Starting phenix.real_space_refine on Fri Dec 15 07:31:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8egs_28129/12_2023/8egs_28129.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8egs_28129/12_2023/8egs_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_28129/12_2023/8egs_28129.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8egs_28129/12_2023/8egs_28129.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8egs_28129/12_2023/8egs_28129.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8egs_28129/12_2023/8egs_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-1.21rc1-5172/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: 15.81, 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: 12.20 Conformation dependent library (CDL) restraints added in 5.7 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: 3.81 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: 11.80 Time building geometry restraints manager: 13.10 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: 3.010 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: 13.760 Check model and map are aligned: 0.520 Set scattering table: 0.320 Process input model: 80.320 Find NCS groups from input model: 2.040 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 103.300 ------------------------------------------------------------------------------- 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 : 3.878 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 outliers start: 12 outliers final: 4 residues processed: 514 average time/residue: 0.4032 time to fit residues: 344.0594 Evaluate side-chains 436 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 432 time to evaluate : 3.524 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2651 time to fit residues: 6.7414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 177 optimal weight: 0.9980 chunk 217 optimal weight: 1.9990 chunk 337 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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 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 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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 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: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 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 0.068 31362 Z= 0.305 Angle : 0.703 8.936 42528 Z= 0.371 Chirality : 0.045 0.191 4644 Planarity : 0.005 0.064 5568 Dihedral : 5.614 32.337 4098 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 5.22 % Allowed : 16.46 % Favored : 78.32 % 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: -0.92 (0.13), residues: 3720 helix: 0.29 (0.18), residues: 840 sheet: 0.04 (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 Y 586 TYR 0.031 0.002 TYR N 457 ARG 0.011 0.001 ARG Q 510 *********************** 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: 180 poor density : 534 time to evaluate : 3.318 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 outliers start: 180 outliers final: 84 residues processed: 652 average time/residue: 0.4187 time to fit residues: 436.7855 Evaluate side-chains 514 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 430 time to evaluate : 3.183 Switching outliers to nearest non-outliers outliers start: 84 outliers final: 0 residues processed: 84 average time/residue: 0.2660 time to fit residues: 46.5273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 187 optimal weight: 3.9990 chunk 104 optimal weight: 0.8980 chunk 281 optimal weight: 0.7980 chunk 230 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 338 optimal weight: 0.8980 chunk 365 optimal weight: 4.9990 chunk 301 optimal weight: 0.5980 chunk 335 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 271 optimal weight: 7.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- 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 101 HIS Y 378 ASN ** Y 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 402 GLN ** 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 378 ASN C 400 GLN ** C 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 471 GLN ** 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 ** F 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 101 HIS F 219 ASN F 378 ASN F 402 GLN ** F 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 72 GLN K 101 HIS K 378 ASN ** K 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 402 GLN ** 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 126 ASN N 378 ASN N 400 GLN ** N 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 471 GLN ** 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 72 GLN ** Q 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 101 HIS Q 219 ASN Q 378 ASN Q 402 GLN Q 471 GLN ** Q 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 31362 Z= 0.247 Angle : 0.590 8.471 42528 Z= 0.310 Chirality : 0.043 0.187 4644 Planarity : 0.004 0.045 5568 Dihedral : 5.272 25.440 4098 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.96 % Allowed : 17.10 % Favored : 79.94 % 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: -1.09 (0.13), residues: 3720 helix: -0.01 (0.18), residues: 876 sheet: -0.01 (0.20), residues: 714 loop : -1.31 (0.13), residues: 2130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Q 568 HIS 0.005 0.001 HIS F 343 PHE 0.025 0.002 PHE Q 54 TYR 0.024 0.002 TYR Y 457 ARG 0.005 0.001 ARG Q 510 *********************** 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 633 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 531 time to evaluate : 3.686 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 outliers start: 102 outliers final: 39 residues processed: 601 average time/residue: 0.3776 time to fit residues: 373.9757 Evaluate side-chains 480 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 441 time to evaluate : 3.310 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.3179 time to fit residues: 26.5274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 334 optimal weight: 0.6980 chunk 254 optimal weight: 2.9990 chunk 175 optimal weight: 0.5980 chunk 37 optimal weight: 0.0470 chunk 161 optimal weight: 1.9990 chunk 227 optimal weight: 0.9990 chunk 339 optimal weight: 4.9990 chunk 359 optimal weight: 7.9990 chunk 177 optimal weight: 0.8980 chunk 321 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 overall best weight: 0.6480 ------------------------------------------------------------------------------- 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 126 ASN Y 378 ASN Y 402 GLN ** Y 403 GLN ** 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 C 405 ASN C 471 GLN C 488 ASN ** F 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 343 HIS ** F 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 509 GLN ** K 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 126 ASN K 378 ASN ** K 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 402 GLN ** N 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 72 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 N 405 ASN N 471 GLN N 488 ASN ** Q 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 126 ASN ** Q 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 31362 Z= 0.189 Angle : 0.572 7.807 42528 Z= 0.299 Chirality : 0.042 0.198 4644 Planarity : 0.004 0.046 5568 Dihedral : 5.200 25.354 4098 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.91 % Allowed : 18.06 % Favored : 80.03 % 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: -1.10 (0.13), residues: 3720 helix: 0.03 (0.18), residues: 870 sheet: 0.04 (0.20), residues: 714 loop : -1.35 (0.13), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 568 HIS 0.003 0.001 HIS Y 300 PHE 0.024 0.001 PHE Q 376 TYR 0.028 0.001 TYR N 457 ARG 0.005 0.000 ARG K 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 572 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 506 time to evaluate : 3.831 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 outliers start: 66 outliers final: 30 residues processed: 530 average time/residue: 0.3026 time to fit residues: 264.7980 Evaluate side-chains 489 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 459 time to evaluate : 2.201 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.1865 time to fit residues: 13.5053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 299 optimal weight: 3.9990 chunk 204 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 267 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 306 optimal weight: 0.9980 chunk 248 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 183 optimal weight: 0.8980 chunk 322 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- 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 93 ASN ** Y 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 GLN ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 ASN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 ASN ** C 402 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 126 ASN F 400 GLN ** F 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 509 GLN ** K 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 93 ASN ** K 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 179 GLN ** N 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 93 ASN ** N 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 491 ASN ** 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 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 471 GLN ** 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: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 31362 Z= 0.395 Angle : 0.672 9.122 42528 Z= 0.349 Chirality : 0.045 0.227 4644 Planarity : 0.004 0.052 5568 Dihedral : 5.472 27.211 4098 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 3.10 % Allowed : 19.28 % Favored : 77.62 % 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: -1.19 (0.14), residues: 3720 helix: -0.01 (0.18), residues: 870 sheet: -0.01 (0.20), residues: 744 loop : -1.45 (0.13), residues: 2106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 532 HIS 0.005 0.002 HIS Q 343 PHE 0.028 0.002 PHE Y 376 TYR 0.028 0.002 TYR F 457 ARG 0.007 0.001 ARG F 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 565 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 458 time to evaluate : 3.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 107 outliers final: 56 residues processed: 521 average time/residue: 0.4010 time to fit residues: 346.7984 Evaluate side-chains 476 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 420 time to evaluate : 3.897 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 0 residues processed: 56 average time/residue: 0.2668 time to fit residues: 33.2485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 120 optimal weight: 1.9990 chunk 323 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 chunk 211 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 359 optimal weight: 4.9990 chunk 298 optimal weight: 2.9990 chunk 166 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 119 optimal weight: 0.9990 chunk 188 optimal weight: 0.0770 overall best weight: 0.7540 ------------------------------------------------------------------------------- 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 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 479 GLN ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 402 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 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 179 GLN ** K 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 402 GLN ** N 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 21 GLN ** 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 400 GLN ** Q 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 488 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 31362 Z= 0.196 Angle : 0.600 11.986 42528 Z= 0.304 Chirality : 0.042 0.174 4644 Planarity : 0.004 0.047 5568 Dihedral : 5.242 25.142 4098 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.03 % Allowed : 20.61 % Favored : 77.36 % 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: -1.13 (0.14), residues: 3720 helix: 0.09 (0.18), residues: 870 sheet: 0.11 (0.21), residues: 708 loop : -1.45 (0.13), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Q 230 HIS 0.003 0.001 HIS Q 343 PHE 0.025 0.002 PHE Y 376 TYR 0.024 0.001 TYR Q 457 ARG 0.010 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 569 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 499 time to evaluate : 3.485 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 outliers start: 70 outliers final: 44 residues processed: 539 average time/residue: 0.4131 time to fit residues: 368.1729 Evaluate side-chains 477 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 433 time to evaluate : 3.521 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 0 residues processed: 44 average time/residue: 0.3277 time to fit residues: 31.5752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 347 optimal weight: 0.9980 chunk 40 optimal weight: 0.0270 chunk 205 optimal weight: 0.4980 chunk 262 optimal weight: 3.9990 chunk 203 optimal weight: 1.9990 chunk 302 optimal weight: 0.9990 chunk 200 optimal weight: 4.9990 chunk 358 optimal weight: 7.9990 chunk 224 optimal weight: 1.9990 chunk 218 optimal weight: 0.7980 chunk 165 optimal weight: 1.9990 overall best weight: 0.6640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: