Processing helix chain 'c' and resid 23 through 38 removed outlier: 4.278A pdb=" N GLU c 36 " --> pdb=" O ASP c 32 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N PHE c 37 " --> pdb=" O ILE c 33 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE c 38 " --> pdb=" O ALA c 34 " (cutoff:3.500A) Processing helix chain 'c' and resid 50 through 73 removed outlier: 4.000A pdb=" N GLU c 54 " --> pdb=" O GLY c 50 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN c 71 " --> pdb=" O LEU c 67 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL c 72 " --> pdb=" O SER c 68 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN c 73 " --> pdb=" O THR c 69 " (cutoff:3.500A) Processing helix chain 'c' and resid 109 through 116 Processing helix chain 'c' and resid 118 through 132 Processing helix chain 'c' and resid 142 through 147 removed outlier: 3.648A pdb=" N ARG c 145 " --> pdb=" O PRO c 142 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY c 146 " --> pdb=" O GLU c 143 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N PHE c 147 " --> pdb=" O ARG c 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 142 through 147' Processing helix chain 'G' and resid 5 through 13 Processing helix chain 'G' and resid 14 through 17 Processing helix chain 'G' and resid 23 through 38 removed outlier: 4.321A pdb=" N GLU G 36 " --> pdb=" O ASP G 32 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N PHE G 37 " --> pdb=" O ILE G 33 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE G 38 " --> pdb=" O ALA G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 73 removed outlier: 4.217A pdb=" N GLU G 54 " --> pdb=" O GLY G 50 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLN G 71 " --> pdb=" O LEU G 67 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N VAL G 72 " --> pdb=" O SER G 68 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLN G 73 " --> pdb=" O THR G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 116 Processing helix chain 'G' and resid 118 through 132 Processing helix chain 'G' and resid 142 through 147 removed outlier: 3.724A pdb=" N ARG G 145 " --> pdb=" O PRO G 142 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE G 147 " --> pdb=" O ARG G 144 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 13 Processing helix chain 'H' and resid 14 through 17 Processing helix chain 'H' and resid 23 through 38 removed outlier: 4.213A pdb=" N GLU H 36 " --> pdb=" O ASP H 32 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N PHE H 37 " --> pdb=" O ILE H 33 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE H 38 " --> pdb=" O ALA H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 50 through 73 removed outlier: 3.547A pdb=" N GLN H 71 " --> pdb=" O LEU H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 109 through 116 Processing helix chain 'H' and resid 118 through 132 Processing helix chain 'H' and resid 142 through 147 removed outlier: 3.712A pdb=" N ARG H 145 " --> pdb=" O PRO H 142 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLY H 146 " --> pdb=" O GLU H 143 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N PHE H 147 " --> pdb=" O ARG H 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 142 through 147' Processing helix chain 'I' and resid 5 through 13 Processing helix chain 'I' and resid 14 through 17 Processing helix chain 'I' and resid 23 through 38 removed outlier: 4.391A pdb=" N GLU I 36 " --> pdb=" O ASP I 32 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N PHE I 37 " --> pdb=" O ILE I 33 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE I 38 " --> pdb=" O ALA I 34 " (cutoff:3.500A) Processing helix chain 'I' and resid 50 through 73 removed outlier: 3.878A pdb=" N GLU I 54 " --> pdb=" O GLY I 50 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLN I 71 " --> pdb=" O LEU I 67 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N VAL I 72 " --> pdb=" O SER I 68 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLN I 73 " --> pdb=" O THR I 69 " (cutoff:3.500A) Processing helix chain 'I' and resid 109 through 116 Processing helix chain 'I' and resid 118 through 132 Processing helix chain 'I' and resid 142 through 147 removed outlier: 3.687A pdb=" N ARG I 145 " --> pdb=" O PRO I 142 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 13 Processing helix chain 'J' and resid 14 through 17 Processing helix chain 'J' and resid 23 through 38 removed outlier: 3.993A pdb=" N GLU J 36 " --> pdb=" O ASP J 32 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N PHE J 37 " --> pdb=" O ILE J 33 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE J 38 " --> pdb=" O ALA J 34 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 74 removed outlier: 4.043A pdb=" N GLU J 54 " --> pdb=" O GLY J 50 " (cutoff:3.500A) Processing helix chain 'J' and resid 109 through 116 Processing helix chain 'J' and resid 118 through 132 Processing helix chain 'J' and resid 142 through 147 removed outlier: 3.680A pdb=" N ARG J 145 " --> pdb=" O PRO J 142 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLY J 146 " --> pdb=" O GLU J 143 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N PHE J 147 " --> pdb=" O ARG J 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 142 through 147' Processing helix chain 'K' and resid 5 through 13 Processing helix chain 'K' and resid 14 through 17 Processing helix chain 'K' and resid 23 through 38 removed outlier: 4.429A pdb=" N GLU K 36 " --> pdb=" O ASP K 32 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N PHE K 37 " --> pdb=" O ILE K 33 " (cutoff:3.500A) Processing helix chain 'K' and resid 50 through 74 removed outlier: 4.027A pdb=" N GLN K 71 " --> pdb=" O LEU K 67 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL K 72 " --> pdb=" O SER K 68 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLN K 73 " --> pdb=" O THR K 69 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLY K 74 " --> pdb=" O MET K 70 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 116 Processing helix chain 'K' and resid 118 through 132 Processing helix chain 'K' and resid 142 through 147 removed outlier: 3.773A pdb=" N ARG K 145 " --> pdb=" O PRO K 142 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE K 147 " --> pdb=" O ARG K 144 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 13 Processing helix chain 'L' and resid 14 through 17 Processing helix chain 'L' and resid 23 through 38 removed outlier: 4.286A pdb=" N GLU L 36 " --> pdb=" O ASP L 32 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N PHE L 37 " --> pdb=" O ILE L 33 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE L 38 " --> pdb=" O ALA L 34 " (cutoff:3.500A) Processing helix chain 'L' and resid 50 through 73 removed outlier: 4.413A pdb=" N GLU L 54 " --> pdb=" O GLY L 50 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN L 71 " --> pdb=" O LEU L 67 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL L 72 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN L 73 " --> pdb=" O THR L 69 " (cutoff:3.500A) Processing helix chain 'L' and resid 109 through 116 Processing helix chain 'L' and resid 118 through 132 Processing helix chain 'L' and resid 142 through 147 removed outlier: 3.606A pdb=" N ARG L 145 " --> pdb=" O PRO L 142 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLY L 146 " --> pdb=" O GLU L 143 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N PHE L 147 " --> pdb=" O ARG L 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 142 through 147' Processing helix chain 'O' and resid 97 through 106 removed outlier: 4.362A pdb=" N GLN O 106 " --> pdb=" O TRP O 102 " (cutoff:3.500A) Processing helix chain 'O' and resid 110 through 118 Processing helix chain 'O' and resid 120 through 135 removed outlier: 4.699A pdb=" N SER O 130 " --> pdb=" O ALA O 126 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N GLY O 131 " --> pdb=" O CYS O 127 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA O 135 " --> pdb=" O GLY O 131 " (cutoff:3.500A) Processing helix chain 'O' and resid 149 through 164 Processing helix chain 'O' and resid 164 through 180 Processing helix chain 'O' and resid 201 through 205 removed outlier: 3.591A pdb=" N VAL O 205 " --> pdb=" O PRO O 202 " (cutoff:3.500A) Processing helix chain 'O' and resid 217 through 219 No H-bonds generated for 'chain 'O' and resid 217 through 219' Processing helix chain 'O' and resid 279 through 303 removed outlier: 5.436A pdb=" N GLU O 285 " --> pdb=" O GLN O 281 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N ARG O 286 " --> pdb=" O ARG O 282 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA O 297 " --> pdb=" O THR O 293 " (cutoff:3.500A) Proline residue: O 298 - end of helix Processing helix chain 'O' and resid 312 through 319 removed outlier: 3.602A pdb=" N ASN O 319 " --> pdb=" O LYS O 315 " (cutoff:3.500A) Processing helix chain 'O' and resid 322 through 333 Processing helix chain 'O' and resid 357 through 373 removed outlier: 3.830A pdb=" N ILE O 361 " --> pdb=" O ASP O 357 " (cutoff:3.500A) Processing helix chain 'O' and resid 376 through 381 removed outlier: 3.593A pdb=" N LEU O 380 " --> pdb=" O PRO O 376 " (cutoff:3.500A) Processing helix chain 'O' and resid 392 through 410 removed outlier: 3.709A pdb=" N THR O 396 " --> pdb=" O GLY O 392 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE O 397 " --> pdb=" O GLU O 393 " (cutoff:3.500A) Processing helix chain 'O' and resid 410 through 427 removed outlier: 4.524A pdb=" N LEU O 414 " --> pdb=" O ILE O 410 " (cutoff:3.500A) Processing helix chain 'O' and resid 443 through 465 removed outlier: 3.540A pdb=" N THR O 457 " --> pdb=" O LYS O 453 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER O 464 " --> pdb=" O ILE O 460 " (cutoff:3.500A) Processing helix chain 'O' and resid 468 through 479 removed outlier: 3.558A pdb=" N VAL O 472 " --> pdb=" O SER O 468 " (cutoff:3.500A) Processing helix chain 'O' and resid 499 through 524 removed outlier: 3.501A pdb=" N ALA O 504 " --> pdb=" O PRO O 500 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA O 514 " --> pdb=" O GLY O 510 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS O 515 " --> pdb=" O ALA O 511 " (cutoff:3.500A) Processing helix chain 'R' and resid 97 through 106 removed outlier: 4.183A pdb=" N GLN R 106 " --> pdb=" O TRP R 102 " (cutoff:3.500A) Processing helix chain 'R' and resid 110 through 118 Processing helix chain 'R' and resid 120 through 135 removed outlier: 4.832A pdb=" N SER R 130 " --> pdb=" O ALA R 126 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N GLY R 131 " --> pdb=" O CYS R 127 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA R 135 " --> pdb=" O GLY R 131 " (cutoff:3.500A) Processing helix chain 'R' and resid 149 through 164 Processing helix chain 'R' and resid 164 through 180 Processing helix chain 'R' and resid 201 through 205 removed outlier: 4.245A pdb=" N VAL R 205 " --> pdb=" O PRO R 202 " (cutoff:3.500A) Processing helix chain 'R' and resid 265 through 269 Processing helix chain 'R' and resid 279 through 303 removed outlier: 5.444A pdb=" N GLU R 285 " --> pdb=" O GLN R 281 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N ARG R 286 " --> pdb=" O ARG R 282 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA R 297 " --> pdb=" O THR R 293 " (cutoff:3.500A) Proline residue: R 298 - end of helix Processing helix chain 'R' and resid 312 through 319 removed outlier: 3.678A pdb=" N ASN R 319 " --> pdb=" O LYS R 315 " (cutoff:3.500A) Processing helix chain 'R' and resid 322 through 333 Processing helix chain 'R' and resid 357 through 373 removed outlier: 3.937A pdb=" N ILE R 361 " --> pdb=" O ASP R 357 " (cutoff:3.500A) Processing helix chain 'R' and resid 376 through 381 removed outlier: 3.513A pdb=" N LEU R 380 " --> pdb=" O PRO R 376 " (cutoff:3.500A) Processing helix chain 'R' and resid 392 through 410 removed outlier: 3.646A pdb=" N ILE R 397 " --> pdb=" O GLU R 393 " (cutoff:3.500A) Processing helix chain 'R' and resid 411 through 426 Processing helix chain 'R' and resid 443 through 464 removed outlier: 3.578A pdb=" N LYS R 453 " --> pdb=" O GLU R 449 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR R 461 " --> pdb=" O THR R 457 " (cutoff:3.500A) Processing helix chain 'R' and resid 468 through 479 removed outlier: 3.521A pdb=" N ARG R 475 " --> pdb=" O GLU R 471 " (cutoff:3.500A) Processing helix chain 'R' and resid 499 through 526 removed outlier: 3.979A pdb=" N GLU R 507 " --> pdb=" O LEU R 503 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS R 508 " --> pdb=" O ALA R 504 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS R 517 " --> pdb=" O SER R 513 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLY R 518 " --> pdb=" O ALA R 514 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLU R 519 " --> pdb=" O LYS R 515 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA R 520 " --> pdb=" O ALA R 516 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA R 525 " --> pdb=" O GLU R 521 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLN R 526 " --> pdb=" O ARG R 522 " (cutoff:3.500A) Processing helix chain 'U' and resid 97 through 106 removed outlier: 4.393A pdb=" N GLN U 106 " --> pdb=" O TRP U 102 " (cutoff:3.500A) Processing helix chain 'U' and resid 110 through 118 Processing helix chain 'U' and resid 120 through 135 removed outlier: 4.620A pdb=" N SER U 130 " --> pdb=" O ALA U 126 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N GLY U 131 " --> pdb=" O CYS U 127 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA U 135 " --> pdb=" O GLY U 131 " (cutoff:3.500A) Processing helix chain 'U' and resid 149 through 164 Processing helix chain 'U' and resid 164 through 180 Processing helix chain 'U' and resid 201 through 205 removed outlier: 3.644A pdb=" N VAL U 205 " --> pdb=" O PRO U 202 " (cutoff:3.500A) Processing helix chain 'U' and resid 278 through 303 removed outlier: 3.656A pdb=" N ARG U 282 " --> pdb=" O PRO U 278 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N GLU U 285 " --> pdb=" O GLN U 281 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N ARG U 286 " --> pdb=" O ARG U 282 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA U 297 " --> pdb=" O THR U 293 " (cutoff:3.500A) Proline residue: U 298 - end of helix Processing helix chain 'U' and resid 312 through 319 removed outlier: 3.732A pdb=" N ASN U 319 " --> pdb=" O LYS U 315 " (cutoff:3.500A) Processing helix chain 'U' and resid 322 through 333 Processing helix chain 'U' and resid 357 through 373 removed outlier: 3.896A pdb=" N ILE U 361 " --> pdb=" O ASP U 357 " (cutoff:3.500A) Processing helix chain 'U' and resid 376 through 381 removed outlier: 3.638A pdb=" N LEU U 380 " --> pdb=" O PRO U 376 " (cutoff:3.500A) Processing helix chain 'U' and resid 393 through 410 Processing helix chain 'U' and resid 410 through 426 removed outlier: 4.597A pdb=" N LEU U 414 " --> pdb=" O ILE U 410 " (cutoff:3.500A) Processing helix chain 'U' and resid 443 through 465 removed outlier: 3.633A pdb=" N THR U 457 " --> pdb=" O LYS U 453 " (cutoff:3.500A) Processing helix chain 'U' and resid 468 through 479 removed outlier: 3.541A pdb=" N VAL U 472 " --> pdb=" O SER U 468 " (cutoff:3.500A) Processing helix chain 'U' and resid 499 through 524 removed outlier: 3.812A pdb=" N ALA U 504 " --> pdb=" O PRO U 500 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU U 505 " --> pdb=" O GLU U 501 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA U 514 " --> pdb=" O GLY U 510 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS U 515 " --> pdb=" O ALA U 511 " (cutoff:3.500A) Processing helix chain 'X' and resid 97 through 106 removed outlier: 4.088A pdb=" N GLN X 106 " --> pdb=" O TRP X 102 " (cutoff:3.500A) Processing helix chain 'X' and resid 110 through 118 Processing helix chain 'X' and resid 120 through 135 removed outlier: 4.906A pdb=" N SER X 130 " --> pdb=" O ALA X 126 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N GLY X 131 " --> pdb=" O CYS X 127 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA X 135 " --> pdb=" O GLY X 131 " (cutoff:3.500A) Processing helix chain 'X' and resid 149 through 162 removed outlier: 3.823A pdb=" N SER X 153 " --> pdb=" O SER X 149 " (cutoff:3.500A) Processing helix chain 'X' and resid 164 through 180 Processing helix chain 'X' and resid 201 through 205 removed outlier: 3.988A pdb=" N VAL X 205 " --> pdb=" O PRO X 202 " (cutoff:3.500A) Processing helix chain 'X' and resid 265 through 267 No H-bonds generated for 'chain 'X' and resid 265 through 267' Processing helix chain 'X' and resid 268 through 273 Processing helix chain 'X' and resid 278 through 303 removed outlier: 3.770A pdb=" N ARG X 282 " --> pdb=" O PRO X 278 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N GLU X 285 " --> pdb=" O GLN X 281 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N ARG X 286 " --> pdb=" O ARG X 282 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA X 297 " --> pdb=" O THR X 293 " (cutoff:3.500A) Proline residue: X 298 - end of helix Processing helix chain 'X' and resid 312 through 319 removed outlier: 3.690A pdb=" N ASN X 319 " --> pdb=" O LYS X 315 " (cutoff:3.500A) Processing helix chain 'X' and resid 322 through 333 Processing helix chain 'X' and resid 357 through 373 removed outlier: 3.813A pdb=" N ILE X 361 " --> pdb=" O ASP X 357 " (cutoff:3.500A) Processing helix chain 'X' and resid 376 through 381 Processing helix chain 'X' and resid 394 through 410 Processing helix chain 'X' and resid 410 through 426 removed outlier: 4.420A pdb=" N LEU X 414 " --> pdb=" O ILE X 410 " (cutoff:3.500A) Processing helix chain 'X' and resid 443 through 464 removed outlier: 3.654A pdb=" N LYS X 453 " --> pdb=" O GLU X 449 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS X 454 " --> pdb=" O LEU X 450 " (cutoff:3.500A) Processing helix chain 'X' and resid 468 through 479 removed outlier: 3.607A pdb=" N VAL X 472 " --> pdb=" O SER X 468 " (cutoff:3.500A) Processing helix chain 'X' and resid 499 through 524 removed outlier: 3.706A pdb=" N GLU X 507 " --> pdb=" O LEU X 503 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS X 508 " --> pdb=" O ALA X 504 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU X 521 " --> pdb=" O LYS X 517 " (cutoff:3.500A) Processing helix chain 'a' and resid 97 through 106 removed outlier: 4.350A pdb=" N GLN a 106 " --> pdb=" O TRP a 102 " (cutoff:3.500A) Processing helix chain 'a' and resid 110 through 118 Processing helix chain 'a' and resid 120 through 135 removed outlier: 4.446A pdb=" N SER a 130 " --> pdb=" O ALA a 126 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLY a 131 " --> pdb=" O CYS a 127 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA a 135 " --> pdb=" O GLY a 131 " (cutoff:3.500A) Processing helix chain 'a' and resid 149 through 164 Processing helix chain 'a' and resid 164 through 180 removed outlier: 3.690A pdb=" N ASN a 168 " --> pdb=" O ARG a 164 " (cutoff:3.500A) Processing helix chain 'a' and resid 201 through 205 Processing helix chain 'a' and resid 278 through 303 removed outlier: 3.716A pdb=" N ARG a 282 " --> pdb=" O PRO a 278 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N GLU a 285 " --> pdb=" O GLN a 281 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N ARG a 286 " --> pdb=" O ARG a 282 " (cutoff:3.500A) Proline residue: a 298 - end of helix removed outlier: 3.598A pdb=" N SER a 303 " --> pdb=" O LEU a 299 " (cutoff:3.500A) Processing helix chain 'a' and resid 312 through 319 removed outlier: 3.572A pdb=" N ALA a 318 " --> pdb=" O GLU a 314 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN a 319 " --> pdb=" O LYS a 315 " (cutoff:3.500A) Processing helix chain 'a' and resid 322 through 333 Processing helix chain 'a' and resid 357 through 373 removed outlier: 3.920A pdb=" N ILE a 361 " --> pdb=" O ASP a 357 " (cutoff:3.500A) Processing helix chain 'a' and resid 376 through 382 removed outlier: 3.568A pdb=" N LEU a 380 " --> pdb=" O PRO a 376 " (cutoff:3.500A) Processing helix chain 'a' and resid 393 through 410 Processing helix chain 'a' and resid 410 through 426 removed outlier: 4.675A pdb=" N LEU a 414 " --> pdb=" O ILE a 410 " (cutoff:3.500A) Processing helix chain 'a' and resid 443 through 465 removed outlier: 3.599A pdb=" N THR a 457 " --> pdb=" O LYS a 453 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER a 464 " --> pdb=" O ILE a 460 " (cutoff:3.500A) Processing helix chain 'a' and resid 468 through 479 removed outlier: 3.941A pdb=" N VAL a 472 " --> pdb=" O SER a 468 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ARG a 473 " --> pdb=" O PRO a 469 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU a 474 " --> pdb=" O ASP a 470 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG a 475 " --> pdb=" O GLU a 471 " (cutoff:3.500A) Processing helix chain 'a' and resid 499 through 526 removed outlier: 3.634A pdb=" N ALA a 504 " --> pdb=" O PRO a 500 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA a 514 " --> pdb=" O GLY a 510 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS a 515 " --> pdb=" O ALA a 511 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG a 522 " --> pdb=" O GLY a 518 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA a 523 " --> pdb=" O GLU a 519 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU a 524 " --> pdb=" O ALA a 520 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA a 525 " --> pdb=" O GLU a 521 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN a 526 " --> pdb=" O ARG a 522 " (cutoff:3.500A) Processing helix chain 'd' and resid 97 through 106 removed outlier: 4.199A pdb=" N GLN d 106 " --> pdb=" O TRP d 102 " (cutoff:3.500A) Processing helix chain 'd' and resid 110 through 118 Processing helix chain 'd' and resid 120 through 135 removed outlier: 4.714A pdb=" N SER d 130 " --> pdb=" O ALA d 126 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLY d 131 " --> pdb=" O CYS d 127 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA d 135 " --> pdb=" O GLY d 131 " (cutoff:3.500A) Processing helix chain 'd' and resid 149 through 162 Processing helix chain 'd' and resid 164 through 180 Processing helix chain 'd' and resid 201 through 205 removed outlier: 3.958A pdb=" N VAL d 205 " --> pdb=" O PRO d 202 " (cutoff:3.500A) Processing helix chain 'd' and resid 265 through 269 Processing helix chain 'd' and resid 278 through 303 removed outlier: 3.647A pdb=" N ARG d 282 " --> pdb=" O PRO d 278 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N GLU d 285 " --> pdb=" O GLN d 281 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N ARG d 286 " --> pdb=" O ARG d 282 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA d 297 " --> pdb=" O THR d 293 " (cutoff:3.500A) Proline residue: d 298 - end of helix removed outlier: 3.601A pdb=" N SER d 303 " --> pdb=" O LEU d 299 " (cutoff:3.500A) Processing helix chain 'd' and resid 312 through 319 removed outlier: 3.797A pdb=" N ASN d 319 " --> pdb=" O LYS d 315 " (cutoff:3.500A) Processing helix chain 'd' and resid 322 through 333 Processing helix chain 'd' and resid 357 through 373 removed outlier: 3.849A pdb=" N ILE d 361 " --> pdb=" O ASP d 357 " (cutoff:3.500A) Processing helix chain 'd' and resid 376 through 381 removed outlier: 3.719A pdb=" N LEU d 380 " --> pdb=" O PRO d 376 " (cutoff:3.500A) Processing helix chain 'd' and resid 392 through 410 removed outlier: 3.875A pdb=" N ILE d 397 " --> pdb=" O GLU d 393 " (cutoff:3.500A) Processing helix chain 'd' and resid 410 through 426 removed outlier: 4.370A pdb=" N LEU d 414 " --> pdb=" O ILE d 410 " (cutoff:3.500A) Processing helix chain 'd' and resid 443 through 464 removed outlier: 3.507A pdb=" N LYS d 453 " --> pdb=" O GLU d 449 " (cutoff:3.500A) Processing helix chain 'd' and resid 470 through 479 removed outlier: 3.563A pdb=" N GLU d 474 " --> pdb=" O ASP d 470 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG d 475 " --> pdb=" O GLU d 471 " (cutoff:3.500A) Processing helix chain 'd' and resid 499 through 524 removed outlier: 3.791A pdb=" N GLU d 507 " --> pdb=" O LEU d 503 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS d 508 " --> pdb=" O ALA d 504 " (cutoff:3.500A) Processing helix chain 'e' and resid 97 through 106 removed outlier: 4.322A pdb=" N GLN e 106 " --> pdb=" O TRP e 102 " (cutoff:3.500A) Processing helix chain 'e' and resid 110 through 118 Processing helix chain 'e' and resid 120 through 135 removed outlier: 4.635A pdb=" N SER e 130 " --> pdb=" O ALA e 126 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N GLY e 131 " --> pdb=" O CYS e 127 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA e 135 " --> pdb=" O GLY e 131 " (cutoff:3.500A) Processing helix chain 'e' and resid 149 through 164 Processing helix chain 'e' and resid 164 through 180 Processing helix chain 'e' and resid 201 through 205 removed outlier: 3.622A pdb=" N VAL e 205 " --> pdb=" O PRO e 202 " (cutoff:3.500A) Processing helix chain 'e' and resid 217 through 219 No H-bonds generated for 'chain 'e' and resid 217 through 219' Processing helix chain 'e' and resid 279 through 303 removed outlier: 5.453A pdb=" N GLU e 285 " --> pdb=" O GLN e 281 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N ARG e 286 " --> pdb=" O ARG e 282 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA e 297 " --> pdb=" O THR e 293 " (cutoff:3.500A) Proline residue: e 298 - end of helix Processing helix chain 'e' and resid 312 through 319 removed outlier: 3.603A pdb=" N ASN e 319 " --> pdb=" O LYS e 315 " (cutoff:3.500A) Processing helix chain 'e' and resid 322 through 333 Processing helix chain 'e' and resid 357 through 373 removed outlier: 3.911A pdb=" N ILE e 361 " --> pdb=" O ASP e 357 " (cutoff:3.500A) Processing helix chain 'e' and resid 376 through 381 removed outlier: 3.581A pdb=" N LEU e 380 " --> pdb=" O PRO e 376 " (cutoff:3.500A) Processing helix chain 'e' and resid 392 through 410 removed outlier: 3.720A pdb=" N THR e 396 " --> pdb=" O GLY e 392 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE e 397 " --> pdb=" O GLU e 393 " (cutoff:3.500A) Processing helix chain 'e' and resid 410 through 426 removed outlier: 4.599A pdb=" N LEU e 414 " --> pdb=" O ILE e 410 " (cutoff:3.500A) Processing helix chain 'e' and resid 443 through 465 removed outlier: 3.590A pdb=" N THR e 457 " --> pdb=" O LYS e 453 " (cutoff:3.500A) Processing helix chain 'e' and resid 468 through 479 removed outlier: 3.839A pdb=" N ARG e 475 " --> pdb=" O GLU e 471 " (cutoff:3.500A) Processing helix chain 'e' and resid 499 through 526 removed outlier: 3.745A pdb=" N ALA e 504 " --> pdb=" O PRO e 500 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE e 506 " --> pdb=" O ASN e 502 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU e 507 " --> pdb=" O LEU e 503 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA e 514 " --> pdb=" O GLY e 510 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLN e 526 " --> pdb=" O ARG e 522 " (cutoff:3.500A) Processing helix chain 'f' and resid 97 through 106 removed outlier: 4.204A pdb=" N GLN f 106 " --> pdb=" O TRP f 102 " (cutoff:3.500A) Processing helix chain 'f' and resid 110 through 118 Processing helix chain 'f' and resid 120 through 135 removed outlier: 4.852A pdb=" N SER f 130 " --> pdb=" O ALA f 126 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N GLY f 131 " --> pdb=" O CYS f 127 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA f 135 " --> pdb=" O GLY f 131 " (cutoff:3.500A) Processing helix chain 'f' and resid 149 through 162 Processing helix chain 'f' and resid 164 through 180 Processing helix chain 'f' and resid 201 through 205 removed outlier: 3.794A pdb=" N GLY f 204 " --> pdb=" O ASN f 201 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL f 205 " --> pdb=" O PRO f 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 201 through 205' Processing helix chain 'f' and resid 278 through 303 removed outlier: 3.789A pdb=" N ARG f 282 " --> pdb=" O PRO f 278 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N GLU f 285 " --> pdb=" O GLN f 281 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ARG f 286 " --> pdb=" O ARG f 282 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA f 297 " --> pdb=" O THR f 293 " (cutoff:3.500A) Proline residue: f 298 - end of helix removed outlier: 3.776A pdb=" N SER f 303 " --> pdb=" O LEU f 299 " (cutoff:3.500A) Processing helix chain 'f' and resid 312 through 319 removed outlier: 3.694A pdb=" N ASN f 319 " --> pdb=" O LYS f 315 " (cutoff:3.500A) Processing helix chain 'f' and resid 322 through 333 Processing helix chain 'f' and resid 357 through 373 removed outlier: 3.831A pdb=" N ILE f 361 " --> pdb=" O ASP f 357 " (cutoff:3.500A) Processing helix chain 'f' and resid 376 through 381 removed outlier: 3.521A pdb=" N LEU f 380 " --> pdb=" O PRO f 376 " (cutoff:3.500A) Processing helix chain 'f' and resid 392 through 410 removed outlier: 3.850A pdb=" N ILE f 397 " --> pdb=" O GLU f 393 " (cutoff:3.500A) Processing helix chain 'f' and resid 410 through 426 removed outlier: 4.460A pdb=" N LEU f 414 " --> pdb=" O ILE f 410 " (cutoff:3.500A) Processing helix chain 'f' and resid 443 through 464 Processing helix chain 'f' and resid 468 through 479 removed outlier: 3.581A pdb=" N VAL f 472 " --> pdb=" O SER f 468 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG f 473 " --> pdb=" O PRO f 469 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU f 474 " --> pdb=" O ASP f 470 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG f 475 " --> pdb=" O GLU f 471 " (cutoff:3.500A) Processing helix chain 'f' and resid 499 through 524 removed outlier: 3.784A pdb=" N GLU f 507 " --> pdb=" O LEU f 503 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS f 508 " --> pdb=" O ALA f 504 " (cutoff:3.500A) Processing helix chain 'g' and resid 97 through 106 removed outlier: 4.355A pdb=" N GLN g 106 " --> pdb=" O TRP g 102 " (cutoff:3.500A) Processing helix chain 'g' and resid 110 through 118 Processing helix chain 'g' and resid 120 through 136 removed outlier: 4.463A pdb=" N SER g 130 " --> pdb=" O ALA g 126 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLY g 131 " --> pdb=" O CYS g 127 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA g 135 " --> pdb=" O GLY g 131 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG g 136 " --> pdb=" O GLU g 132 " (cutoff:3.500A) Processing helix chain 'g' and resid 149 through 164 Processing helix chain 'g' and resid 164 through 180 Processing helix chain 'g' and resid 201 through 205 Processing helix chain 'g' and resid 278 through 303 removed outlier: 3.651A pdb=" N ARG g 282 " --> pdb=" O PRO g 278 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N GLU g 285 " --> pdb=" O GLN g 281 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ARG g 286 " --> pdb=" O ARG g 282 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA g 297 " --> pdb=" O THR g 293 " (cutoff:3.500A) Proline residue: g 298 - end of helix removed outlier: 3.618A pdb=" N SER g 303 " --> pdb=" O LEU g 299 " (cutoff:3.500A) Processing helix chain 'g' and resid 312 through 319 removed outlier: 3.577A pdb=" N ALA g 316 " --> pdb=" O ASP g 312 " (cutoff:3.500A) Processing helix chain 'g' and resid 322 through 333 Processing helix chain 'g' and resid 357 through 373 removed outlier: 3.935A pdb=" N ILE g 361 " --> pdb=" O ASP g 357 " (cutoff:3.500A) Processing helix chain 'g' and resid 376 through 382 removed outlier: 3.621A pdb=" N LEU g 380 " --> pdb=" O PRO g 376 " (cutoff:3.500A) Processing helix chain 'g' and resid 392 through 410 removed outlier: 3.668A pdb=" N SER g 405 " --> pdb=" O GLU g 401 " (cutoff:3.500A) Processing helix chain 'g' and resid 410 through 426 removed outlier: 4.453A pdb=" N LEU g 414 " --> pdb=" O ILE g 410 " (cutoff:3.500A) Processing helix chain 'g' and resid 443 through 465 removed outlier: 3.528A pdb=" N THR g 457 " --> pdb=" O LYS g 453 " (cutoff:3.500A) Processing helix chain 'g' and resid 468 through 479 removed outlier: 3.540A pdb=" N VAL g 472 " --> pdb=" O SER g 468 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP g 478 " --> pdb=" O GLU g 474 " (cutoff:3.500A) Processing helix chain 'g' and resid 499 through 524 removed outlier: 3.549A pdb=" N ALA g 504 " --> pdb=" O PRO g 500 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA g 514 " --> pdb=" O GLY g 510 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS g 515 " --> pdb=" O ALA g 511 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG g 522 " --> pdb=" O GLY g 518 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU g 524 " --> pdb=" O ALA g 520 " (cutoff:3.500A) Processing helix chain 'h' and resid 97 through 106 removed outlier: 4.040A pdb=" N GLN h 106 " --> pdb=" O TRP h 102 " (cutoff:3.500A) Processing helix chain 'h' and resid 110 through 118 Processing helix chain 'h' and resid 120 through 135 removed outlier: 4.852A pdb=" N SER h 130 " --> pdb=" O ALA h 126 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N GLY h 131 " --> pdb=" O CYS h 127 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA h 135 " --> pdb=" O GLY h 131 " (cutoff:3.500A) Processing helix chain 'h' and resid 149 through 162 removed outlier: 3.865A pdb=" N SER h 153 " --> pdb=" O SER h 149 " (cutoff:3.500A) Processing helix chain 'h' and resid 164 through 180 Processing helix chain 'h' and resid 201 through 205 removed outlier: 3.973A pdb=" N VAL h 205 " --> pdb=" O PRO h 202 " (cutoff:3.500A) Processing helix chain 'h' and resid 278 through 303 removed outlier: 3.781A pdb=" N ARG h 282 " --> pdb=" O PRO h 278 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N GLU h 285 " --> pdb=" O GLN h 281 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N ARG h 286 " --> pdb=" O ARG h 282 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA h 297 " --> pdb=" O THR h 293 " (cutoff:3.500A) Proline residue: h 298 - end of helix Processing helix chain 'h' and resid 312 through 319 removed outlier: 3.713A pdb=" N ASN h 319 " --> pdb=" O LYS h 315 " (cutoff:3.500A) Processing helix chain 'h' and resid 322 through 333 Processing helix chain 'h' and resid 357 through 373 removed outlier: 3.798A pdb=" N ILE h 361 " --> pdb=" O ASP h 357 " (cutoff:3.500A) Processing helix chain 'h' and resid 376 through 381 Processing helix chain 'h' and resid 392 through 410 removed outlier: 3.826A pdb=" N ILE h 397 " --> pdb=" O GLU h 393 " (cutoff:3.500A) Processing helix chain 'h' and resid 410 through 426 removed outlier: 4.270A pdb=" N LEU h 414 " --> pdb=" O ILE h 410 " (cutoff:3.500A) Processing helix chain 'h' and resid 443 through 464 removed outlier: 3.803A pdb=" N LYS h 453 " --> pdb=" O GLU h 449 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE h 460 " --> pdb=" O ALA h 456 " (cutoff:3.500A) Processing helix chain 'h' and resid 468 through 479 removed outlier: 3.660A pdb=" N VAL h 472 " --> pdb=" O SER h 468 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG h 473 " --> pdb=" O PRO h 469 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG h 475 " --> pdb=" O GLU h 471 " (cutoff:3.500A) Processing helix chain 'h' and resid 499 through 524 removed outlier: 3.712A pdb=" N GLU h 507 " --> pdb=" O LEU h 503 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS h 508 " --> pdb=" O ALA h 504 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY h 518 " --> pdb=" O ALA h 514 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU h 519 " --> pdb=" O LYS h 515 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA h 520 " --> pdb=" O ALA h 516 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU h 521 " --> pdb=" O LYS h 517 " (cutoff:3.500A) Processing helix chain 'i' and resid 97 through 106 removed outlier: 4.324A pdb=" N GLN i 106 " --> pdb=" O TRP i 102 " (cutoff:3.500A) Processing helix chain 'i' and resid 110 through 118 Processing helix chain 'i' and resid 120 through 135 removed outlier: 4.532A pdb=" N SER i 130 " --> pdb=" O ALA i 126 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLY i 131 " --> pdb=" O CYS i 127 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA i 135 " --> pdb=" O GLY i 131 " (cutoff:3.500A) Processing helix chain 'i' and resid 149 through 164 Processing helix chain 'i' and resid 164 through 180 Processing helix chain 'i' and resid 201 through 205 removed outlier: 3.521A pdb=" N VAL i 205 " --> pdb=" O PRO i 202 " (cutoff:3.500A) Processing helix chain 'i' and resid 217 through 219 No H-bonds generated for 'chain 'i' and resid 217 through 219' Processing helix chain 'i' and resid 278 through 303 removed outlier: 3.673A pdb=" N ARG i 282 " --> pdb=" O PRO i 278 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N GLU i 285 " --> pdb=" O GLN i 281 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N ARG i 286 " --> pdb=" O ARG i 282 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA i 297 " --> pdb=" O THR i 293 " (cutoff:3.500A) Proline residue: i 298 - end of helix Processing helix chain 'i' and resid 312 through 319 removed outlier: 3.618A pdb=" N ASN i 319 " --> pdb=" O LYS i 315 " (cutoff:3.500A) Processing helix chain 'i' and resid 322 through 333 Processing helix chain 'i' and resid 357 through 373 removed outlier: 4.017A pdb=" N ILE i 361 " --> pdb=" O ASP i 357 " (cutoff:3.500A) Processing helix chain 'i' and resid 376 through 381 removed outlier: 3.566A pdb=" N LEU i 380 " --> pdb=" O PRO i 376 " (cutoff:3.500A) Processing helix chain 'i' and resid 392 through 410 removed outlier: 3.793A pdb=" N THR i 396 " --> pdb=" O GLY i 392 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE i 397 " --> pdb=" O GLU i 393 " (cutoff:3.500A) Processing helix chain 'i' and resid 410 through 426 removed outlier: 4.468A pdb=" N LEU i 414 " --> pdb=" O ILE i 410 " (cutoff:3.500A) Processing helix chain 'i' and resid 443 through 465 removed outlier: 3.510A pdb=" N ALA i 456 " --> pdb=" O ASN i 452 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR i 457 " --> pdb=" O LYS i 453 " (cutoff:3.500A) Processing helix chain 'i' and resid 468 through 479 removed outlier: 3.517A pdb=" N VAL i 472 " --> pdb=" O SER i 468 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG i 473 " --> pdb=" O PRO i 469 " (cutoff:3.500A) Processing helix chain 'i' and resid 499 through 526 removed outlier: 3.798A pdb=" N ALA i 504 " --> pdb=" O PRO i 500 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU i 505 " --> pdb=" O GLU i 501 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA i 514 " --> pdb=" O GLY i 510 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS i 515 " --> pdb=" O ALA i 511 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU i 521 " --> pdb=" O LYS i 517 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLN i 526 " --> pdb=" O ARG i 522 " (cutoff:3.500A) Processing helix chain 'j' and resid 97 through 106 removed outlier: 4.195A pdb=" N GLN j 106 " --> pdb=" O TRP j 102 " (cutoff:3.500A) Processing helix chain 'j' and resid 110 through 118 Processing helix chain 'j' and resid 120 through 135 removed outlier: 4.777A pdb=" N SER j 130 " --> pdb=" O ALA j 126 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N GLY j 131 " --> pdb=" O CYS j 127 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ALA j 135 " --> pdb=" O GLY j 131 " (cutoff:3.500A) Processing helix chain 'j' and resid 149 through 164 Processing helix chain 'j' and resid 164 through 180 Processing helix chain 'j' and resid 278 through 303 removed outlier: 3.804A pdb=" N ARG j 282 " --> pdb=" O PRO j 278 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N GLU j 285 " --> pdb=" O GLN j 281 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N ARG j 286 " --> pdb=" O ARG j 282 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA j 297 " --> pdb=" O THR j 293 " (cutoff:3.500A) Proline residue: j 298 - end of helix removed outlier: 3.592A pdb=" N SER j 303 " --> pdb=" O LEU j 299 " (cutoff:3.500A) Processing helix chain 'j' and resid 312 through 319 removed outlier: 3.684A pdb=" N ASN j 319 " --> pdb=" O LYS j 315 " (cutoff:3.500A) Processing helix chain 'j' and resid 322 through 333 Processing helix chain 'j' and resid 357 through 373 removed outlier: 3.847A pdb=" N ILE j 361 " --> pdb=" O ASP j 357 " (cutoff:3.500A) Processing helix chain 'j' and resid 376 through 381 removed outlier: 3.702A pdb=" N LEU j 380 " --> pdb=" O PRO j 376 " (cutoff:3.500A) Processing helix chain 'j' and resid 392 through 410 removed outlier: 3.894A pdb=" N ILE j 397 " --> pdb=" O GLU j 393 " (cutoff:3.500A) Processing helix chain 'j' and resid 410 through 426 removed outlier: 4.374A pdb=" N LEU j 414 " --> pdb=" O ILE j 410 " (cutoff:3.500A) Processing helix chain 'j' and resid 443 through 464 removed outlier: 3.768A pdb=" N LYS j 453 " --> pdb=" O GLU j 449 " (cutoff:3.500A) Processing helix chain 'j' and resid 468 through 479 removed outlier: 3.791A pdb=" N VAL j 472 " --> pdb=" O SER j 468 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ARG j 473 " --> pdb=" O PRO j 469 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU j 474 " --> pdb=" O ASP j 470 " (cutoff:3.500A) Processing helix chain 'j' and resid 499 through 526 removed outlier: 3.758A pdb=" N GLU j 507 " --> pdb=" O LEU j 503 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS j 508 " --> pdb=" O ALA j 504 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA j 525 " --> pdb=" O GLU j 521 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLN j 526 " --> pdb=" O ARG j 522 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 108 through 109 removed outlier: 6.786A pdb=" N TYR C 36 " --> pdb=" O LYS C 30 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LYS C 30 " --> pdb=" O TYR C 36 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N SER C 38 " --> pdb=" O ARG C 28 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ARG C 28 " --> pdb=" O SER C 38 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N PHE C 40 " --> pdb=" O GLU C 26 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N GLU C 26 " --> pdb=" O PHE C 40 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N GLU C 42 " --> pdb=" O LYS C 24 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N LYS C 24 " --> pdb=" O GLU C 42 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG C 21 " --> pdb=" O PHE C 90 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE C 90 " --> pdb=" O ARG C 21 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG C 23 " --> pdb=" O ASP C 88 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 108 through 109 removed outlier: 3.572A pdb=" N MET A 71 " --> pdb=" O GLN A 51 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N TYR A 36 " --> pdb=" O LYS A 30 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LYS A 30 " --> pdb=" O TYR A 36 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N SER A 38 " --> pdb=" O ARG A 28 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ARG A 28 " --> pdb=" O SER A 38 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N PHE A 40 " --> pdb=" O GLU A 26 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N GLU A 26 " --> pdb=" O PHE A 40 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N GLU A 42 " --> pdb=" O LYS A 24 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N LYS A 24 " --> pdb=" O GLU A 42 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ARG A 21 " --> pdb=" O PHE A 90 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE A 90 " --> pdb=" O ARG A 21 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 108 through 109 removed outlier: 3.517A pdb=" N ALA B 74 " --> pdb=" O GLN B 108 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N TYR B 36 " --> pdb=" O LYS B 30 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LYS B 30 " --> pdb=" O TYR B 36 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N SER B 38 " --> pdb=" O ARG B 28 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ARG B 28 " --> pdb=" O SER B 38 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N PHE B 40 " --> pdb=" O GLU B 26 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N GLU B 26 " --> pdb=" O PHE B 40 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N GLU B 42 " --> pdb=" O LYS B 24 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N LYS B 24 " --> pdb=" O GLU B 42 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ARG B 21 " --> pdb=" O PHE B 90 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE B 90 " --> pdb=" O ARG B 21 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 108 through 109 removed outlier: 3.684A pdb=" N ALA D 74 " --> pdb=" O GLN D 108 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N TYR D 36 " --> pdb=" O LYS D 30 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N LYS D 30 " --> pdb=" O TYR D 36 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N SER D 38 " --> pdb=" O ARG D 28 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ARG D 28 " --> pdb=" O SER D 38 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N PHE D 40 " --> pdb=" O GLU D 26 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N GLU D 26 " --> pdb=" O PHE D 40 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N GLU D 42 " --> pdb=" O LYS D 24 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N LYS D 24 " --> pdb=" O GLU D 42 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ARG D 21 " --> pdb=" O PHE D 90 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE D 90 " --> pdb=" O ARG D 21 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 108 through 109 removed outlier: 3.785A pdb=" N MET E 71 " --> pdb=" O GLN E 51 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N TYR E 36 " --> pdb=" O LYS E 30 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LYS E 30 " --> pdb=" O TYR E 36 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N SER E 38 " --> pdb=" O ARG E 28 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ARG E 28 " --> pdb=" O SER E 38 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N PHE E 40 " --> pdb=" O GLU E 26 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N GLU E 26 " --> pdb=" O PHE E 40 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLU E 42 " --> pdb=" O LYS E 24 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N LYS E 24 " --> pdb=" O GLU E 42 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ARG E 21 " --> pdb=" O PHE E 90 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE E 90 " --> pdb=" O ARG E 21 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 108 through 109 removed outlier: 6.985A pdb=" N TYR F 36 " --> pdb=" O LYS F 30 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LYS F 30 " --> pdb=" O TYR F 36 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N SER F 38 " --> pdb=" O ARG F 28 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ARG F 28 " --> pdb=" O SER F 38 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N PHE F 40 " --> pdb=" O GLU F 26 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLU F 26 " --> pdb=" O PHE F 40 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N GLU F 42 " --> pdb=" O LYS F 24 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N LYS F 24 " --> pdb=" O GLU F 42 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ARG F 21 " --> pdb=" O PHE F 90 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE F 90 " --> pdb=" O ARG F 21 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'M' and resid 31 through 34 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 48 through 57 current: chain 'M' and resid 74 through 92 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 74 through 92 current: chain 'M' and resid 155 through 170 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 155 through 170 current: chain 'b' and resid 48 through 56 WARNING: can't find start of bonding for strands! previous: chain 'b' and resid 48 through 56 current: chain 'b' and resid 74 through 83 WARNING: can't find start of bonding for strands! previous: chain 'b' and resid 74 through 83 current: chain 'b' and resid 155 through 170 Processing sheet with id=AA8, first strand: chain 'M' and resid 138 through 139 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 138 through 139 current: chain 'S' and resid 48 through 57 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 48 through 57 current: chain 'S' and resid 74 through 92 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 74 through 92 current: chain 'S' and resid 155 through 170 No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'M' and resid 142 through 143 removed outlier: 3.791A pdb=" N GLU M 151 " --> pdb=" O PHE M 143 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'P' and resid 31 through 34 removed outlier: 3.595A pdb=" N PHE P 51 " --> pdb=" O VAL P 33 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 48 through 57 current: chain 'P' and resid 74 through 92 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 74 through 92 current: chain 'P' and resid 155 through 170 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 155 through 170 current: chain 'V' and resid 48 through 57 WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 48 through 57 current: chain 'V' and resid 74 through 92 WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 74 through 92 current: chain 'V' and resid 155 through 170 Processing sheet with id=AB2, first strand: chain 'P' and resid 142 through 143 Processing sheet with id=AB3, first strand: chain 'S' and resid 142 through 143 Processing sheet with id=AB4, first strand: chain 'V' and resid 142 through 143 Processing sheet with id=AB5, first strand: chain 'Y' and resid 31 through 34 removed outlier: 6.613A pdb=" N GLU Y 31 " --> pdb=" O ILE Y 49 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N PHE Y 51 " --> pdb=" O GLU Y 31 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N VAL Y 33 " --> pdb=" O PHE Y 51 " (cutoff:3.500A) removed outlier: 9.504A pdb=" N LYS Y 53 " --> pdb=" O VAL Y 33 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 48 through 57 current: chain 'Y' and resid 74 through 92 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 74 through 92 current: chain 'Y' and resid 155 through 170 No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'Y' and resid 142 through 143 Processing sheet with id=AB7, first strand: chain 'b' and resid 142 through 143 removed outlier: 3.593A pdb=" N GLU b 151 " --> pdb=" O PHE b 143 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 90 through 95 removed outlier: 5.993A pdb=" N THR N 91 " --> pdb=" O LYS N 102 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N THR L 91 " --> pdb=" O LYS L 102 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N THR K 91 " --> pdb=" O LYS K 102 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N THR J 91 " --> pdb=" O LYS J 102 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL J 98 " --> pdb=" O VAL J 95 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N THR I 91 " --> pdb=" O LYS I 102 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N THR H 91 " --> pdb=" O LYS H 102 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N THR G 91 " --> pdb=" O LYS G 102 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N THR c 91 " --> pdb=" O LYS c 102 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N THR Z 91 " --> pdb=" O LYS Z 102 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N THR W 91 " --> pdb=" O LYS W 102 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL W 98 " --> pdb=" O VAL W 95 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N THR T 91 " --> pdb=" O LYS T 102 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N THR Q 91 " --> pdb=" O LYS Q 102 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'Q' and resid 136 through 137 removed outlier: 6.249A pdb=" N LYS O 340 " --> pdb=" O ILE j 309 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'W' and resid 136 through 137 Processing sheet with id=AC2, first strand: chain 'Z' and resid 136 through 137 Processing sheet with id=AC3, first strand: chain 'c' and resid 136 through 137 removed outlier: 3.891A pdb=" N GLY f 347 " --> pdb=" O HIS f 310 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 136 through 137 Processing sheet with id=AC5, first strand: chain 'H' and resid 136 through 137 Processing sheet with id=AC6, first strand: chain 'J' and resid 136 through 137 Processing sheet with id=AC7, first strand: chain 'K' and resid 136 through 137 removed outlier: 6.741A pdb=" N SER U 307 " --> pdb=" O LYS X 340 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N LEU X 342 " --> pdb=" O SER U 307 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ILE U 309 " --> pdb=" O LEU X 342 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 136 through 137 Processing sheet with id=AC9, first strand: chain 'O' and resid 139 through 142 removed outlier: 3.530A pdb=" N VAL O 435 " --> pdb=" O GLU O 140 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'O' and resid 210 through 216 removed outlier: 3.937A pdb=" N GLY O 212 " --> pdb=" O VAL O 187 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE O 183 " --> pdb=" O ILE O 216 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'O' and resid 221 through 224 removed outlier: 3.662A pdb=" N PHE O 243 " --> pdb=" O GLN O 224 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'O' and resid 347 through 351 Processing sheet with id=AD4, first strand: chain 'R' and resid 139 through 143 Processing sheet with id=AD5, first strand: chain 'R' and resid 210 through 216 removed outlier: 3.919A pdb=" N GLY R 212 " --> pdb=" O VAL R 187 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ILE R 183 " --> pdb=" O ILE R 216 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'R' and resid 221 through 224 removed outlier: 3.659A pdb=" N PHE R 243 " --> pdb=" O GLN R 224 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'U' and resid 139 through 142 removed outlier: 3.639A pdb=" N VAL U 435 " --> pdb=" O GLU U 140 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'U' and resid 210 through 216 removed outlier: 3.941A pdb=" N GLY U 212 " --> pdb=" O VAL U 187 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ILE U 183 " --> pdb=" O ILE U 216 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'U' and resid 221 through 224 removed outlier: 3.521A pdb=" N LYS U 249 " --> pdb=" O ILE U 246 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'X' and resid 139 through 143 Processing sheet with id=AE2, first strand: chain 'X' and resid 210 through 216 removed outlier: 3.906A pdb=" N GLY X 212 " --> pdb=" O VAL X 187 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ILE X 183 " --> pdb=" O ILE X 216 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'X' and resid 221 through 224 Processing sheet with id=AE4, first strand: chain 'a' and resid 139 through 142 Processing sheet with id=AE5, first strand: chain 'a' and resid 210 through 216 removed outlier: 3.821A pdb=" N GLY a 212 " --> pdb=" O VAL a 187 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE a 183 " --> pdb=" O ILE a 216 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'a' and resid 221 through 224 Processing sheet with id=AE7, first strand: chain 'a' and resid 347 through 351 removed outlier: 3.626A pdb=" N GLY a 347 " --> pdb=" O HIS a 310 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'd' and resid 139 through 143 Processing sheet with id=AE9, first strand: chain 'd' and resid 210 through 216 removed outlier: 3.849A pdb=" N GLY d 212 " --> pdb=" O VAL d 187 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ILE d 183 " --> pdb=" O ILE d 216 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'd' and resid 222 through 224 Processing sheet with id=AF2, first strand: chain 'e' and resid 139 through 142 removed outlier: 3.783A pdb=" N VAL e 435 " --> pdb=" O GLU e 140 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS e 142 " --> pdb=" O GLU e 433 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'e' and resid 210 through 216 removed outlier: 3.981A pdb=" N GLY e 212 " --> pdb=" O VAL e 187 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ILE e 183 " --> pdb=" O ILE e 216 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'e' and resid 221 through 224 removed outlier: 3.537A pdb=" N PHE e 243 " --> pdb=" O GLN e 224 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'f' and resid 139 through 143 Processing sheet with id=AF6, first strand: chain 'f' and resid 210 through 216 removed outlier: 3.834A pdb=" N GLY f 212 " --> pdb=" O VAL f 187 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ILE f 183 " --> pdb=" O ILE f 216 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'f' and resid 221 through 224 removed outlier: 3.537A pdb=" N PHE f 243 " --> pdb=" O GLN f 224 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'g' and resid 139 through 142 removed outlier: 3.840A pdb=" N VAL g 435 " --> pdb=" O GLU g 140 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'g' and resid 210 through 216 removed outlier: 4.034A pdb=" N GLY g 212 " --> pdb=" O VAL g 187 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL g 187 " --> pdb=" O GLY g 212 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ILE g 183 " --> pdb=" O ILE g 216 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'g' and resid 221 through 224 Processing sheet with id=AG2, first strand: chain 'h' and resid 139 through 143 Processing sheet with id=AG3, first strand: chain 'h' and resid 210 through 216 removed outlier: 3.885A pdb=" N GLY h 212 " --> pdb=" O VAL h 187 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE h 216 " --> pdb=" O ILE h 183 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ILE h 183 " --> pdb=" O ILE h 216 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'h' and resid 221 through 224 removed outlier: 3.539A pdb=" N PHE h 243 " --> pdb=" O GLN h 224 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'i' and resid 139 through 142 Processing sheet with id=AG6, first strand: chain 'i' and resid 210 through 216 removed outlier: 3.801A pdb=" N GLY i 212 " --> pdb=" O VAL i 187 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ILE i 183 " --> pdb=" O ILE i 216 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'i' and resid 221 through 224 Processing sheet with id=AG8, first strand: chain 'i' and resid 347 through 351 Processing sheet with id=AG9, first strand: chain 'j' and resid 139 through 143 Processing sheet with id=AH1, first strand: chain 'j' and resid 210 through 216 removed outlier: 3.924A pdb=" N GLY j 212 " --> pdb=" O VAL j 187 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ILE j 183 " --> pdb=" O ILE j 216 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'j' and resid 221 through 224 removed outlier: 3.660A pdb=" N PHE j 243 " --> pdb=" O GLN j 224 " (cutoff:3.500A) 3173 hydrogen bonds defined for protein. 9123 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 26.08 Time building geometry restraints manager: 23.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 23531 1.34 - 1.46: 16956 1.46 - 1.58: 31213 1.58 - 1.70: 0 1.70 - 1.82: 414 Bond restraints: 72114 Sorted by residual: bond pdb=" CA ILE Y 57 " pdb=" CB ILE Y 57 " ideal model delta sigma weight residual 1.541 1.526 0.015 1.24e-02 6.50e+03 1.43e+00 bond pdb=" N TRP F 105 " pdb=" CA TRP F 105 " ideal model delta sigma weight residual 1.468 1.454 0.014 1.24e-02 6.50e+03 1.27e+00 bond pdb=" CG GLU e 404 " pdb=" CD GLU e 404 " ideal model delta sigma weight residual 1.516 1.488 0.028 2.50e-02 1.60e+03 1.27e+00 bond pdb=" CD GLU e 404 " pdb=" OE1 GLU e 404 " ideal model delta sigma weight residual 1.249 1.228 0.021 1.90e-02 2.77e+03 1.25e+00 bond pdb=" N GLU U 427 " pdb=" CA GLU U 427 " ideal model delta sigma weight residual 1.457 1.472 -0.014 1.29e-02 6.01e+03 1.25e+00 ... (remaining 72109 not shown) Histogram of bond angle deviations from ideal: 98.74 - 105.81: 1697 105.81 - 112.88: 36980 112.88 - 119.96: 25265 119.96 - 127.03: 32929 127.03 - 134.10: 977 Bond angle restraints: 97848 Sorted by residual: angle pdb=" N VAL A 53 " pdb=" CA VAL A 53 " pdb=" C VAL A 53 " ideal model delta sigma weight residual 113.71 108.28 5.43 9.50e-01 1.11e+00 3.26e+01 angle pdb=" C ARG F 54 " pdb=" N ARG F 55 " pdb=" CA ARG F 55 " ideal model delta sigma weight residual 121.54 132.09 -10.55 1.91e+00 2.74e-01 3.05e+01 angle pdb=" N GLY E 110 " pdb=" CA GLY E 110 " pdb=" C GLY E 110 " ideal model delta sigma weight residual 111.42 118.66 -7.24 1.42e+00 4.96e-01 2.60e+01 angle pdb=" C ARG E 54 " pdb=" N ARG E 55 " pdb=" CA ARG E 55 " ideal model delta sigma weight residual 121.54 131.21 -9.67 1.91e+00 2.74e-01 2.57e+01 angle pdb=" CA ARG A 54 " pdb=" CB ARG A 54 " pdb=" CG ARG A 54 " ideal model delta sigma weight residual 114.10 105.02 9.08 2.00e+00 2.50e-01 2.06e+01 ... (remaining 97843 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 38321 17.96 - 35.91: 3592 35.91 - 53.87: 599 53.87 - 71.82: 162 71.82 - 89.78: 82 Dihedral angle restraints: 42756 sinusoidal: 17082 harmonic: 25674 Sorted by residual: dihedral pdb=" CA GLN F 60 " pdb=" C GLN F 60 " pdb=" N PHE F 61 " pdb=" CA PHE F 61 " ideal model delta harmonic sigma weight residual 180.00 154.11 25.89 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA TYR e 239 " pdb=" C TYR e 239 " pdb=" N GLU e 240 " pdb=" CA GLU e 240 " ideal model delta harmonic sigma weight residual 180.00 155.41 24.59 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA TYR a 239 " pdb=" C TYR a 239 " pdb=" N GLU a 240 " pdb=" CA GLU a 240 " ideal model delta harmonic sigma weight residual 180.00 155.92 24.08 0 5.00e+00 4.00e-02 2.32e+01 ... (remaining 42753 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 9194 0.066 - 0.131: 1152 0.131 - 0.197: 49 0.197 - 0.262: 2 0.262 - 0.328: 7 Chirality restraints: 10404 Sorted by residual: chirality pdb=" CA PHE E 106 " pdb=" N PHE E 106 " pdb=" C PHE E 106 " pdb=" CB PHE E 106 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.69e+00 chirality pdb=" CA ARG A 54 " pdb=" N ARG A 54 " pdb=" C ARG A 54 " pdb=" CB ARG A 54 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" CA ARG E 54 " pdb=" N ARG E 54 " pdb=" C ARG E 54 " pdb=" CB ARG E 54 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.58e+00 ... (remaining 10401 not shown) Planarity restraints: 12912 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE V 57 " -0.041 5.00e-02 4.00e+02 6.20e-02 6.14e+00 pdb=" N PRO V 58 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO V 58 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO V 58 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE S 57 " -0.036 5.00e-02 4.00e+02 5.48e-02 4.80e+00 pdb=" N PRO S 58 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO S 58 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO S 58 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE Y 57 " -0.034 5.00e-02 4.00e+02 5.17e-02 4.27e+00 pdb=" N PRO Y 58 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO Y 58 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO Y 58 " -0.029 5.00e-02 4.00e+02 ... (remaining 12909 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 769 2.62 - 3.19: 62781 3.19 - 3.76: 106287 3.76 - 4.33: 143899 4.33 - 4.90: 243656 Nonbonded interactions: 557392 Sorted by model distance: nonbonded pdb=" OG SER F 101 " pdb=" OD1 ASP F 109 " model vdw 2.050 2.440 nonbonded pdb=" OG SER X 149 " pdb=" OE1 GLN X 152 " model vdw 2.139 2.440 nonbonded pdb=" OG SER h 443 " pdb=" OE1 GLN h 446 " model vdw 2.152 2.440 nonbonded pdb=" OG SER h 149 " pdb=" OE1 GLN h 152 " model vdw 2.154 2.440 nonbonded pdb=" OG SER d 443 " pdb=" OE1 GLN d 446 " model vdw 2.155 2.440 ... (remaining 557387 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'N' selection = chain 'Q' selection = chain 'T' selection = chain 'W' selection = chain 'Z' selection = chain 'c' } ncs_group { reference = chain 'M' selection = chain 'P' selection = chain 'S' selection = chain 'V' selection = chain 'Y' selection = chain 'b' } ncs_group { reference = chain 'O' selection = chain 'R' selection = chain 'U' selection = chain 'X' selection = chain 'a' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.930 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: 0.090 Extract box with map and model: 28.170 Check model and map are aligned: 0.870 Set scattering table: 0.510 Process input model: 145.270 Find NCS groups from input model: 3.920 Set up NCS constraints: 0.590 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 187.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 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 : 0.003 0.034 72114 Z= 0.176 Angle : 0.587 10.757 97848 Z= 0.315 Chirality : 0.043 0.328 10404 Planarity : 0.004 0.070 12912 Dihedral : 14.724 89.779 26268 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.36 % Favored : 95.50 % Rotamer: Outliers : 0.07 % Allowed : 0.26 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.09), residues: 8814 helix: 1.54 (0.09), residues: 3948 sheet: 0.47 (0.16), residues: 1158 loop : -1.00 (0.10), residues: 3708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP E 111 HIS 0.006 0.001 HIS d 337 PHE 0.029 0.001 PHE C 106 TYR 0.016 0.001 TYR W 137 ARG 0.011 0.000 ARG g 136 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17628 Ramachandran restraints generated. 8814 Oldfield, 0 Emsley, 8814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17628 Ramachandran restraints generated. 8814 Oldfield, 0 Emsley, 8814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1691 residues out of total 7380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1686 time to evaluate : 6.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 126 LYS cc_start: 0.9059 (tttp) cc_final: 0.8830 (tttt) REVERT: V 127 GLU cc_start: 0.7893 (pp20) cc_final: 0.7655 (pp20) REVERT: Q 41 ARG cc_start: 0.7495 (mmm-85) cc_final: 0.6972 (tpp80) REVERT: W 47 ILE cc_start: 0.9189 (mm) cc_final: 0.8971 (mm) REVERT: Z 24 ASP cc_start: 0.8054 (t0) cc_final: 0.7733 (t0) REVERT: c 42 ASP cc_start: 0.8054 (t70) cc_final: 0.7825 (t0) REVERT: H 41 ARG cc_start: 0.7496 (mmm-85) cc_final: 0.7018 (tpp80) REVERT: K 24 ASP cc_start: 0.7965 (t0) cc_final: 0.7577 (t0) REVERT: L 42 ASP cc_start: 0.8097 (t70) cc_final: 0.7829 (t0) REVERT: O 101 ASP cc_start: 0.8702 (m-30) cc_final: 0.8440 (m-30) REVERT: O 129 MET cc_start: 0.8265 (mtp) cc_final: 0.8005 (mtp) REVERT: O 159 ARG cc_start: 0.8369 (mmp80) cc_final: 0.8122 (mmp80) REVERT: O 161 MET cc_start: 0.8535 (tpt) cc_final: 0.8081 (mmt) REVERT: R 460 ILE cc_start: 0.9284 (mt) cc_final: 0.9072 (tt) REVERT: R 486 ARG cc_start: 0.7212 (ttp80) cc_final: 0.6604 (tmt-80) REVERT: R 501 GLU cc_start: 0.8632 (pt0) cc_final: 0.8152 (pp20) REVERT: U 101 ASP cc_start: 0.8676 (m-30) cc_final: 0.8414 (m-30) REVERT: U 114 CYS cc_start: 0.8579 (m) cc_final: 0.8369 (m) REVERT: U 123 VAL cc_start: 0.8905 (t) cc_final: 0.8327 (t) REVERT: U 127 CYS cc_start: 0.7881 (m) cc_final: 0.7671 (m) REVERT: U 312 ASP cc_start: 0.7770 (t0) cc_final: 0.7550 (t0) REVERT: U 501 GLU cc_start: 0.9059 (tp30) cc_final: 0.8851 (tp30) REVERT: X 302 MET cc_start: 0.8403 (mmm) cc_final: 0.8194 (mmm) REVERT: a 100 GLN cc_start: 0.9059 (tp40) cc_final: 0.8784 (tp40) REVERT: a 101 ASP cc_start: 0.8676 (m-30) cc_final: 0.8144 (m-30) REVERT: a 171 GLU cc_start: 0.8140 (tm-30) cc_final: 0.7885 (tm-30) REVERT: a 195 TYR cc_start: 0.7292 (t80) cc_final: 0.6957 (t80) REVERT: a 244 TRP cc_start: 0.8594 (m-90) cc_final: 0.8375 (m-90) REVERT: a 386 LYS cc_start: 0.7566 (mttm) cc_final: 0.7182 (mptt) REVERT: a 404 GLU cc_start: 0.8658 (mt-10) cc_final: 0.8309 (mt-10) REVERT: a 491 GLN cc_start: 0.7828 (pp30) cc_final: 0.7622 (pp30) REVERT: d 240 GLU cc_start: 0.8524 (tp30) cc_final: 0.8158 (tp30) REVERT: d 470 ASP cc_start: 0.8466 (p0) cc_final: 0.8194 (p0) REVERT: e 101 ASP cc_start: 0.8642 (m-30) cc_final: 0.8441 (m-30) REVERT: e 401 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7351 (mm-30) REVERT: f 460 ILE cc_start: 0.9309 (mt) cc_final: 0.9047 (tt) REVERT: g 159 ARG cc_start: 0.7918 (mmp80) cc_final: 0.7332 (mmm160) REVERT: g 195 TYR cc_start: 0.7676 (t80) cc_final: 0.7392 (t80) REVERT: g 401 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7746 (mm-30) REVERT: g 449 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8338 (mt-10) REVERT: g 490 ASP cc_start: 0.8072 (m-30) cc_final: 0.7825 (t0) REVERT: h 240 GLU cc_start: 0.7489 (tm-30) cc_final: 0.7169 (tm-30) REVERT: i 101 ASP cc_start: 0.8766 (m-30) cc_final: 0.8279 (m-30) REVERT: i 114 CYS cc_start: 0.8714 (m) cc_final: 0.8465 (m) REVERT: i 345 ASP cc_start: 0.8420 (p0) cc_final: 0.7926 (p0) REVERT: i 346 GLU cc_start: 0.7674 (mp0) cc_final: 0.7377 (mp0) REVERT: i 474 GLU cc_start: 0.8860 (mm-30) cc_final: 0.8601 (mm-30) REVERT: i 475 ARG cc_start: 0.8353 (ttp-170) cc_final: 0.7947 (ptt180) REVERT: i 501 GLU cc_start: 0.9105 (tp30) cc_final: 0.8853 (tp30) REVERT: j 97 THR cc_start: 0.8024 (m) cc_final: 0.7781 (m) REVERT: j 101 ASP cc_start: 0.8798 (m-30) cc_final: 0.8594 (m-30) REVERT: j 240 GLU cc_start: 0.8640 (tp30) cc_final: 0.8180 (tp30) REVERT: j 337 HIS cc_start: 0.7357 (m90) cc_final: 0.6920 (m90) REVERT: j 346 GLU cc_start: 0.7832 (pm20) cc_final: 0.7426 (pm20) REVERT: j 470 ASP cc_start: 0.8329 (p0) cc_final: 0.7992 (p0) REVERT: j 501 GLU cc_start: 0.8709 (pt0) cc_final: 0.8096 (pp20) outliers start: 5 outliers final: 0 residues processed: 1687 average time/residue: 0.6520 time to fit residues: 1878.9024 Evaluate side-chains 1408 residues out of total 7380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1408 time to evaluate : 6.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 876 random chunks: chunk 739 optimal weight: 20.0000 chunk 663 optimal weight: 2.9990 chunk 368 optimal weight: 5.9990 chunk 226 optimal weight: 0.0670 chunk 447 optimal weight: 0.0050 chunk 354 optimal weight: 8.9990 chunk 686 optimal weight: 4.9990 chunk 265 optimal weight: 0.0020 chunk 417 optimal weight: 3.9990 chunk 511 optimal weight: 0.9990 chunk 795 optimal weight: 8.9990 overall best weight: 0.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN A 89 GLN D 89 GLN ** E 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 52 GLN S 95 GLN V 95 GLN b 147 ASN ** N 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 7 HIS ** O 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 237 HIS O 337 HIS R 337 HIS ** U 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 446 GLN ** X 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 237 HIS d 364 ASN e 337 HIS f 337 HIS f 409 HIS g 100 GLN h 119 GLN ** i 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 72114 Z= 0.154 Angle : 0.547 9.002 97848 Z= 0.288 Chirality : 0.042 0.302 10404 Planarity : 0.004 0.047 12912 Dihedral : 4.440 45.688 9660 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.21 % Favored : 95.65 % Rotamer: Outliers : 1.52 % Allowed : 9.34 % Favored : 89.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.09), residues: 8814 helix: 1.68 (0.08), residues: 3996 sheet: 0.90 (0.16), residues: 1170 loop : -0.99 (0.10), residues: 3648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP W 111 HIS 0.008 0.001 HIS H 7 PHE 0.030 0.001 PHE X 506 TYR 0.018 0.001 TYR X 419 ARG 0.012 0.000 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17628 Ramachandran restraints generated. 8814 Oldfield, 0 Emsley, 8814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17628 Ramachandran restraints generated. 8814 Oldfield, 0 Emsley, 8814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1719 residues out of total 7380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 1607 time to evaluate : 6.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 123 LYS cc_start: 0.7535 (mmtm) cc_final: 0.7320 (mmtm) REVERT: M 56 ASP cc_start: 0.7638 (m-30) cc_final: 0.7369 (m-30) REVERT: S 126 LYS cc_start: 0.8988 (tttp) cc_final: 0.8718 (tttt) REVERT: b 145 ASN cc_start: 0.8734 (t0) cc_final: 0.8520 (t0) REVERT: Q 41 ARG cc_start: 0.7565 (mmm-85) cc_final: 0.7017 (tpp80) REVERT: W 8 LYS cc_start: 0.9006 (ttpp) cc_final: 0.8694 (ttpp) REVERT: W 42 ASP cc_start: 0.8532 (t0) cc_final: 0.8306 (t0) REVERT: W 47 ILE cc_start: 0.9143 (mm) cc_final: 0.8937 (mm) REVERT: Z 51 LYS cc_start: 0.8379 (mmmt) cc_final: 0.8143 (mmtp) REVERT: c 42 ASP cc_start: 0.8060 (t70) cc_final: 0.7825 (t0) REVERT: c 45 TYR cc_start: 0.7780 (m-80) cc_final: 0.7527 (m-80) REVERT: H 8 LYS cc_start: 0.8883 (ttpp) cc_final: 0.8680 (ttpp) REVERT: H 41 ARG cc_start: 0.7507 (mmm-85) cc_final: 0.7012 (tpp80) REVERT: J 8 LYS cc_start: 0.8966 (ttpp) cc_final: 0.8635 (ttpp) REVERT: K 6 GLU cc_start: 0.7915 (tt0) cc_final: 0.7372 (tt0) REVERT: L 42 ASP cc_start: 0.8049 (t70) cc_final: 0.7799 (t0) REVERT: O 101 ASP cc_start: 0.8683 (m-30) cc_final: 0.8429 (m-30) REVERT: O 129 MET cc_start: 0.8263 (mtp) cc_final: 0.7981 (mtp) REVERT: O 142 LYS cc_start: 0.7503 (tptt) cc_final: 0.7068 (tptp) REVERT: O 152 GLN cc_start: 0.8740 (mt0) cc_final: 0.8456 (pt0) REVERT: O 159 ARG cc_start: 0.8471 (mmp80) cc_final: 0.8254 (mmp80) REVERT: O 161 MET cc_start: 0.8521 (tpt) cc_final: 0.8167 (mmt) REVERT: R 168 ASN cc_start: 0.8775 (m-40) cc_final: 0.8512 (m-40) REVERT: R 419 TYR cc_start: 0.8781 (m-80) cc_final: 0.8398 (m-80) REVERT: R 486 ARG cc_start: 0.7061 (ttp80) cc_final: 0.6515 (tmt-80) REVERT: R 501 GLU cc_start: 0.8470 (pt0) cc_final: 0.8177 (pp20) REVERT: U 97 THR cc_start: 0.8613 (p) cc_final: 0.8168 (p) REVERT: U 101 ASP cc_start: 0.8670 (m-30) cc_final: 0.8392 (m-30) REVERT: U 114 CYS cc_start: 0.8556 (m) cc_final: 0.8349 (m) REVERT: U 127 CYS cc_start: 0.7875 (m) cc_final: 0.7670 (m) REVERT: U 142 LYS cc_start: 0.7535 (tptp) cc_final: 0.7327 (tptp) REVERT: U 150 ASP cc_start: 0.8650 (m-30) cc_final: 0.8265 (m-30) REVERT: U 312 ASP cc_start: 0.7717 (t0) cc_final: 0.7460 (t0) REVERT: U 346 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7160 (mm-30) REVERT: X 161 MET cc_start: 0.7983 (mmt) cc_final: 0.7728 (mmt) REVERT: X 222 MET cc_start: 0.7714 (mtt) cc_final: 0.7427 (mtp) REVERT: X 406 ILE cc_start: 0.9267 (mm) cc_final: 0.8870 (tp) REVERT: a 97 THR cc_start: 0.9083 (p) cc_final: 0.8476 (p) REVERT: a 100 GLN cc_start: 0.9001 (tp40) cc_final: 0.8690 (tp40) REVERT: a 101 ASP cc_start: 0.8656 (m-30) cc_final: 0.8181 (m-30) REVERT: a 171 GLU cc_start: 0.8168 (tm-30) cc_final: 0.7858 (tm-30) REVERT: a 195 TYR cc_start: 0.7220 (t80) cc_final: 0.6975 (t80) REVERT: a 237 HIS cc_start: 0.8192 (OUTLIER) cc_final: 0.7455 (p-80) REVERT: a 386 LYS cc_start: 0.7508 (mttm) cc_final: 0.7263 (mmtm) REVERT: a 478 ASP cc_start: 0.8002 (m-30) cc_final: 0.7799 (m-30) REVERT: d 216 ILE cc_start: 0.9525 (mt) cc_final: 0.9030 (tp) REVERT: d 240 GLU cc_start: 0.8483 (tp30) cc_final: 0.8178 (tp30) REVERT: d 458 ASP cc_start: 0.8696 (m-30) cc_final: 0.8445 (m-30) REVERT: d 470 ASP cc_start: 0.8565 (p0) cc_final: 0.8219 (p0) REVERT: e 466 VAL cc_start: 0.8943 (t) cc_final: 0.8737 (p) REVERT: f 198 LYS cc_start: 0.8595 (tttm) cc_final: 0.8356 (ttpp) REVERT: g 142 LYS cc_start: 0.7334 (tptp) cc_final: 0.7110 (tptp) REVERT: g 159 ARG cc_start: 0.8101 (mmp80) cc_final: 0.7584 (mmm160) REVERT: g 160 ASP cc_start: 0.8814 (t0) cc_final: 0.8388 (t0) REVERT: g 195 TYR cc_start: 0.7677 (t80) cc_final: 0.7418 (t80) REVERT: g 346 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7482 (mm-30) REVERT: g 381 LEU cc_start: 0.9046 (mp) cc_final: 0.8827 (mp) REVERT: g 401 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7781 (mm-30) REVERT: g 490 ASP cc_start: 0.8068 (m-30) cc_final: 0.7826 (t0) REVERT: h 161 MET cc_start: 0.8190 (mmt) cc_final: 0.7916 (mmt) REVERT: h 240 GLU cc_start: 0.7564 (tm-30) cc_final: 0.7184 (tm-30) REVERT: h 250 LYS cc_start: 0.8672 (mmmt) cc_final: 0.8350 (tttm) REVERT: h 300 LEU cc_start: 0.9369 (tp) cc_final: 0.9055 (mp) REVERT: h 406 ILE cc_start: 0.9257 (mm) cc_final: 0.8934 (tp) REVERT: i 101 ASP cc_start: 0.8718 (m-30) cc_final: 0.8237 (m-30) REVERT: i 114 CYS cc_start: 0.8690 (m) cc_final: 0.8467 (m) REVERT: i 132 GLU cc_start: 0.7956 (tm-30) cc_final: 0.7709 (tm-30) REVERT: i 161 MET cc_start: 0.8576 (mmt) cc_final: 0.8226 (ttp) REVERT: i 345 ASP cc_start: 0.8426 (p0) cc_final: 0.7729 (p0) REVERT: i 346 GLU cc_start: 0.7573 (mp0) cc_final: 0.7196 (mp0) REVERT: i 475 ARG cc_start: 0.8219 (ttp-170) cc_final: 0.7730 (ptt180) REVERT: j 97 THR cc_start: 0.8037 (m) cc_final: 0.7782 (m) REVERT: j 101 ASP cc_start: 0.8798 (m-30) cc_final: 0.8586 (m-30) REVERT: j 240 GLU cc_start: 0.8616 (tp30) cc_final: 0.8149 (tp30) REVERT: j 454 LYS cc_start: 0.8569 (mtmm) cc_final: 0.8315 (mtmp) REVERT: j 501 GLU cc_start: 0.8447 (pt0) cc_final: 0.8072 (pp20) outliers start: 112 outliers final: 89 residues processed: 1642 average time/residue: 0.6646 time to fit residues: 1855.9474 Evaluate side-chains 1569 residues out of total 7380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 1479 time to evaluate : 6.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain B residue 39 MET Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain F residue 42 GLU Chi-restraints excluded: chain F residue 55 ARG Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain M residue 65 ASP Chi-restraints excluded: chain M residue 90 SER Chi-restraints excluded: chain M residue 148 HIS Chi-restraints excluded: chain M residue 181 ILE Chi-restraints excluded: chain P residue 65 ASP Chi-restraints excluded: chain P residue 90 SER Chi-restraints excluded: chain P residue 158 MET Chi-restraints excluded: chain P residue 181 ILE Chi-restraints excluded: chain S residue 90 SER Chi-restraints excluded: chain S residue 181 ILE Chi-restraints excluded: chain V residue 49 ILE Chi-restraints excluded: chain V residue 54 LEU Chi-restraints excluded: chain V residue 65 ASP Chi-restraints excluded: chain V residue 90 SER Chi-restraints excluded: chain Y residue 65 ASP Chi-restraints excluded: chain Y residue 90 SER Chi-restraints excluded: chain b residue 90 SER Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 153 THR Chi-restraints excluded: chain Q residue 25 VAL Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain T residue 97 GLU Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 130 VAL Chi-restraints excluded: chain Z residue 81 THR Chi-restraints excluded: chain Z residue 153 THR Chi-restraints excluded: chain c residue 25 VAL Chi-restraints excluded: chain c residue 72 VAL Chi-restraints excluded: chain G residue 7 HIS Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 54 GLU Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain I residue 7 HIS Chi-restraints excluded: chain J residue 25 VAL Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 123 GLU Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain K residue 7 HIS Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 72 VAL Chi-restraints excluded: chain O residue 144 ASP Chi-restraints excluded: chain O residue 150 ASP Chi-restraints excluded: chain O residue 237 HIS Chi-restraints excluded: chain O residue 308 THR Chi-restraints excluded: chain O residue 415 LEU Chi-restraints excluded: chain R residue 167 ASP Chi-restraints excluded: chain U residue 156 ILE Chi-restraints excluded: chain U residue 485 ASN Chi-restraints excluded: chain X residue 267 ILE Chi-restraints excluded: chain a residue 156 ILE Chi-restraints excluded: chain a residue 167 ASP Chi-restraints excluded: chain a residue 237 HIS Chi-restraints excluded: chain a residue 344 ILE Chi-restraints excluded: chain a residue 357 ASP Chi-restraints excluded: chain d residue 162 GLU Chi-restraints excluded: chain d residue 167 ASP Chi-restraints excluded: chain d residue 308 THR Chi-restraints excluded: chain e residue 117 ILE Chi-restraints excluded: chain e residue 507 GLU Chi-restraints excluded: chain f residue 167 ASP Chi-restraints excluded: chain f residue 409 HIS Chi-restraints excluded: chain f residue 476 LEU Chi-restraints excluded: chain g residue 156 ILE Chi-restraints excluded: chain h residue 167 ASP Chi-restraints excluded: chain h residue 216 ILE Chi-restraints excluded: chain i residue 150 ASP Chi-restraints excluded: chain i residue 156 ILE Chi-restraints excluded: chain i residue 344 ILE Chi-restraints excluded: chain i residue 415 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 876 random chunks: chunk 442 optimal weight: 6.9990 chunk 246 optimal weight: 10.0000 chunk 662 optimal weight: 9.9990 chunk 541 optimal weight: 20.0000 chunk 219 optimal weight: 10.0000 chunk 796 optimal weight: 20.0000 chunk 860 optimal weight: 9.9990 chunk 709 optimal weight: 10.0000 chunk 790 optimal weight: 10.0000 chunk 271 optimal weight: 0.9980 chunk 639 optimal weight: 3.9990 overall best weight: 6.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 62 ASN D 68 ASN P 93 HIS ** P 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 140 ASN ** P 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 52 GLN ** S 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 224 GLN O 237 HIS O 337 HIS R 337 HIS R 364 ASN R 437 ASN ** U 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 337 HIS X 100 GLN ** a 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 409 HIS e 337 HIS e 418 HIS f 337 HIS f 437 ASN g 168 ASN ** i 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 409 HIS ** j 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 72114 Z= 0.407 Angle : 0.651 10.303 97848 Z= 0.345 Chirality : 0.046 0.420 10404 Planarity : 0.004 0.063 12912 Dihedral : 4.937 56.140 9660 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.97 % Favored : 94.89 % Rotamer: Outliers : 2.80 % Allowed : 12.64 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.09), residues: 8814 helix: 1.60 (0.08), residues: 4032 sheet: 0.64 (0.17), residues: 1044 loop : -1.12 (0.10), residues: 3738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP W 111 HIS 0.020 0.001 HIS a 237 PHE 0.030 0.002 PHE V 55 TYR 0.017 0.002 TYR F 69 ARG 0.008 0.001 ARG c 26 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17628 Ramachandran restraints generated. 8814 Oldfield, 0 Emsley, 8814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17628 Ramachandran restraints generated. 8814 Oldfield, 0 Emsley, 8814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1683 residues out of total 7380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 1476 time to evaluate : 6.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 PHE cc_start: 0.7762 (t80) cc_final: 0.7561 (t80) REVERT: B 78 MET cc_start: 0.8375 (ptt) cc_final: 0.7970 (ptt) REVERT: E 101 SER cc_start: 0.7407 (m) cc_final: 0.7129 (m) REVERT: M 56 ASP cc_start: 0.7703 (m-30) cc_final: 0.7359 (m-30) REVERT: P 56 ASP cc_start: 0.7997 (m-30) cc_final: 0.7726 (m-30) REVERT: S 126 LYS cc_start: 0.9097 (tttp) cc_final: 0.8857 (tttt) REVERT: Y 29 ASP cc_start: 0.7308 (m-30) cc_final: 0.7068 (m-30) REVERT: b 56 ASP cc_start: 0.7872 (m-30) cc_final: 0.7577 (m-30) REVERT: Q 41 ARG cc_start: 0.7593 (mmm-85) cc_final: 0.6975 (tpp80) REVERT: c 42 ASP cc_start: 0.8102 (t70) cc_final: 0.7831 (t0) REVERT: H 41 ARG cc_start: 0.7549 (mmm-85) cc_final: 0.7006 (tpp80) REVERT: K 6 GLU cc_start: 0.7561 (tt0) cc_final: 0.6816 (tt0) REVERT: L 42 ASP cc_start: 0.8179 (t70) cc_final: 0.7915 (t0) REVERT: O 101 ASP cc_start: 0.8693 (m-30) cc_final: 0.8445 (m-30) REVERT: O 142 LYS cc_start: 0.7346 (tptt) cc_final: 0.6885 (tptp) REVERT: O 161 MET cc_start: 0.8599 (tpt) cc_final: 0.8260 (mmt) REVERT: O 404 GLU cc_start: 0.8302 (pt0) cc_final: 0.8068 (pt0) REVERT: R 419 TYR cc_start: 0.8768 (m-80) cc_final: 0.8446 (m-80) REVERT: R 424 LYS cc_start: 0.8057 (tptt) cc_final: 0.7826 (tptt) REVERT: R 449 GLU cc_start: 0.8583 (mp0) cc_final: 0.8284 (mp0) REVERT: R 486 ARG cc_start: 0.6953 (ttp80) cc_final: 0.6479 (tmt-80) REVERT: R 501 GLU cc_start: 0.8461 (pt0) cc_final: 0.8165 (pp20) REVERT: U 101 ASP cc_start: 0.8671 (m-30) cc_final: 0.8424 (m-30) REVERT: U 114 CYS cc_start: 0.8639 (m) cc_final: 0.8421 (m) REVERT: U 139 TRP cc_start: 0.8088 (p90) cc_final: 0.7659 (p90) REVERT: U 142 LYS cc_start: 0.7477 (tptp) cc_final: 0.7152 (tptp) REVERT: U 312 ASP cc_start: 0.7855 (t0) cc_final: 0.7549 (t0) REVERT: U 401 GLU cc_start: 0.7954 (tp30) cc_final: 0.7731 (tp30) REVERT: U 489 ASP cc_start: 0.8420 (t0) cc_final: 0.8212 (t0) REVERT: X 161 MET cc_start: 0.8035 (mmt) cc_final: 0.7730 (mmt) REVERT: X 222 MET cc_start: 0.7728 (mtt) cc_final: 0.7419 (mtp) REVERT: a 100 GLN cc_start: 0.9104 (tp40) cc_final: 0.8806 (tp40) REVERT: a 101 ASP cc_start: 0.8694 (m-30) cc_final: 0.8200 (m-30) REVERT: a 171 GLU cc_start: 0.8230 (tm-30) cc_final: 0.7907 (tm-30) REVERT: a 195 TYR cc_start: 0.7358 (t80) cc_final: 0.6981 (t80) REVERT: d 240 GLU cc_start: 0.8519 (tp30) cc_final: 0.8128 (tp30) REVERT: d 458 ASP cc_start: 0.8763 (m-30) cc_final: 0.8537 (m-30) REVERT: d 470 ASP cc_start: 0.8572 (p0) cc_final: 0.8292 (p0) REVERT: e 296 GLU cc_start: 0.8452 (tp30) cc_final: 0.8248 (tp30) REVERT: e 466 VAL cc_start: 0.8992 (t) cc_final: 0.8728 (p) REVERT: f 198 LYS cc_start: 0.8586 (tttm) cc_final: 0.8361 (ttpp) REVERT: g 142 LYS cc_start: 0.7296 (tptp) cc_final: 0.7010 (tptp) REVERT: g 159 ARG cc_start: 0.8139 (mmp80) cc_final: 0.7626 (mmm160) REVERT: g 195 TYR cc_start: 0.7676 (t80) cc_final: 0.7416 (t80) REVERT: g 381 LEU cc_start: 0.9143 (mp) cc_final: 0.8918 (mp) REVERT: g 386 LYS cc_start: 0.7863 (tppt) cc_final: 0.7564 (mmmt) REVERT: g 490 ASP cc_start: 0.7873 (m-30) cc_final: 0.7576 (t0) REVERT: g 505 GLU cc_start: 0.8197 (pt0) cc_final: 0.7976 (pt0) REVERT: h 240 GLU cc_start: 0.7482 (tm-30) cc_final: 0.6978 (tm-30) REVERT: h 250 LYS cc_start: 0.8655 (mmmt) cc_final: 0.8365 (tttm) REVERT: h 424 LYS cc_start: 0.8026 (tptt) cc_final: 0.7667 (tptt) REVERT: h 454 LYS cc_start: 0.8688 (mtmm) cc_final: 0.8406 (mttp) REVERT: i 101 ASP cc_start: 0.8748 (m-30) cc_final: 0.8298 (m-30) REVERT: i 198 LYS cc_start: 0.9003 (tmmt) cc_final: 0.8648 (mttt) REVERT: i 345 ASP cc_start: 0.8502 (p0) cc_final: 0.7802 (p0) REVERT: i 346 GLU cc_start: 0.7692 (mp0) cc_final: 0.7132 (mp0) REVERT: i 475 ARG cc_start: 0.8351 (ttp-170) cc_final: 0.7979 (ptt180) REVERT: j 240 GLU cc_start: 0.8574 (tp30) cc_final: 0.8174 (tp30) REVERT: j 337 HIS cc_start: 0.8136 (m90) cc_final: 0.7881 (m90) REVERT: j 346 GLU cc_start: 0.7851 (pm20) cc_final: 0.7314 (pm20) REVERT: j 424 LYS cc_start: 0.8065 (tptt) cc_final: 0.7772 (tptt) REVERT: j 454 LYS cc_start: 0.8696 (mtmm) cc_final: 0.8332 (mtmp) REVERT: j 486 ARG cc_start: 0.7653 (ttp80) cc_final: 0.7428 (ttp80) outliers start: 207 outliers final: 166 residues processed: 1579 average time/residue: 0.6739 time to fit residues: 1801.1055 Evaluate side-chains 1582 residues out of total 7380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 1416 time to evaluate : 6.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 57 GLN Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 106 PHE Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 118 ASP Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 106 PHE Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain M residue 65 ASP Chi-restraints excluded: chain M residue 69 ASP Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 90 SER Chi-restraints excluded: chain M residue 181 ILE Chi-restraints excluded: chain P residue 65 ASP Chi-restraints excluded: chain P residue 76 VAL Chi-restraints excluded: chain P residue 90 SER Chi-restraints excluded: chain P residue 158 MET Chi-restraints excluded: chain P residue 181 ILE Chi-restraints excluded: chain S residue 6 LEU Chi-restraints excluded: chain S residue 27 PHE Chi-restraints excluded: chain S residue 90 SER Chi-restraints excluded: chain S residue 167 ARG Chi-restraints excluded: chain S residue 181 ILE Chi-restraints excluded: chain V residue 49 ILE Chi-restraints excluded: chain V residue 54 LEU Chi-restraints excluded: chain V residue 65 ASP Chi-restraints excluded: chain V residue 90 SER Chi-restraints excluded: chain Y residue 54 LEU Chi-restraints excluded: chain Y residue 65 ASP Chi-restraints excluded: chain Y residue 90 SER Chi-restraints excluded: chain b residue 90 SER Chi-restraints excluded: chain b residue 100 THR Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 129 SER Chi-restraints excluded: chain N residue 153 THR Chi-restraints excluded: chain Q residue 25 VAL Chi-restraints excluded: chain Q residue 39 SER Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain T residue 97 GLU Chi-restraints excluded: chain T residue 153 THR Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 69 THR Chi-restraints excluded: chain W residue 91 THR Chi-restraints excluded: chain W residue 108 LYS Chi-restraints excluded: chain W residue 130 VAL Chi-restraints excluded: chain Z residue 7 HIS Chi-restraints excluded: chain Z residue 129 SER Chi-restraints excluded: chain Z residue 153 THR Chi-restraints excluded: chain c residue 3 ILE Chi-restraints excluded: chain c residue 25 VAL Chi-restraints excluded: chain c residue 91 THR Chi-restraints excluded: chain c residue 130 VAL Chi-restraints excluded: chain G residue 7 HIS Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 129 SER Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain I residue 7 HIS Chi-restraints excluded: chain I residue 129 SER Chi-restraints excluded: chain I residue 153 THR Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 25 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 108 LYS Chi-restraints excluded: chain J residue 123 GLU Chi-restraints excluded: chain J residue 129 SER Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 153 THR Chi-restraints excluded: chain K residue 7 HIS Chi-restraints excluded: chain K residue 153 THR Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 72 VAL Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain O residue 141 LEU Chi-restraints excluded: chain O residue 144 ASP Chi-restraints excluded: chain O residue 150 ASP Chi-restraints excluded: chain O residue 237 HIS Chi-restraints excluded: chain O residue 308 THR Chi-restraints excluded: chain O residue 391 THR Chi-restraints excluded: chain O residue 415 LEU Chi-restraints excluded: chain R residue 167 ASP Chi-restraints excluded: chain R residue 293 THR Chi-restraints excluded: chain R residue 306 THR Chi-restraints excluded: chain R residue 308 THR Chi-restraints excluded: chain U residue 156 ILE Chi-restraints excluded: chain U residue 357 ASP Chi-restraints excluded: chain U residue 362 ILE Chi-restraints excluded: chain U residue 485 ASN Chi-restraints excluded: chain U residue 505 GLU Chi-restraints excluded: chain X residue 260 ARG Chi-restraints excluded: chain X residue 267 ILE Chi-restraints excluded: chain X residue 398 SER Chi-restraints excluded: chain X residue 442 THR Chi-restraints excluded: chain X residue 472 VAL Chi-restraints excluded: chain a residue 105 SER Chi-restraints excluded: chain a residue 141 LEU Chi-restraints excluded: chain a residue 156 ILE Chi-restraints excluded: chain a residue 167 ASP Chi-restraints excluded: chain a residue 277 ILE Chi-restraints excluded: chain a residue 287 VAL Chi-restraints excluded: chain a residue 302 MET Chi-restraints excluded: chain a residue 344 ILE Chi-restraints excluded: chain a residue 357 ASP Chi-restraints excluded: chain d residue 162 GLU Chi-restraints excluded: chain d residue 167 ASP Chi-restraints excluded: chain d residue 247 SER Chi-restraints excluded: chain d residue 300 LEU Chi-restraints excluded: chain d residue 308 THR Chi-restraints excluded: chain d residue 344 ILE Chi-restraints excluded: chain d residue 415 LEU Chi-restraints excluded: chain d residue 442 THR Chi-restraints excluded: chain e residue 308 THR Chi-restraints excluded: chain e residue 404 GLU Chi-restraints excluded: chain e residue 507 GLU Chi-restraints excluded: chain f residue 167 ASP Chi-restraints excluded: chain f residue 267 ILE Chi-restraints excluded: chain f residue 306 THR Chi-restraints excluded: chain f residue 346 GLU Chi-restraints excluded: chain f residue 442 THR Chi-restraints excluded: chain f residue 476 LEU Chi-restraints excluded: chain g residue 97 THR Chi-restraints excluded: chain g residue 156 ILE Chi-restraints excluded: chain h residue 167 ASP Chi-restraints excluded: chain h residue 398 SER Chi-restraints excluded: chain h residue 442 THR Chi-restraints excluded: chain h residue 472 VAL Chi-restraints excluded: chain h residue 489 ASP Chi-restraints excluded: chain i residue 141 LEU Chi-restraints excluded: chain i residue 150 ASP Chi-restraints excluded: chain i residue 156 ILE Chi-restraints excluded: chain i residue 237 HIS Chi-restraints excluded: chain j residue 167 ASP Chi-restraints excluded: chain j residue 273 ILE Chi-restraints excluded: chain j residue 300 LEU Chi-restraints excluded: chain j residue 311 VAL Chi-restraints excluded: chain j residue 344 ILE Chi-restraints excluded: chain j residue 406 ILE Chi-restraints excluded: chain j residue 415 LEU Chi-restraints excluded: chain j residue 442 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 876 random chunks: chunk 787 optimal weight: 9.9990 chunk 599 optimal weight: 9.9990 chunk 413 optimal weight: 9.9990 chunk 88 optimal weight: 1.9990 chunk 380 optimal weight: 0.6980 chunk 535 optimal weight: 7.9990 chunk 799 optimal weight: 20.0000 chunk 846 optimal weight: 20.0000 chunk 417 optimal weight: 5.9990 chunk 758 optimal weight: 0.4980 chunk 228 optimal weight: 0.4980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 164 GLN S 52 GLN b 93 HIS ** N 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 237 HIS O 337 HIS R 364 ASN ** U 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 337 HIS X 100 GLN ** a 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 337 HIS f 337 HIS f 409 HIS g 100 GLN ** i 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 512 GLN j 100 GLN j 512 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 72114 Z= 0.174 Angle : 0.536 8.239 97848 Z= 0.281 Chirality : 0.042 0.396 10404 Planarity : 0.004 0.053 12912 Dihedral : 4.622 53.816 9660 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.90 % Favored : 95.96 % Rotamer: Outliers : 2.57 % Allowed : 14.96 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.09), residues: 8814 helix: 1.79 (0.08), residues: 3978 sheet: 0.61 (0.17), residues: 1068 loop : -1.06 (0.10), residues: 3768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 111 HIS 0.011 0.001 HIS O 237 PHE 0.033 0.001 PHE C 61 TYR 0.019 0.001 TYR X 419 ARG 0.008 0.000 ARG c 26 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17628 Ramachandran restraints generated. 8814 Oldfield, 0 Emsley, 8814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17628 Ramachandran restraints generated. 8814 Oldfield, 0 Emsley, 8814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1734 residues out of total 7380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 1544 time to evaluate : 6.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 57 GLN cc_start: 0.8062 (OUTLIER) cc_final: 0.6766 (pt0) REVERT: C 123 LYS cc_start: 0.7707 (mmtm) cc_final: 0.7457 (mmtm) REVERT: M 56 ASP cc_start: 0.7559 (m-30) cc_final: 0.7271 (m-30) REVERT: P 56 ASP cc_start: 0.7968 (m-30) cc_final: 0.7614 (m-30) REVERT: S 126 LYS cc_start: 0.9028 (tttp) cc_final: 0.8752 (tttt) REVERT: Y 53 LYS cc_start: 0.8296 (tttt) cc_final: 0.8063 (ttpt) REVERT: b 13 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7048 (mp0) REVERT: b 56 ASP cc_start: 0.7775 (m-30) cc_final: 0.7552 (m-30) REVERT: c 42 ASP cc_start: 0.8127 (t70) cc_final: 0.7853 (t0) REVERT: H 41 ARG cc_start: 0.7568 (mmm-85) cc_final: 0.7008 (tpp80) REVERT: J 8 LYS cc_start: 0.8943 (ttpp) cc_final: 0.8667 (ttpp) REVERT: J 41 ARG cc_start: 0.7593 (tpp80) cc_final: 0.7284 (mmm-85) REVERT: J 42 ASP cc_start: 0.8587 (t0) cc_final: 0.8304 (t0) REVERT: K 6 GLU cc_start: 0.7479 (tt0) cc_final: 0.7048 (tt0) REVERT: L 42 ASP cc_start: 0.8142 (t70) cc_final: 0.7903 (t0) REVERT: O 101 ASP cc_start: 0.8665 (m-30) cc_final: 0.8448 (m-30) REVERT: O 152 GLN cc_start: 0.8716 (mt0) cc_final: 0.8412 (pt0) REVERT: O 161 MET cc_start: 0.8558 (tpt) cc_final: 0.8268 (mmt) REVERT: R 419 TYR cc_start: 0.8751 (m-80) cc_final: 0.8420 (m-80) REVERT: R 424 LYS cc_start: 0.7984 (tptt) cc_final: 0.7734 (tptt) REVERT: R 486 ARG cc_start: 0.6922 (ttp80) cc_final: 0.6511 (tmt-80) REVERT: R 501 GLU cc_start: 0.8489 (pt0) cc_final: 0.8264 (pp20) REVERT: U 101 ASP cc_start: 0.8609 (m-30) cc_final: 0.8364 (m-30) REVERT: U 114 CYS cc_start: 0.8575 (m) cc_final: 0.8369 (m) REVERT: U 139 TRP cc_start: 0.8005 (p90) cc_final: 0.7553 (p90) REVERT: U 142 LYS cc_start: 0.7553 (tptp) cc_final: 0.7179 (tptp) REVERT: U 159 ARG cc_start: 0.7834 (mmm-85) cc_final: 0.7610 (mmm-85) REVERT: U 312 ASP cc_start: 0.7740 (t0) cc_final: 0.7463 (t0) REVERT: X 100 GLN cc_start: 0.8706 (mt0) cc_final: 0.8486 (mt0) REVERT: X 161 MET cc_start: 0.8088 (mmt) cc_final: 0.7772 (mmt) REVERT: X 222 MET cc_start: 0.7744 (mtt) cc_final: 0.7433 (mtp) REVERT: X 424 LYS cc_start: 0.8032 (tptt) cc_final: 0.7774 (tptt) REVERT: X 449 GLU cc_start: 0.8431 (mp0) cc_final: 0.8219 (mp0) REVERT: a 100 GLN cc_start: 0.9059 (tp40) cc_final: 0.8756 (tp40) REVERT: a 101 ASP cc_start: 0.8656 (m-30) cc_final: 0.8159 (m-30) REVERT: a 171 GLU cc_start: 0.8205 (tm-30) cc_final: 0.7903 (tm-30) REVERT: a 195 TYR cc_start: 0.7292 (t80) cc_final: 0.6938 (t80) REVERT: a 404 GLU cc_start: 0.8265 (tp30) cc_final: 0.8029 (tp30) REVERT: d 129 MET cc_start: 0.8027 (mtp) cc_final: 0.7809 (mtp) REVERT: d 216 ILE cc_start: 0.9513 (mt) cc_final: 0.9038 (tp) REVERT: d 240 GLU cc_start: 0.8506 (tp30) cc_final: 0.8142 (tp30) REVERT: d 458 ASP cc_start: 0.8769 (m-30) cc_final: 0.8495 (m-30) REVERT: d 464 SER cc_start: 0.8765 (m) cc_final: 0.8350 (p) REVERT: d 470 ASP cc_start: 0.8691 (p0) cc_final: 0.8427 (p0) REVERT: e 466 VAL cc_start: 0.8971 (t) cc_final: 0.8712 (p) REVERT: e 503 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8351 (mp) REVERT: f 198 LYS cc_start: 0.8582 (tttm) cc_final: 0.8357 (ttpp) REVERT: f 302 MET cc_start: 0.8347 (mmm) cc_final: 0.8000 (mmm) REVERT: f 449 GLU cc_start: 0.8439 (mp0) cc_final: 0.8185 (mp0) REVERT: g 142 LYS cc_start: 0.7496 (tptp) cc_final: 0.6872 (tptp) REVERT: g 160 ASP cc_start: 0.8862 (t0) cc_final: 0.8393 (t0) REVERT: g 195 TYR cc_start: 0.7724 (t80) cc_final: 0.7472 (t80) REVERT: g 381 LEU cc_start: 0.9139 (mp) cc_final: 0.8885 (mp) REVERT: g 490 ASP cc_start: 0.7959 (m-30) cc_final: 0.7699 (t0) REVERT: g 524 GLU cc_start: 0.7585 (mp0) cc_final: 0.7349 (mp0) REVERT: h 161 MET cc_start: 0.8051 (mmt) cc_final: 0.7681 (mmt) REVERT: h 240 GLU cc_start: 0.7479 (tm-30) cc_final: 0.7047 (tm-30) REVERT: h 250 LYS cc_start: 0.8635 (mmmt) cc_final: 0.8270 (tttm) REVERT: h 337 HIS cc_start: 0.7833 (m-70) cc_final: 0.7603 (m90) REVERT: h 406 ILE cc_start: 0.9271 (OUTLIER) cc_final: 0.8937 (tp) REVERT: h 424 LYS cc_start: 0.8150 (tptt) cc_final: 0.7788 (tptt) REVERT: h 454 LYS cc_start: 0.8632 (mtmm) cc_final: 0.8344 (mtmp) REVERT: i 101 ASP cc_start: 0.8714 (m-30) cc_final: 0.8189 (m-30) REVERT: i 198 LYS cc_start: 0.8997 (tmmt) cc_final: 0.8634 (mttt) REVERT: i 224 GLN cc_start: 0.8714 (tt0) cc_final: 0.8453 (tm-30) REVERT: i 345 ASP cc_start: 0.8469 (p0) cc_final: 0.7786 (p0) REVERT: i 346 GLU cc_start: 0.7679 (mp0) cc_final: 0.7027 (mp0) REVERT: i 475 ARG cc_start: 0.8358 (ttp-170) cc_final: 0.7982 (ptt180) REVERT: i 512 GLN cc_start: 0.7239 (OUTLIER) cc_final: 0.6985 (tm130) REVERT: j 240 GLU cc_start: 0.8573 (tp30) cc_final: 0.8153 (tp30) REVERT: j 283 ILE cc_start: 0.9148 (tt) cc_final: 0.8902 (tp) REVERT: j 424 LYS cc_start: 0.8058 (tptt) cc_final: 0.7766 (tptt) REVERT: j 454 LYS cc_start: 0.8673 (mtmm) cc_final: 0.8315 (mtmp) REVERT: j 474 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.8055 (mp0) outliers start: 190 outliers final: 141 residues processed: 1627 average time/residue: 0.6655 time to fit residues: 1844.2940 Evaluate side-chains 1616 residues out of total 7380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 1469 time to evaluate : 6.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 57 GLN Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 106 PHE Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 106 PHE Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain E residue 55 ARG Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 85 MET Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 106 PHE Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 6 ASN Chi-restraints excluded: chain F residue 42 GLU Chi-restraints excluded: chain F residue 55 ARG Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 106 PHE Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain M residue 65 ASP Chi-restraints excluded: chain M residue 90 SER Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain M residue 181 ILE Chi-restraints excluded: chain P residue 65 ASP Chi-restraints excluded: chain P residue 76 VAL Chi-restraints excluded: chain P residue 90 SER Chi-restraints excluded: chain P residue 125 VAL Chi-restraints excluded: chain P residue 181 ILE Chi-restraints excluded: chain S residue 6 LEU Chi-restraints excluded: chain S residue 23 GLU Chi-restraints excluded: chain S residue 90 SER Chi-restraints excluded: chain S residue 102 VAL Chi-restraints excluded: chain S residue 181 ILE Chi-restraints excluded: chain V residue 49 ILE Chi-restraints excluded: chain V residue 54 LEU Chi-restraints excluded: chain V residue 65 ASP Chi-restraints excluded: chain V residue 69 ASP Chi-restraints excluded: chain V residue 90 SER Chi-restraints excluded: chain Y residue 65 ASP Chi-restraints excluded: chain Y residue 90 SER Chi-restraints excluded: chain b residue 13 GLU Chi-restraints excluded: chain b residue 90 SER Chi-restraints excluded: chain b residue 102 VAL Chi-restraints excluded: chain b residue 127 GLU Chi-restraints excluded: chain N residue 153 THR Chi-restraints excluded: chain Q residue 25 VAL Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain T residue 97 GLU Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 85 THR Chi-restraints excluded: chain W residue 130 VAL Chi-restraints excluded: chain Z residue 6 GLU Chi-restraints excluded: chain Z residue 7 HIS Chi-restraints excluded: chain c residue 25 VAL Chi-restraints excluded: chain c residue 72 VAL Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 7 HIS Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 66 SER Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain I residue 7 HIS Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 153 THR Chi-restraints excluded: chain J residue 25 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 108 LYS Chi-restraints excluded: chain J residue 123 GLU Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain K residue 7 HIS Chi-restraints excluded: chain K residue 153 THR Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 72 VAL Chi-restraints excluded: chain O residue 141 LEU Chi-restraints excluded: chain O residue 150 ASP Chi-restraints excluded: chain O residue 415 LEU Chi-restraints excluded: chain R residue 162 GLU Chi-restraints excluded: chain R residue 167 ASP Chi-restraints excluded: chain R residue 409 HIS Chi-restraints excluded: chain R residue 415 LEU Chi-restraints excluded: chain U residue 148 LEU Chi-restraints excluded: chain U residue 156 ILE Chi-restraints excluded: chain U residue 485 ASN Chi-restraints excluded: chain X residue 260 ARG Chi-restraints excluded: chain X residue 267 ILE Chi-restraints excluded: chain X residue 380 LEU Chi-restraints excluded: chain X residue 398 SER Chi-restraints excluded: chain a residue 105 SER Chi-restraints excluded: chain a residue 141 LEU Chi-restraints excluded: chain a residue 148 LEU Chi-restraints excluded: chain a residue 167 ASP Chi-restraints excluded: chain a residue 344 ILE Chi-restraints excluded: chain a residue 357 ASP Chi-restraints excluded: chain d residue 167 ASP Chi-restraints excluded: chain d residue 308 THR Chi-restraints excluded: chain e residue 336 ASN Chi-restraints excluded: chain e residue 404 GLU Chi-restraints excluded: chain e residue 503 LEU Chi-restraints excluded: chain e residue 507 GLU Chi-restraints excluded: chain f residue 162 GLU Chi-restraints excluded: chain f residue 167 ASP Chi-restraints excluded: chain f residue 346 GLU Chi-restraints excluded: chain f residue 409 HIS Chi-restraints excluded: chain f residue 415 LEU Chi-restraints excluded: chain f residue 476 LEU Chi-restraints excluded: chain g residue 97 THR Chi-restraints excluded: chain g residue 155 LEU Chi-restraints excluded: chain g residue 156 ILE Chi-restraints excluded: chain h residue 167 ASP Chi-restraints excluded: chain h residue 183 ILE Chi-restraints excluded: chain h residue 216 ILE Chi-restraints excluded: chain h residue 380 LEU Chi-restraints excluded: chain h residue 398 SER Chi-restraints excluded: chain h residue 406 ILE Chi-restraints excluded: chain i residue 150 ASP Chi-restraints excluded: chain i residue 237 HIS Chi-restraints excluded: chain i residue 512 GLN Chi-restraints excluded: chain j residue 167 ASP Chi-restraints excluded: chain j residue 300 LEU Chi-restraints excluded: chain j residue 311 VAL Chi-restraints excluded: chain j residue 406 ILE Chi-restraints excluded: chain j residue 474 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 876 random chunks: chunk 705 optimal weight: 9.9990 chunk 480 optimal weight: 30.0000 chunk 12 optimal weight: 10.0000 chunk 630 optimal weight: 0.2980 chunk 349 optimal weight: 20.0000 chunk 722 optimal weight: 8.9990 chunk 585 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 432 optimal weight: 20.0000 chunk 760 optimal weight: 30.0000 chunk 213 optimal weight: 3.9990 overall best weight: 6.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 40 GLN ** b 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 237 HIS O 337 HIS R 364 ASN ** U 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 337 HIS ** X 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 337 HIS e 418 HIS ** e 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 512 GLN j 173 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 72114 Z= 0.425 Angle : 0.656 10.548 97848 Z= 0.346 Chirality : 0.046 0.533 10404 Planarity : 0.004 0.065 12912 Dihedral : 5.006 61.313 9660 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.17 % Favored : 94.68 % Rotamer: Outliers : 3.52 % Allowed : 16.30 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.09), residues: 8814 helix: 1.55 (0.08), residues: 4080 sheet: 0.40 (0.17), residues: 1080 loop : -1.23 (0.10), residues: 3654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP J 111 HIS 0.018 0.001 HIS f 409 PHE 0.033 0.002 PHE C 61 TYR 0.016 0.002 TYR i 284 ARG 0.010 0.001 ARG c 26 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17628 Ramachandran restraints generated. 8814 Oldfield, 0 Emsley, 8814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17628 Ramachandran restraints generated. 8814 Oldfield, 0 Emsley, 8814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1726 residues out of total 7380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 260 poor density : 1466 time to evaluate : 6.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 101 SER cc_start: 0.7565 (m) cc_final: 0.7329 (m) REVERT: A 109 ASP cc_start: 0.8479 (OUTLIER) cc_final: 0.8151 (p0) REVERT: E 101 SER cc_start: 0.7491 (m) cc_final: 0.7239 (m) REVERT: M 29 ASP cc_start: 0.7527 (m-30) cc_final: 0.7179 (m-30) REVERT: M 56 ASP cc_start: 0.7733 (m-30) cc_final: 0.7439 (m-30) REVERT: P 56 ASP cc_start: 0.8006 (m-30) cc_final: 0.7597 (m-30) REVERT: S 126 LYS cc_start: 0.9165 (tttp) cc_final: 0.8912 (tttt) REVERT: V 29 ASP cc_start: 0.7658 (m-30) cc_final: 0.7396 (m-30) REVERT: Y 29 ASP cc_start: 0.7311 (m-30) cc_final: 0.7049 (m-30) REVERT: b 13 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7153 (mp0) REVERT: b 56 ASP cc_start: 0.7849 (m-30) cc_final: 0.7547 (m-30) REVERT: Q 41 ARG cc_start: 0.7738 (tpp80) cc_final: 0.7140 (tpp80) REVERT: c 42 ASP cc_start: 0.8131 (t70) cc_final: 0.7868 (t0) REVERT: H 41 ARG cc_start: 0.7627 (mmm-85) cc_final: 0.7035 (tpp80) REVERT: H 143 GLU cc_start: 0.8433 (mm-30) cc_final: 0.8136 (mm-30) REVERT: J 41 ARG cc_start: 0.7663 (tpp80) cc_final: 0.7276 (mmm-85) REVERT: J 42 ASP cc_start: 0.8676 (t0) cc_final: 0.8347 (t0) REVERT: L 42 ASP cc_start: 0.8191 (t70) cc_final: 0.7976 (t0) REVERT: O 101 ASP cc_start: 0.8708 (m-30) cc_final: 0.8472 (m-30) REVERT: O 161 MET cc_start: 0.8598 (tpt) cc_final: 0.8331 (mmt) REVERT: R 161 MET cc_start: 0.7751 (mmt) cc_final: 0.7536 (mmt) REVERT: R 419 TYR cc_start: 0.8785 (m-80) cc_final: 0.8462 (m-80) REVERT: R 424 LYS cc_start: 0.8045 (tptt) cc_final: 0.7776 (tptt) REVERT: R 470 ASP cc_start: 0.8584 (t70) cc_final: 0.8336 (t0) REVERT: R 486 ARG cc_start: 0.6936 (ttp80) cc_final: 0.6534 (tmt-80) REVERT: R 501 GLU cc_start: 0.8493 (pt0) cc_final: 0.8240 (pp20) REVERT: U 101 ASP cc_start: 0.8649 (m-30) cc_final: 0.8399 (m-30) REVERT: U 114 CYS cc_start: 0.8663 (m) cc_final: 0.8381 (m) REVERT: U 142 LYS cc_start: 0.7498 (tptp) cc_final: 0.7201 (tptp) REVERT: U 312 ASP cc_start: 0.7891 (t0) cc_final: 0.7553 (t0) REVERT: U 346 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7304 (mm-30) REVERT: U 404 GLU cc_start: 0.8148 (tp30) cc_final: 0.7947 (tp30) REVERT: X 161 MET cc_start: 0.8039 (mmt) cc_final: 0.7720 (mmt) REVERT: X 424 LYS cc_start: 0.8028 (tptt) cc_final: 0.7780 (tptt) REVERT: a 100 GLN cc_start: 0.9135 (tp40) cc_final: 0.8833 (tp40) REVERT: a 101 ASP cc_start: 0.8681 (m-30) cc_final: 0.8209 (m-30) REVERT: a 171 GLU cc_start: 0.8271 (tm-30) cc_final: 0.7954 (tm-30) REVERT: a 195 TYR cc_start: 0.7464 (t80) cc_final: 0.7067 (t80) REVERT: a 239 TYR cc_start: 0.8815 (m-80) cc_final: 0.8400 (m-80) REVERT: a 474 GLU cc_start: 0.8774 (mp0) cc_final: 0.8488 (mp0) REVERT: d 240 GLU cc_start: 0.8501 (tp30) cc_final: 0.8144 (tp30) REVERT: d 470 ASP cc_start: 0.8630 (p0) cc_final: 0.8417 (p0) REVERT: e 466 VAL cc_start: 0.8963 (t) cc_final: 0.8695 (p) REVERT: f 198 LYS cc_start: 0.8590 (tttm) cc_final: 0.8314 (ttpp) REVERT: g 100 GLN cc_start: 0.9142 (tp40) cc_final: 0.8869 (tp40) REVERT: g 142 LYS cc_start: 0.7404 (tptp) cc_final: 0.7177 (tptp) REVERT: g 159 ARG cc_start: 0.8049 (mmm-85) cc_final: 0.7597 (mmm160) REVERT: g 160 ASP cc_start: 0.8946 (t0) cc_final: 0.8418 (t0) REVERT: g 195 TYR cc_start: 0.7732 (t80) cc_final: 0.7469 (t80) REVERT: g 381 LEU cc_start: 0.9183 (mp) cc_final: 0.8972 (mp) REVERT: g 524 GLU cc_start: 0.7606 (mp0) cc_final: 0.7357 (mp0) REVERT: h 161 MET cc_start: 0.8068 (mmt) cc_final: 0.7844 (mmt) REVERT: h 240 GLU cc_start: 0.7365 (tm-30) cc_final: 0.6719 (tm-30) REVERT: h 250 LYS cc_start: 0.8561 (mmmt) cc_final: 0.8220 (tttm) REVERT: h 424 LYS cc_start: 0.8193 (tptt) cc_final: 0.7817 (tptt) REVERT: i 101 ASP cc_start: 0.8736 (m-30) cc_final: 0.8228 (m-30) REVERT: i 158 ARG cc_start: 0.8840 (ptp-170) cc_final: 0.8600 (ptp-170) REVERT: i 161 MET cc_start: 0.8664 (mmt) cc_final: 0.8270 (ttp) REVERT: i 198 LYS cc_start: 0.8976 (tmmt) cc_final: 0.8687 (tmtt) REVERT: i 345 ASP cc_start: 0.8392 (p0) cc_final: 0.7712 (p0) REVERT: i 346 GLU cc_start: 0.7782 (mp0) cc_final: 0.7083 (mp0) REVERT: i 475 ARG cc_start: 0.8456 (ttp-170) cc_final: 0.8008 (ptt180) REVERT: j 240 GLU cc_start: 0.8575 (tp30) cc_final: 0.8201 (tp30) REVERT: j 346 GLU cc_start: 0.7904 (pm20) cc_final: 0.7118 (pm20) REVERT: j 454 LYS cc_start: 0.8706 (mtmm) cc_final: 0.8362 (mttp) REVERT: j 474 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.8026 (mp0) outliers start: 260 outliers final: 207 residues processed: 1600 average time/residue: 0.6621 time to fit residues: 1800.9166 Evaluate side-chains 1631 residues out of total 7380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 1421 time to evaluate : 6.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 57 GLN Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 106 PHE Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain B residue 10 MET Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain D residue 10 MET Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 106 PHE Chi-restraints excluded: chain E residue 10 MET Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain E residue 55 ARG Chi-restraints excluded: chain E residue 85 MET Chi-restraints excluded: chain E residue 106 PHE Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 118 ASP Chi-restraints excluded: chain F residue 6 ASN Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 106 PHE Chi-restraints excluded: chain M residue 65 ASP Chi-restraints excluded: chain M residue 69 ASP Chi-restraints excluded: chain M residue 90 SER Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain M residue 148 HIS Chi-restraints excluded: chain M residue 181 ILE Chi-restraints excluded: chain P residue 65 ASP Chi-restraints excluded: chain P residue 76 VAL Chi-restraints excluded: chain P residue 90 SER Chi-restraints excluded: chain P residue 125 VAL Chi-restraints excluded: chain P residue 181 ILE Chi-restraints excluded: chain S residue 6 LEU Chi-restraints excluded: chain S residue 27 PHE Chi-restraints excluded: chain S residue 83 VAL Chi-restraints excluded: chain S residue 90 SER Chi-restraints excluded: chain S residue 102 VAL Chi-restraints excluded: chain S residue 167 ARG Chi-restraints excluded: chain S residue 181 ILE Chi-restraints excluded: chain V residue 49 ILE Chi-restraints excluded: chain V residue 54 LEU Chi-restraints excluded: chain V residue 65 ASP Chi-restraints excluded: chain V residue 69 ASP Chi-restraints excluded: chain V residue 90 SER Chi-restraints excluded: chain Y residue 54 LEU Chi-restraints excluded: chain Y residue 65 ASP Chi-restraints excluded: chain Y residue 90 SER Chi-restraints excluded: chain Y residue 103 VAL Chi-restraints excluded: chain b residue 13 GLU Chi-restraints excluded: chain b residue 90 SER Chi-restraints excluded: chain b residue 100 THR Chi-restraints excluded: chain b residue 102 VAL Chi-restraints excluded: chain b residue 127 GLU Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 129 SER Chi-restraints excluded: chain N residue 153 THR Chi-restraints excluded: chain Q residue 25 VAL Chi-restraints excluded: chain Q residue 66 SER Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain T residue 97 GLU Chi-restraints excluded: chain T residue 129 SER Chi-restraints excluded: chain T residue 153 THR Chi-restraints excluded: chain W residue 3 ILE Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 69 THR Chi-restraints excluded: chain W residue 85 THR Chi-restraints excluded: chain W residue 91 THR Chi-restraints excluded: chain W residue 108 LYS Chi-restraints excluded: chain W residue 130 VAL Chi-restraints excluded: chain Z residue 6 GLU Chi-restraints excluded: chain Z residue 7 HIS Chi-restraints excluded: chain Z residue 129 SER Chi-restraints excluded: chain Z residue 153 THR Chi-restraints excluded: chain c residue 3 ILE Chi-restraints excluded: chain c residue 25 VAL Chi-restraints excluded: chain c residue 91 THR Chi-restraints excluded: chain c residue 130 VAL Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 129 SER Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 66 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain I residue 7 HIS Chi-restraints excluded: chain I residue 129 SER Chi-restraints excluded: chain I residue 153 THR Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 25 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 108 LYS Chi-restraints excluded: chain J residue 123 GLU Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 153 THR Chi-restraints excluded: chain K residue 7 HIS Chi-restraints excluded: chain K residue 153 THR Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain L residue 130 VAL Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain O residue 141 LEU Chi-restraints excluded: chain O residue 144 ASP Chi-restraints excluded: chain O residue 148 LEU Chi-restraints excluded: chain O residue 150 ASP Chi-restraints excluded: chain O residue 237 HIS Chi-restraints excluded: chain O residue 259 VAL Chi-restraints excluded: chain O residue 308 THR Chi-restraints excluded: chain O residue 321 GLU Chi-restraints excluded: chain O residue 336 ASN Chi-restraints excluded: chain R residue 162 GLU Chi-restraints excluded: chain R residue 167 ASP Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 293 THR Chi-restraints excluded: chain R residue 308 THR Chi-restraints excluded: chain R residue 409 HIS Chi-restraints excluded: chain R residue 415 LEU Chi-restraints excluded: chain R residue 418 HIS Chi-restraints excluded: chain R residue 442 THR Chi-restraints excluded: chain U residue 148 LEU Chi-restraints excluded: chain U residue 150 ASP Chi-restraints excluded: chain U residue 156 ILE Chi-restraints excluded: chain U residue 357 ASP Chi-restraints excluded: chain U residue 485 ASN Chi-restraints excluded: chain U residue 505 GLU Chi-restraints excluded: chain X residue 260 ARG Chi-restraints excluded: chain X residue 267 ILE Chi-restraints excluded: chain X residue 380 LEU Chi-restraints excluded: chain X residue 398 SER Chi-restraints excluded: chain X residue 442 THR Chi-restraints excluded: chain X residue 472 VAL Chi-restraints excluded: chain a residue 105 SER Chi-restraints excluded: chain a residue 141 LEU Chi-restraints excluded: chain a residue 148 LEU Chi-restraints excluded: chain a residue 156 ILE Chi-restraints excluded: chain a residue 167 ASP Chi-restraints excluded: chain a residue 277 ILE Chi-restraints excluded: chain a residue 302 MET Chi-restraints excluded: chain a residue 344 ILE Chi-restraints excluded: chain a residue 357 ASP Chi-restraints excluded: chain d residue 162 GLU Chi-restraints excluded: chain d residue 167 ASP Chi-restraints excluded: chain d residue 300 LEU Chi-restraints excluded: chain d residue 308 THR Chi-restraints excluded: chain d residue 344 ILE Chi-restraints excluded: chain d residue 415 LEU Chi-restraints excluded: chain d residue 442 THR Chi-restraints excluded: chain d residue 471 GLU Chi-restraints excluded: chain e residue 98 MET Chi-restraints excluded: chain e residue 308 THR Chi-restraints excluded: chain e residue 336 ASN Chi-restraints excluded: chain e residue 404 GLU Chi-restraints excluded: chain e residue 507 GLU Chi-restraints excluded: chain f residue 162 GLU Chi-restraints excluded: chain f residue 167 ASP Chi-restraints excluded: chain f residue 306 THR Chi-restraints excluded: chain f residue 346 GLU Chi-restraints excluded: chain f residue 415 LEU Chi-restraints excluded: chain f residue 418 HIS Chi-restraints excluded: chain f residue 442 THR Chi-restraints excluded: chain f residue 476 LEU Chi-restraints excluded: chain g residue 97 THR Chi-restraints excluded: chain g residue 155 LEU Chi-restraints excluded: chain g residue 156 ILE Chi-restraints excluded: chain g residue 344 ILE Chi-restraints excluded: chain h residue 167 ASP Chi-restraints excluded: chain h residue 183 ILE Chi-restraints excluded: chain h residue 216 ILE Chi-restraints excluded: chain h residue 300 LEU Chi-restraints excluded: chain h residue 380 LEU Chi-restraints excluded: chain h residue 398 SER Chi-restraints excluded: chain h residue 442 THR Chi-restraints excluded: chain i residue 141 LEU Chi-restraints excluded: chain i residue 150 ASP Chi-restraints excluded: chain i residue 237 HIS Chi-restraints excluded: chain i residue 336 ASN Chi-restraints excluded: chain i residue 357 ASP Chi-restraints excluded: chain j residue 167 ASP Chi-restraints excluded: chain j residue 216 ILE Chi-restraints excluded: chain j residue 300 LEU Chi-restraints excluded: chain j residue 311 VAL Chi-restraints excluded: chain j residue 406 ILE Chi-restraints excluded: chain j residue 415 LEU Chi-restraints excluded: chain j residue 442 THR Chi-restraints excluded: chain j residue 472 VAL Chi-restraints excluded: chain j residue 474 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 876 random chunks: chunk 284 optimal weight: 10.0000 chunk 762 optimal weight: 20.0000 chunk 167 optimal weight: 1.9990 chunk 497 optimal weight: 10.0000 chunk 209 optimal weight: 2.9990 chunk 847 optimal weight: 9.9990 chunk 703 optimal weight: 6.9990 chunk 392 optimal weight: 20.0000 chunk 70 optimal weight: 0.9990 chunk 280 optimal weight: 6.9990 chunk 444 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 96 ASN ** V 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 364 ASN ** U 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 337 HIS X 100 GLN ** a 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 337 HIS f 409 HIS ** i 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 100 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 72114 Z= 0.271 Angle : 0.584 10.227 97848 Z= 0.307 Chirality : 0.044 0.476 10404 Planarity : 0.004 0.062 12912 Dihedral : 4.892 62.106 9660 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.58 % Favored : 95.27 % Rotamer: Outliers : 3.39 % Allowed : 17.43 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.09), residues: 8814 helix: 1.73 (0.08), residues: 3966 sheet: 0.42 (0.17), residues: 1068 loop : -1.24 (0.10), residues: 3780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 111 HIS 0.024 0.001 HIS O 237 PHE 0.032 0.002 PHE C 61 TYR 0.020 0.001 TYR X 419 ARG 0.009 0.000 ARG c 26 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17628 Ramachandran restraints generated. 8814 Oldfield, 0 Emsley, 8814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17628 Ramachandran restraints generated. 8814 Oldfield, 0 Emsley, 8814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1735 residues out of total 7380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 250 poor density : 1485 time to evaluate : 6.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 123 LYS cc_start: 0.7823 (mmtm) cc_final: 0.7534 (mmtm) REVERT: A 27 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.7734 (pp30) REVERT: A 109 ASP cc_start: 0.8320 (OUTLIER) cc_final: 0.8095 (p0) REVERT: B 61 PHE cc_start: 0.7571 (t80) cc_final: 0.7356 (t80) REVERT: M 29 ASP cc_start: 0.7427 (m-30) cc_final: 0.7084 (m-30) REVERT: M 56 ASP cc_start: 0.7759 (m-30) cc_final: 0.7468 (m-30) REVERT: P 56 ASP cc_start: 0.7997 (m-30) cc_final: 0.7559 (m-30) REVERT: S 126 LYS cc_start: 0.9162 (tttp) cc_final: 0.8896 (tttt) REVERT: V 127 GLU cc_start: 0.7767 (pp20) cc_final: 0.7494 (pp20) REVERT: Y 29 ASP cc_start: 0.7271 (m-30) cc_final: 0.6989 (m-30) REVERT: b 13 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7118 (mp0) REVERT: b 56 ASP cc_start: 0.7857 (m-30) cc_final: 0.7629 (m-30) REVERT: N 24 ASP cc_start: 0.7634 (t0) cc_final: 0.7409 (t0) REVERT: Q 41 ARG cc_start: 0.7692 (tpp80) cc_final: 0.7067 (tpp80) REVERT: W 8 LYS cc_start: 0.9015 (ttpp) cc_final: 0.8753 (ttpp) REVERT: W 41 ARG cc_start: 0.7626 (tpp80) cc_final: 0.7335 (mmm-85) REVERT: W 42 ASP cc_start: 0.8626 (t0) cc_final: 0.8342 (t0) REVERT: c 42 ASP cc_start: 0.8160 (t70) cc_final: 0.7890 (t0) REVERT: H 143 GLU cc_start: 0.8379 (mm-30) cc_final: 0.8098 (mm-30) REVERT: J 8 LYS cc_start: 0.9005 (ttpp) cc_final: 0.8757 (ttpp) REVERT: J 41 ARG cc_start: 0.7622 (tpp80) cc_final: 0.7234 (mmm-85) REVERT: J 42 ASP cc_start: 0.8714 (t0) cc_final: 0.8363 (t0) REVERT: K 6 GLU cc_start: 0.7602 (tt0) cc_final: 0.7343 (tt0) REVERT: L 42 ASP cc_start: 0.8187 (t70) cc_final: 0.7926 (t0) REVERT: L 143 GLU cc_start: 0.8374 (mm-30) cc_final: 0.8158 (mt-10) REVERT: O 101 ASP cc_start: 0.8667 (m-30) cc_final: 0.8440 (m-30) REVERT: O 161 MET cc_start: 0.8575 (tpt) cc_final: 0.8327 (mmt) REVERT: R 161 MET cc_start: 0.7762 (mmt) cc_final: 0.7546 (mmt) REVERT: R 419 TYR cc_start: 0.8825 (m-80) cc_final: 0.8490 (m-80) REVERT: R 424 LYS cc_start: 0.8043 (tptt) cc_final: 0.7804 (tptt) REVERT: R 446 GLN cc_start: 0.8422 (mp10) cc_final: 0.8067 (mp10) REVERT: R 486 ARG cc_start: 0.6737 (ttp80) cc_final: 0.6444 (tmt-80) REVERT: R 501 GLU cc_start: 0.8502 (pt0) cc_final: 0.8274 (pp20) REVERT: U 101 ASP cc_start: 0.8608 (m-30) cc_final: 0.8368 (m-30) REVERT: U 114 CYS cc_start: 0.8703 (m) cc_final: 0.8494 (m) REVERT: U 142 LYS cc_start: 0.7550 (tptp) cc_final: 0.7223 (tptp) REVERT: U 312 ASP cc_start: 0.7869 (t0) cc_final: 0.7539 (t0) REVERT: U 346 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7513 (mm-30) REVERT: U 404 GLU cc_start: 0.8144 (tp30) cc_final: 0.7904 (tp30) REVERT: U 475 ARG cc_start: 0.8620 (ttp80) cc_final: 0.8070 (tmm-80) REVERT: X 161 MET cc_start: 0.8070 (mmt) cc_final: 0.7797 (mmt) REVERT: X 424 LYS cc_start: 0.8040 (tptt) cc_final: 0.7787 (tptt) REVERT: a 100 GLN cc_start: 0.9121 (tp40) cc_final: 0.8818 (tp40) REVERT: a 101 ASP cc_start: 0.8649 (m-30) cc_final: 0.8182 (m-30) REVERT: a 171 GLU cc_start: 0.8299 (tm-30) cc_final: 0.7981 (tm-30) REVERT: a 195 TYR cc_start: 0.7436 (t80) cc_final: 0.7010 (t80) REVERT: a 239 TYR cc_start: 0.8832 (m-80) cc_final: 0.8391 (m-80) REVERT: a 386 LYS cc_start: 0.7769 (mttm) cc_final: 0.7375 (mmtm) REVERT: a 474 GLU cc_start: 0.8779 (mp0) cc_final: 0.8401 (mp0) REVERT: d 240 GLU cc_start: 0.8485 (tp30) cc_final: 0.8124 (tp30) REVERT: d 424 LYS cc_start: 0.8036 (tptt) cc_final: 0.7683 (tptt) REVERT: d 470 ASP cc_start: 0.8680 (p0) cc_final: 0.8408 (p0) REVERT: e 349 GLU cc_start: 0.7993 (tt0) cc_final: 0.7744 (tt0) REVERT: e 466 VAL cc_start: 0.8904 (t) cc_final: 0.8665 (p) REVERT: f 250 LYS cc_start: 0.8627 (mtpt) cc_final: 0.8313 (tttm) REVERT: f 302 MET cc_start: 0.8378 (mmm) cc_final: 0.8090 (mmm) REVERT: f 424 LYS cc_start: 0.8063 (tptt) cc_final: 0.7809 (tptt) REVERT: f 446 GLN cc_start: 0.8390 (mp10) cc_final: 0.8056 (mp10) REVERT: f 501 GLU cc_start: 0.7589 (pp20) cc_final: 0.7255 (pp20) REVERT: g 100 GLN cc_start: 0.9134 (tp40) cc_final: 0.8901 (tp40) REVERT: g 142 LYS cc_start: 0.7433 (tptp) cc_final: 0.7213 (tptp) REVERT: g 159 ARG cc_start: 0.8205 (mmm-85) cc_final: 0.7657 (mmm160) REVERT: g 160 ASP cc_start: 0.8958 (t0) cc_final: 0.8446 (t0) REVERT: g 195 TYR cc_start: 0.7686 (t80) cc_final: 0.7420 (t80) REVERT: g 381 LEU cc_start: 0.9180 (mp) cc_final: 0.8941 (mp) REVERT: g 524 GLU cc_start: 0.7590 (mp0) cc_final: 0.7378 (mp0) REVERT: h 161 MET cc_start: 0.8087 (mmt) cc_final: 0.7737 (mmt) REVERT: h 240 GLU cc_start: 0.7364 (tm-30) cc_final: 0.6828 (tm-30) REVERT: h 250 LYS cc_start: 0.8574 (mmmt) cc_final: 0.8220 (tttm) REVERT: h 337 HIS cc_start: 0.8113 (m-70) cc_final: 0.7713 (m90) REVERT: h 424 LYS cc_start: 0.8315 (tptt) cc_final: 0.7919 (tptt) REVERT: h 454 LYS cc_start: 0.8576 (mtmm) cc_final: 0.8303 (mtmp) REVERT: i 101 ASP cc_start: 0.8705 (m-30) cc_final: 0.8200 (m-30) REVERT: i 158 ARG cc_start: 0.8821 (ptp-170) cc_final: 0.8591 (ptp-170) REVERT: i 161 MET cc_start: 0.8589 (mmt) cc_final: 0.8207 (ttp) REVERT: i 321 GLU cc_start: 0.8178 (pp20) cc_final: 0.7667 (tm-30) REVERT: i 345 ASP cc_start: 0.8410 (p0) cc_final: 0.7693 (p0) REVERT: i 346 GLU cc_start: 0.7734 (mp0) cc_final: 0.6932 (mp0) REVERT: i 475 ARG cc_start: 0.8434 (ttp-170) cc_final: 0.7962 (ptt180) REVERT: j 240 GLU cc_start: 0.8607 (tp30) cc_final: 0.8165 (tp30) REVERT: j 346 GLU cc_start: 0.7821 (pm20) cc_final: 0.7303 (pm20) REVERT: j 454 LYS cc_start: 0.8702 (mtmm) cc_final: 0.8351 (mttp) REVERT: j 474 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.8035 (mp0) outliers start: 250 outliers final: 203 residues processed: 1615 average time/residue: 0.6613 time to fit residues: 1816.5645 Evaluate side-chains 1653 residues out of total 7380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 1446 time to evaluate : 6.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 57 GLN Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 106 PHE Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain A residue 27 GLN Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain B residue 10 MET Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain D residue 10 MET Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 106 PHE Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain E residue 10 MET Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain E residue 55 ARG Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 85 MET Chi-restraints excluded: chain E residue 106 PHE Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 6 ASN Chi-restraints excluded: chain F residue 42 GLU Chi-restraints excluded: chain F residue 55 ARG Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 106 PHE Chi-restraints excluded: chain M residue 65 ASP Chi-restraints excluded: chain M residue 69 ASP Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 90 SER Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain M residue 148 HIS Chi-restraints excluded: chain M residue 181 ILE Chi-restraints excluded: chain P residue 65 ASP Chi-restraints excluded: chain P residue 76 VAL Chi-restraints excluded: chain P residue 90 SER Chi-restraints excluded: chain P residue 125 VAL Chi-restraints excluded: chain P residue 181 ILE Chi-restraints excluded: chain S residue 6 LEU Chi-restraints excluded: chain S residue 23 GLU Chi-restraints excluded: chain S residue 27 PHE Chi-restraints excluded: chain S residue 90 SER Chi-restraints excluded: chain S residue 102 VAL Chi-restraints excluded: chain S residue 167 ARG Chi-restraints excluded: chain S residue 181 ILE Chi-restraints excluded: chain V residue 49 ILE Chi-restraints excluded: chain V residue 54 LEU Chi-restraints excluded: chain V residue 65 ASP Chi-restraints excluded: chain V residue 69 ASP Chi-restraints excluded: chain V residue 90 SER Chi-restraints excluded: chain Y residue 54 LEU Chi-restraints excluded: chain Y residue 65 ASP Chi-restraints excluded: chain Y residue 90 SER Chi-restraints excluded: chain b residue 13 GLU Chi-restraints excluded: chain b residue 65 ASP Chi-restraints excluded: chain b residue 69 ASP Chi-restraints excluded: chain b residue 90 SER Chi-restraints excluded: chain b residue 100 THR Chi-restraints excluded: chain b residue 102 VAL Chi-restraints excluded: chain b residue 127 GLU Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 118 THR Chi-restraints excluded: chain N residue 153 THR Chi-restraints excluded: chain Q residue 25 VAL Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain T residue 97 GLU Chi-restraints excluded: chain T residue 129 SER Chi-restraints excluded: chain T residue 153 THR Chi-restraints excluded: chain W residue 3 ILE Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 69 THR Chi-restraints excluded: chain W residue 85 THR Chi-restraints excluded: chain W residue 130 VAL Chi-restraints excluded: chain Z residue 6 GLU Chi-restraints excluded: chain Z residue 7 HIS Chi-restraints excluded: chain Z residue 129 SER Chi-restraints excluded: chain Z residue 153 THR Chi-restraints excluded: chain c residue 3 ILE Chi-restraints excluded: chain c residue 25 VAL Chi-restraints excluded: chain c residue 91 THR Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 7 HIS Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 66 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain I residue 7 HIS Chi-restraints excluded: chain I residue 90 ILE Chi-restraints excluded: chain I residue 129 SER Chi-restraints excluded: chain I residue 153 THR Chi-restraints excluded: chain J residue 25 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 108 LYS Chi-restraints excluded: chain J residue 123 GLU Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain K residue 7 HIS Chi-restraints excluded: chain K residue 153 THR Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 72 VAL Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain O residue 141 LEU Chi-restraints excluded: chain O residue 144 ASP Chi-restraints excluded: chain O residue 148 LEU Chi-restraints excluded: chain O residue 150 ASP Chi-restraints excluded: chain O residue 259 VAL Chi-restraints excluded: chain O residue 308 THR Chi-restraints excluded: chain O residue 321 GLU Chi-restraints excluded: chain O residue 336 ASN Chi-restraints excluded: chain R residue 162 GLU Chi-restraints excluded: chain R residue 167 ASP Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 306 THR Chi-restraints excluded: chain R residue 308 THR Chi-restraints excluded: chain R residue 409 HIS Chi-restraints excluded: chain R residue 415 LEU Chi-restraints excluded: chain R residue 418 HIS Chi-restraints excluded: chain R residue 442 THR Chi-restraints excluded: chain R residue 476 LEU Chi-restraints excluded: chain U residue 148 LEU Chi-restraints excluded: chain U residue 156 ILE Chi-restraints excluded: chain U residue 357 ASP Chi-restraints excluded: chain U residue 485 ASN Chi-restraints excluded: chain X residue 162 GLU Chi-restraints excluded: chain X residue 260 ARG Chi-restraints excluded: chain X residue 267 ILE Chi-restraints excluded: chain X residue 339 VAL Chi-restraints excluded: chain X residue 380 LEU Chi-restraints excluded: chain X residue 398 SER Chi-restraints excluded: chain X residue 442 THR Chi-restraints excluded: chain X residue 472 VAL Chi-restraints excluded: chain a residue 105 SER Chi-restraints excluded: chain a residue 141 LEU Chi-restraints excluded: chain a residue 148 LEU Chi-restraints excluded: chain a residue 156 ILE Chi-restraints excluded: chain a residue 167 ASP Chi-restraints excluded: chain a residue 256 LEU Chi-restraints excluded: chain a residue 302 MET Chi-restraints excluded: chain a residue 357 ASP Chi-restraints excluded: chain d residue 162 GLU Chi-restraints excluded: chain d residue 167 ASP Chi-restraints excluded: chain d residue 300 LEU Chi-restraints excluded: chain d residue 308 THR Chi-restraints excluded: chain d residue 442 THR Chi-restraints excluded: chain d residue 471 GLU Chi-restraints excluded: chain e residue 308 THR Chi-restraints excluded: chain e residue 336 ASN Chi-restraints excluded: chain e residue 404 GLU Chi-restraints excluded: chain e residue 507 GLU Chi-restraints excluded: chain f residue 162 GLU Chi-restraints excluded: chain f residue 167 ASP Chi-restraints excluded: chain f residue 187 VAL Chi-restraints excluded: chain f residue 346 GLU Chi-restraints excluded: chain f residue 409 HIS Chi-restraints excluded: chain f residue 415 LEU Chi-restraints excluded: chain f residue 476 LEU Chi-restraints excluded: chain g residue 97 THR Chi-restraints excluded: chain g residue 155 LEU Chi-restraints excluded: chain g residue 156 ILE Chi-restraints excluded: chain g residue 187 VAL Chi-restraints excluded: chain h residue 162 GLU Chi-restraints excluded: chain h residue 167 ASP Chi-restraints excluded: chain h residue 183 ILE Chi-restraints excluded: chain h residue 216 ILE Chi-restraints excluded: chain h residue 300 LEU Chi-restraints excluded: chain h residue 380 LEU Chi-restraints excluded: chain h residue 398 SER Chi-restraints excluded: chain h residue 472 VAL Chi-restraints excluded: chain h residue 476 LEU Chi-restraints excluded: chain i residue 141 LEU Chi-restraints excluded: chain i residue 150 ASP Chi-restraints excluded: chain i residue 237 HIS Chi-restraints excluded: chain i residue 336 ASN Chi-restraints excluded: chain i residue 357 ASP Chi-restraints excluded: chain j residue 167 ASP Chi-restraints excluded: chain j residue 300 LEU Chi-restraints excluded: chain j residue 311 VAL Chi-restraints excluded: chain j residue 406 ILE Chi-restraints excluded: chain j residue 415 LEU Chi-restraints excluded: chain j residue 442 THR Chi-restraints excluded: chain j residue 474 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 876 random chunks: chunk 817 optimal weight: 7.9990 chunk 95 optimal weight: 0.9990 chunk 482 optimal weight: 10.0000 chunk 618 optimal weight: 3.9990 chunk 479 optimal weight: 30.0000 chunk 713 optimal weight: 20.0000 chunk 473 optimal weight: 3.9990 chunk 844 optimal weight: 20.0000 chunk 528 optimal weight: 0.0370 chunk 514 optimal weight: 9.9990 chunk 389 optimal weight: 6.9990 overall best weight: 3.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 62 ASN P 95 GLN ** S 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 237 HIS R 364 ASN ** U 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 337 HIS ** a 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 446 GLN j 100 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 72114 Z= 0.233 Angle : 0.569 11.102 97848 Z= 0.297 Chirality : 0.043 0.485 10404 Planarity : 0.004 0.058 12912 Dihedral : 4.775 62.120 9660 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.92 % Favored : 94.93 % Rotamer: Outliers : 3.28 % Allowed : 18.17 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.09), residues: 8814 helix: 1.79 (0.08), residues: 3966 sheet: 0.44 (0.17), residues: 1068 loop : -1.19 (0.10), residues: 3780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 111 HIS 0.026 0.001 HIS f 409 PHE 0.031 0.001 PHE C 61 TYR 0.019 0.001 TYR h 419 ARG 0.010 0.000 ARG L 26 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17628 Ramachandran restraints generated. 8814 Oldfield, 0 Emsley, 8814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17628 Ramachandran restraints generated. 8814 Oldfield, 0 Emsley, 8814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1736 residues out of total 7380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 242 poor density : 1494 time to evaluate : 6.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 123 LYS cc_start: 0.7826 (mmtm) cc_final: 0.7537 (mmtm) REVERT: A 57 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7258 (pt0) REVERT: A 109 ASP cc_start: 0.8279 (OUTLIER) cc_final: 0.8008 (p0) REVERT: B 61 PHE cc_start: 0.7423 (t80) cc_final: 0.7145 (t80) REVERT: D 65 PHE cc_start: 0.8557 (m-80) cc_final: 0.8226 (m-80) REVERT: M 29 ASP cc_start: 0.7446 (m-30) cc_final: 0.7113 (m-30) REVERT: M 56 ASP cc_start: 0.7756 (m-30) cc_final: 0.7455 (m-30) REVERT: P 56 ASP cc_start: 0.7991 (m-30) cc_final: 0.7528 (m-30) REVERT: S 126 LYS cc_start: 0.9120 (tttp) cc_final: 0.8871 (tttt) REVERT: V 127 GLU cc_start: 0.7766 (pp20) cc_final: 0.7498 (pp20) REVERT: Y 29 ASP cc_start: 0.7265 (m-30) cc_final: 0.6956 (m-30) REVERT: b 13 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7100 (mp0) REVERT: b 56 ASP cc_start: 0.7835 (m-30) cc_final: 0.7621 (m-30) REVERT: Q 41 ARG cc_start: 0.7660 (tpp80) cc_final: 0.7080 (tpp80) REVERT: W 8 LYS cc_start: 0.9001 (ttpp) cc_final: 0.8729 (ttpp) REVERT: c 42 ASP cc_start: 0.8174 (t70) cc_final: 0.7918 (t0) REVERT: H 41 ARG cc_start: 0.7782 (tpp80) cc_final: 0.7224 (tpp80) REVERT: H 143 GLU cc_start: 0.8294 (mm-30) cc_final: 0.8022 (mm-30) REVERT: J 8 LYS cc_start: 0.8945 (ttpp) cc_final: 0.8698 (ttpp) REVERT: J 41 ARG cc_start: 0.7551 (tpp80) cc_final: 0.7238 (mmm-85) REVERT: J 42 ASP cc_start: 0.8733 (t0) cc_final: 0.8368 (t0) REVERT: L 42 ASP cc_start: 0.8182 (t70) cc_final: 0.7921 (t0) REVERT: L 143 GLU cc_start: 0.8364 (mm-30) cc_final: 0.8148 (mt-10) REVERT: O 101 ASP cc_start: 0.8681 (m-30) cc_final: 0.8462 (m-30) REVERT: O 129 MET cc_start: 0.8284 (mtp) cc_final: 0.8013 (mtp) REVERT: O 152 GLN cc_start: 0.8737 (mt0) cc_final: 0.8389 (pt0) REVERT: O 161 MET cc_start: 0.8556 (tpt) cc_final: 0.8299 (mmt) REVERT: O 171 GLU cc_start: 0.7967 (tt0) cc_final: 0.7765 (tm-30) REVERT: R 161 MET cc_start: 0.7823 (mmt) cc_final: 0.7611 (mmt) REVERT: R 419 TYR cc_start: 0.8820 (m-80) cc_final: 0.8448 (m-80) REVERT: R 424 LYS cc_start: 0.8045 (tptt) cc_final: 0.7816 (tptt) REVERT: R 446 GLN cc_start: 0.8484 (mp10) cc_final: 0.8159 (mp10) REVERT: R 486 ARG cc_start: 0.6762 (ttp80) cc_final: 0.6499 (tmt-80) REVERT: R 501 GLU cc_start: 0.8497 (pt0) cc_final: 0.8270 (pp20) REVERT: U 101 ASP cc_start: 0.8600 (m-30) cc_final: 0.8369 (m-30) REVERT: U 114 CYS cc_start: 0.8617 (m) cc_final: 0.8414 (m) REVERT: U 142 LYS cc_start: 0.7538 (tptp) cc_final: 0.7151 (tptp) REVERT: U 186 PHE cc_start: 0.8202 (m-80) cc_final: 0.7872 (m-80) REVERT: U 312 ASP cc_start: 0.7857 (t0) cc_final: 0.7527 (t0) REVERT: U 346 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7545 (mm-30) REVERT: U 404 GLU cc_start: 0.8174 (tp30) cc_final: 0.7919 (tp30) REVERT: U 475 ARG cc_start: 0.8628 (ttp80) cc_final: 0.8065 (tmm-80) REVERT: X 161 MET cc_start: 0.8104 (mmt) cc_final: 0.7827 (mmt) REVERT: X 250 LYS cc_start: 0.8829 (mmmm) cc_final: 0.8564 (mmmm) REVERT: X 424 LYS cc_start: 0.8061 (tptt) cc_final: 0.7815 (tptt) REVERT: a 100 GLN cc_start: 0.9117 (tp40) cc_final: 0.8815 (tp40) REVERT: a 101 ASP cc_start: 0.8644 (m-30) cc_final: 0.8170 (m-30) REVERT: a 171 GLU cc_start: 0.8286 (tm-30) cc_final: 0.7979 (tm-30) REVERT: a 195 TYR cc_start: 0.7450 (t80) cc_final: 0.7017 (t80) REVERT: a 239 TYR cc_start: 0.8833 (m-80) cc_final: 0.8383 (m-80) REVERT: a 386 LYS cc_start: 0.7743 (mttm) cc_final: 0.7365 (mmtm) REVERT: d 132 GLU cc_start: 0.8336 (tp30) cc_final: 0.7920 (tp30) REVERT: d 216 ILE cc_start: 0.9486 (mt) cc_final: 0.9004 (tp) REVERT: d 240 GLU cc_start: 0.8486 (tp30) cc_final: 0.8129 (tp30) REVERT: d 424 LYS cc_start: 0.8030 (tptt) cc_final: 0.7827 (tptt) REVERT: d 464 SER cc_start: 0.8799 (m) cc_final: 0.8449 (p) REVERT: d 486 ARG cc_start: 0.7694 (ttp80) cc_final: 0.7491 (ttp80) REVERT: e 239 TYR cc_start: 0.8480 (m-80) cc_final: 0.7999 (m-80) REVERT: e 349 GLU cc_start: 0.7958 (tt0) cc_final: 0.7732 (tt0) REVERT: e 466 VAL cc_start: 0.8922 (t) cc_final: 0.8685 (p) REVERT: f 250 LYS cc_start: 0.8645 (mtpt) cc_final: 0.8258 (tttm) REVERT: f 424 LYS cc_start: 0.8168 (tptt) cc_final: 0.7901 (tptt) REVERT: f 446 GLN cc_start: 0.8450 (mp10) cc_final: 0.8115 (mp10) REVERT: f 501 GLU cc_start: 0.7537 (pp20) cc_final: 0.7199 (pp20) REVERT: g 100 GLN cc_start: 0.9115 (tp40) cc_final: 0.8911 (tp40) REVERT: g 142 LYS cc_start: 0.7452 (tptp) cc_final: 0.7200 (tptp) REVERT: g 160 ASP cc_start: 0.8950 (t0) cc_final: 0.8494 (t0) REVERT: g 195 TYR cc_start: 0.7793 (t80) cc_final: 0.6963 (t80) REVERT: g 381 LEU cc_start: 0.9186 (mp) cc_final: 0.8939 (mp) REVERT: h 161 MET cc_start: 0.8078 (mmt) cc_final: 0.7723 (mmt) REVERT: h 240 GLU cc_start: 0.7353 (tm-30) cc_final: 0.6846 (tm-30) REVERT: h 250 LYS cc_start: 0.8558 (mmmt) cc_final: 0.8201 (tttm) REVERT: h 292 ARG cc_start: 0.8417 (tpt90) cc_final: 0.8133 (tpt90) REVERT: h 337 HIS cc_start: 0.8100 (m-70) cc_final: 0.7738 (m90) REVERT: h 406 ILE cc_start: 0.9265 (mm) cc_final: 0.8928 (tp) REVERT: h 424 LYS cc_start: 0.8396 (tptt) cc_final: 0.8138 (tptt) REVERT: h 454 LYS cc_start: 0.8548 (mtmm) cc_final: 0.8259 (mtmp) REVERT: i 101 ASP cc_start: 0.8698 (m-30) cc_final: 0.8187 (m-30) REVERT: i 161 MET cc_start: 0.8542 (mmt) cc_final: 0.8145 (ttp) REVERT: i 321 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7667 (tm-30) REVERT: i 345 ASP cc_start: 0.8430 (p0) cc_final: 0.7748 (p0) REVERT: i 346 GLU cc_start: 0.7730 (mp0) cc_final: 0.6874 (mp0) REVERT: i 475 ARG cc_start: 0.8513 (ttp-170) cc_final: 0.8060 (ptt180) REVERT: j 240 GLU cc_start: 0.8609 (tp30) cc_final: 0.8166 (tp30) REVERT: j 346 GLU cc_start: 0.7813 (pm20) cc_final: 0.7280 (pm20) REVERT: j 454 LYS cc_start: 0.8749 (mtmm) cc_final: 0.8441 (mttp) outliers start: 242 outliers final: 201 residues processed: 1621 average time/residue: 0.6630 time to fit residues: 1825.9618 Evaluate side-chains 1665 residues out of total 7380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 1460 time to evaluate : 6.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 57 GLN Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain C residue 106 PHE Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 57 GLN Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain B residue 10 MET Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain D residue 10 MET Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 106 PHE Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain E residue 10 MET Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 55 ARG Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 85 MET Chi-restraints excluded: chain E residue 106 PHE Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 6 ASN Chi-restraints excluded: chain F residue 42 GLU Chi-restraints excluded: chain F residue 55 ARG Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 106 PHE Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain M residue 49 ILE Chi-restraints excluded: chain M residue 65 ASP Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 90 SER Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain M residue 148 HIS Chi-restraints excluded: chain M residue 181 ILE Chi-restraints excluded: chain P residue 48 THR Chi-restraints excluded: chain P residue 76 VAL Chi-restraints excluded: chain P residue 90 SER Chi-restraints excluded: chain P residue 125 VAL Chi-restraints excluded: chain P residue 181 ILE Chi-restraints excluded: chain S residue 6 LEU Chi-restraints excluded: chain S residue 23 GLU Chi-restraints excluded: chain S residue 27 PHE Chi-restraints excluded: chain S residue 90 SER Chi-restraints excluded: chain S residue 102 VAL Chi-restraints excluded: chain S residue 167 ARG Chi-restraints excluded: chain S residue 181 ILE Chi-restraints excluded: chain V residue 49 ILE Chi-restraints excluded: chain V residue 54 LEU Chi-restraints excluded: chain V residue 65 ASP Chi-restraints excluded: chain V residue 69 ASP Chi-restraints excluded: chain V residue 90 SER Chi-restraints excluded: chain Y residue 54 LEU Chi-restraints excluded: chain Y residue 65 ASP Chi-restraints excluded: chain Y residue 90 SER Chi-restraints excluded: chain Y residue 125 VAL Chi-restraints excluded: chain b residue 13 GLU Chi-restraints excluded: chain b residue 65 ASP Chi-restraints excluded: chain b residue 69 ASP Chi-restraints excluded: chain b residue 90 SER Chi-restraints excluded: chain b residue 100 THR Chi-restraints excluded: chain b residue 102 VAL Chi-restraints excluded: chain b residue 127 GLU Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 118 THR Chi-restraints excluded: chain N residue 129 SER Chi-restraints excluded: chain N residue 153 THR Chi-restraints excluded: chain Q residue 25 VAL Chi-restraints excluded: chain Q residue 39 SER Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain T residue 97 GLU Chi-restraints excluded: chain T residue 153 THR Chi-restraints excluded: chain W residue 3 ILE Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 69 THR Chi-restraints excluded: chain W residue 85 THR Chi-restraints excluded: chain W residue 108 LYS Chi-restraints excluded: chain W residue 130 VAL Chi-restraints excluded: chain Z residue 6 GLU Chi-restraints excluded: chain Z residue 7 HIS Chi-restraints excluded: chain Z residue 129 SER Chi-restraints excluded: chain Z residue 153 THR Chi-restraints excluded: chain c residue 25 VAL Chi-restraints excluded: chain c residue 72 VAL Chi-restraints excluded: chain c residue 91 THR Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 7 HIS Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 129 SER Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain I residue 7 HIS Chi-restraints excluded: chain I residue 90 ILE Chi-restraints excluded: chain I residue 129 SER Chi-restraints excluded: chain I residue 153 THR Chi-restraints excluded: chain J residue 25 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 108 LYS Chi-restraints excluded: chain J residue 123 GLU Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain K residue 7 HIS Chi-restraints excluded: chain K residue 153 THR Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain O residue 141 LEU Chi-restraints excluded: chain O residue 148 LEU Chi-restraints excluded: chain O residue 150 ASP Chi-restraints excluded: chain O residue 259 VAL Chi-restraints excluded: chain O residue 308 THR Chi-restraints excluded: chain O residue 321 GLU Chi-restraints excluded: chain O residue 336 ASN Chi-restraints excluded: chain R residue 162 GLU Chi-restraints excluded: chain R residue 167 ASP Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 306 THR Chi-restraints excluded: chain R residue 308 THR Chi-restraints excluded: chain R residue 409 HIS Chi-restraints excluded: chain R residue 415 LEU Chi-restraints excluded: chain R residue 418 HIS Chi-restraints excluded: chain R residue 442 THR Chi-restraints excluded: chain R residue 476 LEU Chi-restraints excluded: chain U residue 148 LEU Chi-restraints excluded: chain U residue 156 ILE Chi-restraints excluded: chain U residue 357 ASP Chi-restraints excluded: chain U residue 485 ASN Chi-restraints excluded: chain X residue 162 GLU Chi-restraints excluded: chain X residue 260 ARG Chi-restraints excluded: chain X residue 380 LEU Chi-restraints excluded: chain X residue 398 SER Chi-restraints excluded: chain X residue 472 VAL Chi-restraints excluded: chain a residue 105 SER Chi-restraints excluded: chain a residue 141 LEU Chi-restraints excluded: chain a residue 148 LEU Chi-restraints excluded: chain a residue 167 ASP Chi-restraints excluded: chain a residue 256 LEU Chi-restraints excluded: chain a residue 302 MET Chi-restraints excluded: chain a residue 357 ASP Chi-restraints excluded: chain d residue 162 GLU Chi-restraints excluded: chain d residue 167 ASP Chi-restraints excluded: chain d residue 300 LEU Chi-restraints excluded: chain d residue 339 VAL Chi-restraints excluded: chain d residue 442 THR Chi-restraints excluded: chain e residue 259 VAL Chi-restraints excluded: chain e residue 308 THR Chi-restraints excluded: chain e residue 336 ASN Chi-restraints excluded: chain e residue 404 GLU Chi-restraints excluded: chain e residue 507 GLU Chi-restraints excluded: chain f residue 162 GLU Chi-restraints excluded: chain f residue 167 ASP Chi-restraints excluded: chain f residue 187 VAL Chi-restraints excluded: chain f residue 346 GLU Chi-restraints excluded: chain f residue 409 HIS Chi-restraints excluded: chain f residue 415 LEU Chi-restraints excluded: chain f residue 442 THR Chi-restraints excluded: chain f residue 476 LEU Chi-restraints excluded: chain g residue 97 THR Chi-restraints excluded: chain g residue 155 LEU Chi-restraints excluded: chain g residue 156 ILE Chi-restraints excluded: chain g residue 187 VAL Chi-restraints excluded: chain g residue 357 ASP Chi-restraints excluded: chain h residue 162 GLU Chi-restraints excluded: chain h residue 167 ASP Chi-restraints excluded: chain h residue 183 ILE Chi-restraints excluded: chain h residue 216 ILE Chi-restraints excluded: chain h residue 380 LEU Chi-restraints excluded: chain h residue 398 SER Chi-restraints excluded: chain h residue 472 VAL Chi-restraints excluded: chain h residue 476 LEU Chi-restraints excluded: chain i residue 141 LEU Chi-restraints excluded: chain i residue 237 HIS Chi-restraints excluded: chain i residue 321 GLU Chi-restraints excluded: chain i residue 336 ASN Chi-restraints excluded: chain i residue 357 ASP Chi-restraints excluded: chain i residue 380 LEU Chi-restraints excluded: chain j residue 167 ASP Chi-restraints excluded: chain j residue 300 LEU Chi-restraints excluded: chain j residue 311 VAL Chi-restraints excluded: chain j residue 406 ILE Chi-restraints excluded: chain j residue 415 LEU Chi-restraints excluded: chain j residue 472 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 876 random chunks: chunk 522 optimal weight: 20.0000 chunk 337 optimal weight: 4.9990 chunk 504 optimal weight: 7.9990 chunk 254 optimal weight: 8.9990 chunk 165 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 536 optimal weight: 5.9990 chunk 575 optimal weight: 8.9990 chunk 417 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 chunk 663 optimal weight: 0.0770 overall best weight: 3.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 364 ASN ** U 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 337 HIS a 152 GLN ** a 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 337 HIS ** d 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 119 GLN f 409 HIS ** g 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 100 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 72114 Z= 0.225 Angle : 0.566 14.144 97848 Z= 0.295 Chirality : 0.043 0.388 10404 Planarity : 0.004 0.056 12912 Dihedral : 4.703 61.881 9660 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.57 % Favored : 95.28 % Rotamer: Outliers : 3.20 % Allowed : 18.78 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.09), residues: 8814 helix: 1.83 (0.08), residues: 3966 sheet: 0.45 (0.17), residues: 1068 loop : -1.16 (0.10), residues: 3780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 111 HIS 0.005 0.001 HIS f 409 PHE 0.031 0.001 PHE X 506 TYR 0.015 0.001 TYR h 419 ARG 0.010 0.000 ARG L 26 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17628 Ramachandran restraints generated. 8814 Oldfield, 0 Emsley, 8814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17628 Ramachandran restraints generated. 8814 Oldfield, 0 Emsley, 8814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1746 residues out of total 7380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 1510 time to evaluate : 6.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 57 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7017 (pt0) REVERT: C 123 LYS cc_start: 0.7803 (mmtm) cc_final: 0.7577 (mmtm) REVERT: A 27 GLN cc_start: 0.8776 (OUTLIER) cc_final: 0.7723 (pp30) REVERT: A 57 GLN cc_start: 0.8256 (OUTLIER) cc_final: 0.7475 (pt0) REVERT: D 6 ASN cc_start: 0.8295 (OUTLIER) cc_final: 0.8087 (p0) REVERT: M 29 ASP cc_start: 0.7466 (m-30) cc_final: 0.7174 (m-30) REVERT: M 56 ASP cc_start: 0.7755 (m-30) cc_final: 0.7426 (m-30) REVERT: P 56 ASP cc_start: 0.7991 (m-30) cc_final: 0.7535 (m-30) REVERT: S 126 LYS cc_start: 0.9115 (tttp) cc_final: 0.8857 (tttt) REVERT: V 127 GLU cc_start: 0.7784 (pp20) cc_final: 0.7499 (pp20) REVERT: Y 29 ASP cc_start: 0.7274 (m-30) cc_final: 0.6956 (m-30) REVERT: b 13 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7067 (mp0) REVERT: Q 41 ARG cc_start: 0.7644 (tpp80) cc_final: 0.7053 (tpp80) REVERT: W 8 LYS cc_start: 0.8974 (ttpp) cc_final: 0.8706 (ttpp) REVERT: W 41 ARG cc_start: 0.7572 (tpp80) cc_final: 0.7274 (mmm-85) REVERT: c 42 ASP cc_start: 0.8169 (t70) cc_final: 0.7910 (t0) REVERT: H 41 ARG cc_start: 0.7751 (tpp80) cc_final: 0.7191 (tpp80) REVERT: H 143 GLU cc_start: 0.8272 (mm-30) cc_final: 0.7982 (mm-30) REVERT: J 8 LYS cc_start: 0.8944 (ttpp) cc_final: 0.8689 (ttpp) REVERT: J 41 ARG cc_start: 0.7586 (tpp80) cc_final: 0.7247 (mmm-85) REVERT: J 42 ASP cc_start: 0.8725 (t0) cc_final: 0.8399 (t0) REVERT: L 1 MET cc_start: 0.4800 (ttt) cc_final: 0.4543 (ttt) REVERT: L 42 ASP cc_start: 0.8174 (t70) cc_final: 0.7906 (t0) REVERT: L 143 GLU cc_start: 0.8357 (mm-30) cc_final: 0.8144 (mt-10) REVERT: O 101 ASP cc_start: 0.8675 (m-30) cc_final: 0.8453 (m-30) REVERT: O 129 MET cc_start: 0.8301 (mtp) cc_final: 0.8021 (mtp) REVERT: O 152 GLN cc_start: 0.8694 (mt0) cc_final: 0.8359 (pt0) REVERT: O 161 MET cc_start: 0.8551 (tpt) cc_final: 0.8258 (mmt) REVERT: O 171 GLU cc_start: 0.7937 (tt0) cc_final: 0.7655 (tm-30) REVERT: R 161 MET cc_start: 0.7841 (mmt) cc_final: 0.7624 (mmt) REVERT: R 337 HIS cc_start: 0.8283 (m90) cc_final: 0.7841 (m90) REVERT: R 419 TYR cc_start: 0.8779 (m-80) cc_final: 0.8443 (m-80) REVERT: R 424 LYS cc_start: 0.8147 (tptt) cc_final: 0.7889 (tptt) REVERT: R 446 GLN cc_start: 0.8515 (mp10) cc_final: 0.8173 (mp10) REVERT: R 486 ARG cc_start: 0.6649 (ttp80) cc_final: 0.6410 (tmt-80) REVERT: R 501 GLU cc_start: 0.8489 (pt0) cc_final: 0.8278 (pp20) REVERT: U 101 ASP cc_start: 0.8581 (m-30) cc_final: 0.8347 (m-30) REVERT: U 114 CYS cc_start: 0.8601 (m) cc_final: 0.8389 (m) REVERT: U 142 LYS cc_start: 0.7609 (tptp) cc_final: 0.7248 (tptp) REVERT: U 186 PHE cc_start: 0.8211 (m-80) cc_final: 0.7887 (m-80) REVERT: U 312 ASP cc_start: 0.7855 (t0) cc_final: 0.7518 (t0) REVERT: U 346 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7567 (mm-30) REVERT: U 404 GLU cc_start: 0.8135 (tp30) cc_final: 0.7882 (tp30) REVERT: U 475 ARG cc_start: 0.8631 (ttp80) cc_final: 0.8051 (tmm-80) REVERT: X 161 MET cc_start: 0.8122 (mmt) cc_final: 0.7828 (mmt) REVERT: X 250 LYS cc_start: 0.8837 (mmmm) cc_final: 0.8563 (mmmm) REVERT: X 424 LYS cc_start: 0.8099 (tptt) cc_final: 0.7893 (tptt) REVERT: a 100 GLN cc_start: 0.9113 (tp40) cc_final: 0.8813 (tp40) REVERT: a 101 ASP cc_start: 0.8641 (m-30) cc_final: 0.8167 (m-30) REVERT: a 171 GLU cc_start: 0.8274 (tm-30) cc_final: 0.7972 (tm-30) REVERT: a 195 TYR cc_start: 0.7472 (t80) cc_final: 0.7039 (t80) REVERT: a 239 TYR cc_start: 0.8815 (m-80) cc_final: 0.8349 (m-80) REVERT: d 132 GLU cc_start: 0.8302 (tp30) cc_final: 0.7843 (tp30) REVERT: d 216 ILE cc_start: 0.9476 (mt) cc_final: 0.8998 (tp) REVERT: d 240 GLU cc_start: 0.8480 (tp30) cc_final: 0.8124 (tp30) REVERT: d 292 ARG cc_start: 0.8342 (tpt90) cc_final: 0.7980 (tpt90) REVERT: d 464 SER cc_start: 0.8666 (m) cc_final: 0.8347 (p) REVERT: d 470 ASP cc_start: 0.8925 (p0) cc_final: 0.8414 (p0) REVERT: e 239 TYR cc_start: 0.8481 (m-80) cc_final: 0.7996 (m-80) REVERT: e 349 GLU cc_start: 0.7976 (tt0) cc_final: 0.7741 (tt0) REVERT: e 466 VAL cc_start: 0.8934 (t) cc_final: 0.8698 (p) REVERT: f 250 LYS cc_start: 0.8674 (mtpt) cc_final: 0.8271 (tttm) REVERT: f 282 ARG cc_start: 0.8507 (mtm180) cc_final: 0.7847 (mtm-85) REVERT: f 337 HIS cc_start: 0.8282 (m90) cc_final: 0.7851 (m90) REVERT: f 424 LYS cc_start: 0.8170 (tptt) cc_final: 0.7921 (tptt) REVERT: f 446 GLN cc_start: 0.8464 (mp10) cc_final: 0.8115 (mp10) REVERT: f 454 LYS cc_start: 0.8724 (mttp) cc_final: 0.8391 (mttp) REVERT: f 501 GLU cc_start: 0.7602 (pp20) cc_final: 0.7238 (pp20) REVERT: g 100 GLN cc_start: 0.9125 (tp40) cc_final: 0.8867 (tp40) REVERT: g 142 LYS cc_start: 0.7445 (tptp) cc_final: 0.7238 (tptp) REVERT: g 159 ARG cc_start: 0.8151 (mmm-85) cc_final: 0.7655 (mmm-85) REVERT: g 160 ASP cc_start: 0.8971 (t0) cc_final: 0.8504 (t0) REVERT: g 195 TYR cc_start: 0.7800 (t80) cc_final: 0.6963 (t80) REVERT: g 381 LEU cc_start: 0.9180 (mp) cc_final: 0.8934 (mp) REVERT: h 161 MET cc_start: 0.8091 (mmt) cc_final: 0.7740 (mmt) REVERT: h 240 GLU cc_start: 0.7382 (tm-30) cc_final: 0.6845 (tm-30) REVERT: h 250 LYS cc_start: 0.8563 (mmmt) cc_final: 0.8201 (tttm) REVERT: h 292 ARG cc_start: 0.8436 (tpt90) cc_final: 0.8134 (tpt90) REVERT: h 337 HIS cc_start: 0.8101 (m-70) cc_final: 0.7750 (m90) REVERT: h 406 ILE cc_start: 0.9261 (mm) cc_final: 0.8929 (tp) REVERT: h 424 LYS cc_start: 0.8380 (tptt) cc_final: 0.8136 (tptt) REVERT: h 454 LYS cc_start: 0.8530 (mtmm) cc_final: 0.8235 (mtmp) REVERT: i 101 ASP cc_start: 0.8693 (m-30) cc_final: 0.8179 (m-30) REVERT: i 161 MET cc_start: 0.8468 (mmt) cc_final: 0.8146 (ttp) REVERT: i 321 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7607 (tm-30) REVERT: i 345 ASP cc_start: 0.8450 (p0) cc_final: 0.7771 (p0) REVERT: i 346 GLU cc_start: 0.7722 (mp0) cc_final: 0.6861 (mp0) REVERT: i 475 ARG cc_start: 0.8519 (ttp-170) cc_final: 0.8049 (ptt180) REVERT: j 240 GLU cc_start: 0.8562 (tp30) cc_final: 0.8132 (tp30) REVERT: j 346 GLU cc_start: 0.7831 (pm20) cc_final: 0.7294 (pm20) REVERT: j 454 LYS cc_start: 0.8727 (mtmm) cc_final: 0.8417 (mttp) outliers start: 236 outliers final: 209 residues processed: 1629 average time/residue: 0.6756 time to fit residues: 1869.8715 Evaluate side-chains 1684 residues out of total 7380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 1469 time to evaluate : 6.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 57 GLN Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain C residue 106 PHE Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain A residue 27 GLN Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 57 GLN Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain B residue 10 MET Chi-restraints excluded: chain B residue 39 MET Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain D residue 6 ASN Chi-restraints excluded: chain D residue 10 MET Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 106 PHE Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain E residue 10 MET Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 85 MET Chi-restraints excluded: chain E residue 106 PHE Chi-restraints excluded: chain F residue 6 ASN Chi-restraints excluded: chain F residue 42 GLU Chi-restraints excluded: chain F residue 55 ARG Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 106 PHE Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain M residue 49 ILE Chi-restraints excluded: chain M residue 65 ASP Chi-restraints excluded: chain M residue 69 ASP Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 90 SER Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain M residue 148 HIS Chi-restraints excluded: chain M residue 181 ILE Chi-restraints excluded: chain P residue 48 THR Chi-restraints excluded: chain P residue 65 ASP Chi-restraints excluded: chain P residue 76 VAL Chi-restraints excluded: chain P residue 90 SER Chi-restraints excluded: chain P residue 125 VAL Chi-restraints excluded: chain P residue 181 ILE Chi-restraints excluded: chain S residue 6 LEU Chi-restraints excluded: chain S residue 23 GLU Chi-restraints excluded: chain S residue 27 PHE Chi-restraints excluded: chain S residue 90 SER Chi-restraints excluded: chain S residue 102 VAL Chi-restraints excluded: chain S residue 167 ARG Chi-restraints excluded: chain S residue 181 ILE Chi-restraints excluded: chain V residue 49 ILE Chi-restraints excluded: chain V residue 54 LEU Chi-restraints excluded: chain V residue 65 ASP Chi-restraints excluded: chain V residue 69 ASP Chi-restraints excluded: chain V residue 90 SER Chi-restraints excluded: chain Y residue 54 LEU Chi-restraints excluded: chain Y residue 65 ASP Chi-restraints excluded: chain Y residue 90 SER Chi-restraints excluded: chain Y residue 125 VAL Chi-restraints excluded: chain b residue 13 GLU Chi-restraints excluded: chain b residue 65 ASP Chi-restraints excluded: chain b residue 69 ASP Chi-restraints excluded: chain b residue 90 SER Chi-restraints excluded: chain b residue 100 THR Chi-restraints excluded: chain b residue 102 VAL Chi-restraints excluded: chain b residue 127 GLU Chi-restraints excluded: chain N residue 6 GLU Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 118 THR Chi-restraints excluded: chain N residue 129 SER Chi-restraints excluded: chain N residue 153 THR Chi-restraints excluded: chain Q residue 25 VAL Chi-restraints excluded: chain Q residue 39 SER Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain T residue 97 GLU Chi-restraints excluded: chain T residue 129 SER Chi-restraints excluded: chain T residue 153 THR Chi-restraints excluded: chain W residue 3 ILE Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 69 THR Chi-restraints excluded: chain W residue 85 THR Chi-restraints excluded: chain W residue 108 LYS Chi-restraints excluded: chain W residue 130 VAL Chi-restraints excluded: chain Z residue 6 GLU Chi-restraints excluded: chain Z residue 7 HIS Chi-restraints excluded: chain Z residue 129 SER Chi-restraints excluded: chain Z residue 153 THR Chi-restraints excluded: chain c residue 25 VAL Chi-restraints excluded: chain c residue 72 VAL Chi-restraints excluded: chain c residue 91 THR Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 7 HIS Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 66 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain I residue 7 HIS Chi-restraints excluded: chain I residue 90 ILE Chi-restraints excluded: chain I residue 129 SER Chi-restraints excluded: chain I residue 150 VAL Chi-restraints excluded: chain I residue 153 THR Chi-restraints excluded: chain J residue 25 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 108 LYS Chi-restraints excluded: chain J residue 123 GLU Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain K residue 7 HIS Chi-restraints excluded: chain K residue 153 THR Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 72 VAL Chi-restraints excluded: chain O residue 141 LEU Chi-restraints excluded: chain O residue 148 LEU Chi-restraints excluded: chain O residue 150 ASP Chi-restraints excluded: chain O residue 259 VAL Chi-restraints excluded: chain O residue 308 THR Chi-restraints excluded: chain O residue 321 GLU Chi-restraints excluded: chain O residue 336 ASN Chi-restraints excluded: chain O residue 391 THR Chi-restraints excluded: chain R residue 162 GLU Chi-restraints excluded: chain R residue 167 ASP Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 306 THR Chi-restraints excluded: chain R residue 308 THR Chi-restraints excluded: chain R residue 409 HIS Chi-restraints excluded: chain R residue 415 LEU Chi-restraints excluded: chain R residue 442 THR Chi-restraints excluded: chain R residue 476 LEU Chi-restraints excluded: chain U residue 148 LEU Chi-restraints excluded: chain U residue 156 ILE Chi-restraints excluded: chain U residue 357 ASP Chi-restraints excluded: chain U residue 485 ASN Chi-restraints excluded: chain X residue 162 GLU Chi-restraints excluded: chain X residue 260 ARG Chi-restraints excluded: chain X residue 299 LEU Chi-restraints excluded: chain X residue 339 VAL Chi-restraints excluded: chain X residue 380 LEU Chi-restraints excluded: chain X residue 398 SER Chi-restraints excluded: chain X residue 442 THR Chi-restraints excluded: chain X residue 472 VAL Chi-restraints excluded: chain a residue 105 SER Chi-restraints excluded: chain a residue 141 LEU Chi-restraints excluded: chain a residue 148 LEU Chi-restraints excluded: chain a residue 167 ASP Chi-restraints excluded: chain a residue 256 LEU Chi-restraints excluded: chain a residue 302 MET Chi-restraints excluded: chain a residue 357 ASP Chi-restraints excluded: chain d residue 162 GLU Chi-restraints excluded: chain d residue 167 ASP Chi-restraints excluded: chain d residue 300 LEU Chi-restraints excluded: chain d residue 339 VAL Chi-restraints excluded: chain d residue 442 THR Chi-restraints excluded: chain e residue 308 THR Chi-restraints excluded: chain e residue 336 ASN Chi-restraints excluded: chain e residue 383 THR Chi-restraints excluded: chain e residue 404 GLU Chi-restraints excluded: chain e residue 507 GLU Chi-restraints excluded: chain f residue 162 GLU Chi-restraints excluded: chain f residue 167 ASP Chi-restraints excluded: chain f residue 187 VAL Chi-restraints excluded: chain f residue 306 THR Chi-restraints excluded: chain f residue 346 GLU Chi-restraints excluded: chain f residue 409 HIS Chi-restraints excluded: chain f residue 442 THR Chi-restraints excluded: chain f residue 476 LEU Chi-restraints excluded: chain g residue 97 THR Chi-restraints excluded: chain g residue 155 LEU Chi-restraints excluded: chain g residue 156 ILE Chi-restraints excluded: chain g residue 187 VAL Chi-restraints excluded: chain g residue 357 ASP Chi-restraints excluded: chain h residue 162 GLU Chi-restraints excluded: chain h residue 167 ASP Chi-restraints excluded: chain h residue 183 ILE Chi-restraints excluded: chain h residue 216 ILE Chi-restraints excluded: chain h residue 380 LEU Chi-restraints excluded: chain h residue 398 SER Chi-restraints excluded: chain h residue 442 THR Chi-restraints excluded: chain h residue 472 VAL Chi-restraints excluded: chain h residue 476 LEU Chi-restraints excluded: chain i residue 237 HIS Chi-restraints excluded: chain i residue 321 GLU Chi-restraints excluded: chain i residue 336 ASN Chi-restraints excluded: chain i residue 357 ASP Chi-restraints excluded: chain i residue 380 LEU Chi-restraints excluded: chain j residue 167 ASP Chi-restraints excluded: chain j residue 187 VAL Chi-restraints excluded: chain j residue 216 ILE Chi-restraints excluded: chain j residue 300 LEU Chi-restraints excluded: chain j residue 311 VAL Chi-restraints excluded: chain j residue 442 THR Chi-restraints excluded: chain j residue 472 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 876 random chunks: chunk 768 optimal weight: 5.9990 chunk 808 optimal weight: 6.9990 chunk 737 optimal weight: 0.9980 chunk 786 optimal weight: 20.0000 chunk 473 optimal weight: 4.9990 chunk 342 optimal weight: 8.9990 chunk 617 optimal weight: 9.9990 chunk 241 optimal weight: 1.9990 chunk 710 optimal weight: 5.9990 chunk 744 optimal weight: 0.8980 chunk 784 optimal weight: 8.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 364 ASN ** U 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 337 HIS ** a 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 337 HIS ** d 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 119 GLN f 409 HIS j 100 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 72114 Z= 0.225 Angle : 0.573 15.529 97848 Z= 0.297 Chirality : 0.043 0.399 10404 Planarity : 0.004 0.056 12912 Dihedral : 4.664 61.617 9660 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.97 % Favored : 94.88 % Rotamer: Outliers : 3.28 % Allowed : 19.08 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.09), residues: 8814 helix: 1.80 (0.08), residues: 4038 sheet: 0.47 (0.17), residues: 1068 loop : -1.10 (0.10), residues: 3708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 111 HIS 0.018 0.001 HIS f 409 PHE 0.031 0.001 PHE h 506 TYR 0.015 0.001 TYR h 419 ARG 0.009 0.000 ARG c 26 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17628 Ramachandran restraints generated. 8814 Oldfield, 0 Emsley, 8814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17628 Ramachandran restraints generated. 8814 Oldfield, 0 Emsley, 8814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1737 residues out of total 7380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 242 poor density : 1495 time to evaluate : 6.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 123 LYS cc_start: 0.7771 (mmtm) cc_final: 0.7491 (mmtm) REVERT: A 27 GLN cc_start: 0.8776 (OUTLIER) cc_final: 0.7723 (pp30) REVERT: A 57 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.7446 (pm20) REVERT: D 6 ASN cc_start: 0.8304 (OUTLIER) cc_final: 0.8092 (p0) REVERT: D 65 PHE cc_start: 0.8500 (m-80) cc_final: 0.8287 (m-80) REVERT: M 29 ASP cc_start: 0.7461 (m-30) cc_final: 0.7165 (m-30) REVERT: M 56 ASP cc_start: 0.7759 (m-30) cc_final: 0.7428 (m-30) REVERT: P 56 ASP cc_start: 0.7966 (m-30) cc_final: 0.7635 (m-30) REVERT: S 126 LYS cc_start: 0.9112 (tttp) cc_final: 0.8847 (tttt) REVERT: V 127 GLU cc_start: 0.7788 (pp20) cc_final: 0.7516 (pp20) REVERT: Y 29 ASP cc_start: 0.7260 (m-30) cc_final: 0.6941 (m-30) REVERT: b 13 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7094 (mp0) REVERT: Q 41 ARG cc_start: 0.7631 (tpp80) cc_final: 0.7043 (tpp80) REVERT: W 8 LYS cc_start: 0.8961 (ttpp) cc_final: 0.8682 (ttpp) REVERT: W 41 ARG cc_start: 0.7635 (tpp80) cc_final: 0.7273 (mmm-85) REVERT: c 42 ASP cc_start: 0.8164 (t70) cc_final: 0.7910 (t0) REVERT: H 41 ARG cc_start: 0.7771 (tpp80) cc_final: 0.7196 (tpp80) REVERT: H 143 GLU cc_start: 0.8275 (mm-30) cc_final: 0.8004 (mm-30) REVERT: J 8 LYS cc_start: 0.8937 (ttpp) cc_final: 0.8695 (ttpp) REVERT: J 41 ARG cc_start: 0.7590 (tpp80) cc_final: 0.7248 (mmm-85) REVERT: J 42 ASP cc_start: 0.8722 (t0) cc_final: 0.8384 (t0) REVERT: L 1 MET cc_start: 0.4871 (ttt) cc_final: 0.4622 (ttt) REVERT: L 42 ASP cc_start: 0.8168 (t70) cc_final: 0.7903 (t0) REVERT: L 143 GLU cc_start: 0.8356 (mm-30) cc_final: 0.8148 (mt-10) REVERT: O 101 ASP cc_start: 0.8675 (m-30) cc_final: 0.8452 (m-30) REVERT: O 129 MET cc_start: 0.8298 (mtp) cc_final: 0.8011 (mtp) REVERT: O 152 GLN cc_start: 0.8707 (mt0) cc_final: 0.8440 (pt0) REVERT: O 161 MET cc_start: 0.8593 (tpt) cc_final: 0.8282 (mmt) REVERT: O 171 GLU cc_start: 0.7915 (tt0) cc_final: 0.7625 (tm-30) REVERT: R 161 MET cc_start: 0.7839 (mmt) cc_final: 0.7618 (mmt) REVERT: R 337 HIS cc_start: 0.8305 (m90) cc_final: 0.7865 (m90) REVERT: R 419 TYR cc_start: 0.8811 (m-80) cc_final: 0.8460 (m-80) REVERT: R 446 GLN cc_start: 0.8532 (mp10) cc_final: 0.8176 (mp10) REVERT: R 486 ARG cc_start: 0.6628 (ttp80) cc_final: 0.6399 (tmt-80) REVERT: R 501 GLU cc_start: 0.8506 (pt0) cc_final: 0.8272 (pp20) REVERT: U 101 ASP cc_start: 0.8582 (m-30) cc_final: 0.8347 (m-30) REVERT: U 114 CYS cc_start: 0.8597 (m) cc_final: 0.8385 (m) REVERT: U 142 LYS cc_start: 0.7576 (tptp) cc_final: 0.7204 (tptp) REVERT: U 186 PHE cc_start: 0.8212 (m-80) cc_final: 0.7887 (m-80) REVERT: U 312 ASP cc_start: 0.7862 (t0) cc_final: 0.7526 (t0) REVERT: U 346 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7555 (mm-30) REVERT: U 404 GLU cc_start: 0.8180 (tp30) cc_final: 0.7901 (tp30) REVERT: U 475 ARG cc_start: 0.8634 (ttp80) cc_final: 0.8042 (tmm-80) REVERT: X 250 LYS cc_start: 0.8815 (mmmm) cc_final: 0.8532 (mmmm) REVERT: X 424 LYS cc_start: 0.8101 (tptt) cc_final: 0.7889 (tptt) REVERT: a 100 GLN cc_start: 0.9112 (tp40) cc_final: 0.8817 (tp40) REVERT: a 101 ASP cc_start: 0.8665 (m-30) cc_final: 0.8166 (m-30) REVERT: a 171 GLU cc_start: 0.8270 (tm-30) cc_final: 0.7965 (tm-30) REVERT: a 195 TYR cc_start: 0.7583 (t80) cc_final: 0.7131 (t80) REVERT: a 239 TYR cc_start: 0.8862 (m-80) cc_final: 0.8405 (m-80) REVERT: a 404 GLU cc_start: 0.8224 (tp30) cc_final: 0.7929 (tp30) REVERT: d 132 GLU cc_start: 0.8283 (tp30) cc_final: 0.7761 (tp30) REVERT: d 216 ILE cc_start: 0.9478 (mt) cc_final: 0.9005 (tp) REVERT: d 240 GLU cc_start: 0.8476 (tp30) cc_final: 0.8119 (tp30) REVERT: d 292 ARG cc_start: 0.8331 (tpt90) cc_final: 0.7967 (tpt90) REVERT: d 464 SER cc_start: 0.8645 (m) cc_final: 0.8333 (p) REVERT: d 470 ASP cc_start: 0.8925 (p0) cc_final: 0.8503 (p0) REVERT: e 239 TYR cc_start: 0.8481 (m-80) cc_final: 0.7972 (m-80) REVERT: e 349 GLU cc_start: 0.7962 (tt0) cc_final: 0.7733 (tt0) REVERT: e 466 VAL cc_start: 0.8951 (t) cc_final: 0.8713 (p) REVERT: f 282 ARG cc_start: 0.8519 (mtm180) cc_final: 0.7881 (mtm-85) REVERT: f 337 HIS cc_start: 0.8301 (m90) cc_final: 0.7871 (m90) REVERT: f 424 LYS cc_start: 0.8167 (tptt) cc_final: 0.7917 (tptt) REVERT: f 446 GLN cc_start: 0.8463 (mp10) cc_final: 0.8107 (mp10) REVERT: f 454 LYS cc_start: 0.8728 (mttp) cc_final: 0.8394 (mttp) REVERT: f 501 GLU cc_start: 0.7610 (pp20) cc_final: 0.7257 (pp20) REVERT: g 100 GLN cc_start: 0.9119 (tp40) cc_final: 0.8881 (tp40) REVERT: g 142 LYS cc_start: 0.7450 (tptp) cc_final: 0.7239 (tptp) REVERT: g 159 ARG cc_start: 0.8109 (mmm-85) cc_final: 0.7623 (mmm-85) REVERT: g 160 ASP cc_start: 0.8976 (t0) cc_final: 0.8523 (t0) REVERT: g 195 TYR cc_start: 0.7829 (t80) cc_final: 0.6997 (t80) REVERT: g 381 LEU cc_start: 0.9177 (mp) cc_final: 0.8929 (mp) REVERT: h 101 ASP cc_start: 0.8529 (m-30) cc_final: 0.8304 (m-30) REVERT: h 161 MET cc_start: 0.8146 (mmt) cc_final: 0.7903 (mmt) REVERT: h 240 GLU cc_start: 0.7412 (tm-30) cc_final: 0.6872 (tm-30) REVERT: h 250 LYS cc_start: 0.8565 (mmmt) cc_final: 0.8202 (tttm) REVERT: h 292 ARG cc_start: 0.8432 (tpt90) cc_final: 0.8137 (tpt90) REVERT: h 337 HIS cc_start: 0.8076 (m-70) cc_final: 0.7725 (m90) REVERT: h 406 ILE cc_start: 0.9262 (mm) cc_final: 0.8935 (tp) REVERT: h 424 LYS cc_start: 0.8369 (tptt) cc_final: 0.8117 (tptt) REVERT: h 454 LYS cc_start: 0.8617 (mtmm) cc_final: 0.8375 (mtmp) REVERT: h 498 MET cc_start: 0.7536 (mmp) cc_final: 0.6997 (mmp) REVERT: i 101 ASP cc_start: 0.8693 (m-30) cc_final: 0.8180 (m-30) REVERT: i 161 MET cc_start: 0.8486 (mmt) cc_final: 0.8166 (ttp) REVERT: i 345 ASP cc_start: 0.8507 (p0) cc_final: 0.7940 (p0) REVERT: i 346 GLU cc_start: 0.7725 (mp0) cc_final: 0.6837 (mp0) REVERT: i 475 ARG cc_start: 0.8530 (ttp-170) cc_final: 0.8049 (ptt180) REVERT: j 240 GLU cc_start: 0.8562 (tp30) cc_final: 0.8133 (tp30) REVERT: j 346 GLU cc_start: 0.7849 (pm20) cc_final: 0.7285 (pm20) REVERT: j 454 LYS cc_start: 0.8715 (mtmm) cc_final: 0.8405 (mttp) outliers start: 242 outliers final: 218 residues processed: 1620 average time/residue: 0.6731 time to fit residues: 1862.7252 Evaluate side-chains 1693 residues out of total 7380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 1471 time to evaluate : 6.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 57 GLN Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain C residue 106 PHE Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain A residue 27 GLN Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 57 GLN Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain B residue 10 MET Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain D residue 6 ASN Chi-restraints excluded: chain D residue 10 MET Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 106 PHE Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain E residue 10 MET Chi-restraints excluded: chain E residue 32 ASP Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 85 MET Chi-restraints excluded: chain E residue 106 PHE Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 6 ASN Chi-restraints excluded: chain F residue 32 ASP Chi-restraints excluded: chain F residue 42 GLU Chi-restraints excluded: chain F residue 55 ARG Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 106 PHE Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain M residue 49 ILE Chi-restraints excluded: chain M residue 65 ASP Chi-restraints excluded: chain M residue 69 ASP Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 90 SER Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain M residue 148 HIS Chi-restraints excluded: chain M residue 181 ILE Chi-restraints excluded: chain P residue 48 THR Chi-restraints excluded: chain P residue 65 ASP Chi-restraints excluded: chain P residue 76 VAL Chi-restraints excluded: chain P residue 90 SER Chi-restraints excluded: chain P residue 125 VAL Chi-restraints excluded: chain P residue 181 ILE Chi-restraints excluded: chain S residue 6 LEU Chi-restraints excluded: chain S residue 23 GLU Chi-restraints excluded: chain S residue 27 PHE Chi-restraints excluded: chain S residue 90 SER Chi-restraints excluded: chain S residue 102 VAL Chi-restraints excluded: chain S residue 167 ARG Chi-restraints excluded: chain S residue 181 ILE Chi-restraints excluded: chain V residue 49 ILE Chi-restraints excluded: chain V residue 54 LEU Chi-restraints excluded: chain V residue 65 ASP Chi-restraints excluded: chain V residue 69 ASP Chi-restraints excluded: chain V residue 90 SER Chi-restraints excluded: chain Y residue 54 LEU Chi-restraints excluded: chain Y residue 65 ASP Chi-restraints excluded: chain Y residue 90 SER Chi-restraints excluded: chain Y residue 125 VAL Chi-restraints excluded: chain Y residue 166 ILE Chi-restraints excluded: chain b residue 13 GLU Chi-restraints excluded: chain b residue 65 ASP Chi-restraints excluded: chain b residue 69 ASP Chi-restraints excluded: chain b residue 90 SER Chi-restraints excluded: chain b residue 100 THR Chi-restraints excluded: chain b residue 102 VAL Chi-restraints excluded: chain b residue 127 GLU Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 118 THR Chi-restraints excluded: chain N residue 129 SER Chi-restraints excluded: chain N residue 153 THR Chi-restraints excluded: chain Q residue 25 VAL Chi-restraints excluded: chain Q residue 39 SER Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain T residue 97 GLU Chi-restraints excluded: chain T residue 129 SER Chi-restraints excluded: chain T residue 153 THR Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 69 THR Chi-restraints excluded: chain W residue 85 THR Chi-restraints excluded: chain W residue 108 LYS Chi-restraints excluded: chain W residue 130 VAL Chi-restraints excluded: chain Z residue 6 GLU Chi-restraints excluded: chain Z residue 7 HIS Chi-restraints excluded: chain Z residue 129 SER Chi-restraints excluded: chain Z residue 153 THR Chi-restraints excluded: chain c residue 25 VAL Chi-restraints excluded: chain c residue 72 VAL Chi-restraints excluded: chain c residue 91 THR Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 7 HIS Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 129 SER Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 66 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain I residue 7 HIS Chi-restraints excluded: chain I residue 54 GLU Chi-restraints excluded: chain I residue 90 ILE Chi-restraints excluded: chain I residue 129 SER Chi-restraints excluded: chain I residue 150 VAL Chi-restraints excluded: chain I residue 153 THR Chi-restraints excluded: chain J residue 25 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 108 LYS Chi-restraints excluded: chain J residue 123 GLU Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain K residue 7 HIS Chi-restraints excluded: chain K residue 153 THR Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 72 VAL Chi-restraints excluded: chain O residue 141 LEU Chi-restraints excluded: chain O residue 150 ASP Chi-restraints excluded: chain O residue 259 VAL Chi-restraints excluded: chain O residue 308 THR Chi-restraints excluded: chain O residue 321 GLU Chi-restraints excluded: chain O residue 336 ASN Chi-restraints excluded: chain O residue 391 THR Chi-restraints excluded: chain R residue 162 GLU Chi-restraints excluded: chain R residue 167 ASP Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 306 THR Chi-restraints excluded: chain R residue 308 THR Chi-restraints excluded: chain R residue 409 HIS Chi-restraints excluded: chain R residue 415 LEU Chi-restraints excluded: chain R residue 418 HIS Chi-restraints excluded: chain R residue 442 THR Chi-restraints excluded: chain R residue 476 LEU Chi-restraints excluded: chain U residue 148 LEU Chi-restraints excluded: chain U residue 150 ASP Chi-restraints excluded: chain U residue 156 ILE Chi-restraints excluded: chain U residue 357 ASP Chi-restraints excluded: chain U residue 485 ASN Chi-restraints excluded: chain U residue 505 GLU Chi-restraints excluded: chain X residue 299 LEU Chi-restraints excluded: chain X residue 339 VAL Chi-restraints excluded: chain X residue 380 LEU Chi-restraints excluded: chain X residue 398 SER Chi-restraints excluded: chain X residue 442 THR Chi-restraints excluded: chain X residue 472 VAL Chi-restraints excluded: chain a residue 105 SER Chi-restraints excluded: chain a residue 141 LEU Chi-restraints excluded: chain a residue 148 LEU Chi-restraints excluded: chain a residue 167 ASP Chi-restraints excluded: chain a residue 256 LEU Chi-restraints excluded: chain a residue 302 MET Chi-restraints excluded: chain a residue 357 ASP Chi-restraints excluded: chain d residue 162 GLU Chi-restraints excluded: chain d residue 167 ASP Chi-restraints excluded: chain d residue 300 LEU Chi-restraints excluded: chain d residue 442 THR Chi-restraints excluded: chain d residue 471 GLU Chi-restraints excluded: chain e residue 259 VAL Chi-restraints excluded: chain e residue 308 THR Chi-restraints excluded: chain e residue 336 ASN Chi-restraints excluded: chain e residue 383 THR Chi-restraints excluded: chain e residue 404 GLU Chi-restraints excluded: chain e residue 507 GLU Chi-restraints excluded: chain f residue 162 GLU Chi-restraints excluded: chain f residue 167 ASP Chi-restraints excluded: chain f residue 187 VAL Chi-restraints excluded: chain f residue 346 GLU Chi-restraints excluded: chain f residue 409 HIS Chi-restraints excluded: chain f residue 442 THR Chi-restraints excluded: chain f residue 476 LEU Chi-restraints excluded: chain f residue 489 ASP Chi-restraints excluded: chain g residue 97 THR Chi-restraints excluded: chain g residue 155 LEU Chi-restraints excluded: chain g residue 156 ILE Chi-restraints excluded: chain g residue 187 VAL Chi-restraints excluded: chain g residue 357 ASP Chi-restraints excluded: chain h residue 167 ASP Chi-restraints excluded: chain h residue 183 ILE Chi-restraints excluded: chain h residue 216 ILE Chi-restraints excluded: chain h residue 300 LEU Chi-restraints excluded: chain h residue 380 LEU Chi-restraints excluded: chain h residue 398 SER Chi-restraints excluded: chain h residue 442 THR Chi-restraints excluded: chain h residue 472 VAL Chi-restraints excluded: chain h residue 476 LEU Chi-restraints excluded: chain i residue 141 LEU Chi-restraints excluded: chain i residue 237 HIS Chi-restraints excluded: chain i residue 336 ASN Chi-restraints excluded: chain i residue 357 ASP Chi-restraints excluded: chain i residue 380 LEU Chi-restraints excluded: chain j residue 167 ASP Chi-restraints excluded: chain j residue 187 VAL Chi-restraints excluded: chain j residue 216 ILE Chi-restraints excluded: chain j residue 300 LEU Chi-restraints excluded: chain j residue 311 VAL Chi-restraints excluded: chain j residue 406 ILE Chi-restraints excluded: chain j residue 415 LEU Chi-restraints excluded: chain j residue 442 THR Chi-restraints excluded: chain j residue 472 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 876 random chunks: chunk 516 optimal weight: 0.9980 chunk 831 optimal weight: 6.9990 chunk 507 optimal weight: 9.9990 chunk 394 optimal weight: 20.0000 chunk 578 optimal weight: 9.9990 chunk 872 optimal weight: 6.9990 chunk 803 optimal weight: 20.0000 chunk 694 optimal weight: 0.0570 chunk 72 optimal weight: 0.9980 chunk 536 optimal weight: 10.0000 chunk 426 optimal weight: 2.9990 overall best weight: 2.4102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 164 GLN Y 110 ASN ** N 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 364 ASN ** U 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 337 HIS ** a 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 337 HIS ** d 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 119 GLN f 364 ASN f 409 HIS j 100 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 72114 Z= 0.201 Angle : 0.568 14.855 97848 Z= 0.294 Chirality : 0.042 0.408 10404 Planarity : 0.004 0.056 12912 Dihedral : 4.591 60.585 9660 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.59 % Favored : 95.26 % Rotamer: Outliers : 2.94 % Allowed : 19.39 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.09), residues: 8814 helix: 1.83 (0.08), residues: 4038 sheet: 0.50 (0.16), residues: 1188 loop : -1.10 (0.10), residues: 3588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP F 111 HIS 0.010 0.001 HIS f 409 PHE 0.031 0.001 PHE h 506 TYR 0.014 0.001 TYR h 419 ARG 0.010 0.000 ARG A 95 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17628 Ramachandran restraints generated. 8814 Oldfield, 0 Emsley, 8814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17628 Ramachandran restraints generated. 8814 Oldfield, 0 Emsley, 8814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1724 residues out of total 7380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 217 poor density : 1507 time to evaluate : 6.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 57 GLN cc_start: 0.8029 (OUTLIER) cc_final: 0.6795 (pt0) REVERT: C 123 LYS cc_start: 0.7994 (mmtm) cc_final: 0.7717 (mmtm) REVERT: A 27 GLN cc_start: 0.8767 (OUTLIER) cc_final: 0.7767 (pp30) REVERT: A 57 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.7400 (pm20) REVERT: A 61 PHE cc_start: 0.7351 (t80) cc_final: 0.7062 (t80) REVERT: D 6 ASN cc_start: 0.8280 (OUTLIER) cc_final: 0.8072 (p0) REVERT: M 56 ASP cc_start: 0.7746 (m-30) cc_final: 0.7415 (m-30) REVERT: P 56 ASP cc_start: 0.7976 (m-30) cc_final: 0.7629 (m-30) REVERT: S 126 LYS cc_start: 0.9115 (tttp) cc_final: 0.8843 (tttt) REVERT: V 127 GLU cc_start: 0.7771 (pp20) cc_final: 0.7506 (pp20) REVERT: Y 29 ASP cc_start: 0.7226 (m-30) cc_final: 0.6898 (m-30) REVERT: b 13 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7078 (mp0) REVERT: N 1 MET cc_start: 0.5860 (ttt) cc_final: 0.5161 (ttt) REVERT: W 8 LYS cc_start: 0.8959 (ttpp) cc_final: 0.8700 (ttpp) REVERT: W 41 ARG cc_start: 0.7669 (tpp80) cc_final: 0.7233 (mmm-85) REVERT: Z 71 GLN cc_start: 0.8021 (mp10) cc_final: 0.7813 (mm-40) REVERT: c 42 ASP cc_start: 0.8114 (t70) cc_final: 0.7854 (t0) REVERT: H 41 ARG cc_start: 0.7743 (tpp80) cc_final: 0.7208 (tpp80) REVERT: H 143 GLU cc_start: 0.8279 (mm-30) cc_final: 0.8011 (mm-30) REVERT: J 8 LYS cc_start: 0.8923 (ttpp) cc_final: 0.8676 (ttpp) REVERT: J 41 ARG cc_start: 0.7587 (tpp80) cc_final: 0.7244 (mmm-85) REVERT: J 42 ASP cc_start: 0.8717 (t0) cc_final: 0.8387 (t0) REVERT: L 1 MET cc_start: 0.4920 (ttt) cc_final: 0.4669 (ttt) REVERT: L 42 ASP cc_start: 0.8154 (t70) cc_final: 0.7900 (t0) REVERT: O 101 ASP cc_start: 0.8673 (m-30) cc_final: 0.8464 (m-30) REVERT: O 129 MET cc_start: 0.8287 (mtp) cc_final: 0.7999 (mtp) REVERT: O 161 MET cc_start: 0.8586 (tpt) cc_final: 0.8283 (mmt) REVERT: O 171 GLU cc_start: 0.7899 (tt0) cc_final: 0.7594 (tm-30) REVERT: R 162 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8219 (mp0) REVERT: R 337 HIS cc_start: 0.8278 (m90) cc_final: 0.7865 (m90) REVERT: R 419 TYR cc_start: 0.8828 (m-80) cc_final: 0.8455 (m-80) REVERT: R 446 GLN cc_start: 0.8563 (mp10) cc_final: 0.8218 (mp10) REVERT: R 486 ARG cc_start: 0.6635 (ttp80) cc_final: 0.6404 (tmt-80) REVERT: R 501 GLU cc_start: 0.8495 (pt0) cc_final: 0.8274 (pp20) REVERT: U 101 ASP cc_start: 0.8578 (m-30) cc_final: 0.8342 (m-30) REVERT: U 114 CYS cc_start: 0.8583 (m) cc_final: 0.8377 (m) REVERT: U 142 LYS cc_start: 0.7605 (tptp) cc_final: 0.7237 (tptp) REVERT: U 186 PHE cc_start: 0.8204 (m-80) cc_final: 0.7888 (m-80) REVERT: U 312 ASP cc_start: 0.7845 (t0) cc_final: 0.7529 (t0) REVERT: U 346 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7588 (mm-30) REVERT: U 404 GLU cc_start: 0.8177 (tp30) cc_final: 0.7897 (tp30) REVERT: U 475 ARG cc_start: 0.8641 (ttp80) cc_final: 0.8032 (tmm-80) REVERT: X 216 ILE cc_start: 0.9501 (mt) cc_final: 0.8923 (tp) REVERT: X 250 LYS cc_start: 0.8825 (mmmm) cc_final: 0.8539 (mmmm) REVERT: X 424 LYS cc_start: 0.8100 (tptt) cc_final: 0.7881 (tptt) REVERT: a 100 GLN cc_start: 0.9104 (tp40) cc_final: 0.8814 (tp40) REVERT: a 101 ASP cc_start: 0.8663 (m-30) cc_final: 0.8164 (m-30) REVERT: a 171 GLU cc_start: 0.8255 (tm-30) cc_final: 0.7959 (tm-30) REVERT: a 195 TYR cc_start: 0.7604 (t80) cc_final: 0.7137 (t80) REVERT: a 239 TYR cc_start: 0.8837 (m-80) cc_final: 0.8344 (m-80) REVERT: a 404 GLU cc_start: 0.8227 (tp30) cc_final: 0.7926 (tp30) REVERT: d 132 GLU cc_start: 0.8239 (tp30) cc_final: 0.7756 (tp30) REVERT: d 216 ILE cc_start: 0.9458 (mt) cc_final: 0.8981 (tp) REVERT: d 240 GLU cc_start: 0.8485 (tp30) cc_final: 0.8112 (tp30) REVERT: d 292 ARG cc_start: 0.8320 (tpt90) cc_final: 0.7962 (tpt90) REVERT: d 470 ASP cc_start: 0.8956 (p0) cc_final: 0.8390 (p0) REVERT: d 519 GLU cc_start: 0.8414 (tp30) cc_final: 0.8053 (tp30) REVERT: e 239 TYR cc_start: 0.8477 (m-80) cc_final: 0.7966 (m-80) REVERT: e 466 VAL cc_start: 0.8958 (t) cc_final: 0.8722 (p) REVERT: f 250 LYS cc_start: 0.8534 (mtpt) cc_final: 0.8110 (tttm) REVERT: f 282 ARG cc_start: 0.8514 (mtm180) cc_final: 0.7877 (mtm-85) REVERT: f 337 HIS cc_start: 0.8291 (m90) cc_final: 0.7872 (m90) REVERT: f 424 LYS cc_start: 0.8160 (tptt) cc_final: 0.7926 (tptt) REVERT: f 446 GLN cc_start: 0.8497 (mp10) cc_final: 0.8198 (mp10) REVERT: f 454 LYS cc_start: 0.8726 (mttp) cc_final: 0.8389 (mttp) REVERT: f 464 SER cc_start: 0.8790 (m) cc_final: 0.8415 (p) REVERT: f 501 GLU cc_start: 0.7548 (pp20) cc_final: 0.7182 (pp20) REVERT: g 100 GLN cc_start: 0.9104 (tp40) cc_final: 0.8891 (tp40) REVERT: g 142 LYS cc_start: 0.7416 (tptp) cc_final: 0.7153 (tptp) REVERT: g 159 ARG cc_start: 0.8102 (mmm-85) cc_final: 0.7621 (mmm-85) REVERT: g 160 ASP cc_start: 0.8973 (t0) cc_final: 0.8524 (t0) REVERT: g 195 TYR cc_start: 0.7828 (t80) cc_final: 0.7013 (t80) REVERT: g 381 LEU cc_start: 0.9165 (mp) cc_final: 0.8912 (mp) REVERT: h 101 ASP cc_start: 0.8523 (m-30) cc_final: 0.8290 (m-30) REVERT: h 161 MET cc_start: 0.8214 (mmt) cc_final: 0.7855 (mmt) REVERT: h 240 GLU cc_start: 0.7413 (tm-30) cc_final: 0.6869 (tm-30) REVERT: h 250 LYS cc_start: 0.8570 (mmmt) cc_final: 0.8202 (tttm) REVERT: h 292 ARG cc_start: 0.8394 (tpt90) cc_final: 0.8107 (tpt90) REVERT: h 337 HIS cc_start: 0.8040 (m-70) cc_final: 0.7717 (m90) REVERT: h 406 ILE cc_start: 0.9258 (mm) cc_final: 0.8906 (tp) REVERT: h 424 LYS cc_start: 0.8363 (tptt) cc_final: 0.8129 (tptt) REVERT: h 454 LYS cc_start: 0.8604 (mtmm) cc_final: 0.8361 (mtmp) REVERT: h 498 MET cc_start: 0.7505 (mmp) cc_final: 0.6970 (mmp) REVERT: i 101 ASP cc_start: 0.8690 (m-30) cc_final: 0.8175 (m-30) REVERT: i 159 ARG cc_start: 0.8203 (mmp80) cc_final: 0.7708 (mmp-170) REVERT: i 161 MET cc_start: 0.8480 (mmt) cc_final: 0.8143 (ttp) REVERT: i 346 GLU cc_start: 0.7720 (mp0) cc_final: 0.7021 (mp0) REVERT: i 475 ARG cc_start: 0.8557 (ttp-170) cc_final: 0.8081 (ptt180) REVERT: j 240 GLU cc_start: 0.8564 (tp30) cc_final: 0.8132 (tp30) REVERT: j 454 LYS cc_start: 0.8689 (mtmm) cc_final: 0.8399 (mttp) outliers start: 217 outliers final: 201 residues processed: 1617 average time/residue: 0.6559 time to fit residues: 1801.8321 Evaluate side-chains 1675 residues out of total 7380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 1468 time to evaluate : 6.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 57 GLN Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain C residue 106 PHE Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain A residue 27 GLN Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 57 GLN Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain B residue 10 MET Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain D residue 6 ASN Chi-restraints excluded: chain D residue 10 MET Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 106 PHE Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain E residue 6 ASN Chi-restraints excluded: chain E residue 10 MET Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 85 MET Chi-restraints excluded: chain E residue 106 PHE Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 6 ASN Chi-restraints excluded: chain F residue 32 ASP Chi-restraints excluded: chain F residue 42 GLU Chi-restraints excluded: chain F residue 55 ARG Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 106 PHE Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain M residue 49 ILE Chi-restraints excluded: chain M residue 65 ASP Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 90 SER Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain M residue 148 HIS Chi-restraints excluded: chain M residue 181 ILE Chi-restraints excluded: chain P residue 48 THR Chi-restraints excluded: chain P residue 65 ASP Chi-restraints excluded: chain P residue 76 VAL Chi-restraints excluded: chain P residue 90 SER Chi-restraints excluded: chain P residue 125 VAL Chi-restraints excluded: chain P residue 181 ILE Chi-restraints excluded: chain S residue 6 LEU Chi-restraints excluded: chain S residue 23 GLU Chi-restraints excluded: chain S residue 90 SER Chi-restraints excluded: chain S residue 102 VAL Chi-restraints excluded: chain S residue 167 ARG Chi-restraints excluded: chain S residue 181 ILE Chi-restraints excluded: chain V residue 49 ILE Chi-restraints excluded: chain V residue 54 LEU Chi-restraints excluded: chain V residue 65 ASP Chi-restraints excluded: chain V residue 69 ASP Chi-restraints excluded: chain V residue 90 SER Chi-restraints excluded: chain Y residue 54 LEU Chi-restraints excluded: chain Y residue 65 ASP Chi-restraints excluded: chain Y residue 90 SER Chi-restraints excluded: chain Y residue 125 VAL Chi-restraints excluded: chain Y residue 166 ILE Chi-restraints excluded: chain b residue 13 GLU Chi-restraints excluded: chain b residue 65 ASP Chi-restraints excluded: chain b residue 69 ASP Chi-restraints excluded: chain b residue 90 SER Chi-restraints excluded: chain b residue 100 THR Chi-restraints excluded: chain b residue 102 VAL Chi-restraints excluded: chain b residue 127 GLU Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 118 THR Chi-restraints excluded: chain N residue 129 SER Chi-restraints excluded: chain N residue 153 THR Chi-restraints excluded: chain Q residue 25 VAL Chi-restraints excluded: chain Q residue 39 SER Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain T residue 97 GLU Chi-restraints excluded: chain T residue 129 SER Chi-restraints excluded: chain T residue 153 THR Chi-restraints excluded: chain W residue 3 ILE Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 69 THR Chi-restraints excluded: chain W residue 85 THR Chi-restraints excluded: chain W residue 108 LYS Chi-restraints excluded: chain W residue 130 VAL Chi-restraints excluded: chain Z residue 6 GLU Chi-restraints excluded: chain Z residue 7 HIS Chi-restraints excluded: chain Z residue 153 THR Chi-restraints excluded: chain c residue 25 VAL Chi-restraints excluded: chain c residue 72 VAL Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 7 HIS Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 129 SER Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 66 SER Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain I residue 7 HIS Chi-restraints excluded: chain I residue 54 GLU Chi-restraints excluded: chain I residue 90 ILE Chi-restraints excluded: chain I residue 129 SER Chi-restraints excluded: chain I residue 150 VAL Chi-restraints excluded: chain I residue 153 THR Chi-restraints excluded: chain J residue 25 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 123 GLU Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain K residue 7 HIS Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 72 VAL Chi-restraints excluded: chain O residue 141 LEU Chi-restraints excluded: chain O residue 150 ASP Chi-restraints excluded: chain O residue 259 VAL Chi-restraints excluded: chain O residue 308 THR Chi-restraints excluded: chain O residue 321 GLU Chi-restraints excluded: chain O residue 336 ASN Chi-restraints excluded: chain O residue 391 THR Chi-restraints excluded: chain R residue 162 GLU Chi-restraints excluded: chain R residue 167 ASP Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 300 LEU Chi-restraints excluded: chain R residue 306 THR Chi-restraints excluded: chain R residue 339 VAL Chi-restraints excluded: chain R residue 409 HIS Chi-restraints excluded: chain R residue 415 LEU Chi-restraints excluded: chain R residue 418 HIS Chi-restraints excluded: chain R residue 476 LEU Chi-restraints excluded: chain U residue 148 LEU Chi-restraints excluded: chain U residue 156 ILE Chi-restraints excluded: chain U residue 357 ASP Chi-restraints excluded: chain U residue 485 ASN Chi-restraints excluded: chain X residue 299 LEU Chi-restraints excluded: chain X residue 339 VAL Chi-restraints excluded: chain X residue 380 LEU Chi-restraints excluded: chain X residue 398 SER Chi-restraints excluded: chain X residue 442 THR Chi-restraints excluded: chain X residue 472 VAL Chi-restraints excluded: chain a residue 105 SER Chi-restraints excluded: chain a residue 141 LEU Chi-restraints excluded: chain a residue 148 LEU Chi-restraints excluded: chain a residue 167 ASP Chi-restraints excluded: chain a residue 256 LEU Chi-restraints excluded: chain a residue 302 MET Chi-restraints excluded: chain a residue 357 ASP Chi-restraints excluded: chain d residue 162 GLU Chi-restraints excluded: chain d residue 167 ASP Chi-restraints excluded: chain d residue 300 LEU Chi-restraints excluded: chain d residue 471 GLU Chi-restraints excluded: chain e residue 259 VAL Chi-restraints excluded: chain e residue 308 THR Chi-restraints excluded: chain e residue 336 ASN Chi-restraints excluded: chain e residue 383 THR Chi-restraints excluded: chain e residue 404 GLU Chi-restraints excluded: chain e residue 507 GLU Chi-restraints excluded: chain f residue 162 GLU Chi-restraints excluded: chain f residue 167 ASP Chi-restraints excluded: chain f residue 187 VAL Chi-restraints excluded: chain f residue 306 THR Chi-restraints excluded: chain f residue 346 GLU Chi-restraints excluded: chain f residue 409 HIS Chi-restraints excluded: chain f residue 476 LEU Chi-restraints excluded: chain g residue 97 THR Chi-restraints excluded: chain g residue 155 LEU Chi-restraints excluded: chain g residue 156 ILE Chi-restraints excluded: chain g residue 187 VAL Chi-restraints excluded: chain g residue 357 ASP Chi-restraints excluded: chain h residue 167 ASP Chi-restraints excluded: chain h residue 183 ILE Chi-restraints excluded: chain h residue 216 ILE Chi-restraints excluded: chain h residue 380 LEU Chi-restraints excluded: chain h residue 398 SER Chi-restraints excluded: chain h residue 442 THR Chi-restraints excluded: chain h residue 472 VAL Chi-restraints excluded: chain h residue 476 LEU Chi-restraints excluded: chain i residue 141 LEU Chi-restraints excluded: chain i residue 237 HIS Chi-restraints excluded: chain i residue 336 ASN Chi-restraints excluded: chain i residue 357 ASP Chi-restraints excluded: chain i residue 380 LEU Chi-restraints excluded: chain j residue 167 ASP Chi-restraints excluded: chain j residue 187 VAL Chi-restraints excluded: chain j residue 216 ILE Chi-restraints excluded: chain j residue 300 LEU Chi-restraints excluded: chain j residue 311 VAL Chi-restraints excluded: chain j residue 415 LEU Chi-restraints excluded: chain j residue 442 THR Chi-restraints excluded: chain j residue 472 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 876 random chunks: chunk 552 optimal weight: 10.0000 chunk 740 optimal weight: 9.9990 chunk 212 optimal weight: 5.9990 chunk 640 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 chunk 193 optimal weight: 8.9990 chunk 696 optimal weight: 2.9990 chunk 291 optimal weight: 7.9990 chunk 714 optimal weight: 8.9990 chunk 88 optimal weight: 4.9990 chunk 128 optimal weight: 0.0970 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 164 GLN Y 110 ASN ** N 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 364 ASN ** U 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 337 HIS ** a 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 337 HIS d 173 ASN f 364 ASN f 409 HIS g 350 GLN j 100 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.128749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.094450 restraints weight = 132694.498| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.81 r_work: 0.3114 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 72114 Z= 0.192 Angle : 0.568 14.572 97848 Z= 0.293 Chirality : 0.042 0.360 10404 Planarity : 0.004 0.056 12912 Dihedral : 4.523 59.376 9660 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.75 % Favored : 95.10 % Rotamer: Outliers : 3.05 % Allowed : 19.46 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.09), residues: 8814 helix: 1.83 (0.08), residues: 4038 sheet: 0.46 (0.17), residues: 1080 loop : -1.03 (0.10), residues: 3696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP F 111 HIS 0.007 0.001 HIS f 409 PHE 0.031 0.001 PHE h 506 TYR 0.014 0.001 TYR H 137 ARG 0.009 0.000 ARG L 26 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25070.99 seconds wall clock time: 436 minutes 3.95 seconds (26163.95 seconds total)