Starting phenix.real_space_refine on Thu Mar 21 17:09:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8egs_28129/03_2024/8egs_28129.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8egs_28129/03_2024/8egs_28129.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8egs_28129/03_2024/8egs_28129.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8egs_28129/03_2024/8egs_28129.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8egs_28129/03_2024/8egs_28129.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8egs_28129/03_2024/8egs_28129.pdb" } resolution = 3.92 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 108 5.16 5 C 19506 2.51 5 N 5154 2.21 5 O 5928 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "J ASP 192": "OD1" <-> "OD2" Residue "J TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 185": "OD1" <-> "OD2" Residue "I ASP 187": "OD1" <-> "OD2" Residue "Y GLU 39": "OE1" <-> "OE2" Residue "Y PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 64": "OE1" <-> "OE2" Residue "Y ASP 82": "OD1" <-> "OD2" Residue "Y PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 96": "OE1" <-> "OE2" Residue "Y TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 130": "OE1" <-> "OE2" Residue "Y GLU 166": "OE1" <-> "OE2" Residue "Y ASP 180": "OD1" <-> "OD2" Residue "Y GLU 190": "OE1" <-> "OE2" Residue "Y GLU 216": "OE1" <-> "OE2" Residue "Y GLU 276": "OE1" <-> "OE2" Residue "Y GLU 285": "OE1" <-> "OE2" Residue "Y GLU 297": "OE1" <-> "OE2" Residue "Y TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 310": "OE1" <-> "OE2" Residue "Y TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 322": "OD1" <-> "OD2" Residue "Y GLU 328": "OE1" <-> "OE2" Residue "Y ASP 352": "OD1" <-> "OD2" Residue "Y ASP 366": "OD1" <-> "OD2" Residue "Y ASP 372": "OD1" <-> "OD2" Residue "Y PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 504": "OD1" <-> "OD2" Residue "Y GLU 518": "OE1" <-> "OE2" Residue "Y TYR 544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 550": "OD1" <-> "OD2" Residue "Y GLU 562": "OE1" <-> "OE2" Residue "Y PHE 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 192": "OD1" <-> "OD2" Residue "A TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 185": "OD1" <-> "OD2" Residue "B ASP 187": "OD1" <-> "OD2" Residue "C GLU 39": "OE1" <-> "OE2" Residue "C PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 64": "OE1" <-> "OE2" Residue "C ASP 82": "OD1" <-> "OD2" Residue "C PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 96": "OE1" <-> "OE2" Residue "C TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 130": "OE1" <-> "OE2" Residue "C GLU 166": "OE1" <-> "OE2" Residue "C ASP 180": "OD1" <-> "OD2" Residue "C GLU 190": "OE1" <-> "OE2" Residue "C GLU 216": "OE1" <-> "OE2" Residue "C GLU 276": "OE1" <-> "OE2" Residue "C GLU 285": "OE1" <-> "OE2" Residue "C GLU 297": "OE1" <-> "OE2" Residue "C TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 310": "OE1" <-> "OE2" Residue "C TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 322": "OD1" <-> "OD2" Residue "C GLU 328": "OE1" <-> "OE2" Residue "C ASP 352": "OD1" <-> "OD2" Residue "C ASP 366": "OD1" <-> "OD2" Residue "C ASP 372": "OD1" <-> "OD2" Residue "C PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 504": "OD1" <-> "OD2" Residue "C GLU 518": "OE1" <-> "OE2" Residue "C TYR 544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 550": "OD1" <-> "OD2" Residue "C GLU 562": "OE1" <-> "OE2" Residue "C PHE 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 192": "OD1" <-> "OD2" Residue "D TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 185": "OD1" <-> "OD2" Residue "E ASP 187": "OD1" <-> "OD2" Residue "F GLU 39": "OE1" <-> "OE2" Residue "F PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 64": "OE1" <-> "OE2" Residue "F ASP 82": "OD1" <-> "OD2" Residue "F PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 96": "OE1" <-> "OE2" Residue "F TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 130": "OE1" <-> "OE2" Residue "F GLU 166": "OE1" <-> "OE2" Residue "F ASP 180": "OD1" <-> "OD2" Residue "F GLU 190": "OE1" <-> "OE2" Residue "F GLU 216": "OE1" <-> "OE2" Residue "F GLU 276": "OE1" <-> "OE2" Residue "F GLU 285": "OE1" <-> "OE2" Residue "F GLU 297": "OE1" <-> "OE2" Residue "F TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 310": "OE1" <-> "OE2" Residue "F TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 322": "OD1" <-> "OD2" Residue "F GLU 328": "OE1" <-> "OE2" Residue "F ASP 352": "OD1" <-> "OD2" Residue "F ASP 366": "OD1" <-> "OD2" Residue "F ASP 372": "OD1" <-> "OD2" Residue "F PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 504": "OD1" <-> "OD2" Residue "F GLU 518": "OE1" <-> "OE2" Residue "F TYR 544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 550": "OD1" <-> "OD2" Residue "F GLU 562": "OE1" <-> "OE2" Residue "F PHE 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 192": "OD1" <-> "OD2" Residue "G TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 185": "OD1" <-> "OD2" Residue "H ASP 187": "OD1" <-> "OD2" Residue "K GLU 39": "OE1" <-> "OE2" Residue "K PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 64": "OE1" <-> "OE2" Residue "K ASP 82": "OD1" <-> "OD2" Residue "K PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 96": "OE1" <-> "OE2" Residue "K TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 130": "OE1" <-> "OE2" Residue "K GLU 166": "OE1" <-> "OE2" Residue "K ASP 180": "OD1" <-> "OD2" Residue "K GLU 190": "OE1" <-> "OE2" Residue "K GLU 216": "OE1" <-> "OE2" Residue "K GLU 276": "OE1" <-> "OE2" Residue "K GLU 285": "OE1" <-> "OE2" Residue "K GLU 297": "OE1" <-> "OE2" Residue "K TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 310": "OE1" <-> "OE2" Residue "K TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 322": "OD1" <-> "OD2" Residue "K GLU 328": "OE1" <-> "OE2" Residue "K ASP 352": "OD1" <-> "OD2" Residue "K ASP 366": "OD1" <-> "OD2" Residue "K ASP 372": "OD1" <-> "OD2" Residue "K PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 504": "OD1" <-> "OD2" Residue "K GLU 518": "OE1" <-> "OE2" Residue "K TYR 544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 550": "OD1" <-> "OD2" Residue "K GLU 562": "OE1" <-> "OE2" Residue "K PHE 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 192": "OD1" <-> "OD2" Residue "L TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 185": "OD1" <-> "OD2" Residue "M ASP 187": "OD1" <-> "OD2" Residue "N GLU 39": "OE1" <-> "OE2" Residue "N PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 64": "OE1" <-> "OE2" Residue "N ASP 82": "OD1" <-> "OD2" Residue "N PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 96": "OE1" <-> "OE2" Residue "N TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 130": "OE1" <-> "OE2" Residue "N GLU 166": "OE1" <-> "OE2" Residue "N ASP 180": "OD1" <-> "OD2" Residue "N GLU 190": "OE1" <-> "OE2" Residue "N GLU 216": "OE1" <-> "OE2" Residue "N GLU 276": "OE1" <-> "OE2" Residue "N GLU 285": "OE1" <-> "OE2" Residue "N GLU 297": "OE1" <-> "OE2" Residue "N TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 310": "OE1" <-> "OE2" Residue "N TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 322": "OD1" <-> "OD2" Residue "N GLU 328": "OE1" <-> "OE2" Residue "N ASP 352": "OD1" <-> "OD2" Residue "N ASP 366": "OD1" <-> "OD2" Residue "N ASP 372": "OD1" <-> "OD2" Residue "N PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 504": "OD1" <-> "OD2" Residue "N GLU 518": "OE1" <-> "OE2" Residue "N TYR 544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 550": "OD1" <-> "OD2" Residue "N GLU 562": "OE1" <-> "OE2" Residue "N PHE 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 192": "OD1" <-> "OD2" Residue "O TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 185": "OD1" <-> "OD2" Residue "P ASP 187": "OD1" <-> "OD2" Residue "Q GLU 39": "OE1" <-> "OE2" Residue "Q PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 64": "OE1" <-> "OE2" Residue "Q ASP 82": "OD1" <-> "OD2" Residue "Q PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 96": "OE1" <-> "OE2" Residue "Q TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 130": "OE1" <-> "OE2" Residue "Q GLU 166": "OE1" <-> "OE2" Residue "Q ASP 180": "OD1" <-> "OD2" Residue "Q GLU 190": "OE1" <-> "OE2" Residue "Q GLU 216": "OE1" <-> "OE2" Residue "Q GLU 276": "OE1" <-> "OE2" Residue "Q GLU 285": "OE1" <-> "OE2" Residue "Q GLU 297": "OE1" <-> "OE2" Residue "Q TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 310": "OE1" <-> "OE2" Residue "Q TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 322": "OD1" <-> "OD2" Residue "Q GLU 328": "OE1" <-> "OE2" Residue "Q ASP 352": "OD1" <-> "OD2" Residue "Q ASP 366": "OD1" <-> "OD2" Residue "Q ASP 372": "OD1" <-> "OD2" Residue "Q PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 504": "OD1" <-> "OD2" Residue "Q GLU 518": "OE1" <-> "OE2" Residue "Q TYR 544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 550": "OD1" <-> "OD2" Residue "Q GLU 562": "OE1" <-> "OE2" Residue "Q PHE 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 30696 Number of models: 1 Model: "" Number of chains: 18 Chain: "J" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 153 Classifications: {'peptide': 20} Link IDs: {'PTRANS': 1, 'TRANS': 18} Chain: "I" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 153 Classifications: {'peptide': 20} Link IDs: {'PTRANS': 1, 'TRANS': 18} Chain: "Y" Number of atoms: 4810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 586, 4810 Classifications: {'peptide': 586} Link IDs: {'PTRANS': 22, 'TRANS': 563} Chain: "A" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 153 Classifications: {'peptide': 20} Link IDs: {'PTRANS': 1, 'TRANS': 18} Chain: "B" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 153 Classifications: {'peptide': 20} Link IDs: {'PTRANS': 1, 'TRANS': 18} Chain: "C" Number of atoms: 4810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 586, 4810 Classifications: {'peptide': 586} Link IDs: {'PTRANS': 22, 'TRANS': 563} Chain: "D" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 153 Classifications: {'peptide': 20} Link IDs: {'PTRANS': 1, 'TRANS': 18} Chain: "E" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 153 Classifications: {'peptide': 20} Link IDs: {'PTRANS': 1, 'TRANS': 18} Chain: "F" Number of atoms: 4810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 586, 4810 Classifications: {'peptide': 586} Link IDs: {'PTRANS': 22, 'TRANS': 563} Chain: "G" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 153 Classifications: {'peptide': 20} Link IDs: {'PTRANS': 1, 'TRANS': 18} Chain: "H" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 153 Classifications: {'peptide': 20} Link IDs: {'PTRANS': 1, 'TRANS': 18} Chain: "K" Number of atoms: 4810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 586, 4810 Classifications: {'peptide': 586} Link IDs: {'PTRANS': 22, 'TRANS': 563} Chain: "L" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 153 Classifications: {'peptide': 20} Link IDs: {'PTRANS': 1, 'TRANS': 18} Chain: "M" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 153 Classifications: {'peptide': 20} Link IDs: {'PTRANS': 1, 'TRANS': 18} Chain: "N" Number of atoms: 4810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 586, 4810 Classifications: {'peptide': 586} Link IDs: {'PTRANS': 22, 'TRANS': 563} Chain: "O" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 153 Classifications: {'peptide': 20} Link IDs: {'PTRANS': 1, 'TRANS': 18} Chain: "P" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 153 Classifications: {'peptide': 20} Link IDs: {'PTRANS': 1, 'TRANS': 18} Chain: "Q" Number of atoms: 4810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 586, 4810 Classifications: {'peptide': 586} Link IDs: {'PTRANS': 22, 'TRANS': 563} Time building chain proxies: 16.03, per 1000 atoms: 0.52 Number of scatterers: 30696 At special positions: 0 Unit cell: (110.224, 110.224, 171.312, 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 108 16.00 O 5928 8.00 N 5154 7.00 C 19506 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: 12.96 Conformation dependent library (CDL) restraints added in 6.0 seconds 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7224 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 48 sheets defined 27.3% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.89 Creating SS restraints... Processing helix chain 'Y' and resid 28 through 38 Processing helix chain 'Y' and resid 67 through 72 Processing helix chain 'Y' and resid 110 through 116 Processing helix chain 'Y' and resid 119 through 124 Processing helix chain 'Y' and resid 135 through 148 Proline residue: Y 144 - end of helix Processing helix chain 'Y' and resid 200 through 204 removed outlier: 4.389A pdb=" N TYR Y 203 " --> pdb=" O THR Y 200 " (cutoff:3.500A) Processing helix chain 'Y' and resid 214 through 226 removed outlier: 4.138A pdb=" N ASN Y 219 " --> pdb=" O ARG Y 215 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASN Y 220 " --> pdb=" O GLU Y 216 " (cutoff:3.500A) Processing helix chain 'Y' and resid 228 through 234 removed outlier: 3.562A pdb=" N THR Y 232 " --> pdb=" O TYR Y 228 " (cutoff:3.500A) Processing helix chain 'Y' and resid 283 through 291 Processing helix chain 'Y' and resid 295 through 302 removed outlier: 4.578A pdb=" N HIS Y 300 " --> pdb=" O GLU Y 297 " (cutoff:3.500A) Processing helix chain 'Y' and resid 398 through 406 Processing helix chain 'Y' and resid 417 through 420 removed outlier: 4.004A pdb=" N ASN Y 420 " --> pdb=" O ASN Y 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 417 through 420' Processing helix chain 'Y' and resid 425 through 438 Processing helix chain 'Y' and resid 445 through 450 removed outlier: 3.716A pdb=" N SER Y 449 " --> pdb=" O THR Y 445 " (cutoff:3.500A) Processing helix chain 'Y' and resid 454 through 462 removed outlier: 3.599A pdb=" N ARG Y 462 " --> pdb=" O TYR Y 458 " (cutoff:3.500A) Processing helix chain 'Y' and resid 482 through 488 removed outlier: 3.515A pdb=" N ILE Y 486 " --> pdb=" O ASN Y 482 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN Y 488 " --> pdb=" O PHE Y 484 " (cutoff:3.500A) Processing helix chain 'Y' and resid 501 through 516 Processing helix chain 'Y' and resid 550 through 564 Processing helix chain 'Y' and resid 580 through 584 Processing helix chain 'C' and resid 28 through 38 Processing helix chain 'C' and resid 67 through 72 Processing helix chain 'C' and resid 110 through 116 Processing helix chain 'C' and resid 119 through 124 Processing helix chain 'C' and resid 135 through 148 Proline residue: C 144 - end of helix Processing helix chain 'C' and resid 200 through 204 removed outlier: 4.389A pdb=" N TYR C 203 " --> pdb=" O THR C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 226 removed outlier: 4.138A pdb=" N ASN C 219 " --> pdb=" O ARG C 215 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASN C 220 " --> pdb=" O GLU C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 234 removed outlier: 3.562A pdb=" N THR C 232 " --> pdb=" O TYR C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 291 Processing helix chain 'C' and resid 295 through 302 removed outlier: 4.578A pdb=" N HIS C 300 " --> pdb=" O GLU C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 406 Processing helix chain 'C' and resid 417 through 420 removed outlier: 4.004A pdb=" N ASN C 420 " --> pdb=" O ASN C 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 417 through 420' Processing helix chain 'C' and resid 425 through 438 Processing helix chain 'C' and resid 445 through 450 removed outlier: 3.716A pdb=" N SER C 449 " --> pdb=" O THR C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 462 removed outlier: 3.600A pdb=" N ARG C 462 " --> pdb=" O TYR C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 488 removed outlier: 3.515A pdb=" N ILE C 486 " --> pdb=" O ASN C 482 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN C 488 " --> pdb=" O PHE C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 516 Processing helix chain 'C' and resid 550 through 564 Processing helix chain 'C' and resid 580 through 584 Processing helix chain 'F' and resid 28 through 38 Processing helix chain 'F' and resid 67 through 72 Processing helix chain 'F' and resid 110 through 116 Processing helix chain 'F' and resid 119 through 124 Processing helix chain 'F' and resid 135 through 148 Proline residue: F 144 - end of helix Processing helix chain 'F' and resid 200 through 204 removed outlier: 4.389A pdb=" N TYR F 203 " --> pdb=" O THR F 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 226 removed outlier: 4.138A pdb=" N ASN F 219 " --> pdb=" O ARG F 215 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASN F 220 " --> pdb=" O GLU F 216 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 234 removed outlier: 3.562A pdb=" N THR F 232 " --> pdb=" O TYR F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 283 through 291 Processing helix chain 'F' and resid 295 through 302 removed outlier: 4.578A pdb=" N HIS F 300 " --> pdb=" O GLU F 297 " (cutoff:3.500A) Processing helix chain 'F' and resid 398 through 406 Processing helix chain 'F' and resid 417 through 420 removed outlier: 4.003A pdb=" N ASN F 420 " --> pdb=" O ASN F 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 417 through 420' Processing helix chain 'F' and resid 425 through 438 Processing helix chain 'F' and resid 445 through 450 removed outlier: 3.716A pdb=" N SER F 449 " --> pdb=" O THR F 445 " (cutoff:3.500A) Processing helix chain 'F' and resid 454 through 462 removed outlier: 3.600A pdb=" N ARG F 462 " --> pdb=" O TYR F 458 " (cutoff:3.500A) Processing helix chain 'F' and resid 482 through 488 removed outlier: 3.516A pdb=" N ILE F 486 " --> pdb=" O ASN F 482 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN F 488 " --> pdb=" O PHE F 484 " (cutoff:3.500A) Processing helix chain 'F' and resid 501 through 516 Processing helix chain 'F' and resid 550 through 564 Processing helix chain 'F' and resid 580 through 584 Processing helix chain 'K' and resid 28 through 38 Processing helix chain 'K' and resid 67 through 72 Processing helix chain 'K' and resid 110 through 116 Processing helix chain 'K' and resid 119 through 124 Processing helix chain 'K' and resid 135 through 148 Proline residue: K 144 - end of helix Processing helix chain 'K' and resid 200 through 204 removed outlier: 4.389A pdb=" N TYR K 203 " --> pdb=" O THR K 200 " (cutoff:3.500A) Processing helix chain 'K' and resid 214 through 226 removed outlier: 4.138A pdb=" N ASN K 219 " --> pdb=" O ARG K 215 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASN K 220 " --> pdb=" O GLU K 216 " (cutoff:3.500A) Processing helix chain 'K' and resid 228 through 234 removed outlier: 3.562A pdb=" N THR K 232 " --> pdb=" O TYR K 228 " (cutoff:3.500A) Processing helix chain 'K' and resid 283 through 291 Processing helix chain 'K' and resid 295 through 302 removed outlier: 4.578A pdb=" N HIS K 300 " --> pdb=" O GLU K 297 " (cutoff:3.500A) Processing helix chain 'K' and resid 398 through 406 Processing helix chain 'K' and resid 417 through 420 removed outlier: 4.004A pdb=" N ASN K 420 " --> pdb=" O ASN K 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 417 through 420' Processing helix chain 'K' and resid 425 through 438 Processing helix chain 'K' and resid 445 through 450 removed outlier: 3.716A pdb=" N SER K 449 " --> pdb=" O THR K 445 " (cutoff:3.500A) Processing helix chain 'K' and resid 454 through 462 removed outlier: 3.599A pdb=" N ARG K 462 " --> pdb=" O TYR K 458 " (cutoff:3.500A) Processing helix chain 'K' and resid 482 through 488 removed outlier: 3.515A pdb=" N ILE K 486 " --> pdb=" O ASN K 482 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN K 488 " --> pdb=" O PHE K 484 " (cutoff:3.500A) Processing helix chain 'K' and resid 501 through 516 Processing helix chain 'K' and resid 550 through 564 Processing helix chain 'K' and resid 580 through 584 Processing helix chain 'N' and resid 28 through 38 Processing helix chain 'N' and resid 67 through 72 Processing helix chain 'N' and resid 110 through 116 Processing helix chain 'N' and resid 119 through 124 Processing helix chain 'N' and resid 135 through 148 Proline residue: N 144 - end of helix Processing helix chain 'N' and resid 200 through 204 removed outlier: 4.389A pdb=" N TYR N 203 " --> pdb=" O THR N 200 " (cutoff:3.500A) Processing helix chain 'N' and resid 214 through 226 removed outlier: 4.138A pdb=" N ASN N 219 " --> pdb=" O ARG N 215 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASN N 220 " --> pdb=" O GLU N 216 " (cutoff:3.500A) Processing helix chain 'N' and resid 228 through 234 removed outlier: 3.562A pdb=" N THR N 232 " --> pdb=" O TYR N 228 " (cutoff:3.500A) Processing helix chain 'N' and resid 283 through 291 Processing helix chain 'N' and resid 295 through 302 removed outlier: 4.578A pdb=" N HIS N 300 " --> pdb=" O GLU N 297 " (cutoff:3.500A) Processing helix chain 'N' and resid 398 through 406 Processing helix chain 'N' and resid 417 through 420 removed outlier: 4.004A pdb=" N ASN N 420 " --> pdb=" O ASN N 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 417 through 420' Processing helix chain 'N' and resid 425 through 438 Processing helix chain 'N' and resid 445 through 450 removed outlier: 3.716A pdb=" N SER N 449 " --> pdb=" O THR N 445 " (cutoff:3.500A) Processing helix chain 'N' and resid 454 through 462 removed outlier: 3.600A pdb=" N ARG N 462 " --> pdb=" O TYR N 458 " (cutoff:3.500A) Processing helix chain 'N' and resid 482 through 488 removed outlier: 3.515A pdb=" N ILE N 486 " --> pdb=" O ASN N 482 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN N 488 " --> pdb=" O PHE N 484 " (cutoff:3.500A) Processing helix chain 'N' and resid 501 through 516 Processing helix chain 'N' and resid 550 through 564 Processing helix chain 'N' and resid 580 through 584 Processing helix chain 'Q' and resid 28 through 38 Processing helix chain 'Q' and resid 67 through 72 Processing helix chain 'Q' and resid 110 through 116 Processing helix chain 'Q' and resid 119 through 124 Processing helix chain 'Q' and resid 135 through 148 Proline residue: Q 144 - end of helix Processing helix chain 'Q' and resid 200 through 204 removed outlier: 4.389A pdb=" N TYR Q 203 " --> pdb=" O THR Q 200 " (cutoff:3.500A) Processing helix chain 'Q' and resid 214 through 226 removed outlier: 4.138A pdb=" N ASN Q 219 " --> pdb=" O ARG Q 215 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASN Q 220 " --> pdb=" O GLU Q 216 " (cutoff:3.500A) Processing helix chain 'Q' and resid 228 through 234 removed outlier: 3.562A pdb=" N THR Q 232 " --> pdb=" O TYR Q 228 " (cutoff:3.500A) Processing helix chain 'Q' and resid 283 through 291 Processing helix chain 'Q' and resid 295 through 302 removed outlier: 4.578A pdb=" N HIS Q 300 " --> pdb=" O GLU Q 297 " (cutoff:3.500A) Processing helix chain 'Q' and resid 398 through 406 Processing helix chain 'Q' and resid 417 through 420 removed outlier: 4.003A pdb=" N ASN Q 420 " --> pdb=" O ASN Q 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 417 through 420' Processing helix chain 'Q' and resid 425 through 438 Processing helix chain 'Q' and resid 445 through 450 removed outlier: 3.716A pdb=" N SER Q 449 " --> pdb=" O THR Q 445 " (cutoff:3.500A) Processing helix chain 'Q' and resid 454 through 462 removed outlier: 3.600A pdb=" N ARG Q 462 " --> pdb=" O TYR Q 458 " (cutoff:3.500A) Processing helix chain 'Q' and resid 482 through 488 removed outlier: 3.516A pdb=" N ILE Q 486 " --> pdb=" O ASN Q 482 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN Q 488 " --> pdb=" O PHE Q 484 " (cutoff:3.500A) Processing helix chain 'Q' and resid 501 through 516 Processing helix chain 'Q' and resid 550 through 564 Processing helix chain 'Q' and resid 580 through 584 Processing sheet with id= 1, first strand: chain 'Y' and resid 44 through 46 removed outlier: 4.327A pdb=" N TYR Y 76 " --> pdb=" O PHE Y 12 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'Y' and resid 22 through 25 removed outlier: 6.394A pdb=" N THR Y 23 " --> pdb=" O TRP Y 568 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE Y 567 " --> pdb=" O ASN Y 536 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'Y' and resid 61 through 63 removed outlier: 3.753A pdb=" N LEU Y 63 " --> pdb=" O THR Y 103 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR Y 103 " --> pdb=" O LEU Y 63 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL Y 102 " --> pdb=" O VAL Y 98 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL Y 98 " --> pdb=" O VAL Y 102 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'Y' and resid 158 through 165 removed outlier: 6.603A pdb=" N ILE Y 497 " --> pdb=" O LEU Y 161 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ASN Y 163 " --> pdb=" O MET Y 495 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N MET Y 495 " --> pdb=" O ASN Y 163 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'Y' and resid 235 through 237 removed outlier: 3.667A pdb=" N LYS Y 237 " --> pdb=" O GLN Y 176 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'Y' and resid 235 through 237 removed outlier: 3.667A pdb=" N LYS Y 237 " --> pdb=" O GLN Y 176 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N LEU Y 210 " --> pdb=" O LEU Y 266 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU Y 266 " --> pdb=" O LEU Y 210 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'Y' and resid 281 through 282 removed outlier: 3.680A pdb=" N VAL Y 282 " --> pdb=" O VAL Y 332 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'Y' and resid 413 through 415 Processing sheet with id= 9, first strand: chain 'C' and resid 44 through 46 removed outlier: 4.327A pdb=" N TYR C 76 " --> pdb=" O PHE C 12 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'C' and resid 22 through 25 removed outlier: 6.394A pdb=" N THR C 23 " --> pdb=" O TRP C 568 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE C 567 " --> pdb=" O ASN C 536 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'C' and resid 61 through 63 removed outlier: 3.753A pdb=" N LEU C 63 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR C 103 " --> pdb=" O LEU C 63 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL C 102 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL C 98 " --> pdb=" O VAL C 102 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'C' and resid 158 through 165 removed outlier: 6.604A pdb=" N ILE C 497 " --> pdb=" O LEU C 161 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ASN C 163 " --> pdb=" O MET C 495 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N MET C 495 " --> pdb=" O ASN C 163 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'C' and resid 235 through 237 removed outlier: 3.667A pdb=" N LYS C 237 " --> pdb=" O GLN C 176 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'C' and resid 235 through 237 removed outlier: 3.667A pdb=" N LYS C 237 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N LEU C 210 " --> pdb=" O LEU C 266 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU C 266 " --> pdb=" O LEU C 210 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'C' and resid 281 through 282 removed outlier: 3.679A pdb=" N VAL C 282 " --> pdb=" O VAL C 332 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'C' and resid 413 through 415 Processing sheet with id= 17, first strand: chain 'F' and resid 44 through 46 removed outlier: 4.328A pdb=" N TYR F 76 " --> pdb=" O PHE F 12 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'F' and resid 22 through 25 removed outlier: 6.394A pdb=" N THR F 23 " --> pdb=" O TRP F 568 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE F 567 " --> pdb=" O ASN F 536 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'F' and resid 61 through 63 removed outlier: 3.753A pdb=" N LEU F 63 " --> pdb=" O THR F 103 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR F 103 " --> pdb=" O LEU F 63 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL F 102 " --> pdb=" O VAL F 98 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL F 98 " --> pdb=" O VAL F 102 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'F' and resid 158 through 165 removed outlier: 6.603A pdb=" N ILE F 497 " --> pdb=" O LEU F 161 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ASN F 163 " --> pdb=" O MET F 495 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N MET F 495 " --> pdb=" O ASN F 163 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'F' and resid 235 through 237 removed outlier: 3.666A pdb=" N LYS F 237 " --> pdb=" O GLN F 176 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'F' and resid 235 through 237 removed outlier: 3.666A pdb=" N LYS F 237 " --> pdb=" O GLN F 176 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N LEU F 210 " --> pdb=" O LEU F 266 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU F 266 " --> pdb=" O LEU F 210 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'F' and resid 281 through 282 removed outlier: 3.679A pdb=" N VAL F 282 " --> pdb=" O VAL F 332 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'F' and resid 413 through 415 Processing sheet with id= 25, first strand: chain 'K' and resid 44 through 46 removed outlier: 4.327A pdb=" N TYR K 76 " --> pdb=" O PHE K 12 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'K' and resid 22 through 25 removed outlier: 6.394A pdb=" N THR K 23 " --> pdb=" O TRP K 568 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE K 567 " --> pdb=" O ASN K 536 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'K' and resid 61 through 63 removed outlier: 3.753A pdb=" N LEU K 63 " --> pdb=" O THR K 103 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR K 103 " --> pdb=" O LEU K 63 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL K 102 " --> pdb=" O VAL K 98 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL K 98 " --> pdb=" O VAL K 102 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'K' and resid 158 through 165 removed outlier: 6.603A pdb=" N ILE K 497 " --> pdb=" O LEU K 161 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ASN K 163 " --> pdb=" O MET K 495 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N MET K 495 " --> pdb=" O ASN K 163 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'K' and resid 235 through 237 removed outlier: 3.667A pdb=" N LYS K 237 " --> pdb=" O GLN K 176 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'K' and resid 235 through 237 removed outlier: 3.667A pdb=" N LYS K 237 " --> pdb=" O GLN K 176 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N LEU K 210 " --> pdb=" O LEU K 266 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU K 266 " --> pdb=" O LEU K 210 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'K' and resid 281 through 282 removed outlier: 3.680A pdb=" N VAL K 282 " --> pdb=" O VAL K 332 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'K' and resid 413 through 415 Processing sheet with id= 33, first strand: chain 'N' and resid 44 through 46 removed outlier: 4.327A pdb=" N TYR N 76 " --> pdb=" O PHE N 12 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'N' and resid 22 through 25 removed outlier: 6.394A pdb=" N THR N 23 " --> pdb=" O TRP N 568 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE N 567 " --> pdb=" O ASN N 536 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'N' and resid 61 through 63 removed outlier: 3.753A pdb=" N LEU N 63 " --> pdb=" O THR N 103 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR N 103 " --> pdb=" O LEU N 63 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL N 102 " --> pdb=" O VAL N 98 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL N 98 " --> pdb=" O VAL N 102 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'N' and resid 158 through 165 removed outlier: 6.604A pdb=" N ILE N 497 " --> pdb=" O LEU N 161 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ASN N 163 " --> pdb=" O MET N 495 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N MET N 495 " --> pdb=" O ASN N 163 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'N' and resid 235 through 237 removed outlier: 3.667A pdb=" N LYS N 237 " --> pdb=" O GLN N 176 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'N' and resid 235 through 237 removed outlier: 3.667A pdb=" N LYS N 237 " --> pdb=" O GLN N 176 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N LEU N 210 " --> pdb=" O LEU N 266 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU N 266 " --> pdb=" O LEU N 210 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'N' and resid 281 through 282 removed outlier: 3.679A pdb=" N VAL N 282 " --> pdb=" O VAL N 332 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'N' and resid 413 through 415 Processing sheet with id= 41, first strand: chain 'Q' and resid 44 through 46 removed outlier: 4.328A pdb=" N TYR Q 76 " --> pdb=" O PHE Q 12 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'Q' and resid 22 through 25 removed outlier: 6.394A pdb=" N THR Q 23 " --> pdb=" O TRP Q 568 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE Q 567 " --> pdb=" O ASN Q 536 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'Q' and resid 61 through 63 removed outlier: 3.753A pdb=" N LEU Q 63 " --> pdb=" O THR Q 103 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR Q 103 " --> pdb=" O LEU Q 63 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL Q 102 " --> pdb=" O VAL Q 98 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL Q 98 " --> pdb=" O VAL Q 102 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'Q' and resid 158 through 165 removed outlier: 6.603A pdb=" N ILE Q 497 " --> pdb=" O LEU Q 161 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ASN Q 163 " --> pdb=" O MET Q 495 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N MET Q 495 " --> pdb=" O ASN Q 163 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'Q' and resid 235 through 237 removed outlier: 3.666A pdb=" N LYS Q 237 " --> pdb=" O GLN Q 176 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'Q' and resid 235 through 237 removed outlier: 3.666A pdb=" N LYS Q 237 " --> pdb=" O GLN Q 176 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N LEU Q 210 " --> pdb=" O LEU Q 266 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU Q 266 " --> pdb=" O LEU Q 210 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'Q' and resid 281 through 282 removed outlier: 3.680A pdb=" N VAL Q 282 " --> pdb=" O VAL Q 332 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'Q' and resid 413 through 415 882 hydrogen bonds defined for protein. 2250 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: 10.85 Time building geometry restraints manager: 13.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 10092 1.34 - 1.46: 6743 1.46 - 1.58: 14317 1.58 - 1.69: 6 1.69 - 1.81: 204 Bond restraints: 31362 Sorted by residual: bond pdb=" CB PRO B 178 " pdb=" CG PRO B 178 " ideal model delta sigma weight residual 1.492 1.627 -0.135 5.00e-02 4.00e+02 7.31e+00 bond pdb=" CB PRO M 178 " pdb=" CG PRO M 178 " ideal model delta sigma weight residual 1.492 1.627 -0.135 5.00e-02 4.00e+02 7.31e+00 bond pdb=" CB PRO E 178 " pdb=" CG PRO E 178 " ideal model delta sigma weight residual 1.492 1.627 -0.135 5.00e-02 4.00e+02 7.30e+00 bond pdb=" CB PRO P 178 " pdb=" CG PRO P 178 " ideal model delta sigma weight residual 1.492 1.627 -0.135 5.00e-02 4.00e+02 7.30e+00 bond pdb=" CB PRO I 178 " pdb=" CG PRO I 178 " ideal model delta sigma weight residual 1.492 1.627 -0.135 5.00e-02 4.00e+02 7.30e+00 ... (remaining 31357 not shown) Histogram of bond angle deviations from ideal: 100.07 - 106.86: 760 106.86 - 113.64: 16908 113.64 - 120.43: 11944 120.43 - 127.21: 12652 127.21 - 134.00: 264 Bond angle restraints: 42528 Sorted by residual: angle pdb=" CA PRO E 178 " pdb=" N PRO E 178 " pdb=" CD PRO E 178 " ideal model delta sigma weight residual 112.00 103.26 8.74 1.40e+00 5.10e-01 3.89e+01 angle pdb=" CA PRO P 178 " pdb=" N PRO P 178 " pdb=" CD PRO P 178 " ideal model delta sigma weight residual 112.00 103.26 8.74 1.40e+00 5.10e-01 3.89e+01 angle pdb=" CA PRO H 178 " pdb=" N PRO H 178 " pdb=" CD PRO H 178 " ideal model delta sigma weight residual 112.00 103.28 8.72 1.40e+00 5.10e-01 3.88e+01 angle pdb=" CA PRO I 178 " pdb=" N PRO I 178 " pdb=" CD PRO I 178 " ideal model delta sigma weight residual 112.00 103.28 8.72 1.40e+00 5.10e-01 3.88e+01 angle pdb=" CA PRO B 178 " pdb=" N PRO B 178 " pdb=" CD PRO B 178 " ideal model delta sigma weight residual 112.00 103.28 8.72 1.40e+00 5.10e-01 3.88e+01 ... (remaining 42523 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 16616 17.98 - 35.96: 1864 35.96 - 53.93: 336 53.93 - 71.91: 48 71.91 - 89.89: 12 Dihedral angle restraints: 18876 sinusoidal: 7698 harmonic: 11178 Sorted by residual: dihedral pdb=" CA TYR C 312 " pdb=" C TYR C 312 " pdb=" N SER C 313 " pdb=" CA SER C 313 " ideal model delta harmonic sigma weight residual 180.00 161.62 18.38 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA TYR N 312 " pdb=" C TYR N 312 " pdb=" N SER N 313 " pdb=" CA SER N 313 " ideal model delta harmonic sigma weight residual 180.00 161.62 18.38 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA TYR Q 312 " pdb=" C TYR Q 312 " pdb=" N SER Q 313 " pdb=" CA SER Q 313 " ideal model delta harmonic sigma weight residual 180.00 161.64 18.36 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 18873 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 3045 0.029 - 0.059: 1080 0.059 - 0.088: 211 0.088 - 0.117: 232 0.117 - 0.146: 76 Chirality restraints: 4644 Sorted by residual: chirality pdb=" CA ILE C 95 " pdb=" N ILE C 95 " pdb=" C ILE C 95 " pdb=" CB ILE C 95 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.35e-01 chirality pdb=" CA ILE N 95 " pdb=" N ILE N 95 " pdb=" C ILE N 95 " pdb=" CB ILE N 95 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.35e-01 chirality pdb=" CA ILE K 95 " pdb=" N ILE K 95 " pdb=" C ILE K 95 " pdb=" CB ILE K 95 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.15e-01 ... (remaining 4641 not shown) Planarity restraints: 5568 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU P 177 " 0.058 5.00e-02 4.00e+02 8.24e-02 1.09e+01 pdb=" N PRO P 178 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO P 178 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO P 178 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 177 " 0.058 5.00e-02 4.00e+02 8.24e-02 1.09e+01 pdb=" N PRO E 178 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO E 178 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO E 178 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU H 177 " -0.058 5.00e-02 4.00e+02 8.22e-02 1.08e+01 pdb=" N PRO H 178 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO H 178 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO H 178 " -0.045 5.00e-02 4.00e+02 ... (remaining 5565 not shown) Histogram of nonbonded interaction distances: 0.36 - 1.27: 234 1.27 - 2.17: 870 2.17 - 3.08: 25566 3.08 - 3.99: 77661 3.99 - 4.90: 145092 Warning: very small nonbonded interaction distances. Nonbonded interactions: 249423 Sorted by model distance: nonbonded pdb=" CD LYS D 181 " pdb=" CD2 TYR H 193 " model vdw 0.357 3.740 nonbonded pdb=" CD2 TYR I 193 " pdb=" CD LYS O 181 " model vdw 0.357 3.740 nonbonded pdb=" CD LYS L 181 " pdb=" CD2 TYR P 193 " model vdw 0.357 3.740 nonbonded pdb=" CD LYS A 181 " pdb=" CD2 TYR E 193 " model vdw 0.357 3.740 nonbonded pdb=" CD LYS J 181 " pdb=" CD2 TYR B 193 " model vdw 0.358 3.740 ... (remaining 249418 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 'D' selection = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'L' selection = chain 'M' selection = chain 'O' selection = chain 'P' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'K' selection = chain 'N' selection = chain 'Q' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.140 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: 0.020 Extract box with map and model: 13.790 Check model and map are aligned: 0.510 Set scattering table: 0.320 Process input model: 82.220 Find NCS groups from input model: 2.110 Set up NCS constraints: 0.230 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:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 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 0.135 31362 Z= 0.223 Angle : 0.570 8.737 42528 Z= 0.323 Chirality : 0.039 0.146 4644 Planarity : 0.004 0.082 5568 Dihedral : 14.973 89.889 11652 Min Nonbonded Distance : 0.357 Molprobity Statistics. All-atom Clashscore : 27.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.35 % Allowed : 19.30 % Favored : 80.35 % 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: -0.21 (0.14), residues: 3720 helix: 1.32 (0.20), residues: 792 sheet: 0.46 (0.22), residues: 684 loop : -0.90 (0.13), residues: 2244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 275 HIS 0.004 0.001 HIS K 101 PHE 0.018 0.002 PHE Q 432 TYR 0.011 0.001 TYR K 455 ARG 0.006 0.001 ARG Y 56 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 502 time to evaluate : 3.440 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 577 MET cc_start: 0.7311 (ttm) cc_final: 0.7053 (ttm) REVERT: C 338 SER cc_start: 0.8612 (m) cc_final: 0.8214 (p) REVERT: K 577 MET cc_start: 0.7292 (ttm) cc_final: 0.7041 (ttm) REVERT: N 338 SER cc_start: 0.8623 (m) cc_final: 0.8227 (p) outliers start: 12 outliers final: 4 residues processed: 514 average time/residue: 0.3785 time to fit residues: 321.1397 Evaluate side-chains 438 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 434 time to evaluate : 3.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 55 ILE Chi-restraints excluded: chain Y residue 354 ASN Chi-restraints excluded: chain K residue 55 ILE Chi-restraints excluded: chain K residue 354 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 314 optimal weight: 5.9990 chunk 281 optimal weight: 2.9990 chunk 156 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 190 optimal weight: 5.9990 chunk 150 optimal weight: 1.9990 chunk 291 optimal weight: 7.9990 chunk 112 optimal weight: 0.5980 chunk 177 optimal weight: 0.9980 chunk 217 optimal weight: 1.9990 chunk 337 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 72 GLN Y 126 ASN Y 343 HIS Y 378 ASN ** Y 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 441 ASN ** Y 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 509 GLN B 179 GLN ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 GLN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 ASN C 343 HIS C 378 ASN ** C 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 441 ASN ** C 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 509 GLN E 179 GLN ** F 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 72 GLN ** F 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 126 ASN F 343 HIS F 378 ASN ** F 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 441 ASN ** F 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 509 GLN ** K 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 72 GLN K 126 ASN K 343 HIS K 378 ASN ** K 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 441 ASN ** K 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 509 GLN M 179 GLN ** N 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 72 GLN ** N 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 126 ASN N 343 HIS N 378 ASN ** N 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 441 ASN ** N 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 509 GLN P 179 GLN ** Q 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 72 GLN ** Q 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 126 ASN Q 343 HIS Q 378 ASN ** Q 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 441 ASN ** Q 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 509 GLN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 31362 Z= 0.301 Angle : 0.697 8.332 42528 Z= 0.372 Chirality : 0.045 0.195 4644 Planarity : 0.005 0.057 5568 Dihedral : 5.725 36.393 4106 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 5.16 % Allowed : 16.70 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.13), residues: 3720 helix: 0.32 (0.18), residues: 840 sheet: 0.05 (0.21), residues: 714 loop : -1.23 (0.13), residues: 2166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 68 HIS 0.005 0.001 HIS Q 300 PHE 0.013 0.002 PHE K 586 TYR 0.028 0.002 TYR K 342 ARG 0.011 0.001 ARG K 541 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 714 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 536 time to evaluate : 3.732 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: J 180 SER cc_start: 0.8198 (OUTLIER) cc_final: 0.7713 (p) REVERT: Y 213 MET cc_start: 0.8510 (ptm) cc_final: 0.8074 (ptm) REVERT: Y 488 ASN cc_start: 0.7751 (m-40) cc_final: 0.7422 (m-40) REVERT: A 180 SER cc_start: 0.7904 (OUTLIER) cc_final: 0.7522 (p) REVERT: C 105 MET cc_start: 0.8298 (mtp) cc_final: 0.8001 (mtp) REVERT: C 338 SER cc_start: 0.8620 (m) cc_final: 0.8377 (p) REVERT: C 555 GLU cc_start: 0.6962 (tp30) cc_final: 0.6568 (tp30) REVERT: D 180 SER cc_start: 0.8059 (OUTLIER) cc_final: 0.7717 (p) REVERT: F 105 MET cc_start: 0.7951 (mtp) cc_final: 0.7747 (mtp) REVERT: F 168 PHE cc_start: 0.7956 (OUTLIER) cc_final: 0.7055 (p90) REVERT: F 377 LEU cc_start: 0.7547 (OUTLIER) cc_final: 0.7224 (mp) REVERT: F 455 TYR cc_start: 0.6528 (t80) cc_final: 0.6213 (t80) REVERT: G 180 SER cc_start: 0.8199 (OUTLIER) cc_final: 0.7713 (p) REVERT: K 213 MET cc_start: 0.8508 (ptm) cc_final: 0.8049 (ptm) REVERT: K 488 ASN cc_start: 0.7752 (m-40) cc_final: 0.7430 (m-40) REVERT: L 180 SER cc_start: 0.7899 (OUTLIER) cc_final: 0.7526 (p) REVERT: N 105 MET cc_start: 0.8285 (mtp) cc_final: 0.8008 (mtp) REVERT: N 338 SER cc_start: 0.8625 (m) cc_final: 0.8368 (p) REVERT: N 555 GLU cc_start: 0.6973 (tp30) cc_final: 0.6593 (tp30) REVERT: O 180 SER cc_start: 0.8061 (OUTLIER) cc_final: 0.7777 (p) REVERT: Q 105 MET cc_start: 0.7960 (mtp) cc_final: 0.7755 (mtp) REVERT: Q 168 PHE cc_start: 0.7960 (OUTLIER) cc_final: 0.7057 (p90) REVERT: Q 377 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.7242 (mp) REVERT: Q 455 TYR cc_start: 0.6529 (t80) cc_final: 0.6192 (t80) outliers start: 178 outliers final: 80 residues processed: 652 average time/residue: 0.4151 time to fit residues: 431.9576 Evaluate side-chains 526 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 436 time to evaluate : 3.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 180 SER Chi-restraints excluded: chain Y residue 18 THR Chi-restraints excluded: chain Y residue 55 ILE Chi-restraints excluded: chain Y residue 59 ASN Chi-restraints excluded: chain Y residue 123 THR Chi-restraints excluded: chain Y residue 152 VAL Chi-restraints excluded: chain Y residue 153 ILE Chi-restraints excluded: chain Y residue 168 PHE Chi-restraints excluded: chain Y residue 212 VAL Chi-restraints excluded: chain Y residue 226 SER Chi-restraints excluded: chain Y residue 256 THR Chi-restraints excluded: chain Y residue 344 ASN Chi-restraints excluded: chain Y residue 563 THR Chi-restraints excluded: chain Y residue 565 VAL Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 226 SER Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 290 MET Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 565 VAL Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain F residue 14 ASN Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 168 PHE Chi-restraints excluded: chain F residue 204 ILE Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 226 SER Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain F residue 256 THR Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 391 ILE Chi-restraints excluded: chain F residue 563 THR Chi-restraints excluded: chain F residue 565 VAL Chi-restraints excluded: chain G residue 180 SER Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 55 ILE Chi-restraints excluded: chain K residue 59 ASN Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 152 VAL Chi-restraints excluded: chain K residue 153 ILE Chi-restraints excluded: chain K residue 168 PHE Chi-restraints excluded: chain K residue 212 VAL Chi-restraints excluded: chain K residue 226 SER Chi-restraints excluded: chain K residue 256 THR Chi-restraints excluded: chain K residue 344 ASN Chi-restraints excluded: chain K residue 563 THR Chi-restraints excluded: chain K residue 565 VAL Chi-restraints excluded: chain L residue 180 SER Chi-restraints excluded: chain M residue 185 ASP Chi-restraints excluded: chain N residue 18 THR Chi-restraints excluded: chain N residue 95 ILE Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain N residue 153 ILE Chi-restraints excluded: chain N residue 168 PHE Chi-restraints excluded: chain N residue 212 VAL Chi-restraints excluded: chain N residue 226 SER Chi-restraints excluded: chain N residue 232 THR Chi-restraints excluded: chain N residue 256 THR Chi-restraints excluded: chain N residue 290 MET Chi-restraints excluded: chain N residue 563 THR Chi-restraints excluded: chain N residue 565 VAL Chi-restraints excluded: chain O residue 180 SER Chi-restraints excluded: chain P residue 185 ASP Chi-restraints excluded: chain Q residue 14 ASN Chi-restraints excluded: chain Q residue 18 THR Chi-restraints excluded: chain Q residue 77 CYS Chi-restraints excluded: chain Q residue 95 ILE Chi-restraints excluded: chain Q residue 168 PHE Chi-restraints excluded: chain Q residue 204 ILE Chi-restraints excluded: chain Q residue 212 VAL Chi-restraints excluded: chain Q residue 226 SER Chi-restraints excluded: chain Q residue 232 THR Chi-restraints excluded: chain Q residue 241 ILE Chi-restraints excluded: chain Q residue 256 THR Chi-restraints excluded: chain Q residue 377 LEU Chi-restraints excluded: chain Q residue 391 ILE Chi-restraints excluded: chain Q residue 563 THR Chi-restraints excluded: chain Q residue 565 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 187 optimal weight: 4.9990 chunk 104 optimal weight: 0.7980 chunk 281 optimal weight: 0.6980 chunk 230 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 338 optimal weight: 4.9990 chunk 365 optimal weight: 5.9990 chunk 301 optimal weight: 5.9990 chunk 335 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 271 optimal weight: 7.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 72 GLN Y 126 ASN ** Y 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 378 ASN ** Y 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 402 GLN ** Y 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 GLN A 183 ASN ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 ASN C 219 ASN C 378 ASN ** C 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 378 ASN ** F 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 72 GLN K 126 ASN ** K 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 378 ASN ** K 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 402 GLN ** K 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 179 GLN L 183 ASN ** N 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 126 ASN N 219 ASN N 378 ASN ** N 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 219 ASN Q 378 ASN ** Q 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.051 31362 Z= 0.525 Angle : 0.729 8.067 42528 Z= 0.385 Chirality : 0.047 0.191 4644 Planarity : 0.005 0.051 5568 Dihedral : 5.878 43.230 4102 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 6.46 % Allowed : 16.84 % Favored : 76.70 % 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: -1.29 (0.13), residues: 3720 helix: -0.26 (0.17), residues: 870 sheet: -0.05 (0.21), residues: 744 loop : -1.44 (0.13), residues: 2106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 532 HIS 0.006 0.002 HIS Q 25 PHE 0.030 0.003 PHE F 54 TYR 0.027 0.002 TYR Y 457 ARG 0.013 0.001 ARG F 541 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 454 time to evaluate : 3.922 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: Y 6 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8628 (mt) REVERT: Y 115 TYR cc_start: 0.8355 (m-80) cc_final: 0.8060 (m-10) REVERT: Y 159 TYR cc_start: 0.9005 (OUTLIER) cc_final: 0.8626 (p90) REVERT: Y 213 MET cc_start: 0.8699 (ptm) cc_final: 0.8282 (ptm) REVERT: C 105 MET cc_start: 0.8311 (mtp) cc_final: 0.8058 (mtp) REVERT: C 159 TYR cc_start: 0.9055 (OUTLIER) cc_final: 0.8843 (p90) REVERT: C 555 GLU cc_start: 0.6870 (tp30) cc_final: 0.6625 (tp30) REVERT: D 181 LYS cc_start: 0.7538 (mmtm) cc_final: 0.7167 (tppt) REVERT: F 168 PHE cc_start: 0.8262 (OUTLIER) cc_final: 0.6889 (p90) REVERT: K 6 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8472 (mt) REVERT: K 115 TYR cc_start: 0.8347 (m-80) cc_final: 0.8043 (m-10) REVERT: K 159 TYR cc_start: 0.9003 (OUTLIER) cc_final: 0.8619 (p90) REVERT: K 213 MET cc_start: 0.8693 (ptm) cc_final: 0.8265 (ptm) REVERT: N 105 MET cc_start: 0.8300 (mtp) cc_final: 0.8060 (mtp) REVERT: N 159 TYR cc_start: 0.9053 (OUTLIER) cc_final: 0.8843 (p90) REVERT: N 555 GLU cc_start: 0.6865 (tp30) cc_final: 0.6611 (tp30) REVERT: Q 168 PHE cc_start: 0.8268 (OUTLIER) cc_final: 0.6889 (p90) REVERT: Q 219 ASN cc_start: 0.6795 (m-40) cc_final: 0.6586 (m-40) outliers start: 223 outliers final: 144 residues processed: 612 average time/residue: 0.4236 time to fit residues: 430.6979 Evaluate side-chains 552 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 400 time to evaluate : 3.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 177 LEU Chi-restraints excluded: chain J residue 179 GLN Chi-restraints excluded: chain I residue 185 ASP Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 18 THR Chi-restraints excluded: chain Y residue 55 ILE Chi-restraints excluded: chain Y residue 59 ASN Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 123 THR Chi-restraints excluded: chain Y residue 152 VAL Chi-restraints excluded: chain Y residue 153 ILE Chi-restraints excluded: chain Y residue 159 TYR Chi-restraints excluded: chain Y residue 168 PHE Chi-restraints excluded: chain Y residue 204 ILE Chi-restraints excluded: chain Y residue 212 VAL Chi-restraints excluded: chain Y residue 226 SER Chi-restraints excluded: chain Y residue 232 THR Chi-restraints excluded: chain Y residue 256 THR Chi-restraints excluded: chain Y residue 375 SER Chi-restraints excluded: chain Y residue 421 ASN Chi-restraints excluded: chain Y residue 459 LYS Chi-restraints excluded: chain Y residue 468 LEU Chi-restraints excluded: chain Y residue 495 MET Chi-restraints excluded: chain Y residue 515 LEU Chi-restraints excluded: chain Y residue 519 THR Chi-restraints excluded: chain Y residue 559 VAL Chi-restraints excluded: chain Y residue 563 THR Chi-restraints excluded: chain Y residue 565 VAL Chi-restraints excluded: chain Y residue 586 PHE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain C residue 8 HIS Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 159 TYR Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 185 PHE Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 226 SER Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 290 MET Chi-restraints excluded: chain C residue 339 ILE Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 421 ASN Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain C residue 547 ASP Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 179 GLN Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain F residue 14 ASN Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 168 PHE Chi-restraints excluded: chain F residue 204 ILE Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 226 SER Chi-restraints excluded: chain F residue 256 THR Chi-restraints excluded: chain F residue 391 ILE Chi-restraints excluded: chain F residue 417 ASN Chi-restraints excluded: chain F residue 553 LEU Chi-restraints excluded: chain F residue 563 THR Chi-restraints excluded: chain F residue 565 VAL Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain G residue 179 GLN Chi-restraints excluded: chain H residue 185 ASP Chi-restraints excluded: chain K residue 6 LEU Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 55 ILE Chi-restraints excluded: chain K residue 59 ASN Chi-restraints excluded: chain K residue 102 VAL Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 152 VAL Chi-restraints excluded: chain K residue 153 ILE Chi-restraints excluded: chain K residue 159 TYR Chi-restraints excluded: chain K residue 168 PHE Chi-restraints excluded: chain K residue 204 ILE Chi-restraints excluded: chain K residue 212 VAL Chi-restraints excluded: chain K residue 226 SER Chi-restraints excluded: chain K residue 232 THR Chi-restraints excluded: chain K residue 256 THR Chi-restraints excluded: chain K residue 375 SER Chi-restraints excluded: chain K residue 421 ASN Chi-restraints excluded: chain K residue 459 LYS Chi-restraints excluded: chain K residue 468 LEU Chi-restraints excluded: chain K residue 495 MET Chi-restraints excluded: chain K residue 515 LEU Chi-restraints excluded: chain K residue 519 THR Chi-restraints excluded: chain K residue 559 VAL Chi-restraints excluded: chain K residue 563 THR Chi-restraints excluded: chain K residue 565 VAL Chi-restraints excluded: chain K residue 586 PHE Chi-restraints excluded: chain L residue 177 LEU Chi-restraints excluded: chain M residue 185 ASP Chi-restraints excluded: chain N residue 8 HIS Chi-restraints excluded: chain N residue 18 THR Chi-restraints excluded: chain N residue 95 ILE Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain N residue 153 ILE Chi-restraints excluded: chain N residue 159 TYR Chi-restraints excluded: chain N residue 168 PHE Chi-restraints excluded: chain N residue 185 PHE Chi-restraints excluded: chain N residue 204 ILE Chi-restraints excluded: chain N residue 212 VAL Chi-restraints excluded: chain N residue 226 SER Chi-restraints excluded: chain N residue 256 THR Chi-restraints excluded: chain N residue 280 LEU Chi-restraints excluded: chain N residue 290 MET Chi-restraints excluded: chain N residue 339 ILE Chi-restraints excluded: chain N residue 375 SER Chi-restraints excluded: chain N residue 391 ILE Chi-restraints excluded: chain N residue 415 ILE Chi-restraints excluded: chain N residue 421 ASN Chi-restraints excluded: chain N residue 519 THR Chi-restraints excluded: chain N residue 547 ASP Chi-restraints excluded: chain N residue 563 THR Chi-restraints excluded: chain O residue 177 LEU Chi-restraints excluded: chain O residue 179 GLN Chi-restraints excluded: chain O residue 180 SER Chi-restraints excluded: chain P residue 185 ASP Chi-restraints excluded: chain Q residue 14 ASN Chi-restraints excluded: chain Q residue 18 THR Chi-restraints excluded: chain Q residue 77 CYS Chi-restraints excluded: chain Q residue 95 ILE Chi-restraints excluded: chain Q residue 102 VAL Chi-restraints excluded: chain Q residue 111 THR Chi-restraints excluded: chain Q residue 153 ILE Chi-restraints excluded: chain Q residue 168 PHE Chi-restraints excluded: chain Q residue 204 ILE Chi-restraints excluded: chain Q residue 212 VAL Chi-restraints excluded: chain Q residue 226 SER Chi-restraints excluded: chain Q residue 256 THR Chi-restraints excluded: chain Q residue 391 ILE Chi-restraints excluded: chain Q residue 417 ASN Chi-restraints excluded: chain Q residue 553 LEU Chi-restraints excluded: chain Q residue 563 THR Chi-restraints excluded: chain Q residue 565 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 334 optimal weight: 0.9980 chunk 254 optimal weight: 0.9990 chunk 175 optimal weight: 5.9990 chunk 37 optimal weight: 0.2980 chunk 161 optimal weight: 2.9990 chunk 227 optimal weight: 5.9990 chunk 339 optimal weight: 0.6980 chunk 359 optimal weight: 4.9990 chunk 177 optimal weight: 0.8980 chunk 321 optimal weight: 0.6980 chunk 96 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 72 GLN ** F 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 219 ASN ** F 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 402 GLN F 471 GLN ** F 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 72 GLN ** Q 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 402 GLN Q 471 GLN ** Q 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 31362 Z= 0.189 Angle : 0.570 7.415 42528 Z= 0.299 Chirality : 0.042 0.161 4644 Planarity : 0.004 0.048 5568 Dihedral : 5.433 46.854 4102 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 4.49 % Allowed : 19.16 % Favored : 76.35 % 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: -1.16 (0.13), residues: 3720 helix: -0.08 (0.17), residues: 870 sheet: 0.06 (0.21), residues: 714 loop : -1.39 (0.13), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 68 HIS 0.003 0.001 HIS C 300 PHE 0.018 0.002 PHE Q 54 TYR 0.020 0.001 TYR F 159 ARG 0.006 0.000 ARG Q 541 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 506 time to evaluate : 3.732 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: I 183 ASN cc_start: 0.7357 (t0) cc_final: 0.6363 (t0) REVERT: Y 115 TYR cc_start: 0.8322 (m-80) cc_final: 0.8066 (m-10) REVERT: Y 159 TYR cc_start: 0.8903 (OUTLIER) cc_final: 0.8541 (p90) REVERT: Y 213 MET cc_start: 0.8799 (ptm) cc_final: 0.8366 (ptm) REVERT: Y 222 MET cc_start: 0.7582 (tpp) cc_final: 0.7347 (tpp) REVERT: Y 376 PHE cc_start: 0.8369 (t80) cc_final: 0.7711 (t80) REVERT: Y 459 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.8168 (mmmm) REVERT: C 61 VAL cc_start: 0.8581 (OUTLIER) cc_final: 0.8247 (p) REVERT: C 219 ASN cc_start: 0.6494 (m-40) cc_final: 0.6227 (m-40) REVERT: C 376 PHE cc_start: 0.8294 (t80) cc_final: 0.7455 (t80) REVERT: C 515 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8287 (mm) REVERT: F 168 PHE cc_start: 0.7962 (OUTLIER) cc_final: 0.6885 (p90) REVERT: F 219 ASN cc_start: 0.5803 (m-40) cc_final: 0.5586 (m-40) REVERT: H 183 ASN cc_start: 0.7364 (t0) cc_final: 0.6397 (t0) REVERT: K 115 TYR cc_start: 0.8336 (m-80) cc_final: 0.8064 (m-10) REVERT: K 159 TYR cc_start: 0.8889 (OUTLIER) cc_final: 0.8533 (p90) REVERT: K 213 MET cc_start: 0.8802 (ptm) cc_final: 0.8358 (ptm) REVERT: K 222 MET cc_start: 0.7563 (tpp) cc_final: 0.7323 (tpp) REVERT: K 376 PHE cc_start: 0.8366 (t80) cc_final: 0.7715 (t80) REVERT: K 400 GLN cc_start: 0.5668 (mm110) cc_final: 0.5272 (mm-40) REVERT: K 459 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8243 (mmmm) REVERT: N 61 VAL cc_start: 0.8567 (OUTLIER) cc_final: 0.8241 (p) REVERT: N 219 ASN cc_start: 0.6495 (m-40) cc_final: 0.6213 (m-40) REVERT: N 376 PHE cc_start: 0.8284 (t80) cc_final: 0.7460 (t80) REVERT: N 515 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8289 (mm) REVERT: Q 168 PHE cc_start: 0.7966 (OUTLIER) cc_final: 0.6889 (p90) REVERT: Q 219 ASN cc_start: 0.6433 (m-40) cc_final: 0.6171 (m-40) outliers start: 155 outliers final: 87 residues processed: 609 average time/residue: 0.3538 time to fit residues: 357.2079 Evaluate side-chains 550 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 453 time to evaluate : 2.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 8 HIS Chi-restraints excluded: chain Y residue 55 ILE Chi-restraints excluded: chain Y residue 111 THR Chi-restraints excluded: chain Y residue 123 THR Chi-restraints excluded: chain Y residue 152 VAL Chi-restraints excluded: chain Y residue 159 TYR Chi-restraints excluded: chain Y residue 168 PHE Chi-restraints excluded: chain Y residue 212 VAL Chi-restraints excluded: chain Y residue 226 SER Chi-restraints excluded: chain Y residue 375 SER Chi-restraints excluded: chain Y residue 389 VAL Chi-restraints excluded: chain Y residue 415 ILE Chi-restraints excluded: chain Y residue 459 LYS Chi-restraints excluded: chain Y residue 563 THR Chi-restraints excluded: chain Y residue 586 PHE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 226 SER Chi-restraints excluded: chain C residue 255 LYS Chi-restraints excluded: chain C residue 339 ILE Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 495 MET Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain C residue 547 ASP Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain F residue 8 HIS Chi-restraints excluded: chain F residue 14 ASN Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 168 PHE Chi-restraints excluded: chain F residue 204 ILE Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 226 SER Chi-restraints excluded: chain F residue 336 THR Chi-restraints excluded: chain F residue 391 ILE Chi-restraints excluded: chain F residue 421 ASN Chi-restraints excluded: chain F residue 563 THR Chi-restraints excluded: chain K residue 8 HIS Chi-restraints excluded: chain K residue 102 VAL Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 152 VAL Chi-restraints excluded: chain K residue 159 TYR Chi-restraints excluded: chain K residue 168 PHE Chi-restraints excluded: chain K residue 212 VAL Chi-restraints excluded: chain K residue 226 SER Chi-restraints excluded: chain K residue 375 SER Chi-restraints excluded: chain K residue 389 VAL Chi-restraints excluded: chain K residue 415 ILE Chi-restraints excluded: chain K residue 459 LYS Chi-restraints excluded: chain K residue 563 THR Chi-restraints excluded: chain K residue 586 PHE Chi-restraints excluded: chain L residue 177 LEU Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain N residue 153 ILE Chi-restraints excluded: chain N residue 168 PHE Chi-restraints excluded: chain N residue 226 SER Chi-restraints excluded: chain N residue 255 LYS Chi-restraints excluded: chain N residue 339 ILE Chi-restraints excluded: chain N residue 369 ILE Chi-restraints excluded: chain N residue 375 SER Chi-restraints excluded: chain N residue 391 ILE Chi-restraints excluded: chain N residue 415 ILE Chi-restraints excluded: chain N residue 438 ILE Chi-restraints excluded: chain N residue 495 MET Chi-restraints excluded: chain N residue 515 LEU Chi-restraints excluded: chain N residue 519 THR Chi-restraints excluded: chain N residue 547 ASP Chi-restraints excluded: chain N residue 563 THR Chi-restraints excluded: chain O residue 177 LEU Chi-restraints excluded: chain O residue 179 GLN Chi-restraints excluded: chain P residue 185 ASP Chi-restraints excluded: chain Q residue 8 HIS Chi-restraints excluded: chain Q residue 14 ASN Chi-restraints excluded: chain Q residue 102 VAL Chi-restraints excluded: chain Q residue 168 PHE Chi-restraints excluded: chain Q residue 204 ILE Chi-restraints excluded: chain Q residue 212 VAL Chi-restraints excluded: chain Q residue 226 SER Chi-restraints excluded: chain Q residue 241 ILE Chi-restraints excluded: chain Q residue 336 THR Chi-restraints excluded: chain Q residue 339 ILE Chi-restraints excluded: chain Q residue 391 ILE Chi-restraints excluded: chain Q residue 421 ASN Chi-restraints excluded: chain Q residue 563 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 299 optimal weight: 0.6980 chunk 204 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 267 optimal weight: 1.9990 chunk 148 optimal weight: 0.7980 chunk 306 optimal weight: 0.9980 chunk 248 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 183 optimal weight: 1.9990 chunk 322 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 179 GLN ** Y 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 93 ASN ** Y 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 183 ASN ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 ASN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN ** F 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 126 ASN ** F 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 522 GLN ** K 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 93 ASN ** K 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 183 ASN ** N 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 72 GLN N 93 ASN ** N 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 179 GLN ** Q 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 93 ASN ** Q 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 126 ASN ** Q 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 522 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 31362 Z= 0.234 Angle : 0.593 9.464 42528 Z= 0.306 Chirality : 0.042 0.236 4644 Planarity : 0.004 0.047 5568 Dihedral : 5.310 47.170 4100 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 4.75 % Allowed : 19.33 % Favored : 75.91 % 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: -1.15 (0.14), residues: 3720 helix: 0.04 (0.18), residues: 870 sheet: 0.01 (0.20), residues: 744 loop : -1.43 (0.13), residues: 2106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP Q 230 HIS 0.002 0.001 HIS C 300 PHE 0.025 0.002 PHE F 376 TYR 0.018 0.001 TYR Q 312 ARG 0.012 0.000 ARG K 541 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 653 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 489 time to evaluate : 3.733 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: J 183 ASN cc_start: 0.8175 (m-40) cc_final: 0.7858 (m-40) REVERT: Y 115 TYR cc_start: 0.8334 (m-80) cc_final: 0.8050 (m-10) REVERT: Y 159 TYR cc_start: 0.8903 (OUTLIER) cc_final: 0.8583 (p90) REVERT: Y 213 MET cc_start: 0.8753 (ptm) cc_final: 0.8353 (ptm) REVERT: Y 376 PHE cc_start: 0.8344 (t80) cc_final: 0.7599 (t80) REVERT: Y 459 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8100 (mmmm) REVERT: C 61 VAL cc_start: 0.8609 (OUTLIER) cc_final: 0.8220 (p) REVERT: C 219 ASN cc_start: 0.6453 (m-40) cc_final: 0.6160 (m-40) REVERT: C 468 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8637 (mt) REVERT: C 515 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8279 (mm) REVERT: F 168 PHE cc_start: 0.8044 (OUTLIER) cc_final: 0.6794 (p90) REVERT: F 213 MET cc_start: 0.8501 (ptp) cc_final: 0.8104 (ptm) REVERT: F 515 LEU cc_start: 0.8411 (mm) cc_final: 0.8096 (mm) REVERT: G 183 ASN cc_start: 0.8191 (m-40) cc_final: 0.7866 (m-40) REVERT: K 115 TYR cc_start: 0.8348 (m-80) cc_final: 0.8062 (m-10) REVERT: K 159 TYR cc_start: 0.8895 (OUTLIER) cc_final: 0.8565 (p90) REVERT: K 175 PHE cc_start: 0.6968 (t80) cc_final: 0.6750 (t80) REVERT: K 213 MET cc_start: 0.8742 (ptm) cc_final: 0.8368 (ptm) REVERT: K 376 PHE cc_start: 0.8301 (t80) cc_final: 0.7547 (t80) REVERT: K 459 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.8051 (mmmm) REVERT: K 480 MET cc_start: 0.8336 (mmp) cc_final: 0.7837 (mmp) REVERT: N 61 VAL cc_start: 0.8636 (OUTLIER) cc_final: 0.8225 (p) REVERT: N 219 ASN cc_start: 0.6451 (m-40) cc_final: 0.6150 (m-40) REVERT: N 468 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8641 (mt) REVERT: N 515 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8279 (mm) REVERT: Q 168 PHE cc_start: 0.8047 (OUTLIER) cc_final: 0.6806 (p90) REVERT: Q 213 MET cc_start: 0.8571 (ptp) cc_final: 0.8263 (ptm) REVERT: Q 515 LEU cc_start: 0.8408 (mm) cc_final: 0.8096 (mm) outliers start: 164 outliers final: 117 residues processed: 598 average time/residue: 0.3694 time to fit residues: 366.2770 Evaluate side-chains 577 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 448 time to evaluate : 3.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 177 LEU Chi-restraints excluded: chain Y residue 8 HIS Chi-restraints excluded: chain Y residue 18 THR Chi-restraints excluded: chain Y residue 78 THR Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 111 THR Chi-restraints excluded: chain Y residue 123 THR Chi-restraints excluded: chain Y residue 152 VAL Chi-restraints excluded: chain Y residue 153 ILE Chi-restraints excluded: chain Y residue 159 TYR Chi-restraints excluded: chain Y residue 168 PHE Chi-restraints excluded: chain Y residue 212 VAL Chi-restraints excluded: chain Y residue 226 SER Chi-restraints excluded: chain Y residue 256 THR Chi-restraints excluded: chain Y residue 336 THR Chi-restraints excluded: chain Y residue 375 SER Chi-restraints excluded: chain Y residue 389 VAL Chi-restraints excluded: chain Y residue 459 LYS Chi-restraints excluded: chain Y residue 519 THR Chi-restraints excluded: chain Y residue 563 THR Chi-restraints excluded: chain Y residue 586 PHE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain C residue 8 HIS Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 226 SER Chi-restraints excluded: chain C residue 255 LYS Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 339 ILE Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 400 GLN Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain C residue 547 ASP Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain F residue 8 HIS Chi-restraints excluded: chain F residue 14 ASN Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 168 PHE Chi-restraints excluded: chain F residue 175 PHE Chi-restraints excluded: chain F residue 204 ILE Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 226 SER Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain F residue 256 THR Chi-restraints excluded: chain F residue 336 THR Chi-restraints excluded: chain F residue 391 ILE Chi-restraints excluded: chain F residue 417 ASN Chi-restraints excluded: chain F residue 421 ASN Chi-restraints excluded: chain F residue 563 THR Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain K residue 8 HIS Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 102 VAL Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 152 VAL Chi-restraints excluded: chain K residue 153 ILE Chi-restraints excluded: chain K residue 159 TYR Chi-restraints excluded: chain K residue 168 PHE Chi-restraints excluded: chain K residue 212 VAL Chi-restraints excluded: chain K residue 226 SER Chi-restraints excluded: chain K residue 256 THR Chi-restraints excluded: chain K residue 336 THR Chi-restraints excluded: chain K residue 375 SER Chi-restraints excluded: chain K residue 389 VAL Chi-restraints excluded: chain K residue 459 LYS Chi-restraints excluded: chain K residue 519 THR Chi-restraints excluded: chain K residue 563 THR Chi-restraints excluded: chain K residue 586 PHE Chi-restraints excluded: chain L residue 177 LEU Chi-restraints excluded: chain N residue 8 HIS Chi-restraints excluded: chain N residue 18 THR Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain N residue 153 ILE Chi-restraints excluded: chain N residue 168 PHE Chi-restraints excluded: chain N residue 226 SER Chi-restraints excluded: chain N residue 255 LYS Chi-restraints excluded: chain N residue 256 THR Chi-restraints excluded: chain N residue 339 ILE Chi-restraints excluded: chain N residue 375 SER Chi-restraints excluded: chain N residue 391 ILE Chi-restraints excluded: chain N residue 400 GLN Chi-restraints excluded: chain N residue 415 ILE Chi-restraints excluded: chain N residue 438 ILE Chi-restraints excluded: chain N residue 468 LEU Chi-restraints excluded: chain N residue 515 LEU Chi-restraints excluded: chain N residue 519 THR Chi-restraints excluded: chain N residue 547 ASP Chi-restraints excluded: chain N residue 563 THR Chi-restraints excluded: chain O residue 177 LEU Chi-restraints excluded: chain P residue 185 ASP Chi-restraints excluded: chain Q residue 8 HIS Chi-restraints excluded: chain Q residue 14 ASN Chi-restraints excluded: chain Q residue 18 THR Chi-restraints excluded: chain Q residue 77 CYS Chi-restraints excluded: chain Q residue 102 VAL Chi-restraints excluded: chain Q residue 153 ILE Chi-restraints excluded: chain Q residue 168 PHE Chi-restraints excluded: chain Q residue 175 PHE Chi-restraints excluded: chain Q residue 204 ILE Chi-restraints excluded: chain Q residue 212 VAL Chi-restraints excluded: chain Q residue 226 SER Chi-restraints excluded: chain Q residue 241 ILE Chi-restraints excluded: chain Q residue 256 THR Chi-restraints excluded: chain Q residue 336 THR Chi-restraints excluded: chain Q residue 391 ILE Chi-restraints excluded: chain Q residue 417 ASN Chi-restraints excluded: chain Q residue 421 ASN Chi-restraints excluded: chain Q residue 563 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 120 optimal weight: 3.9990 chunk 323 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 211 optimal weight: 0.6980 chunk 88 optimal weight: 0.8980 chunk 359 optimal weight: 3.9990 chunk 298 optimal weight: 7.9990 chunk 166 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 119 optimal weight: 0.7980 chunk 188 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 179 GLN ** Y 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 402 GLN ** Y 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 405 ASN ** C 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 GLN E 179 GLN ** F 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 ASN ** F 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 343 HIS ** F 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 509 GLN G 179 GLN ** K 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 179 GLN ** Q 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 509 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 31362 Z= 0.220 Angle : 0.584 10.083 42528 Z= 0.300 Chirality : 0.042 0.235 4644 Planarity : 0.004 0.047 5568 Dihedral : 5.133 25.527 4098 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 5.22 % Allowed : 20.12 % Favored : 74.67 % 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: -1.06 (0.14), residues: 3720 helix: 0.12 (0.18), residues: 864 sheet: 0.05 (0.20), residues: 744 loop : -1.37 (0.13), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Y 230 HIS 0.002 0.001 HIS C 300 PHE 0.035 0.002 PHE Q 376 TYR 0.031 0.001 TYR E 193 ARG 0.011 0.000 ARG Y 541 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 498 time to evaluate : 3.852 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: J 179 GLN cc_start: 0.8000 (OUTLIER) cc_final: 0.7727 (pm20) REVERT: Y 115 TYR cc_start: 0.8284 (m-80) cc_final: 0.7897 (m-10) REVERT: Y 159 TYR cc_start: 0.8897 (OUTLIER) cc_final: 0.8608 (p90) REVERT: Y 165 LEU cc_start: 0.7835 (tt) cc_final: 0.7631 (tt) REVERT: Y 213 MET cc_start: 0.8764 (ptm) cc_final: 0.8287 (ptm) REVERT: Y 376 PHE cc_start: 0.8273 (t80) cc_final: 0.7551 (t80) REVERT: Y 459 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.8104 (mmmm) REVERT: Y 480 MET cc_start: 0.8008 (mmp) cc_final: 0.7314 (mmp) REVERT: B 193 TYR cc_start: 0.5319 (m-10) cc_final: 0.4972 (m-80) REVERT: C 61 VAL cc_start: 0.8780 (OUTLIER) cc_final: 0.8476 (p) REVERT: C 219 ASN cc_start: 0.6454 (m-40) cc_final: 0.6064 (m-40) REVERT: C 468 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8629 (mt) REVERT: D 179 GLN cc_start: 0.8092 (pt0) cc_final: 0.7494 (pm20) REVERT: F 168 PHE cc_start: 0.8046 (OUTLIER) cc_final: 0.6846 (p90) REVERT: F 175 PHE cc_start: 0.7031 (OUTLIER) cc_final: 0.6660 (m-80) REVERT: F 185 PHE cc_start: 0.6781 (m-80) cc_final: 0.6499 (m-10) REVERT: F 213 MET cc_start: 0.8425 (ptp) cc_final: 0.8199 (ptm) REVERT: F 515 LEU cc_start: 0.8588 (mm) cc_final: 0.8306 (mm) REVERT: G 179 GLN cc_start: 0.7993 (OUTLIER) cc_final: 0.7712 (pm20) REVERT: K 115 TYR cc_start: 0.8310 (m-80) cc_final: 0.7897 (m-10) REVERT: K 159 TYR cc_start: 0.8881 (OUTLIER) cc_final: 0.8599 (p90) REVERT: K 165 LEU cc_start: 0.7852 (tt) cc_final: 0.7650 (tt) REVERT: K 213 MET cc_start: 0.8771 (ptm) cc_final: 0.8310 (ptm) REVERT: K 376 PHE cc_start: 0.8277 (t80) cc_final: 0.7550 (t80) REVERT: K 459 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.8005 (mmmm) REVERT: K 480 MET cc_start: 0.8066 (mmp) cc_final: 0.7842 (mmp) REVERT: M 193 TYR cc_start: 0.5295 (m-10) cc_final: 0.4952 (m-80) REVERT: N 61 VAL cc_start: 0.8760 (OUTLIER) cc_final: 0.8461 (p) REVERT: N 219 ASN cc_start: 0.6447 (m-40) cc_final: 0.6052 (m-40) REVERT: N 468 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8633 (mt) REVERT: Q 168 PHE cc_start: 0.8049 (OUTLIER) cc_final: 0.6845 (p90) REVERT: Q 175 PHE cc_start: 0.7062 (OUTLIER) cc_final: 0.6675 (m-80) REVERT: Q 185 PHE cc_start: 0.6788 (m-80) cc_final: 0.6489 (m-10) REVERT: Q 515 LEU cc_start: 0.8595 (mm) cc_final: 0.8313 (mm) outliers start: 180 outliers final: 122 residues processed: 621 average time/residue: 0.3691 time to fit residues: 382.1745 Evaluate side-chains 589 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 453 time to evaluate : 3.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 179 GLN Chi-restraints excluded: chain Y residue 8 HIS Chi-restraints excluded: chain Y residue 18 THR Chi-restraints excluded: chain Y residue 78 THR Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 111 THR Chi-restraints excluded: chain Y residue 123 THR Chi-restraints excluded: chain Y residue 152 VAL Chi-restraints excluded: chain Y residue 153 ILE Chi-restraints excluded: chain Y residue 159 TYR Chi-restraints excluded: chain Y residue 168 PHE Chi-restraints excluded: chain Y residue 212 VAL Chi-restraints excluded: chain Y residue 232 THR Chi-restraints excluded: chain Y residue 256 THR Chi-restraints excluded: chain Y residue 336 THR Chi-restraints excluded: chain Y residue 375 SER Chi-restraints excluded: chain Y residue 389 VAL Chi-restraints excluded: chain Y residue 459 LYS Chi-restraints excluded: chain Y residue 475 VAL Chi-restraints excluded: chain Y residue 563 THR Chi-restraints excluded: chain Y residue 586 PHE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain C residue 8 HIS Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 255 LYS Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 290 MET Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 339 ILE Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain C residue 547 ASP Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain F residue 8 HIS Chi-restraints excluded: chain F residue 14 ASN Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 60 MET Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 168 PHE Chi-restraints excluded: chain F residue 175 PHE Chi-restraints excluded: chain F residue 204 ILE Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain F residue 256 THR Chi-restraints excluded: chain F residue 336 THR Chi-restraints excluded: chain F residue 391 ILE Chi-restraints excluded: chain F residue 421 ASN Chi-restraints excluded: chain F residue 438 ILE Chi-restraints excluded: chain F residue 475 VAL Chi-restraints excluded: chain F residue 519 THR Chi-restraints excluded: chain F residue 553 LEU Chi-restraints excluded: chain F residue 563 THR Chi-restraints excluded: chain G residue 179 GLN Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain K residue 8 HIS Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 102 VAL Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 152 VAL Chi-restraints excluded: chain K residue 153 ILE Chi-restraints excluded: chain K residue 159 TYR Chi-restraints excluded: chain K residue 168 PHE Chi-restraints excluded: chain K residue 212 VAL Chi-restraints excluded: chain K residue 232 THR Chi-restraints excluded: chain K residue 256 THR Chi-restraints excluded: chain K residue 336 THR Chi-restraints excluded: chain K residue 375 SER Chi-restraints excluded: chain K residue 389 VAL Chi-restraints excluded: chain K residue 459 LYS Chi-restraints excluded: chain K residue 475 VAL Chi-restraints excluded: chain K residue 563 THR Chi-restraints excluded: chain K residue 586 PHE Chi-restraints excluded: chain L residue 177 LEU Chi-restraints excluded: chain M residue 175 SER Chi-restraints excluded: chain M residue 189 THR Chi-restraints excluded: chain N residue 8 HIS Chi-restraints excluded: chain N residue 18 THR Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain N residue 153 ILE Chi-restraints excluded: chain N residue 168 PHE Chi-restraints excluded: chain N residue 255 LYS Chi-restraints excluded: chain N residue 256 THR Chi-restraints excluded: chain N residue 290 MET Chi-restraints excluded: chain N residue 327 THR Chi-restraints excluded: chain N residue 339 ILE Chi-restraints excluded: chain N residue 375 SER Chi-restraints excluded: chain N residue 391 ILE Chi-restraints excluded: chain N residue 415 ILE Chi-restraints excluded: chain N residue 438 ILE Chi-restraints excluded: chain N residue 468 LEU Chi-restraints excluded: chain N residue 475 VAL Chi-restraints excluded: chain N residue 519 THR Chi-restraints excluded: chain N residue 547 ASP Chi-restraints excluded: chain N residue 563 THR Chi-restraints excluded: chain P residue 189 THR Chi-restraints excluded: chain Q residue 8 HIS Chi-restraints excluded: chain Q residue 14 ASN Chi-restraints excluded: chain Q residue 18 THR Chi-restraints excluded: chain Q residue 60 MET Chi-restraints excluded: chain Q residue 77 CYS Chi-restraints excluded: chain Q residue 102 VAL Chi-restraints excluded: chain Q residue 168 PHE Chi-restraints excluded: chain Q residue 175 PHE Chi-restraints excluded: chain Q residue 204 ILE Chi-restraints excluded: chain Q residue 212 VAL Chi-restraints excluded: chain Q residue 241 ILE Chi-restraints excluded: chain Q residue 256 THR Chi-restraints excluded: chain Q residue 336 THR Chi-restraints excluded: chain Q residue 391 ILE Chi-restraints excluded: chain Q residue 421 ASN Chi-restraints excluded: chain Q residue 438 ILE Chi-restraints excluded: chain Q residue 475 VAL Chi-restraints excluded: chain Q residue 519 THR Chi-restraints excluded: chain Q residue 553 LEU Chi-restraints excluded: chain Q residue 563 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 347 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 205 optimal weight: 0.8980 chunk 262 optimal weight: 0.9990 chunk 203 optimal weight: 1.9990 chunk 302 optimal weight: 2.9990 chunk 200 optimal weight: 0.9990 chunk 358 optimal weight: 6.9990 chunk 224 optimal weight: 2.9990 chunk 218 optimal weight: 0.6980 chunk 165 optimal weight: 0.7980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 179 GLN ** Y 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 GLN ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 402 GLN ** C 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 488 ASN F 509 GLN G 179 GLN ** K 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 72 GLN K 93 ASN ** K 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 179 GLN ** N 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 72 GLN ** N 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 402 GLN ** N 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 179 GLN ** Q 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 488 ASN Q 509 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.3911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31362 Z= 0.204 Angle : 0.585 10.828 42528 Z= 0.297 Chirality : 0.041 0.235 4644 Planarity : 0.004 0.047 5568 Dihedral : 5.093 27.230 4098 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 5.30 % Allowed : 21.19 % Favored : 73.51 % 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: -1.02 (0.14), residues: 3720 helix: 0.14 (0.18), residues: 864 sheet: 0.10 (0.20), residues: 738 loop : -1.35 (0.13), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Q 68 HIS 0.004 0.001 HIS F 343 PHE 0.013 0.001 PHE F 175 TYR 0.031 0.001 TYR E 193 ARG 0.009 0.000 ARG F 541 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 667 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 484 time to evaluate : 3.029 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: Y 115 TYR cc_start: 0.8230 (m-80) cc_final: 0.7799 (m-10) REVERT: Y 159 TYR cc_start: 0.8883 (OUTLIER) cc_final: 0.8524 (p90) REVERT: Y 165 LEU cc_start: 0.7891 (tt) cc_final: 0.7638 (tt) REVERT: Y 213 MET cc_start: 0.8750 (ptm) cc_final: 0.8273 (ptm) REVERT: Y 376 PHE cc_start: 0.8195 (t80) cc_final: 0.7502 (t80) REVERT: Y 459 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.8050 (mmmm) REVERT: B 183 ASN cc_start: 0.7369 (t0) cc_final: 0.7077 (t0) REVERT: C 61 VAL cc_start: 0.8786 (OUTLIER) cc_final: 0.8468 (p) REVERT: C 213 MET cc_start: 0.8305 (ptm) cc_final: 0.8054 (ptm) REVERT: C 219 ASN cc_start: 0.6252 (m-40) cc_final: 0.5775 (m-40) REVERT: C 468 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8656 (mt) REVERT: D 179 GLN cc_start: 0.7834 (pt0) cc_final: 0.7479 (pm20) REVERT: F 168 PHE cc_start: 0.8024 (OUTLIER) cc_final: 0.6776 (p90) REVERT: F 175 PHE cc_start: 0.6978 (OUTLIER) cc_final: 0.6668 (m-80) REVERT: F 185 PHE cc_start: 0.6673 (m-80) cc_final: 0.6467 (m-10) REVERT: F 213 MET cc_start: 0.8403 (ptp) cc_final: 0.8199 (ptm) REVERT: F 515 LEU cc_start: 0.8623 (mm) cc_final: 0.8325 (mm) REVERT: K 115 TYR cc_start: 0.8239 (m-80) cc_final: 0.7806 (m-10) REVERT: K 159 TYR cc_start: 0.8871 (OUTLIER) cc_final: 0.8517 (p90) REVERT: K 165 LEU cc_start: 0.7909 (tt) cc_final: 0.7652 (tt) REVERT: K 213 MET cc_start: 0.8768 (ptm) cc_final: 0.8282 (ptm) REVERT: K 376 PHE cc_start: 0.8190 (t80) cc_final: 0.7497 (t80) REVERT: K 459 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.8000 (mmmm) REVERT: M 183 ASN cc_start: 0.7358 (t0) cc_final: 0.7072 (t0) REVERT: N 61 VAL cc_start: 0.8812 (OUTLIER) cc_final: 0.8491 (p) REVERT: N 213 MET cc_start: 0.8307 (ptm) cc_final: 0.8043 (ptm) REVERT: N 219 ASN cc_start: 0.6245 (m-40) cc_final: 0.5758 (m-40) REVERT: N 468 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8658 (mt) REVERT: O 179 GLN cc_start: 0.8139 (pt0) cc_final: 0.7768 (pm20) REVERT: Q 168 PHE cc_start: 0.8032 (OUTLIER) cc_final: 0.6773 (p90) REVERT: Q 175 PHE cc_start: 0.6984 (OUTLIER) cc_final: 0.6668 (m-80) REVERT: Q 185 PHE cc_start: 0.6676 (m-80) cc_final: 0.6444 (m-10) REVERT: Q 515 LEU cc_start: 0.8621 (mm) cc_final: 0.8325 (mm) outliers start: 183 outliers final: 130 residues processed: 617 average time/residue: 0.3645 time to fit residues: 375.6154 Evaluate side-chains 593 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 451 time to evaluate : 3.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 177 LEU Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain Y residue 8 HIS Chi-restraints excluded: chain Y residue 18 THR Chi-restraints excluded: chain Y residue 78 THR Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 111 THR Chi-restraints excluded: chain Y residue 123 THR Chi-restraints excluded: chain Y residue 152 VAL Chi-restraints excluded: chain Y residue 153 ILE Chi-restraints excluded: chain Y residue 159 TYR Chi-restraints excluded: chain Y residue 168 PHE Chi-restraints excluded: chain Y residue 212 VAL Chi-restraints excluded: chain Y residue 232 THR Chi-restraints excluded: chain Y residue 256 THR Chi-restraints excluded: chain Y residue 336 THR Chi-restraints excluded: chain Y residue 375 SER Chi-restraints excluded: chain Y residue 389 VAL Chi-restraints excluded: chain Y residue 438 ILE Chi-restraints excluded: chain Y residue 459 LYS Chi-restraints excluded: chain Y residue 475 VAL Chi-restraints excluded: chain Y residue 519 THR Chi-restraints excluded: chain Y residue 563 THR Chi-restraints excluded: chain Y residue 586 PHE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain C residue 8 HIS Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 255 LYS Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 290 MET Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 339 ILE Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 495 MET Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain C residue 547 ASP Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain F residue 8 HIS Chi-restraints excluded: chain F residue 14 ASN Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 60 MET Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 168 PHE Chi-restraints excluded: chain F residue 175 PHE Chi-restraints excluded: chain F residue 204 ILE Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain F residue 256 THR Chi-restraints excluded: chain F residue 336 THR Chi-restraints excluded: chain F residue 391 ILE Chi-restraints excluded: chain F residue 421 ASN Chi-restraints excluded: chain F residue 438 ILE Chi-restraints excluded: chain F residue 475 VAL Chi-restraints excluded: chain F residue 519 THR Chi-restraints excluded: chain F residue 553 LEU Chi-restraints excluded: chain F residue 563 THR Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain K residue 8 HIS Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 102 VAL Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 152 VAL Chi-restraints excluded: chain K residue 153 ILE Chi-restraints excluded: chain K residue 159 TYR Chi-restraints excluded: chain K residue 168 PHE Chi-restraints excluded: chain K residue 212 VAL Chi-restraints excluded: chain K residue 232 THR Chi-restraints excluded: chain K residue 256 THR Chi-restraints excluded: chain K residue 336 THR Chi-restraints excluded: chain K residue 375 SER Chi-restraints excluded: chain K residue 389 VAL Chi-restraints excluded: chain K residue 438 ILE Chi-restraints excluded: chain K residue 459 LYS Chi-restraints excluded: chain K residue 475 VAL Chi-restraints excluded: chain K residue 519 THR Chi-restraints excluded: chain K residue 563 THR Chi-restraints excluded: chain K residue 586 PHE Chi-restraints excluded: chain L residue 177 LEU Chi-restraints excluded: chain M residue 175 SER Chi-restraints excluded: chain N residue 8 HIS Chi-restraints excluded: chain N residue 18 THR Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain N residue 153 ILE Chi-restraints excluded: chain N residue 168 PHE Chi-restraints excluded: chain N residue 205 THR Chi-restraints excluded: chain N residue 255 LYS Chi-restraints excluded: chain N residue 256 THR Chi-restraints excluded: chain N residue 327 THR Chi-restraints excluded: chain N residue 336 THR Chi-restraints excluded: chain N residue 339 ILE Chi-restraints excluded: chain N residue 375 SER Chi-restraints excluded: chain N residue 391 ILE Chi-restraints excluded: chain N residue 468 LEU Chi-restraints excluded: chain N residue 475 VAL Chi-restraints excluded: chain N residue 519 THR Chi-restraints excluded: chain N residue 547 ASP Chi-restraints excluded: chain N residue 563 THR Chi-restraints excluded: chain O residue 177 LEU Chi-restraints excluded: chain P residue 189 THR Chi-restraints excluded: chain Q residue 8 HIS Chi-restraints excluded: chain Q residue 14 ASN Chi-restraints excluded: chain Q residue 18 THR Chi-restraints excluded: chain Q residue 60 MET Chi-restraints excluded: chain Q residue 77 CYS Chi-restraints excluded: chain Q residue 102 VAL Chi-restraints excluded: chain Q residue 153 ILE Chi-restraints excluded: chain Q residue 168 PHE Chi-restraints excluded: chain Q residue 175 PHE Chi-restraints excluded: chain Q residue 204 ILE Chi-restraints excluded: chain Q residue 212 VAL Chi-restraints excluded: chain Q residue 241 ILE Chi-restraints excluded: chain Q residue 256 THR Chi-restraints excluded: chain Q residue 336 THR Chi-restraints excluded: chain Q residue 391 ILE Chi-restraints excluded: chain Q residue 421 ASN Chi-restraints excluded: chain Q residue 438 ILE Chi-restraints excluded: chain Q residue 475 VAL Chi-restraints excluded: chain Q residue 519 THR Chi-restraints excluded: chain Q residue 553 LEU Chi-restraints excluded: chain Q residue 563 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 221 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 chunk 214 optimal weight: 3.9990 chunk 108 optimal weight: 8.9990 chunk 70 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 227 optimal weight: 0.2980 chunk 244 optimal weight: 2.9990 chunk 177 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 281 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 GLN ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 GLN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 358 ASN ** C 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN ** F 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 509 GLN ** K 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 179 GLN ** N 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 179 GLN ** Q 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 509 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.4079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 31362 Z= 0.184 Angle : 0.589 10.965 42528 Z= 0.297 Chirality : 0.041 0.222 4644 Planarity : 0.004 0.047 5568 Dihedral : 4.994 24.787 4098 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 4.61 % Allowed : 22.72 % Favored : 72.67 % 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: -1.00 (0.14), residues: 3720 helix: 0.23 (0.18), residues: 864 sheet: 0.18 (0.21), residues: 708 loop : -1.38 (0.13), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 68 HIS 0.004 0.001 HIS F 343 PHE 0.012 0.001 PHE F 503 TYR 0.016 0.001 TYR E 193 ARG 0.008 0.000 ARG Y 541 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 645 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 486 time to evaluate : 3.759 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: Y 115 TYR cc_start: 0.8151 (m-80) cc_final: 0.7739 (m-10) REVERT: Y 159 TYR cc_start: 0.8848 (OUTLIER) cc_final: 0.8481 (p90) REVERT: Y 165 LEU cc_start: 0.8056 (tt) cc_final: 0.7809 (tt) REVERT: Y 213 MET cc_start: 0.8754 (ptm) cc_final: 0.8291 (ptm) REVERT: Y 376 PHE cc_start: 0.8165 (t80) cc_final: 0.7519 (t80) REVERT: Y 388 GLU cc_start: 0.6638 (mt-10) cc_final: 0.6351 (mt-10) REVERT: Y 458 TYR cc_start: 0.7347 (m-10) cc_final: 0.7042 (m-10) REVERT: Y 459 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.8028 (mmmm) REVERT: C 61 VAL cc_start: 0.8591 (OUTLIER) cc_final: 0.8252 (p) REVERT: C 213 MET cc_start: 0.8330 (ptm) cc_final: 0.8089 (ptm) REVERT: C 219 ASN cc_start: 0.6147 (m-40) cc_final: 0.5684 (m-40) REVERT: C 468 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8808 (mt) REVERT: D 179 GLN cc_start: 0.7736 (pt0) cc_final: 0.7394 (pm20) REVERT: F 168 PHE cc_start: 0.7961 (OUTLIER) cc_final: 0.6563 (p90) REVERT: F 175 PHE cc_start: 0.7282 (OUTLIER) cc_final: 0.6879 (m-80) REVERT: F 515 LEU cc_start: 0.8662 (mm) cc_final: 0.8348 (mm) REVERT: K 115 TYR cc_start: 0.8055 (m-80) cc_final: 0.7625 (m-10) REVERT: K 159 TYR cc_start: 0.8843 (OUTLIER) cc_final: 0.8485 (p90) REVERT: K 165 LEU cc_start: 0.8071 (tt) cc_final: 0.7823 (tt) REVERT: K 213 MET cc_start: 0.8759 (ptm) cc_final: 0.8274 (ptm) REVERT: K 376 PHE cc_start: 0.8159 (t80) cc_final: 0.7516 (t80) REVERT: K 459 LYS cc_start: 0.8314 (OUTLIER) cc_final: 0.7953 (mmmm) REVERT: N 61 VAL cc_start: 0.8577 (OUTLIER) cc_final: 0.8252 (p) REVERT: N 213 MET cc_start: 0.8325 (ptm) cc_final: 0.8081 (ptm) REVERT: N 219 ASN cc_start: 0.6156 (m-40) cc_final: 0.5671 (m-40) REVERT: N 468 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8808 (mt) REVERT: O 179 GLN cc_start: 0.7977 (pt0) cc_final: 0.7723 (pm20) REVERT: Q 168 PHE cc_start: 0.7957 (OUTLIER) cc_final: 0.6581 (p90) REVERT: Q 175 PHE cc_start: 0.7307 (OUTLIER) cc_final: 0.6827 (m-80) REVERT: Q 213 MET cc_start: 0.8470 (ptm) cc_final: 0.8148 (ptm) REVERT: Q 515 LEU cc_start: 0.8647 (mm) cc_final: 0.8342 (mm) outliers start: 159 outliers final: 119 residues processed: 605 average time/residue: 0.3775 time to fit residues: 382.9899 Evaluate side-chains 583 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 452 time to evaluate : 3.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 177 LEU Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain Y residue 8 HIS Chi-restraints excluded: chain Y residue 18 THR Chi-restraints excluded: chain Y residue 78 THR Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 111 THR Chi-restraints excluded: chain Y residue 123 THR Chi-restraints excluded: chain Y residue 152 VAL Chi-restraints excluded: chain Y residue 159 TYR Chi-restraints excluded: chain Y residue 168 PHE Chi-restraints excluded: chain Y residue 175 PHE Chi-restraints excluded: chain Y residue 212 VAL Chi-restraints excluded: chain Y residue 232 THR Chi-restraints excluded: chain Y residue 256 THR Chi-restraints excluded: chain Y residue 336 THR Chi-restraints excluded: chain Y residue 375 SER Chi-restraints excluded: chain Y residue 389 VAL Chi-restraints excluded: chain Y residue 438 ILE Chi-restraints excluded: chain Y residue 459 LYS Chi-restraints excluded: chain Y residue 475 VAL Chi-restraints excluded: chain Y residue 519 THR Chi-restraints excluded: chain Y residue 563 THR Chi-restraints excluded: chain Y residue 586 PHE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain C residue 8 HIS Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 255 LYS Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 339 ILE Chi-restraints excluded: chain C residue 358 ASN Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain F residue 8 HIS Chi-restraints excluded: chain F residue 14 ASN Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 168 PHE Chi-restraints excluded: chain F residue 175 PHE Chi-restraints excluded: chain F residue 204 ILE Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 256 THR Chi-restraints excluded: chain F residue 336 THR Chi-restraints excluded: chain F residue 391 ILE Chi-restraints excluded: chain F residue 421 ASN Chi-restraints excluded: chain F residue 438 ILE Chi-restraints excluded: chain F residue 475 VAL Chi-restraints excluded: chain F residue 519 THR Chi-restraints excluded: chain F residue 563 THR Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain K residue 8 HIS Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 102 VAL Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 152 VAL Chi-restraints excluded: chain K residue 159 TYR Chi-restraints excluded: chain K residue 168 PHE Chi-restraints excluded: chain K residue 212 VAL Chi-restraints excluded: chain K residue 232 THR Chi-restraints excluded: chain K residue 256 THR Chi-restraints excluded: chain K residue 336 THR Chi-restraints excluded: chain K residue 375 SER Chi-restraints excluded: chain K residue 389 VAL Chi-restraints excluded: chain K residue 438 ILE Chi-restraints excluded: chain K residue 459 LYS Chi-restraints excluded: chain K residue 475 VAL Chi-restraints excluded: chain K residue 515 LEU Chi-restraints excluded: chain K residue 519 THR Chi-restraints excluded: chain K residue 563 THR Chi-restraints excluded: chain K residue 586 PHE Chi-restraints excluded: chain L residue 177 LEU Chi-restraints excluded: chain M residue 175 SER Chi-restraints excluded: chain M residue 189 THR Chi-restraints excluded: chain N residue 8 HIS Chi-restraints excluded: chain N residue 18 THR Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain N residue 153 ILE Chi-restraints excluded: chain N residue 168 PHE Chi-restraints excluded: chain N residue 255 LYS Chi-restraints excluded: chain N residue 256 THR Chi-restraints excluded: chain N residue 290 MET Chi-restraints excluded: chain N residue 327 THR Chi-restraints excluded: chain N residue 339 ILE Chi-restraints excluded: chain N residue 375 SER Chi-restraints excluded: chain N residue 391 ILE Chi-restraints excluded: chain N residue 438 ILE Chi-restraints excluded: chain N residue 468 LEU Chi-restraints excluded: chain N residue 475 VAL Chi-restraints excluded: chain N residue 519 THR Chi-restraints excluded: chain N residue 540 MET Chi-restraints excluded: chain N residue 563 THR Chi-restraints excluded: chain P residue 189 THR Chi-restraints excluded: chain Q residue 8 HIS Chi-restraints excluded: chain Q residue 14 ASN Chi-restraints excluded: chain Q residue 102 VAL Chi-restraints excluded: chain Q residue 153 ILE Chi-restraints excluded: chain Q residue 168 PHE Chi-restraints excluded: chain Q residue 175 PHE Chi-restraints excluded: chain Q residue 204 ILE Chi-restraints excluded: chain Q residue 212 VAL Chi-restraints excluded: chain Q residue 241 ILE Chi-restraints excluded: chain Q residue 256 THR Chi-restraints excluded: chain Q residue 336 THR Chi-restraints excluded: chain Q residue 391 ILE Chi-restraints excluded: chain Q residue 421 ASN Chi-restraints excluded: chain Q residue 438 ILE Chi-restraints excluded: chain Q residue 475 VAL Chi-restraints excluded: chain Q residue 519 THR Chi-restraints excluded: chain Q residue 563 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 326 optimal weight: 2.9990 chunk 343 optimal weight: 2.9990 chunk 313 optimal weight: 0.8980 chunk 334 optimal weight: 0.9990 chunk 201 optimal weight: 2.9990 chunk 145 optimal weight: 5.9990 chunk 262 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 301 optimal weight: 0.6980 chunk 316 optimal weight: 0.8980 chunk 332 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 69 GLN ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 358 ASN C 378 ASN ** C 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 403 GLN ** C 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 471 GLN F 479 GLN ** F 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 509 GLN ** K 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 72 GLN ** N 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 378 ASN ** N 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 403 GLN ** N 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 471 GLN Q 479 GLN ** Q 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 509 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.4134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 31362 Z= 0.226 Angle : 0.614 11.891 42528 Z= 0.308 Chirality : 0.042 0.137 4644 Planarity : 0.004 0.048 5568 Dihedral : 5.029 25.707 4098 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 4.58 % Allowed : 22.35 % Favored : 73.07 % 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: -0.99 (0.14), residues: 3720 helix: 0.20 (0.18), residues: 864 sheet: 0.12 (0.20), residues: 738 loop : -1.34 (0.13), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 68 HIS 0.003 0.001 HIS F 343 PHE 0.011 0.001 PHE Q 175 TYR 0.022 0.001 TYR M 193 ARG 0.009 0.000 ARG K 541 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 473 time to evaluate : 3.832 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: Y 115 TYR cc_start: 0.8179 (m-80) cc_final: 0.7769 (m-10) REVERT: Y 159 TYR cc_start: 0.8872 (OUTLIER) cc_final: 0.8502 (p90) REVERT: Y 165 LEU cc_start: 0.8204 (tt) cc_final: 0.7993 (tt) REVERT: Y 213 MET cc_start: 0.8745 (ptm) cc_final: 0.8249 (ptm) REVERT: Y 376 PHE cc_start: 0.8213 (t80) cc_final: 0.7433 (t80) REVERT: Y 480 MET cc_start: 0.7662 (mmp) cc_final: 0.7278 (mmp) REVERT: C 61 VAL cc_start: 0.8642 (OUTLIER) cc_final: 0.8336 (p) REVERT: C 219 ASN cc_start: 0.6241 (m-40) cc_final: 0.5744 (m-40) REVERT: D 179 GLN cc_start: 0.7735 (pt0) cc_final: 0.7245 (pm20) REVERT: D 181 LYS cc_start: 0.7244 (OUTLIER) cc_final: 0.6898 (tptt) REVERT: F 168 PHE cc_start: 0.7994 (OUTLIER) cc_final: 0.6412 (p90) REVERT: F 175 PHE cc_start: 0.6985 (OUTLIER) cc_final: 0.6622 (m-80) REVERT: F 515 LEU cc_start: 0.8600 (mm) cc_final: 0.8213 (mm) REVERT: K 115 TYR cc_start: 0.8187 (m-80) cc_final: 0.7773 (m-10) REVERT: K 159 TYR cc_start: 0.8866 (OUTLIER) cc_final: 0.8506 (p90) REVERT: K 165 LEU cc_start: 0.8218 (tt) cc_final: 0.8018 (tt) REVERT: K 213 MET cc_start: 0.8765 (ptm) cc_final: 0.8279 (ptm) REVERT: K 222 MET cc_start: 0.7442 (tpp) cc_final: 0.7178 (mtp) REVERT: K 376 PHE cc_start: 0.8209 (t80) cc_final: 0.7425 (t80) REVERT: N 61 VAL cc_start: 0.8658 (OUTLIER) cc_final: 0.8346 (p) REVERT: N 219 ASN cc_start: 0.6230 (m-40) cc_final: 0.5735 (m-40) REVERT: O 179 GLN cc_start: 0.8034 (pt0) cc_final: 0.7766 (pm20) REVERT: Q 168 PHE cc_start: 0.7999 (OUTLIER) cc_final: 0.6469 (p90) REVERT: Q 515 LEU cc_start: 0.8592 (mm) cc_final: 0.8219 (mm) outliers start: 158 outliers final: 128 residues processed: 592 average time/residue: 0.3743 time to fit residues: 369.6627 Evaluate side-chains 578 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 442 time to evaluate : 3.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 177 LEU Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain Y residue 8 HIS Chi-restraints excluded: chain Y residue 18 THR Chi-restraints excluded: chain Y residue 78 THR Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 111 THR Chi-restraints excluded: chain Y residue 123 THR Chi-restraints excluded: chain Y residue 152 VAL Chi-restraints excluded: chain Y residue 153 ILE Chi-restraints excluded: chain Y residue 159 TYR Chi-restraints excluded: chain Y residue 168 PHE Chi-restraints excluded: chain Y residue 175 PHE Chi-restraints excluded: chain Y residue 212 VAL Chi-restraints excluded: chain Y residue 232 THR Chi-restraints excluded: chain Y residue 256 THR Chi-restraints excluded: chain Y residue 336 THR Chi-restraints excluded: chain Y residue 375 SER Chi-restraints excluded: chain Y residue 389 VAL Chi-restraints excluded: chain Y residue 421 ASN Chi-restraints excluded: chain Y residue 438 ILE Chi-restraints excluded: chain Y residue 475 VAL Chi-restraints excluded: chain Y residue 519 THR Chi-restraints excluded: chain Y residue 563 THR Chi-restraints excluded: chain Y residue 586 PHE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain C residue 8 HIS Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 255 LYS Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 290 MET Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 339 ILE Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain C residue 540 MET Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain D residue 181 LYS Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain F residue 8 HIS Chi-restraints excluded: chain F residue 14 ASN Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 168 PHE Chi-restraints excluded: chain F residue 175 PHE Chi-restraints excluded: chain F residue 204 ILE Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 256 THR Chi-restraints excluded: chain F residue 336 THR Chi-restraints excluded: chain F residue 358 ASN Chi-restraints excluded: chain F residue 391 ILE Chi-restraints excluded: chain F residue 421 ASN Chi-restraints excluded: chain F residue 438 ILE Chi-restraints excluded: chain F residue 475 VAL Chi-restraints excluded: chain F residue 519 THR Chi-restraints excluded: chain F residue 563 THR Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain K residue 8 HIS Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 102 VAL Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 152 VAL Chi-restraints excluded: chain K residue 153 ILE Chi-restraints excluded: chain K residue 159 TYR Chi-restraints excluded: chain K residue 168 PHE Chi-restraints excluded: chain K residue 212 VAL Chi-restraints excluded: chain K residue 232 THR Chi-restraints excluded: chain K residue 256 THR Chi-restraints excluded: chain K residue 336 THR Chi-restraints excluded: chain K residue 375 SER Chi-restraints excluded: chain K residue 421 ASN Chi-restraints excluded: chain K residue 475 VAL Chi-restraints excluded: chain K residue 519 THR Chi-restraints excluded: chain K residue 563 THR Chi-restraints excluded: chain K residue 586 PHE Chi-restraints excluded: chain L residue 177 LEU Chi-restraints excluded: chain M residue 175 SER Chi-restraints excluded: chain M residue 189 THR Chi-restraints excluded: chain N residue 8 HIS Chi-restraints excluded: chain N residue 18 THR Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 95 ILE Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain N residue 153 ILE Chi-restraints excluded: chain N residue 168 PHE Chi-restraints excluded: chain N residue 255 LYS Chi-restraints excluded: chain N residue 256 THR Chi-restraints excluded: chain N residue 290 MET Chi-restraints excluded: chain N residue 327 THR Chi-restraints excluded: chain N residue 336 THR Chi-restraints excluded: chain N residue 339 ILE Chi-restraints excluded: chain N residue 375 SER Chi-restraints excluded: chain N residue 391 ILE Chi-restraints excluded: chain N residue 438 ILE Chi-restraints excluded: chain N residue 475 VAL Chi-restraints excluded: chain N residue 519 THR Chi-restraints excluded: chain N residue 540 MET Chi-restraints excluded: chain N residue 563 THR Chi-restraints excluded: chain P residue 186 VAL Chi-restraints excluded: chain P residue 189 THR Chi-restraints excluded: chain Q residue 8 HIS Chi-restraints excluded: chain Q residue 14 ASN Chi-restraints excluded: chain Q residue 77 CYS Chi-restraints excluded: chain Q residue 153 ILE Chi-restraints excluded: chain Q residue 168 PHE Chi-restraints excluded: chain Q residue 175 PHE Chi-restraints excluded: chain Q residue 204 ILE Chi-restraints excluded: chain Q residue 212 VAL Chi-restraints excluded: chain Q residue 241 ILE Chi-restraints excluded: chain Q residue 256 THR Chi-restraints excluded: chain Q residue 336 THR Chi-restraints excluded: chain Q residue 358 ASN Chi-restraints excluded: chain Q residue 391 ILE Chi-restraints excluded: chain Q residue 421 ASN Chi-restraints excluded: chain Q residue 438 ILE Chi-restraints excluded: chain Q residue 475 VAL Chi-restraints excluded: chain Q residue 519 THR Chi-restraints excluded: chain Q residue 563 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 219 optimal weight: 0.9990 chunk 353 optimal weight: 4.9990 chunk 215 optimal weight: 6.9990 chunk 167 optimal weight: 3.9990 chunk 245 optimal weight: 0.9980 chunk 370 optimal weight: 5.9990 chunk 341 optimal weight: 6.9990 chunk 295 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 227 optimal weight: 1.9990 chunk 180 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 72 GLN ** Y 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.4158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 31362 Z= 0.404 Angle : 0.713 12.468 42528 Z= 0.364 Chirality : 0.045 0.187 4644 Planarity : 0.004 0.048 5568 Dihedral : 5.399 24.358 4098 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 15.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 4.20 % Allowed : 22.87 % Favored : 72.93 % 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: -1.08 (0.14), residues: 3720 helix: 0.10 (0.18), residues: 864 sheet: 0.09 (0.20), residues: 744 loop : -1.40 (0.13), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Y 532 HIS 0.004 0.001 HIS Y 569 PHE 0.022 0.002 PHE Y 175 TYR 0.039 0.002 TYR M 193 ARG 0.009 0.000 ARG Y 541 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 406 time to evaluate : 4.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 115 TYR cc_start: 0.8296 (m-80) cc_final: 0.7901 (m-10) REVERT: Y 159 TYR cc_start: 0.8914 (OUTLIER) cc_final: 0.8691 (p90) REVERT: Y 213 MET cc_start: 0.8826 (ptm) cc_final: 0.8382 (ptm) REVERT: Y 480 MET cc_start: 0.7907 (mmp) cc_final: 0.7657 (mmp) REVERT: C 219 ASN cc_start: 0.6586 (m-40) cc_final: 0.5967 (m-40) REVERT: F 168 PHE cc_start: 0.8178 (OUTLIER) cc_final: 0.6713 (p90) REVERT: F 515 LEU cc_start: 0.8226 (mm) cc_final: 0.7923 (mm) REVERT: K 115 TYR cc_start: 0.8327 (m-80) cc_final: 0.7898 (m-10) REVERT: K 159 TYR cc_start: 0.8892 (OUTLIER) cc_final: 0.8632 (p90) REVERT: K 213 MET cc_start: 0.8881 (ptm) cc_final: 0.8350 (ptm) REVERT: N 219 ASN cc_start: 0.6587 (m-40) cc_final: 0.5953 (m-40) REVERT: N 388 GLU cc_start: 0.6876 (mp0) cc_final: 0.6573 (mp0) REVERT: O 179 GLN cc_start: 0.8093 (pt0) cc_final: 0.7875 (pm20) REVERT: Q 168 PHE cc_start: 0.8224 (OUTLIER) cc_final: 0.6720 (p90) REVERT: Q 213 MET cc_start: 0.8557 (ptm) cc_final: 0.8150 (ptm) REVERT: Q 515 LEU cc_start: 0.8228 (mm) cc_final: 0.7927 (mm) outliers start: 145 outliers final: 128 residues processed: 516 average time/residue: 0.3651 time to fit residues: 318.7317 Evaluate side-chains 534 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 402 time to evaluate : 3.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 177 LEU Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain Y residue 8 HIS Chi-restraints excluded: chain Y residue 18 THR Chi-restraints excluded: chain Y residue 78 THR Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 111 THR Chi-restraints excluded: chain Y residue 123 THR Chi-restraints excluded: chain Y residue 152 VAL Chi-restraints excluded: chain Y residue 153 ILE Chi-restraints excluded: chain Y residue 159 TYR Chi-restraints excluded: chain Y residue 168 PHE Chi-restraints excluded: chain Y residue 175 PHE Chi-restraints excluded: chain Y residue 185 PHE Chi-restraints excluded: chain Y residue 212 VAL Chi-restraints excluded: chain Y residue 232 THR Chi-restraints excluded: chain Y residue 256 THR Chi-restraints excluded: chain Y residue 375 SER Chi-restraints excluded: chain Y residue 421 ASN Chi-restraints excluded: chain Y residue 475 VAL Chi-restraints excluded: chain Y residue 519 THR Chi-restraints excluded: chain Y residue 563 THR Chi-restraints excluded: chain Y residue 586 PHE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain C residue 8 HIS Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 255 LYS Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 339 ILE Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 480 MET Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain F residue 8 HIS Chi-restraints excluded: chain F residue 14 ASN Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 168 PHE Chi-restraints excluded: chain F residue 175 PHE Chi-restraints excluded: chain F residue 204 ILE Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 256 THR Chi-restraints excluded: chain F residue 336 THR Chi-restraints excluded: chain F residue 358 ASN Chi-restraints excluded: chain F residue 391 ILE Chi-restraints excluded: chain F residue 417 ASN Chi-restraints excluded: chain F residue 421 ASN Chi-restraints excluded: chain F residue 475 VAL Chi-restraints excluded: chain F residue 519 THR Chi-restraints excluded: chain F residue 563 THR Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain K residue 8 HIS Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 102 VAL Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 152 VAL Chi-restraints excluded: chain K residue 153 ILE Chi-restraints excluded: chain K residue 159 TYR Chi-restraints excluded: chain K residue 168 PHE Chi-restraints excluded: chain K residue 212 VAL Chi-restraints excluded: chain K residue 232 THR Chi-restraints excluded: chain K residue 256 THR Chi-restraints excluded: chain K residue 375 SER Chi-restraints excluded: chain K residue 421 ASN Chi-restraints excluded: chain K residue 438 ILE Chi-restraints excluded: chain K residue 475 VAL Chi-restraints excluded: chain K residue 519 THR Chi-restraints excluded: chain K residue 563 THR Chi-restraints excluded: chain K residue 586 PHE Chi-restraints excluded: chain L residue 177 LEU Chi-restraints excluded: chain M residue 175 SER Chi-restraints excluded: chain M residue 189 THR Chi-restraints excluded: chain N residue 8 HIS Chi-restraints excluded: chain N residue 18 THR Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 95 ILE Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain N residue 153 ILE Chi-restraints excluded: chain N residue 168 PHE Chi-restraints excluded: chain N residue 255 LYS Chi-restraints excluded: chain N residue 256 THR Chi-restraints excluded: chain N residue 327 THR Chi-restraints excluded: chain N residue 336 THR Chi-restraints excluded: chain N residue 339 ILE Chi-restraints excluded: chain N residue 375 SER Chi-restraints excluded: chain N residue 391 ILE Chi-restraints excluded: chain N residue 438 ILE Chi-restraints excluded: chain N residue 475 VAL Chi-restraints excluded: chain N residue 519 THR Chi-restraints excluded: chain N residue 563 THR Chi-restraints excluded: chain P residue 186 VAL Chi-restraints excluded: chain P residue 189 THR Chi-restraints excluded: chain Q residue 8 HIS Chi-restraints excluded: chain Q residue 14 ASN Chi-restraints excluded: chain Q residue 77 CYS Chi-restraints excluded: chain Q residue 95 ILE Chi-restraints excluded: chain Q residue 153 ILE Chi-restraints excluded: chain Q residue 168 PHE Chi-restraints excluded: chain Q residue 175 PHE Chi-restraints excluded: chain Q residue 204 ILE Chi-restraints excluded: chain Q residue 212 VAL Chi-restraints excluded: chain Q residue 256 THR Chi-restraints excluded: chain Q residue 336 THR Chi-restraints excluded: chain Q residue 358 ASN Chi-restraints excluded: chain Q residue 391 ILE Chi-restraints excluded: chain Q residue 417 ASN Chi-restraints excluded: chain Q residue 421 ASN Chi-restraints excluded: chain Q residue 475 VAL Chi-restraints excluded: chain Q residue 519 THR Chi-restraints excluded: chain Q residue 553 LEU Chi-restraints excluded: chain Q residue 563 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 234 optimal weight: 0.0770 chunk 314 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 272 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 295 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 303 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 overall best weight: 0.8540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 72 GLN ** F 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 378 ASN ** F 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 69 GLN ** K 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 402 GLN ** N 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 405 ASN ** Q 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 72 GLN ** Q 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 378 ASN ** Q 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.107455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.087696 restraints weight = 53559.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.091110 restraints weight = 28574.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.093459 restraints weight = 18489.565| |-----------------------------------------------------------------------------| r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 31362 Z= 0.205 Angle : 0.625 11.756 42528 Z= 0.315 Chirality : 0.042 0.170 4644 Planarity : 0.004 0.047 5568 Dihedral : 5.129 21.412 4098 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 3.80 % Allowed : 23.36 % Favored : 72.84 % 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: -1.06 (0.14), residues: 3720 helix: 0.17 (0.18), residues: 864 sheet: 0.17 (0.20), residues: 708 loop : -1.42 (0.13), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 68 HIS 0.003 0.001 HIS F 343 PHE 0.014 0.001 PHE Y 376 TYR 0.017 0.001 TYR C 457 ARG 0.009 0.000 ARG Y 541 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6851.33 seconds wall clock time: 127 minutes 43.84 seconds (7663.84 seconds total)