Starting phenix.real_space_refine on Thu Feb 15 22:25:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sn9_25215/02_2024/7sn9_25215.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sn9_25215/02_2024/7sn9_25215.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sn9_25215/02_2024/7sn9_25215.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sn9_25215/02_2024/7sn9_25215.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sn9_25215/02_2024/7sn9_25215.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sn9_25215/02_2024/7sn9_25215.pdb" } resolution = 3.5 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= 0.003 sd= 0.033 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 294 5.16 5 C 72828 2.51 5 N 20370 2.21 5 O 25662 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 334": "OD1" <-> "OD2" Residue "A GLU 338": "OE1" <-> "OE2" Residue "A ASP 345": "OD1" <-> "OD2" Residue "A GLU 361": "OE1" <-> "OE2" Residue "P GLU 86": "OE1" <-> "OE2" Residue "P ASP 334": "OD1" <-> "OD2" Residue "B TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 90": "OE1" <-> "OE2" Residue "B PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 334": "OD1" <-> "OD2" Residue "W TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 86": "OE1" <-> "OE2" Residue "W TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 334": "OD1" <-> "OD2" Residue "W ASP 358": "OD1" <-> "OD2" Residue "C TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 90": "OE1" <-> "OE2" Residue "C PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 205": "OE1" <-> "OE2" Residue "C PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 338": "OE1" <-> "OE2" Residue "C ASP 345": "OD1" <-> "OD2" Residue "C GLU 348": "OE1" <-> "OE2" Residue "X TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 86": "OE1" <-> "OE2" Residue "X GLU 111": "OE1" <-> "OE2" Residue "X TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 334": "OD1" <-> "OD2" Residue "X GLU 338": "OE1" <-> "OE2" Residue "X ASP 345": "OD1" <-> "OD2" Residue "D TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 82": "OE1" <-> "OE2" Residue "D PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 205": "OE1" <-> "OE2" Residue "D PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 334": "OD1" <-> "OD2" Residue "D ASP 345": "OD1" <-> "OD2" Residue "D GLU 361": "OE1" <-> "OE2" Residue "Y GLU 86": "OE1" <-> "OE2" Residue "Y TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 358": "OD1" <-> "OD2" Residue "E GLU 82": "OE1" <-> "OE2" Residue "E GLU 90": "OE1" <-> "OE2" Residue "E GLU 100": "OE1" <-> "OE2" Residue "E PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 345": "OD1" <-> "OD2" Residue "E GLU 348": "OE1" <-> "OE2" Residue "E GLU 361": "OE1" <-> "OE2" Residue "Z ASP 56": "OD1" <-> "OD2" Residue "Z GLU 86": "OE1" <-> "OE2" Residue "Z TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 216": "OE1" <-> "OE2" Residue "Z GLU 338": "OE1" <-> "OE2" Residue "Z GLU 348": "OE1" <-> "OE2" Residue "Z ASP 358": "OD1" <-> "OD2" Residue "F TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 90": "OE1" <-> "OE2" Residue "F GLU 100": "OE1" <-> "OE2" Residue "F PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 334": "OD1" <-> "OD2" Residue "F ASP 345": "OD1" <-> "OD2" Residue "a ASP 313": "OD1" <-> "OD2" Residue "G TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 90": "OE1" <-> "OE2" Residue "G PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 338": "OE1" <-> "OE2" Residue "G ASP 345": "OD1" <-> "OD2" Residue "b GLU 86": "OE1" <-> "OE2" Residue "b GLU 216": "OE1" <-> "OE2" Residue "b ASP 334": "OD1" <-> "OD2" Residue "b GLU 338": "OE1" <-> "OE2" Residue "b GLU 348": "OE1" <-> "OE2" Residue "H GLU 82": "OE1" <-> "OE2" Residue "H GLU 90": "OE1" <-> "OE2" Residue "H PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 334": "OD1" <-> "OD2" Residue "H GLU 348": "OE1" <-> "OE2" Residue "c ASP 56": "OD1" <-> "OD2" Residue "c GLU 86": "OE1" <-> "OE2" Residue "c GLU 348": "OE1" <-> "OE2" Residue "I TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 82": "OE1" <-> "OE2" Residue "I GLU 86": "OE1" <-> "OE2" Residue "I GLU 90": "OE1" <-> "OE2" Residue "I GLU 100": "OE1" <-> "OE2" Residue "I PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 185": "OD1" <-> "OD2" Residue "I GLU 338": "OE1" <-> "OE2" Residue "I ASP 345": "OD1" <-> "OD2" Residue "d ASP 56": "OD1" <-> "OD2" Residue "d ASP 75": "OD1" <-> "OD2" Residue "d GLU 86": "OE1" <-> "OE2" Residue "d TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 216": "OE1" <-> "OE2" Residue "d GLU 338": "OE1" <-> "OE2" Residue "d ASP 345": "OD1" <-> "OD2" Residue "J TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 82": "OE1" <-> "OE2" Residue "J PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 185": "OD1" <-> "OD2" Residue "J GLU 205": "OE1" <-> "OE2" Residue "J TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 338": "OE1" <-> "OE2" Residue "J ASP 345": "OD1" <-> "OD2" Residue "e ASP 56": "OD1" <-> "OD2" Residue "e ASP 75": "OD1" <-> "OD2" Residue "e GLU 86": "OE1" <-> "OE2" Residue "e TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 345": "OD1" <-> "OD2" Residue "K TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 111": "OE1" <-> "OE2" Residue "K PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 334": "OD1" <-> "OD2" Residue "K GLU 338": "OE1" <-> "OE2" Residue "K ASP 345": "OD1" <-> "OD2" Residue "K GLU 361": "OE1" <-> "OE2" Residue "f TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 86": "OE1" <-> "OE2" Residue "f GLU 205": "OE1" <-> "OE2" Residue "f ASP 334": "OD1" <-> "OD2" Residue "f GLU 338": "OE1" <-> "OE2" Residue "f GLU 348": "OE1" <-> "OE2" Residue "L TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 90": "OE1" <-> "OE2" Residue "L PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 334": "OD1" <-> "OD2" Residue "L GLU 338": "OE1" <-> "OE2" Residue "g GLU 86": "OE1" <-> "OE2" Residue "g GLU 111": "OE1" <-> "OE2" Residue "g GLU 216": "OE1" <-> "OE2" Residue "g ASP 313": "OD1" <-> "OD2" Residue "g ASP 334": "OD1" <-> "OD2" Residue "g GLU 338": "OE1" <-> "OE2" Residue "g ASP 345": "OD1" <-> "OD2" Residue "M GLU 82": "OE1" <-> "OE2" Residue "M PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 185": "OD1" <-> "OD2" Residue "M TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 345": "OD1" <-> "OD2" Residue "h GLU 25": "OE1" <-> "OE2" Residue "h ASP 75": "OD1" <-> "OD2" Residue "h TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 86": "OE1" <-> "OE2" Residue "h TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 334": "OD1" <-> "OD2" Residue "N TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 185": "OD1" <-> "OD2" Residue "N TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 318": "OD1" <-> "OD2" Residue "N ASP 345": "OD1" <-> "OD2" Residue "N GLU 348": "OE1" <-> "OE2" Residue "N GLU 361": "OE1" <-> "OE2" Residue "i ASP 56": "OD1" <-> "OD2" Residue "i ASP 75": "OD1" <-> "OD2" Residue "i GLU 86": "OE1" <-> "OE2" Residue "i GLU 216": "OE1" <-> "OE2" Residue "i ASP 345": "OD1" <-> "OD2" Residue "i GLU 348": "OE1" <-> "OE2" Residue "i ASP 358": "OD1" <-> "OD2" Residue "O TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 82": "OE1" <-> "OE2" Residue "O GLU 111": "OE1" <-> "OE2" Residue "O PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 338": "OE1" <-> "OE2" Residue "O ASP 345": "OD1" <-> "OD2" Residue "O GLU 361": "OE1" <-> "OE2" Residue "j ASP 75": "OD1" <-> "OD2" Residue "j TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 86": "OE1" <-> "OE2" Residue "j GLU 111": "OE1" <-> "OE2" Residue "j TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 216": "OE1" <-> "OE2" Residue "j GLU 338": "OE1" <-> "OE2" Residue "j ASP 345": "OD1" <-> "OD2" Residue "Q GLU 82": "OE1" <-> "OE2" Residue "Q GLU 90": "OE1" <-> "OE2" Residue "Q PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 334": "OD1" <-> "OD2" Residue "Q ASP 345": "OD1" <-> "OD2" Residue "Q ASP 356": "OD1" <-> "OD2" Residue "Q GLU 361": "OE1" <-> "OE2" Residue "k GLU 86": "OE1" <-> "OE2" Residue "k GLU 216": "OE1" <-> "OE2" Residue "k ASP 334": "OD1" <-> "OD2" Residue "k GLU 338": "OE1" <-> "OE2" Residue "k GLU 348": "OE1" <-> "OE2" Residue "R TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 131": "OE1" <-> "OE2" Residue "R PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 345": "OD1" <-> "OD2" Residue "l GLU 86": "OE1" <-> "OE2" Residue "l GLU 216": "OE1" <-> "OE2" Residue "l ASP 358": "OD1" <-> "OD2" Residue "S TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 345": "OD1" <-> "OD2" Residue "m GLU 86": "OE1" <-> "OE2" Residue "m GLU 216": "OE1" <-> "OE2" Residue "m ASP 334": "OD1" <-> "OD2" Residue "m ASP 345": "OD1" <-> "OD2" Residue "m ASP 358": "OD1" <-> "OD2" Residue "T GLU 82": "OE1" <-> "OE2" Residue "T GLU 111": "OE1" <-> "OE2" Residue "T PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 185": "OD1" <-> "OD2" Residue "T TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 345": "OD1" <-> "OD2" Residue "T GLU 348": "OE1" <-> "OE2" Residue "n ASP 56": "OD1" <-> "OD2" Residue "n ASP 75": "OD1" <-> "OD2" Residue "n GLU 86": "OE1" <-> "OE2" Residue "n TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ASP 345": "OD1" <-> "OD2" Residue "n GLU 348": "OE1" <-> "OE2" Residue "U TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 82": "OE1" <-> "OE2" Residue "U PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 334": "OD1" <-> "OD2" Residue "U GLU 338": "OE1" <-> "OE2" Residue "U ASP 345": "OD1" <-> "OD2" Residue "o GLU 86": "OE1" <-> "OE2" Residue "o TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 216": "OE1" <-> "OE2" Residue "o ASP 345": "OD1" <-> "OD2" Residue "o GLU 348": "OE1" <-> "OE2" Residue "V GLU 82": "OE1" <-> "OE2" Residue "V PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 334": "OD1" <-> "OD2" Residue "V GLU 338": "OE1" <-> "OE2" Residue "V ASP 345": "OD1" <-> "OD2" Residue "V GLU 348": "OE1" <-> "OE2" Residue "p TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 86": "OE1" <-> "OE2" Residue "p GLU 111": "OE1" <-> "OE2" Residue "p TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 205": "OE1" <-> "OE2" Residue "p GLU 216": "OE1" <-> "OE2" Residue "p ASP 313": "OD1" <-> "OD2" Time to flip residues: 0.26s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 119154 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 2837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2837 Classifications: {'peptide': 394} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 392} Chain: "P" Number of atoms: 2837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2837 Classifications: {'peptide': 394} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 392} Chain: "B" Number of atoms: 2837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2837 Classifications: {'peptide': 394} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 392} Chain: "W" Number of atoms: 2837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2837 Classifications: {'peptide': 394} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 392} Chain: "C" Number of atoms: 2837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2837 Classifications: {'peptide': 394} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 392} Chain: "X" Number of atoms: 2837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2837 Classifications: {'peptide': 394} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 392} Chain: "D" Number of atoms: 2837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2837 Classifications: {'peptide': 394} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 392} Chain: "Y" Number of atoms: 2837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2837 Classifications: {'peptide': 394} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 392} Chain: "E" Number of atoms: 2837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2837 Classifications: {'peptide': 394} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 392} Chain: "Z" Number of atoms: 2837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2837 Classifications: {'peptide': 394} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 392} Chain: "F" Number of atoms: 2837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2837 Classifications: {'peptide': 394} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 392} Chain: "a" Number of atoms: 2837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2837 Classifications: {'peptide': 394} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 392} Chain: "G" Number of atoms: 2837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2837 Classifications: {'peptide': 394} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 392} Chain: "b" Number of atoms: 2837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2837 Classifications: {'peptide': 394} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 392} Chain: "H" Number of atoms: 2837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2837 Classifications: {'peptide': 394} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 392} Chain: "c" Number of atoms: 2837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2837 Classifications: {'peptide': 394} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 392} Chain: "I" Number of atoms: 2837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2837 Classifications: {'peptide': 394} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 392} Chain: "d" Number of atoms: 2837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2837 Classifications: {'peptide': 394} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 392} Chain: "J" Number of atoms: 2837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2837 Classifications: {'peptide': 394} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 392} Chain: "e" Number of atoms: 2837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2837 Classifications: {'peptide': 394} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 392} Chain: "K" Number of atoms: 2837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2837 Classifications: {'peptide': 394} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 392} Chain: "f" Number of atoms: 2837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2837 Classifications: {'peptide': 394} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 392} Chain: "L" Number of atoms: 2837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2837 Classifications: {'peptide': 394} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 392} Chain: "g" Number of atoms: 2837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2837 Classifications: {'peptide': 394} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 392} Chain: "M" Number of atoms: 2837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2837 Classifications: {'peptide': 394} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 392} Chain: "h" Number of atoms: 2837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2837 Classifications: {'peptide': 394} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 392} Chain: "N" Number of atoms: 2837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2837 Classifications: {'peptide': 394} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 392} Chain: "i" Number of atoms: 2837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2837 Classifications: {'peptide': 394} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 392} Chain: "O" Number of atoms: 2837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2837 Classifications: {'peptide': 394} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 392} Chain: "j" Number of atoms: 2837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2837 Classifications: {'peptide': 394} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 392} Chain: "Q" Number of atoms: 2837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2837 Classifications: {'peptide': 394} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 392} Chain: "k" Number of atoms: 2837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2837 Classifications: {'peptide': 394} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 392} Chain: "R" Number of atoms: 2837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2837 Classifications: {'peptide': 394} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 392} Chain: "l" Number of atoms: 2837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2837 Classifications: {'peptide': 394} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 392} Chain: "S" Number of atoms: 2837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2837 Classifications: {'peptide': 394} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 392} Chain: "m" Number of atoms: 2837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2837 Classifications: {'peptide': 394} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 392} Chain: "T" Number of atoms: 2837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2837 Classifications: {'peptide': 394} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 392} Chain: "n" Number of atoms: 2837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2837 Classifications: {'peptide': 394} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 392} Chain: "U" Number of atoms: 2837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2837 Classifications: {'peptide': 394} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 392} Chain: "o" Number of atoms: 2837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2837 Classifications: {'peptide': 394} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 392} Chain: "V" Number of atoms: 2837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2837 Classifications: {'peptide': 394} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 392} Chain: "p" Number of atoms: 2837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2837 Classifications: {'peptide': 394} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 392} Time building chain proxies: 42.94, per 1000 atoms: 0.36 Number of scatterers: 119154 At special positions: 0 Unit cell: (191.16, 191.16, 370.44, 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 294 16.00 O 25662 8.00 N 20370 7.00 C 72828 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: 36.24 Conformation dependent library (CDL) restraints added in 16.7 seconds 32928 Ramachandran restraints generated. 16464 Oldfield, 0 Emsley, 16464 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 30492 Finding SS restraints... Secondary structure from input PDB file: 345 helices and 126 sheets defined 53.8% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.76 Creating SS restraints... Processing helix chain 'A' and resid 7 through 34 Processing helix chain 'A' and resid 43 through 99 Processing helix chain 'A' and resid 104 through 126 removed outlier: 4.223A pdb=" N ILE A 108 " --> pdb=" O ASP A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 221 removed outlier: 3.685A pdb=" N ALA A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 295 removed outlier: 3.795A pdb=" N ILE A 295 " --> pdb=" O VAL A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 356 Processing helix chain 'A' and resid 358 through 387 removed outlier: 3.523A pdb=" N GLU A 362 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 395 Processing helix chain 'P' and resid 7 through 34 Processing helix chain 'P' and resid 43 through 98 Processing helix chain 'P' and resid 104 through 126 removed outlier: 4.456A pdb=" N ILE P 108 " --> pdb=" O ASP P 104 " (cutoff:3.500A) Processing helix chain 'P' and resid 214 through 222 removed outlier: 3.613A pdb=" N GLY P 222 " --> pdb=" O LEU P 218 " (cutoff:3.500A) Processing helix chain 'P' and resid 291 through 295 removed outlier: 3.881A pdb=" N ILE P 295 " --> pdb=" O VAL P 292 " (cutoff:3.500A) Processing helix chain 'P' and resid 301 through 356 Processing helix chain 'P' and resid 358 through 386 removed outlier: 3.933A pdb=" N GLU P 362 " --> pdb=" O ASP P 358 " (cutoff:3.500A) Processing helix chain 'P' and resid 387 through 389 No H-bonds generated for 'chain 'P' and resid 387 through 389' Processing helix chain 'P' and resid 390 through 395 removed outlier: 4.239A pdb=" N PHE P 394 " --> pdb=" O VAL P 390 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG P 395 " --> pdb=" O LEU P 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 390 through 395' Processing helix chain 'B' and resid 7 through 34 Processing helix chain 'B' and resid 43 through 99 Processing helix chain 'B' and resid 104 through 126 removed outlier: 4.186A pdb=" N ILE B 108 " --> pdb=" O ASP B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 221 removed outlier: 3.646A pdb=" N ALA B 221 " --> pdb=" O SER B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 295 removed outlier: 3.760A pdb=" N ILE B 295 " --> pdb=" O VAL B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 356 Processing helix chain 'B' and resid 358 through 387 removed outlier: 3.812A pdb=" N SER B 387 " --> pdb=" O ALA B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 395 Processing helix chain 'W' and resid 7 through 34 Processing helix chain 'W' and resid 43 through 98 Processing helix chain 'W' and resid 104 through 126 removed outlier: 4.485A pdb=" N ILE W 108 " --> pdb=" O ASP W 104 " (cutoff:3.500A) Processing helix chain 'W' and resid 214 through 222 removed outlier: 3.604A pdb=" N GLY W 222 " --> pdb=" O LEU W 218 " (cutoff:3.500A) Processing helix chain 'W' and resid 301 through 356 Processing helix chain 'W' and resid 358 through 386 removed outlier: 3.890A pdb=" N GLU W 362 " --> pdb=" O ASP W 358 " (cutoff:3.500A) Processing helix chain 'W' and resid 387 through 389 No H-bonds generated for 'chain 'W' and resid 387 through 389' Processing helix chain 'W' and resid 390 through 395 removed outlier: 4.273A pdb=" N PHE W 394 " --> pdb=" O VAL W 390 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG W 395 " --> pdb=" O LEU W 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 390 through 395' Processing helix chain 'C' and resid 7 through 34 Processing helix chain 'C' and resid 43 through 99 Processing helix chain 'C' and resid 104 through 126 removed outlier: 4.206A pdb=" N ILE C 108 " --> pdb=" O ASP C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 221 removed outlier: 3.651A pdb=" N ALA C 221 " --> pdb=" O SER C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 356 Processing helix chain 'C' and resid 358 through 387 removed outlier: 3.612A pdb=" N GLU C 362 " --> pdb=" O ASP C 358 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER C 387 " --> pdb=" O ALA C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 388 through 393 Processing helix chain 'X' and resid 7 through 34 Processing helix chain 'X' and resid 43 through 99 Processing helix chain 'X' and resid 104 through 126 removed outlier: 4.531A pdb=" N ILE X 108 " --> pdb=" O ASP X 104 " (cutoff:3.500A) Processing helix chain 'X' and resid 214 through 222 removed outlier: 3.612A pdb=" N GLY X 222 " --> pdb=" O LEU X 218 " (cutoff:3.500A) Processing helix chain 'X' and resid 291 through 295 removed outlier: 3.866A pdb=" N ILE X 295 " --> pdb=" O VAL X 292 " (cutoff:3.500A) Processing helix chain 'X' and resid 301 through 356 Processing helix chain 'X' and resid 358 through 386 removed outlier: 3.935A pdb=" N GLU X 362 " --> pdb=" O ASP X 358 " (cutoff:3.500A) Processing helix chain 'X' and resid 387 through 389 No H-bonds generated for 'chain 'X' and resid 387 through 389' Processing helix chain 'X' and resid 390 through 395 removed outlier: 4.207A pdb=" N PHE X 394 " --> pdb=" O VAL X 390 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG X 395 " --> pdb=" O LEU X 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 390 through 395' Processing helix chain 'D' and resid 7 through 34 Processing helix chain 'D' and resid 43 through 99 Processing helix chain 'D' and resid 104 through 126 removed outlier: 4.218A pdb=" N ILE D 108 " --> pdb=" O ASP D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 221 removed outlier: 3.703A pdb=" N ALA D 221 " --> pdb=" O SER D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 295 removed outlier: 3.802A pdb=" N ILE D 295 " --> pdb=" O VAL D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 356 Processing helix chain 'D' and resid 358 through 387 removed outlier: 3.622A pdb=" N GLU D 362 " --> pdb=" O ASP D 358 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER D 387 " --> pdb=" O ALA D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 393 removed outlier: 3.504A pdb=" N SER D 392 " --> pdb=" O ASN D 389 " (cutoff:3.500A) Processing helix chain 'Y' and resid 7 through 34 Processing helix chain 'Y' and resid 43 through 99 Processing helix chain 'Y' and resid 104 through 126 removed outlier: 4.512A pdb=" N ILE Y 108 " --> pdb=" O ASP Y 104 " (cutoff:3.500A) Processing helix chain 'Y' and resid 214 through 222 removed outlier: 3.616A pdb=" N GLY Y 222 " --> pdb=" O LEU Y 218 " (cutoff:3.500A) Processing helix chain 'Y' and resid 291 through 295 removed outlier: 3.905A pdb=" N ILE Y 295 " --> pdb=" O VAL Y 292 " (cutoff:3.500A) Processing helix chain 'Y' and resid 301 through 356 Processing helix chain 'Y' and resid 358 through 386 removed outlier: 3.906A pdb=" N GLU Y 362 " --> pdb=" O ASP Y 358 " (cutoff:3.500A) Processing helix chain 'Y' and resid 387 through 389 No H-bonds generated for 'chain 'Y' and resid 387 through 389' Processing helix chain 'Y' and resid 390 through 395 removed outlier: 4.273A pdb=" N PHE Y 394 " --> pdb=" O VAL Y 390 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG Y 395 " --> pdb=" O LEU Y 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 390 through 395' Processing helix chain 'E' and resid 7 through 34 Processing helix chain 'E' and resid 43 through 99 Processing helix chain 'E' and resid 104 through 126 removed outlier: 4.221A pdb=" N ILE E 108 " --> pdb=" O ASP E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 214 through 221 removed outlier: 3.651A pdb=" N ALA E 221 " --> pdb=" O SER E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 295 removed outlier: 3.780A pdb=" N ILE E 295 " --> pdb=" O VAL E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 304 through 356 Processing helix chain 'E' and resid 358 through 387 removed outlier: 3.608A pdb=" N GLU E 362 " --> pdb=" O ASP E 358 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N SER E 387 " --> pdb=" O ALA E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 388 through 393 Processing helix chain 'Z' and resid 7 through 34 Processing helix chain 'Z' and resid 43 through 99 Processing helix chain 'Z' and resid 104 through 126 removed outlier: 4.515A pdb=" N ILE Z 108 " --> pdb=" O ASP Z 104 " (cutoff:3.500A) Processing helix chain 'Z' and resid 214 through 222 removed outlier: 3.594A pdb=" N GLY Z 222 " --> pdb=" O LEU Z 218 " (cutoff:3.500A) Processing helix chain 'Z' and resid 291 through 295 removed outlier: 3.885A pdb=" N ILE Z 295 " --> pdb=" O VAL Z 292 " (cutoff:3.500A) Processing helix chain 'Z' and resid 301 through 356 Processing helix chain 'Z' and resid 358 through 386 removed outlier: 3.892A pdb=" N GLU Z 362 " --> pdb=" O ASP Z 358 " (cutoff:3.500A) Processing helix chain 'Z' and resid 387 through 389 No H-bonds generated for 'chain 'Z' and resid 387 through 389' Processing helix chain 'Z' and resid 390 through 395 removed outlier: 4.276A pdb=" N PHE Z 394 " --> pdb=" O VAL Z 390 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG Z 395 " --> pdb=" O LEU Z 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 390 through 395' Processing helix chain 'F' and resid 7 through 34 Processing helix chain 'F' and resid 43 through 99 Processing helix chain 'F' and resid 104 through 126 removed outlier: 4.226A pdb=" N ILE F 108 " --> pdb=" O ASP F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 221 removed outlier: 3.641A pdb=" N ALA F 221 " --> pdb=" O SER F 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 304 through 356 Processing helix chain 'F' and resid 358 through 387 removed outlier: 3.601A pdb=" N GLU F 362 " --> pdb=" O ASP F 358 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER F 387 " --> pdb=" O ALA F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 388 through 393 Processing helix chain 'a' and resid 7 through 34 Processing helix chain 'a' and resid 43 through 98 Processing helix chain 'a' and resid 104 through 126 removed outlier: 4.479A pdb=" N ILE a 108 " --> pdb=" O ASP a 104 " (cutoff:3.500A) Processing helix chain 'a' and resid 214 through 222 removed outlier: 3.603A pdb=" N GLY a 222 " --> pdb=" O LEU a 218 " (cutoff:3.500A) Processing helix chain 'a' and resid 301 through 356 Processing helix chain 'a' and resid 358 through 386 removed outlier: 3.929A pdb=" N GLU a 362 " --> pdb=" O ASP a 358 " (cutoff:3.500A) Processing helix chain 'a' and resid 387 through 389 No H-bonds generated for 'chain 'a' and resid 387 through 389' Processing helix chain 'a' and resid 390 through 395 removed outlier: 4.214A pdb=" N PHE a 394 " --> pdb=" O VAL a 390 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG a 395 " --> pdb=" O LEU a 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 390 through 395' Processing helix chain 'G' and resid 7 through 34 Processing helix chain 'G' and resid 43 through 99 Processing helix chain 'G' and resid 104 through 126 removed outlier: 4.186A pdb=" N ILE G 108 " --> pdb=" O ASP G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 214 through 221 removed outlier: 3.635A pdb=" N ALA G 221 " --> pdb=" O SER G 217 " (cutoff:3.500A) Processing helix chain 'G' and resid 291 through 295 removed outlier: 3.759A pdb=" N ILE G 295 " --> pdb=" O VAL G 292 " (cutoff:3.500A) Processing helix chain 'G' and resid 304 through 356 Processing helix chain 'G' and resid 358 through 387 removed outlier: 3.567A pdb=" N GLU G 362 " --> pdb=" O ASP G 358 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER G 387 " --> pdb=" O ALA G 383 " (cutoff:3.500A) Processing helix chain 'G' and resid 388 through 393 Processing helix chain 'b' and resid 7 through 34 Processing helix chain 'b' and resid 43 through 98 Processing helix chain 'b' and resid 104 through 126 removed outlier: 4.467A pdb=" N ILE b 108 " --> pdb=" O ASP b 104 " (cutoff:3.500A) Processing helix chain 'b' and resid 214 through 222 removed outlier: 3.620A pdb=" N GLY b 222 " --> pdb=" O LEU b 218 " (cutoff:3.500A) Processing helix chain 'b' and resid 291 through 295 removed outlier: 3.876A pdb=" N ILE b 295 " --> pdb=" O VAL b 292 " (cutoff:3.500A) Processing helix chain 'b' and resid 301 through 356 Processing helix chain 'b' and resid 358 through 386 removed outlier: 3.883A pdb=" N GLU b 362 " --> pdb=" O ASP b 358 " (cutoff:3.500A) Processing helix chain 'b' and resid 387 through 389 No H-bonds generated for 'chain 'b' and resid 387 through 389' Processing helix chain 'b' and resid 390 through 395 removed outlier: 4.205A pdb=" N PHE b 394 " --> pdb=" O VAL b 390 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG b 395 " --> pdb=" O LEU b 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 390 through 395' Processing helix chain 'H' and resid 7 through 34 Processing helix chain 'H' and resid 43 through 99 Processing helix chain 'H' and resid 104 through 126 removed outlier: 4.225A pdb=" N ILE H 108 " --> pdb=" O ASP H 104 " (cutoff:3.500A) Processing helix chain 'H' and resid 214 through 221 removed outlier: 3.677A pdb=" N ALA H 221 " --> pdb=" O SER H 217 " (cutoff:3.500A) Processing helix chain 'H' and resid 304 through 356 Processing helix chain 'H' and resid 358 through 387 removed outlier: 3.541A pdb=" N GLU H 362 " --> pdb=" O ASP H 358 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER H 387 " --> pdb=" O ALA H 383 " (cutoff:3.500A) Processing helix chain 'H' and resid 388 through 395 removed outlier: 3.505A pdb=" N ARG H 395 " --> pdb=" O SER H 392 " (cutoff:3.500A) Processing helix chain 'c' and resid 7 through 34 Processing helix chain 'c' and resid 43 through 98 Processing helix chain 'c' and resid 104 through 126 removed outlier: 4.479A pdb=" N ILE c 108 " --> pdb=" O ASP c 104 " (cutoff:3.500A) Processing helix chain 'c' and resid 214 through 222 removed outlier: 3.619A pdb=" N GLY c 222 " --> pdb=" O LEU c 218 " (cutoff:3.500A) Processing helix chain 'c' and resid 291 through 295 removed outlier: 3.874A pdb=" N ILE c 295 " --> pdb=" O VAL c 292 " (cutoff:3.500A) Processing helix chain 'c' and resid 301 through 356 Processing helix chain 'c' and resid 358 through 386 removed outlier: 3.899A pdb=" N GLU c 362 " --> pdb=" O ASP c 358 " (cutoff:3.500A) Processing helix chain 'c' and resid 387 through 389 No H-bonds generated for 'chain 'c' and resid 387 through 389' Processing helix chain 'c' and resid 390 through 395 removed outlier: 4.256A pdb=" N PHE c 394 " --> pdb=" O VAL c 390 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG c 395 " --> pdb=" O LEU c 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 390 through 395' Processing helix chain 'I' and resid 7 through 34 Processing helix chain 'I' and resid 43 through 99 Processing helix chain 'I' and resid 104 through 126 removed outlier: 4.224A pdb=" N ILE I 108 " --> pdb=" O ASP I 104 " (cutoff:3.500A) Processing helix chain 'I' and resid 214 through 221 removed outlier: 3.645A pdb=" N ALA I 221 " --> pdb=" O SER I 217 " (cutoff:3.500A) Processing helix chain 'I' and resid 291 through 295 removed outlier: 3.754A pdb=" N ILE I 295 " --> pdb=" O VAL I 292 " (cutoff:3.500A) Processing helix chain 'I' and resid 304 through 356 Processing helix chain 'I' and resid 358 through 387 removed outlier: 3.683A pdb=" N GLU I 362 " --> pdb=" O ASP I 358 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER I 387 " --> pdb=" O ALA I 383 " (cutoff:3.500A) Processing helix chain 'I' and resid 388 through 395 removed outlier: 3.540A pdb=" N ARG I 395 " --> pdb=" O SER I 392 " (cutoff:3.500A) Processing helix chain 'd' and resid 7 through 34 Processing helix chain 'd' and resid 43 through 99 Processing helix chain 'd' and resid 104 through 126 removed outlier: 4.436A pdb=" N ILE d 108 " --> pdb=" O ASP d 104 " (cutoff:3.500A) Processing helix chain 'd' and resid 214 through 222 removed outlier: 3.616A pdb=" N GLY d 222 " --> pdb=" O LEU d 218 " (cutoff:3.500A) Processing helix chain 'd' and resid 291 through 295 removed outlier: 3.886A pdb=" N ILE d 295 " --> pdb=" O VAL d 292 " (cutoff:3.500A) Processing helix chain 'd' and resid 301 through 356 Processing helix chain 'd' and resid 358 through 386 removed outlier: 3.910A pdb=" N GLU d 362 " --> pdb=" O ASP d 358 " (cutoff:3.500A) Processing helix chain 'd' and resid 387 through 389 No H-bonds generated for 'chain 'd' and resid 387 through 389' Processing helix chain 'd' and resid 390 through 395 removed outlier: 4.135A pdb=" N PHE d 394 " --> pdb=" O VAL d 390 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG d 395 " --> pdb=" O LEU d 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 390 through 395' Processing helix chain 'J' and resid 7 through 34 Processing helix chain 'J' and resid 43 through 99 removed outlier: 3.567A pdb=" N TRP J 47 " --> pdb=" O ASN J 43 " (cutoff:3.500A) Processing helix chain 'J' and resid 104 through 126 removed outlier: 4.208A pdb=" N ILE J 108 " --> pdb=" O ASP J 104 " (cutoff:3.500A) Processing helix chain 'J' and resid 214 through 221 removed outlier: 3.675A pdb=" N ALA J 221 " --> pdb=" O SER J 217 " (cutoff:3.500A) Processing helix chain 'J' and resid 291 through 295 removed outlier: 3.737A pdb=" N ILE J 295 " --> pdb=" O VAL J 292 " (cutoff:3.500A) Processing helix chain 'J' and resid 304 through 356 Processing helix chain 'J' and resid 358 through 388 removed outlier: 3.594A pdb=" N GLU J 362 " --> pdb=" O ASP J 358 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER J 387 " --> pdb=" O ALA J 383 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N GLN J 388 " --> pdb=" O ASN J 384 " (cutoff:3.500A) Processing helix chain 'J' and resid 389 through 393 Processing helix chain 'e' and resid 7 through 34 Processing helix chain 'e' and resid 43 through 98 Processing helix chain 'e' and resid 104 through 126 removed outlier: 4.468A pdb=" N ILE e 108 " --> pdb=" O ASP e 104 " (cutoff:3.500A) Processing helix chain 'e' and resid 214 through 222 removed outlier: 3.593A pdb=" N GLY e 222 " --> pdb=" O LEU e 218 " (cutoff:3.500A) Processing helix chain 'e' and resid 291 through 295 removed outlier: 3.860A pdb=" N ILE e 295 " --> pdb=" O VAL e 292 " (cutoff:3.500A) Processing helix chain 'e' and resid 301 through 356 Processing helix chain 'e' and resid 358 through 386 removed outlier: 3.909A pdb=" N GLU e 362 " --> pdb=" O ASP e 358 " (cutoff:3.500A) Processing helix chain 'e' and resid 387 through 389 No H-bonds generated for 'chain 'e' and resid 387 through 389' Processing helix chain 'e' and resid 390 through 395 removed outlier: 4.305A pdb=" N PHE e 394 " --> pdb=" O VAL e 390 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG e 395 " --> pdb=" O LEU e 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 390 through 395' Processing helix chain 'K' and resid 7 through 34 Processing helix chain 'K' and resid 43 through 99 Processing helix chain 'K' and resid 104 through 126 removed outlier: 4.211A pdb=" N ILE K 108 " --> pdb=" O ASP K 104 " (cutoff:3.500A) Processing helix chain 'K' and resid 214 through 221 removed outlier: 3.645A pdb=" N ALA K 221 " --> pdb=" O SER K 217 " (cutoff:3.500A) Processing helix chain 'K' and resid 291 through 295 removed outlier: 3.748A pdb=" N ILE K 295 " --> pdb=" O VAL K 292 " (cutoff:3.500A) Processing helix chain 'K' and resid 304 through 356 Processing helix chain 'K' and resid 358 through 387 removed outlier: 3.738A pdb=" N GLU K 362 " --> pdb=" O ASP K 358 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER K 387 " --> pdb=" O ALA K 383 " (cutoff:3.500A) Processing helix chain 'K' and resid 388 through 395 removed outlier: 3.545A pdb=" N ARG K 395 " --> pdb=" O SER K 392 " (cutoff:3.500A) Processing helix chain 'f' and resid 7 through 34 Processing helix chain 'f' and resid 43 through 98 Processing helix chain 'f' and resid 104 through 126 removed outlier: 4.475A pdb=" N ILE f 108 " --> pdb=" O ASP f 104 " (cutoff:3.500A) Processing helix chain 'f' and resid 214 through 222 removed outlier: 3.622A pdb=" N GLY f 222 " --> pdb=" O LEU f 218 " (cutoff:3.500A) Processing helix chain 'f' and resid 291 through 295 removed outlier: 3.867A pdb=" N ILE f 295 " --> pdb=" O VAL f 292 " (cutoff:3.500A) Processing helix chain 'f' and resid 301 through 356 Processing helix chain 'f' and resid 358 through 386 removed outlier: 3.895A pdb=" N GLU f 362 " --> pdb=" O ASP f 358 " (cutoff:3.500A) Processing helix chain 'f' and resid 387 through 389 No H-bonds generated for 'chain 'f' and resid 387 through 389' Processing helix chain 'f' and resid 390 through 395 removed outlier: 4.219A pdb=" N PHE f 394 " --> pdb=" O VAL f 390 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG f 395 " --> pdb=" O LEU f 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 390 through 395' Processing helix chain 'L' and resid 7 through 34 Processing helix chain 'L' and resid 43 through 99 Processing helix chain 'L' and resid 104 through 126 removed outlier: 4.205A pdb=" N ILE L 108 " --> pdb=" O ASP L 104 " (cutoff:3.500A) Processing helix chain 'L' and resid 214 through 221 removed outlier: 3.631A pdb=" N ALA L 221 " --> pdb=" O SER L 217 " (cutoff:3.500A) Processing helix chain 'L' and resid 291 through 295 removed outlier: 3.760A pdb=" N ILE L 295 " --> pdb=" O VAL L 292 " (cutoff:3.500A) Processing helix chain 'L' and resid 304 through 356 Processing helix chain 'L' and resid 358 through 387 removed outlier: 3.545A pdb=" N GLU L 362 " --> pdb=" O ASP L 358 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER L 387 " --> pdb=" O ALA L 383 " (cutoff:3.500A) Processing helix chain 'L' and resid 388 through 395 Processing helix chain 'g' and resid 7 through 34 Processing helix chain 'g' and resid 43 through 98 Processing helix chain 'g' and resid 104 through 126 removed outlier: 4.470A pdb=" N ILE g 108 " --> pdb=" O ASP g 104 " (cutoff:3.500A) Processing helix chain 'g' and resid 214 through 222 removed outlier: 3.588A pdb=" N GLY g 222 " --> pdb=" O LEU g 218 " (cutoff:3.500A) Processing helix chain 'g' and resid 291 through 295 removed outlier: 3.879A pdb=" N ILE g 295 " --> pdb=" O VAL g 292 " (cutoff:3.500A) Processing helix chain 'g' and resid 301 through 356 Processing helix chain 'g' and resid 358 through 386 removed outlier: 3.883A pdb=" N GLU g 362 " --> pdb=" O ASP g 358 " (cutoff:3.500A) Processing helix chain 'g' and resid 387 through 389 No H-bonds generated for 'chain 'g' and resid 387 through 389' Processing helix chain 'g' and resid 390 through 395 removed outlier: 4.254A pdb=" N PHE g 394 " --> pdb=" O VAL g 390 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG g 395 " --> pdb=" O LEU g 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 390 through 395' Processing helix chain 'M' and resid 7 through 34 Processing helix chain 'M' and resid 43 through 99 Processing helix chain 'M' and resid 104 through 126 removed outlier: 4.214A pdb=" N ILE M 108 " --> pdb=" O ASP M 104 " (cutoff:3.500A) Processing helix chain 'M' and resid 214 through 221 removed outlier: 3.700A pdb=" N ALA M 221 " --> pdb=" O SER M 217 " (cutoff:3.500A) Processing helix chain 'M' and resid 291 through 295 removed outlier: 3.765A pdb=" N ILE M 295 " --> pdb=" O VAL M 292 " (cutoff:3.500A) Processing helix chain 'M' and resid 304 through 356 Processing helix chain 'M' and resid 358 through 387 removed outlier: 3.592A pdb=" N GLU M 362 " --> pdb=" O ASP M 358 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER M 387 " --> pdb=" O ALA M 383 " (cutoff:3.500A) Processing helix chain 'M' and resid 388 through 395 Processing helix chain 'h' and resid 7 through 34 Processing helix chain 'h' and resid 43 through 99 Processing helix chain 'h' and resid 105 through 126 Processing helix chain 'h' and resid 214 through 222 removed outlier: 3.607A pdb=" N GLY h 222 " --> pdb=" O LEU h 218 " (cutoff:3.500A) Processing helix chain 'h' and resid 301 through 356 Processing helix chain 'h' and resid 358 through 386 removed outlier: 3.861A pdb=" N GLU h 362 " --> pdb=" O ASP h 358 " (cutoff:3.500A) Processing helix chain 'h' and resid 387 through 389 No H-bonds generated for 'chain 'h' and resid 387 through 389' Processing helix chain 'h' and resid 390 through 395 removed outlier: 4.178A pdb=" N PHE h 394 " --> pdb=" O VAL h 390 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG h 395 " --> pdb=" O LEU h 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 390 through 395' Processing helix chain 'N' and resid 7 through 34 Processing helix chain 'N' and resid 43 through 99 Processing helix chain 'N' and resid 104 through 126 removed outlier: 4.200A pdb=" N ILE N 108 " --> pdb=" O ASP N 104 " (cutoff:3.500A) Processing helix chain 'N' and resid 214 through 221 removed outlier: 3.651A pdb=" N ALA N 221 " --> pdb=" O SER N 217 " (cutoff:3.500A) Processing helix chain 'N' and resid 291 through 295 removed outlier: 3.781A pdb=" N ILE N 295 " --> pdb=" O VAL N 292 " (cutoff:3.500A) Processing helix chain 'N' and resid 304 through 356 Processing helix chain 'N' and resid 358 through 387 removed outlier: 3.565A pdb=" N GLU N 362 " --> pdb=" O ASP N 358 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER N 387 " --> pdb=" O ALA N 383 " (cutoff:3.500A) Processing helix chain 'N' and resid 388 through 395 Processing helix chain 'i' and resid 7 through 34 Processing helix chain 'i' and resid 43 through 98 Processing helix chain 'i' and resid 104 through 126 removed outlier: 4.480A pdb=" N ILE i 108 " --> pdb=" O ASP i 104 " (cutoff:3.500A) Processing helix chain 'i' and resid 214 through 222 removed outlier: 3.630A pdb=" N GLY i 222 " --> pdb=" O LEU i 218 " (cutoff:3.500A) Processing helix chain 'i' and resid 291 through 295 removed outlier: 3.875A pdb=" N ILE i 295 " --> pdb=" O VAL i 292 " (cutoff:3.500A) Processing helix chain 'i' and resid 301 through 356 Processing helix chain 'i' and resid 358 through 386 removed outlier: 3.971A pdb=" N GLU i 362 " --> pdb=" O ASP i 358 " (cutoff:3.500A) Processing helix chain 'i' and resid 387 through 389 No H-bonds generated for 'chain 'i' and resid 387 through 389' Processing helix chain 'i' and resid 390 through 395 removed outlier: 4.195A pdb=" N PHE i 394 " --> pdb=" O VAL i 390 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG i 395 " --> pdb=" O LEU i 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 390 through 395' Processing helix chain 'O' and resid 7 through 34 Processing helix chain 'O' and resid 43 through 99 Processing helix chain 'O' and resid 104 through 126 removed outlier: 4.281A pdb=" N ILE O 108 " --> pdb=" O ASP O 104 " (cutoff:3.500A) Processing helix chain 'O' and resid 214 through 221 removed outlier: 3.666A pdb=" N ALA O 221 " --> pdb=" O SER O 217 " (cutoff:3.500A) Processing helix chain 'O' and resid 304 through 356 Processing helix chain 'O' and resid 358 through 387 removed outlier: 3.734A pdb=" N GLU O 362 " --> pdb=" O ASP O 358 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N SER O 387 " --> pdb=" O ALA O 383 " (cutoff:3.500A) Processing helix chain 'O' and resid 388 through 395 Processing helix chain 'j' and resid 7 through 34 Processing helix chain 'j' and resid 43 through 98 Processing helix chain 'j' and resid 104 through 126 removed outlier: 4.454A pdb=" N ILE j 108 " --> pdb=" O ASP j 104 " (cutoff:3.500A) Processing helix chain 'j' and resid 214 through 222 removed outlier: 3.628A pdb=" N GLY j 222 " --> pdb=" O LEU j 218 " (cutoff:3.500A) Processing helix chain 'j' and resid 301 through 356 Processing helix chain 'j' and resid 358 through 386 removed outlier: 3.994A pdb=" N GLU j 362 " --> pdb=" O ASP j 358 " (cutoff:3.500A) Processing helix chain 'j' and resid 387 through 389 No H-bonds generated for 'chain 'j' and resid 387 through 389' Processing helix chain 'j' and resid 390 through 395 removed outlier: 4.278A pdb=" N PHE j 394 " --> pdb=" O VAL j 390 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG j 395 " --> pdb=" O LEU j 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 390 through 395' Processing helix chain 'Q' and resid 7 through 34 Processing helix chain 'Q' and resid 43 through 99 Processing helix chain 'Q' and resid 104 through 126 removed outlier: 4.210A pdb=" N ILE Q 108 " --> pdb=" O ASP Q 104 " (cutoff:3.500A) Processing helix chain 'Q' and resid 214 through 221 removed outlier: 3.673A pdb=" N ALA Q 221 " --> pdb=" O SER Q 217 " (cutoff:3.500A) Processing helix chain 'Q' and resid 291 through 295 removed outlier: 3.725A pdb=" N ILE Q 295 " --> pdb=" O VAL Q 292 " (cutoff:3.500A) Processing helix chain 'Q' and resid 304 through 356 Processing helix chain 'Q' and resid 358 through 387 removed outlier: 3.571A pdb=" N GLU Q 362 " --> pdb=" O ASP Q 358 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER Q 387 " --> pdb=" O ALA Q 383 " (cutoff:3.500A) Processing helix chain 'Q' and resid 388 through 395 Processing helix chain 'k' and resid 7 through 34 Processing helix chain 'k' and resid 43 through 98 Processing helix chain 'k' and resid 104 through 126 removed outlier: 4.480A pdb=" N ILE k 108 " --> pdb=" O ASP k 104 " (cutoff:3.500A) Processing helix chain 'k' and resid 214 through 222 removed outlier: 3.611A pdb=" N GLY k 222 " --> pdb=" O LEU k 218 " (cutoff:3.500A) Processing helix chain 'k' and resid 291 through 295 removed outlier: 3.873A pdb=" N ILE k 295 " --> pdb=" O VAL k 292 " (cutoff:3.500A) Processing helix chain 'k' and resid 301 through 356 Processing helix chain 'k' and resid 358 through 386 removed outlier: 4.000A pdb=" N GLU k 362 " --> pdb=" O ASP k 358 " (cutoff:3.500A) Processing helix chain 'k' and resid 387 through 389 No H-bonds generated for 'chain 'k' and resid 387 through 389' Processing helix chain 'k' and resid 390 through 395 removed outlier: 4.232A pdb=" N PHE k 394 " --> pdb=" O VAL k 390 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG k 395 " --> pdb=" O LEU k 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 390 through 395' Processing helix chain 'R' and resid 7 through 34 Processing helix chain 'R' and resid 43 through 99 Processing helix chain 'R' and resid 104 through 126 removed outlier: 4.191A pdb=" N ILE R 108 " --> pdb=" O ASP R 104 " (cutoff:3.500A) Processing helix chain 'R' and resid 214 through 221 removed outlier: 3.669A pdb=" N ALA R 221 " --> pdb=" O SER R 217 " (cutoff:3.500A) Processing helix chain 'R' and resid 291 through 295 removed outlier: 3.800A pdb=" N ILE R 295 " --> pdb=" O VAL R 292 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 356 Processing helix chain 'R' and resid 358 through 387 removed outlier: 3.607A pdb=" N GLU R 362 " --> pdb=" O ASP R 358 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER R 387 " --> pdb=" O ALA R 383 " (cutoff:3.500A) Processing helix chain 'R' and resid 388 through 395 Processing helix chain 'l' and resid 7 through 34 Processing helix chain 'l' and resid 43 through 98 Processing helix chain 'l' and resid 104 through 126 removed outlier: 4.464A pdb=" N ILE l 108 " --> pdb=" O ASP l 104 " (cutoff:3.500A) Processing helix chain 'l' and resid 214 through 222 removed outlier: 3.593A pdb=" N GLY l 222 " --> pdb=" O LEU l 218 " (cutoff:3.500A) Processing helix chain 'l' and resid 301 through 356 Processing helix chain 'l' and resid 358 through 386 removed outlier: 3.982A pdb=" N GLU l 362 " --> pdb=" O ASP l 358 " (cutoff:3.500A) Processing helix chain 'l' and resid 387 through 389 No H-bonds generated for 'chain 'l' and resid 387 through 389' Processing helix chain 'l' and resid 390 through 395 removed outlier: 4.225A pdb=" N PHE l 394 " --> pdb=" O VAL l 390 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG l 395 " --> pdb=" O LEU l 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 390 through 395' Processing helix chain 'S' and resid 7 through 34 Processing helix chain 'S' and resid 43 through 99 Processing helix chain 'S' and resid 104 through 126 removed outlier: 4.206A pdb=" N ILE S 108 " --> pdb=" O ASP S 104 " (cutoff:3.500A) Processing helix chain 'S' and resid 214 through 221 removed outlier: 3.655A pdb=" N ALA S 221 " --> pdb=" O SER S 217 " (cutoff:3.500A) Processing helix chain 'S' and resid 304 through 356 Processing helix chain 'S' and resid 358 through 387 removed outlier: 3.530A pdb=" N GLU S 362 " --> pdb=" O ASP S 358 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER S 387 " --> pdb=" O ALA S 383 " (cutoff:3.500A) Processing helix chain 'S' and resid 388 through 395 removed outlier: 3.516A pdb=" N ARG S 395 " --> pdb=" O SER S 392 " (cutoff:3.500A) Processing helix chain 'm' and resid 7 through 34 Processing helix chain 'm' and resid 43 through 98 Processing helix chain 'm' and resid 104 through 126 removed outlier: 4.482A pdb=" N ILE m 108 " --> pdb=" O ASP m 104 " (cutoff:3.500A) Processing helix chain 'm' and resid 214 through 222 removed outlier: 3.606A pdb=" N GLY m 222 " --> pdb=" O LEU m 218 " (cutoff:3.500A) Processing helix chain 'm' and resid 291 through 295 removed outlier: 3.871A pdb=" N ILE m 295 " --> pdb=" O VAL m 292 " (cutoff:3.500A) Processing helix chain 'm' and resid 301 through 356 Processing helix chain 'm' and resid 358 through 386 removed outlier: 3.969A pdb=" N GLU m 362 " --> pdb=" O ASP m 358 " (cutoff:3.500A) Processing helix chain 'm' and resid 387 through 389 No H-bonds generated for 'chain 'm' and resid 387 through 389' Processing helix chain 'm' and resid 390 through 395 removed outlier: 4.112A pdb=" N PHE m 394 " --> pdb=" O VAL m 390 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG m 395 " --> pdb=" O LEU m 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 390 through 395' Processing helix chain 'T' and resid 7 through 34 Processing helix chain 'T' and resid 43 through 99 Processing helix chain 'T' and resid 104 through 126 removed outlier: 4.377A pdb=" N ILE T 108 " --> pdb=" O ASP T 104 " (cutoff:3.500A) Processing helix chain 'T' and resid 214 through 221 removed outlier: 3.645A pdb=" N ALA T 221 " --> pdb=" O SER T 217 " (cutoff:3.500A) Processing helix chain 'T' and resid 304 through 356 Processing helix chain 'T' and resid 358 through 387 removed outlier: 3.692A pdb=" N GLU T 362 " --> pdb=" O ASP T 358 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER T 387 " --> pdb=" O ALA T 383 " (cutoff:3.500A) Processing helix chain 'T' and resid 388 through 395 Processing helix chain 'n' and resid 7 through 34 Processing helix chain 'n' and resid 43 through 98 Processing helix chain 'n' and resid 104 through 126 removed outlier: 4.481A pdb=" N ILE n 108 " --> pdb=" O ASP n 104 " (cutoff:3.500A) Processing helix chain 'n' and resid 214 through 222 removed outlier: 3.604A pdb=" N GLY n 222 " --> pdb=" O LEU n 218 " (cutoff:3.500A) Processing helix chain 'n' and resid 291 through 295 removed outlier: 3.865A pdb=" N ILE n 295 " --> pdb=" O VAL n 292 " (cutoff:3.500A) Processing helix chain 'n' and resid 301 through 356 Processing helix chain 'n' and resid 358 through 386 removed outlier: 3.987A pdb=" N GLU n 362 " --> pdb=" O ASP n 358 " (cutoff:3.500A) Processing helix chain 'n' and resid 387 through 389 No H-bonds generated for 'chain 'n' and resid 387 through 389' Processing helix chain 'n' and resid 390 through 395 removed outlier: 4.234A pdb=" N PHE n 394 " --> pdb=" O VAL n 390 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG n 395 " --> pdb=" O LEU n 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 390 through 395' Processing helix chain 'U' and resid 7 through 34 Processing helix chain 'U' and resid 43 through 99 Processing helix chain 'U' and resid 104 through 126 removed outlier: 4.313A pdb=" N ILE U 108 " --> pdb=" O ASP U 104 " (cutoff:3.500A) Processing helix chain 'U' and resid 214 through 221 removed outlier: 3.658A pdb=" N ALA U 221 " --> pdb=" O SER U 217 " (cutoff:3.500A) Processing helix chain 'U' and resid 304 through 356 Processing helix chain 'U' and resid 358 through 387 removed outlier: 3.729A pdb=" N GLU U 362 " --> pdb=" O ASP U 358 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER U 387 " --> pdb=" O ALA U 383 " (cutoff:3.500A) Processing helix chain 'U' and resid 388 through 395 Processing helix chain 'o' and resid 7 through 34 Processing helix chain 'o' and resid 43 through 98 Processing helix chain 'o' and resid 104 through 126 removed outlier: 4.502A pdb=" N ILE o 108 " --> pdb=" O ASP o 104 " (cutoff:3.500A) Processing helix chain 'o' and resid 214 through 222 removed outlier: 3.614A pdb=" N GLY o 222 " --> pdb=" O LEU o 218 " (cutoff:3.500A) Processing helix chain 'o' and resid 291 through 295 removed outlier: 3.870A pdb=" N ILE o 295 " --> pdb=" O VAL o 292 " (cutoff:3.500A) Processing helix chain 'o' and resid 301 through 356 Processing helix chain 'o' and resid 358 through 386 removed outlier: 4.005A pdb=" N GLU o 362 " --> pdb=" O ASP o 358 " (cutoff:3.500A) Processing helix chain 'o' and resid 387 through 389 No H-bonds generated for 'chain 'o' and resid 387 through 389' Processing helix chain 'o' and resid 390 through 395 removed outlier: 4.144A pdb=" N PHE o 394 " --> pdb=" O VAL o 390 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG o 395 " --> pdb=" O LEU o 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 390 through 395' Processing helix chain 'V' and resid 7 through 34 Processing helix chain 'V' and resid 43 through 99 Processing helix chain 'V' and resid 104 through 126 removed outlier: 4.285A pdb=" N ILE V 108 " --> pdb=" O ASP V 104 " (cutoff:3.500A) Processing helix chain 'V' and resid 214 through 221 removed outlier: 3.663A pdb=" N ALA V 221 " --> pdb=" O SER V 217 " (cutoff:3.500A) Processing helix chain 'V' and resid 291 through 295 removed outlier: 3.738A pdb=" N ILE V 295 " --> pdb=" O VAL V 292 " (cutoff:3.500A) Processing helix chain 'V' and resid 304 through 356 Processing helix chain 'V' and resid 358 through 388 removed outlier: 3.717A pdb=" N GLU V 362 " --> pdb=" O ASP V 358 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER V 387 " --> pdb=" O ALA V 383 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLN V 388 " --> pdb=" O ASN V 384 " (cutoff:3.500A) Processing helix chain 'V' and resid 389 through 395 Processing helix chain 'p' and resid 7 through 34 Processing helix chain 'p' and resid 43 through 98 Processing helix chain 'p' and resid 104 through 126 removed outlier: 4.484A pdb=" N ILE p 108 " --> pdb=" O ASP p 104 " (cutoff:3.500A) Processing helix chain 'p' and resid 214 through 222 removed outlier: 3.614A pdb=" N GLY p 222 " --> pdb=" O LEU p 218 " (cutoff:3.500A) Processing helix chain 'p' and resid 291 through 295 removed outlier: 3.867A pdb=" N ILE p 295 " --> pdb=" O VAL p 292 " (cutoff:3.500A) Processing helix chain 'p' and resid 301 through 356 Processing helix chain 'p' and resid 358 through 386 removed outlier: 3.993A pdb=" N GLU p 362 " --> pdb=" O ASP p 358 " (cutoff:3.500A) Processing helix chain 'p' and resid 387 through 389 No H-bonds generated for 'chain 'p' and resid 387 through 389' Processing helix chain 'p' and resid 390 through 395 removed outlier: 4.281A pdb=" N PHE p 394 " --> pdb=" O VAL p 390 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG p 395 " --> pdb=" O LEU p 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 390 through 395' Processing sheet with id=AA1, first strand: chain 'A' and resid 143 through 154 removed outlier: 6.043A pdb=" N THR A 144 " --> pdb=" O LEU A 168 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LEU A 168 " --> pdb=" O THR A 144 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N SER A 146 " --> pdb=" O TYR A 166 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N TYR A 166 " --> pdb=" O SER A 146 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N VAL A 148 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N VAL A 164 " --> pdb=" O VAL A 148 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER A 150 " --> pdb=" O LYS A 162 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER A 158 " --> pdb=" O ASP A 154 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 194 through 198 Processing sheet with id=AA3, first strand: chain 'A' and resid 224 through 226 removed outlier: 3.882A pdb=" N GLU A 224 " --> pdb=" O LEU A 231 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N SER A 236 " --> pdb=" O ALA A 247 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'P' and resid 144 through 154 removed outlier: 5.462A pdb=" N SER P 146 " --> pdb=" O TYR P 166 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N TYR P 166 " --> pdb=" O SER P 146 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N VAL P 148 " --> pdb=" O VAL P 164 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N VAL P 164 " --> pdb=" O VAL P 148 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER P 158 " --> pdb=" O ASP P 154 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'P' and resid 194 through 201 Processing sheet with id=AA6, first strand: chain 'P' and resid 224 through 226 removed outlier: 4.877A pdb=" N SER P 236 " --> pdb=" O ALA P 247 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 143 through 154 removed outlier: 6.063A pdb=" N THR B 144 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LEU B 168 " --> pdb=" O THR B 144 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N SER B 146 " --> pdb=" O TYR B 166 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N TYR B 166 " --> pdb=" O SER B 146 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N VAL B 148 " --> pdb=" O VAL B 164 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N VAL B 164 " --> pdb=" O VAL B 148 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER B 150 " --> pdb=" O LYS B 162 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER B 158 " --> pdb=" O ASP B 154 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 194 through 198 Processing sheet with id=AA9, first strand: chain 'B' and resid 224 through 226 removed outlier: 3.917A pdb=" N GLU B 224 " --> pdb=" O LEU B 231 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N SER B 236 " --> pdb=" O ALA B 247 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'W' and resid 144 through 154 removed outlier: 5.446A pdb=" N SER W 146 " --> pdb=" O TYR W 166 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N TYR W 166 " --> pdb=" O SER W 146 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N VAL W 148 " --> pdb=" O VAL W 164 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N VAL W 164 " --> pdb=" O VAL W 148 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER W 158 " --> pdb=" O ASP W 154 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'W' and resid 194 through 201 Processing sheet with id=AB3, first strand: chain 'W' and resid 224 through 226 removed outlier: 4.871A pdb=" N SER W 236 " --> pdb=" O ALA W 247 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 143 through 154 removed outlier: 6.075A pdb=" N THR C 144 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LEU C 168 " --> pdb=" O THR C 144 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N SER C 146 " --> pdb=" O TYR C 166 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N TYR C 166 " --> pdb=" O SER C 146 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N VAL C 148 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N VAL C 164 " --> pdb=" O VAL C 148 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER C 150 " --> pdb=" O LYS C 162 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER C 158 " --> pdb=" O ASP C 154 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 194 through 198 Processing sheet with id=AB6, first strand: chain 'C' and resid 224 through 226 removed outlier: 3.864A pdb=" N GLU C 224 " --> pdb=" O LEU C 231 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL C 276 " --> pdb=" O ILE C 259 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N ILE C 259 " --> pdb=" O VAL C 276 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'X' and resid 144 through 154 removed outlier: 6.818A pdb=" N LYS X 162 " --> pdb=" O GLY X 149 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N PHE X 151 " --> pdb=" O ALA X 160 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ALA X 160 " --> pdb=" O PHE X 151 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ARG X 153 " --> pdb=" O SER X 158 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N SER X 158 " --> pdb=" O ARG X 153 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'X' and resid 194 through 201 Processing sheet with id=AB9, first strand: chain 'X' and resid 224 through 226 removed outlier: 4.827A pdb=" N SER X 236 " --> pdb=" O ALA X 247 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 143 through 154 removed outlier: 6.039A pdb=" N THR D 144 " --> pdb=" O LEU D 168 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N LEU D 168 " --> pdb=" O THR D 144 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N SER D 146 " --> pdb=" O TYR D 166 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N TYR D 166 " --> pdb=" O SER D 146 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N VAL D 148 " --> pdb=" O VAL D 164 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N VAL D 164 " --> pdb=" O VAL D 148 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER D 150 " --> pdb=" O LYS D 162 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER D 158 " --> pdb=" O ASP D 154 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 194 through 198 Processing sheet with id=AC3, first strand: chain 'D' and resid 224 through 226 removed outlier: 3.840A pdb=" N GLU D 224 " --> pdb=" O LEU D 231 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'Y' and resid 144 through 154 removed outlier: 5.451A pdb=" N SER Y 146 " --> pdb=" O TYR Y 166 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N TYR Y 166 " --> pdb=" O SER Y 146 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N VAL Y 148 " --> pdb=" O VAL Y 164 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N VAL Y 164 " --> pdb=" O VAL Y 148 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER Y 158 " --> pdb=" O ASP Y 154 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'Y' and resid 194 through 201 Processing sheet with id=AC6, first strand: chain 'Y' and resid 224 through 226 removed outlier: 4.861A pdb=" N SER Y 236 " --> pdb=" O ALA Y 247 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL Y 276 " --> pdb=" O ILE Y 259 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N ILE Y 259 " --> pdb=" O VAL Y 276 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 143 through 154 removed outlier: 6.044A pdb=" N THR E 144 " --> pdb=" O LEU E 168 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LEU E 168 " --> pdb=" O THR E 144 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N SER E 146 " --> pdb=" O TYR E 166 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N TYR E 166 " --> pdb=" O SER E 146 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N VAL E 148 " --> pdb=" O VAL E 164 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N VAL E 164 " --> pdb=" O VAL E 148 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER E 150 " --> pdb=" O LYS E 162 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER E 158 " --> pdb=" O ASP E 154 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 194 through 198 Processing sheet with id=AC9, first strand: chain 'E' and resid 224 through 226 removed outlier: 3.898A pdb=" N GLU E 224 " --> pdb=" O LEU E 231 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N SER E 236 " --> pdb=" O ALA E 247 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'Z' and resid 144 through 154 removed outlier: 5.453A pdb=" N SER Z 146 " --> pdb=" O TYR Z 166 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N TYR Z 166 " --> pdb=" O SER Z 146 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N VAL Z 148 " --> pdb=" O VAL Z 164 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N VAL Z 164 " --> pdb=" O VAL Z 148 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER Z 158 " --> pdb=" O ASP Z 154 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'Z' and resid 194 through 201 Processing sheet with id=AD3, first strand: chain 'Z' and resid 224 through 226 removed outlier: 4.945A pdb=" N SER Z 236 " --> pdb=" O ALA Z 247 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 143 through 154 removed outlier: 6.059A pdb=" N THR F 144 " --> pdb=" O LEU F 168 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LEU F 168 " --> pdb=" O THR F 144 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N SER F 146 " --> pdb=" O TYR F 166 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N TYR F 166 " --> pdb=" O SER F 146 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N VAL F 148 " --> pdb=" O VAL F 164 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N VAL F 164 " --> pdb=" O VAL F 148 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER F 150 " --> pdb=" O LYS F 162 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER F 158 " --> pdb=" O ASP F 154 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 194 through 198 Processing sheet with id=AD6, first strand: chain 'F' and resid 224 through 226 removed outlier: 3.842A pdb=" N GLU F 224 " --> pdb=" O LEU F 231 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'a' and resid 144 through 154 removed outlier: 6.771A pdb=" N LYS a 162 " --> pdb=" O GLY a 149 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N PHE a 151 " --> pdb=" O ALA a 160 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ALA a 160 " --> pdb=" O PHE a 151 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ARG a 153 " --> pdb=" O SER a 158 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N SER a 158 " --> pdb=" O ARG a 153 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'a' and resid 194 through 201 Processing sheet with id=AD9, first strand: chain 'a' and resid 224 through 226 removed outlier: 4.896A pdb=" N SER a 236 " --> pdb=" O ALA a 247 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N VAL a 276 " --> pdb=" O ILE a 259 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N ILE a 259 " --> pdb=" O VAL a 276 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 143 through 154 removed outlier: 6.084A pdb=" N THR G 144 " --> pdb=" O LEU G 168 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LEU G 168 " --> pdb=" O THR G 144 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N SER G 146 " --> pdb=" O TYR G 166 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N TYR G 166 " --> pdb=" O SER G 146 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N VAL G 148 " --> pdb=" O VAL G 164 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N VAL G 164 " --> pdb=" O VAL G 148 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER G 150 " --> pdb=" O LYS G 162 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER G 158 " --> pdb=" O ASP G 154 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 194 through 198 Processing sheet with id=AE3, first strand: chain 'G' and resid 224 through 226 removed outlier: 3.885A pdb=" N GLU G 224 " --> pdb=" O LEU G 231 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N SER G 236 " --> pdb=" O ALA G 247 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'b' and resid 144 through 154 removed outlier: 6.771A pdb=" N LYS b 162 " --> pdb=" O GLY b 149 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N PHE b 151 " --> pdb=" O ALA b 160 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ALA b 160 " --> pdb=" O PHE b 151 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ARG b 153 " --> pdb=" O SER b 158 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N SER b 158 " --> pdb=" O ARG b 153 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'b' and resid 194 through 201 Processing sheet with id=AE6, first strand: chain 'b' and resid 224 through 226 removed outlier: 4.847A pdb=" N SER b 236 " --> pdb=" O ALA b 247 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N VAL b 276 " --> pdb=" O ILE b 259 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N ILE b 259 " --> pdb=" O VAL b 276 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 143 through 154 removed outlier: 6.056A pdb=" N THR H 144 " --> pdb=" O LEU H 168 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LEU H 168 " --> pdb=" O THR H 144 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N SER H 146 " --> pdb=" O TYR H 166 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N TYR H 166 " --> pdb=" O SER H 146 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N VAL H 148 " --> pdb=" O VAL H 164 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N VAL H 164 " --> pdb=" O VAL H 148 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER H 150 " --> pdb=" O LYS H 162 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER H 158 " --> pdb=" O ASP H 154 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 194 through 198 Processing sheet with id=AE9, first strand: chain 'H' and resid 224 through 226 removed outlier: 3.921A pdb=" N GLU H 224 " --> pdb=" O LEU H 231 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N SER H 236 " --> pdb=" O ALA H 247 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL H 276 " --> pdb=" O ILE H 259 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N ILE H 259 " --> pdb=" O VAL H 276 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'c' and resid 144 through 154 removed outlier: 5.446A pdb=" N SER c 146 " --> pdb=" O TYR c 166 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N TYR c 166 " --> pdb=" O SER c 146 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N VAL c 148 " --> pdb=" O VAL c 164 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N VAL c 164 " --> pdb=" O VAL c 148 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER c 158 " --> pdb=" O ASP c 154 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'c' and resid 194 through 201 Processing sheet with id=AF3, first strand: chain 'c' and resid 224 through 226 removed outlier: 4.968A pdb=" N SER c 236 " --> pdb=" O ALA c 247 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL c 276 " --> pdb=" O ILE c 259 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N ILE c 259 " --> pdb=" O VAL c 276 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 143 through 154 removed outlier: 6.083A pdb=" N THR I 144 " --> pdb=" O LEU I 168 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N LEU I 168 " --> pdb=" O THR I 144 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N SER I 146 " --> pdb=" O TYR I 166 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N TYR I 166 " --> pdb=" O SER I 146 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N VAL I 148 " --> pdb=" O VAL I 164 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N VAL I 164 " --> pdb=" O VAL I 148 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER I 150 " --> pdb=" O LYS I 162 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER I 158 " --> pdb=" O ASP I 154 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 194 through 198 Processing sheet with id=AF6, first strand: chain 'I' and resid 224 through 226 removed outlier: 3.848A pdb=" N GLU I 224 " --> pdb=" O LEU I 231 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N SER I 236 " --> pdb=" O ALA I 247 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'd' and resid 144 through 154 removed outlier: 5.494A pdb=" N SER d 146 " --> pdb=" O TYR d 166 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N TYR d 166 " --> pdb=" O SER d 146 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N VAL d 148 " --> pdb=" O VAL d 164 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N VAL d 164 " --> pdb=" O VAL d 148 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER d 158 " --> pdb=" O ASP d 154 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'd' and resid 194 through 201 Processing sheet with id=AF9, first strand: chain 'd' and resid 224 through 226 removed outlier: 4.847A pdb=" N SER d 236 " --> pdb=" O ALA d 247 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL d 276 " --> pdb=" O ILE d 259 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N ILE d 259 " --> pdb=" O VAL d 276 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'J' and resid 143 through 154 removed outlier: 6.044A pdb=" N THR J 144 " --> pdb=" O LEU J 168 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LEU J 168 " --> pdb=" O THR J 144 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N SER J 146 " --> pdb=" O TYR J 166 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N TYR J 166 " --> pdb=" O SER J 146 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N VAL J 148 " --> pdb=" O VAL J 164 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N VAL J 164 " --> pdb=" O VAL J 148 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER J 150 " --> pdb=" O LYS J 162 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER J 158 " --> pdb=" O ASP J 154 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'J' and resid 194 through 198 Processing sheet with id=AG3, first strand: chain 'J' and resid 224 through 226 removed outlier: 3.881A pdb=" N GLU J 224 " --> pdb=" O LEU J 231 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N SER J 236 " --> pdb=" O ALA J 247 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'e' and resid 144 through 154 removed outlier: 6.808A pdb=" N LYS e 162 " --> pdb=" O GLY e 149 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N PHE e 151 " --> pdb=" O ALA e 160 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ALA e 160 " --> pdb=" O PHE e 151 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ARG e 153 " --> pdb=" O SER e 158 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N SER e 158 " --> pdb=" O ARG e 153 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'e' and resid 194 through 201 Processing sheet with id=AG6, first strand: chain 'e' and resid 224 through 226 removed outlier: 4.806A pdb=" N SER e 236 " --> pdb=" O ALA e 247 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL e 276 " --> pdb=" O ILE e 259 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N ILE e 259 " --> pdb=" O VAL e 276 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'K' and resid 143 through 154 removed outlier: 6.066A pdb=" N THR K 144 " --> pdb=" O LEU K 168 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LEU K 168 " --> pdb=" O THR K 144 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N SER K 146 " --> pdb=" O TYR K 166 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N TYR K 166 " --> pdb=" O SER K 146 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N VAL K 148 " --> pdb=" O VAL K 164 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N VAL K 164 " --> pdb=" O VAL K 148 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER K 150 " --> pdb=" O LYS K 162 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER K 158 " --> pdb=" O ASP K 154 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'K' and resid 194 through 198 Processing sheet with id=AG9, first strand: chain 'K' and resid 224 through 226 removed outlier: 3.895A pdb=" N GLU K 224 " --> pdb=" O LEU K 231 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N SER K 236 " --> pdb=" O ALA K 247 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'f' and resid 144 through 154 removed outlier: 6.819A pdb=" N LYS f 162 " --> pdb=" O GLY f 149 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N PHE f 151 " --> pdb=" O ALA f 160 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ALA f 160 " --> pdb=" O PHE f 151 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ARG f 153 " --> pdb=" O SER f 158 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N SER f 158 " --> pdb=" O ARG f 153 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'f' and resid 194 through 201 Processing sheet with id=AH3, first strand: chain 'f' and resid 224 through 226 removed outlier: 4.959A pdb=" N SER f 236 " --> pdb=" O ALA f 247 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL f 276 " --> pdb=" O ILE f 259 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N ILE f 259 " --> pdb=" O VAL f 276 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'L' and resid 143 through 154 removed outlier: 6.046A pdb=" N THR L 144 " --> pdb=" O LEU L 168 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LEU L 168 " --> pdb=" O THR L 144 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N SER L 146 " --> pdb=" O TYR L 166 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N TYR L 166 " --> pdb=" O SER L 146 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N VAL L 148 " --> pdb=" O VAL L 164 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N VAL L 164 " --> pdb=" O VAL L 148 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER L 150 " --> pdb=" O LYS L 162 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER L 158 " --> pdb=" O ASP L 154 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'L' and resid 194 through 198 Processing sheet with id=AH6, first strand: chain 'L' and resid 224 through 226 removed outlier: 3.827A pdb=" N GLU L 224 " --> pdb=" O LEU L 231 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N SER L 236 " --> pdb=" O ALA L 247 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'g' and resid 144 through 154 removed outlier: 5.423A pdb=" N SER g 146 " --> pdb=" O TYR g 166 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N TYR g 166 " --> pdb=" O SER g 146 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N VAL g 148 " --> pdb=" O VAL g 164 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N VAL g 164 " --> pdb=" O VAL g 148 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER g 158 " --> pdb=" O ASP g 154 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'g' and resid 194 through 201 Processing sheet with id=AH9, first strand: chain 'g' and resid 224 through 226 removed outlier: 4.877A pdb=" N SER g 236 " --> pdb=" O ALA g 247 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL g 276 " --> pdb=" O ILE g 259 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N ILE g 259 " --> pdb=" O VAL g 276 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'M' and resid 143 through 154 removed outlier: 6.051A pdb=" N THR M 144 " --> pdb=" O LEU M 168 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N LEU M 168 " --> pdb=" O THR M 144 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N SER M 146 " --> pdb=" O TYR M 166 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N TYR M 166 " --> pdb=" O SER M 146 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N VAL M 148 " --> pdb=" O VAL M 164 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N VAL M 164 " --> pdb=" O VAL M 148 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER M 150 " --> pdb=" O LYS M 162 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER M 158 " --> pdb=" O ASP M 154 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'M' and resid 194 through 198 Processing sheet with id=AI3, first strand: chain 'M' and resid 224 through 226 removed outlier: 3.896A pdb=" N GLU M 224 " --> pdb=" O LEU M 231 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N SER M 236 " --> pdb=" O ALA M 247 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'h' and resid 144 through 154 removed outlier: 6.814A pdb=" N LYS h 162 " --> pdb=" O GLY h 149 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N PHE h 151 " --> pdb=" O ALA h 160 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ALA h 160 " --> pdb=" O PHE h 151 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ARG h 153 " --> pdb=" O SER h 158 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N SER h 158 " --> pdb=" O ARG h 153 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'h' and resid 194 through 201 Processing sheet with id=AI6, first strand: chain 'h' and resid 224 through 226 removed outlier: 4.880A pdb=" N SER h 236 " --> pdb=" O ALA h 247 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL h 276 " --> pdb=" O ILE h 259 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N ILE h 259 " --> pdb=" O VAL h 276 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'N' and resid 143 through 154 removed outlier: 6.075A pdb=" N THR N 144 " --> pdb=" O LEU N 168 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LEU N 168 " --> pdb=" O THR N 144 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N SER N 146 " --> pdb=" O TYR N 166 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N TYR N 166 " --> pdb=" O SER N 146 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N VAL N 148 " --> pdb=" O VAL N 164 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N VAL N 164 " --> pdb=" O VAL N 148 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER N 150 " --> pdb=" O LYS N 162 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER N 158 " --> pdb=" O ASP N 154 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'N' and resid 194 through 198 Processing sheet with id=AI9, first strand: chain 'N' and resid 224 through 226 removed outlier: 3.836A pdb=" N GLU N 224 " --> pdb=" O LEU N 231 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N SER N 236 " --> pdb=" O ALA N 247 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'i' and resid 144 through 154 removed outlier: 6.838A pdb=" N LYS i 162 " --> pdb=" O GLY i 149 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N PHE i 151 " --> pdb=" O ALA i 160 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ALA i 160 " --> pdb=" O PHE i 151 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ARG i 153 " --> pdb=" O SER i 158 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N SER i 158 " --> pdb=" O ARG i 153 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'i' and resid 194 through 201 Processing sheet with id=AJ3, first strand: chain 'i' and resid 224 through 226 removed outlier: 4.846A pdb=" N SER i 236 " --> pdb=" O ALA i 247 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL i 276 " --> pdb=" O ILE i 259 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ILE i 259 " --> pdb=" O VAL i 276 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'O' and resid 143 through 154 removed outlier: 6.060A pdb=" N THR O 144 " --> pdb=" O LEU O 168 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N LEU O 168 " --> pdb=" O THR O 144 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N SER O 146 " --> pdb=" O TYR O 166 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N TYR O 166 " --> pdb=" O SER O 146 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N VAL O 148 " --> pdb=" O VAL O 164 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N VAL O 164 " --> pdb=" O VAL O 148 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER O 150 " --> pdb=" O LYS O 162 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER O 158 " --> pdb=" O ASP O 154 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'O' and resid 194 through 198 Processing sheet with id=AJ6, first strand: chain 'O' and resid 224 through 226 removed outlier: 3.880A pdb=" N GLU O 224 " --> pdb=" O LEU O 231 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N SER O 236 " --> pdb=" O ALA O 247 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL O 276 " --> pdb=" O ILE O 259 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N ILE O 259 " --> pdb=" O VAL O 276 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'j' and resid 144 through 154 removed outlier: 5.452A pdb=" N SER j 146 " --> pdb=" O TYR j 166 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N TYR j 166 " --> pdb=" O SER j 146 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N VAL j 148 " --> pdb=" O VAL j 164 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N VAL j 164 " --> pdb=" O VAL j 148 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER j 158 " --> pdb=" O ASP j 154 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'j' and resid 194 through 201 Processing sheet with id=AJ9, first strand: chain 'j' and resid 224 through 226 removed outlier: 4.860A pdb=" N SER j 236 " --> pdb=" O ALA j 247 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL j 276 " --> pdb=" O ILE j 259 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N ILE j 259 " --> pdb=" O VAL j 276 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'Q' and resid 143 through 154 removed outlier: 6.062A pdb=" N THR Q 144 " --> pdb=" O LEU Q 168 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N LEU Q 168 " --> pdb=" O THR Q 144 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N SER Q 146 " --> pdb=" O TYR Q 166 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N TYR Q 166 " --> pdb=" O SER Q 146 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N VAL Q 148 " --> pdb=" O VAL Q 164 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N VAL Q 164 " --> pdb=" O VAL Q 148 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER Q 150 " --> pdb=" O LYS Q 162 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER Q 158 " --> pdb=" O ASP Q 154 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'Q' and resid 194 through 198 Processing sheet with id=AK3, first strand: chain 'Q' and resid 224 through 226 removed outlier: 3.907A pdb=" N GLU Q 224 " --> pdb=" O LEU Q 231 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N SER Q 236 " --> pdb=" O ALA Q 247 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'k' and resid 144 through 154 removed outlier: 5.457A pdb=" N SER k 146 " --> pdb=" O TYR k 166 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N TYR k 166 " --> pdb=" O SER k 146 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N VAL k 148 " --> pdb=" O VAL k 164 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N VAL k 164 " --> pdb=" O VAL k 148 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER k 158 " --> pdb=" O ASP k 154 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'k' and resid 194 through 201 Processing sheet with id=AK6, first strand: chain 'k' and resid 224 through 226 removed outlier: 4.826A pdb=" N SER k 236 " --> pdb=" O ALA k 247 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL k 276 " --> pdb=" O ILE k 259 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N ILE k 259 " --> pdb=" O VAL k 276 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'R' and resid 143 through 154 removed outlier: 6.046A pdb=" N THR R 144 " --> pdb=" O LEU R 168 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LEU R 168 " --> pdb=" O THR R 144 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N SER R 146 " --> pdb=" O TYR R 166 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N TYR R 166 " --> pdb=" O SER R 146 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N VAL R 148 " --> pdb=" O VAL R 164 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N VAL R 164 " --> pdb=" O VAL R 148 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER R 150 " --> pdb=" O LYS R 162 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER R 158 " --> pdb=" O ASP R 154 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'R' and resid 194 through 198 Processing sheet with id=AK9, first strand: chain 'R' and resid 224 through 226 removed outlier: 3.848A pdb=" N GLU R 224 " --> pdb=" O LEU R 231 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'l' and resid 144 through 154 removed outlier: 6.823A pdb=" N LYS l 162 " --> pdb=" O GLY l 149 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N PHE l 151 " --> pdb=" O ALA l 160 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ALA l 160 " --> pdb=" O PHE l 151 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ARG l 153 " --> pdb=" O SER l 158 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N SER l 158 " --> pdb=" O ARG l 153 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'l' and resid 194 through 201 Processing sheet with id=AL3, first strand: chain 'l' and resid 224 through 226 removed outlier: 4.880A pdb=" N SER l 236 " --> pdb=" O ALA l 247 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'S' and resid 143 through 154 removed outlier: 6.073A pdb=" N THR S 144 " --> pdb=" O LEU S 168 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LEU S 168 " --> pdb=" O THR S 144 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N SER S 146 " --> pdb=" O TYR S 166 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N TYR S 166 " --> pdb=" O SER S 146 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N VAL S 148 " --> pdb=" O VAL S 164 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N VAL S 164 " --> pdb=" O VAL S 148 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER S 150 " --> pdb=" O LYS S 162 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER S 158 " --> pdb=" O ASP S 154 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'S' and resid 194 through 198 Processing sheet with id=AL6, first strand: chain 'S' and resid 224 through 226 removed outlier: 3.877A pdb=" N GLU S 224 " --> pdb=" O LEU S 231 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N SER S 236 " --> pdb=" O ALA S 247 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'm' and resid 144 through 154 removed outlier: 5.474A pdb=" N SER m 146 " --> pdb=" O TYR m 166 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N TYR m 166 " --> pdb=" O SER m 146 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N VAL m 148 " --> pdb=" O VAL m 164 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N VAL m 164 " --> pdb=" O VAL m 148 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER m 158 " --> pdb=" O ASP m 154 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'm' and resid 194 through 201 Processing sheet with id=AL9, first strand: chain 'm' and resid 224 through 226 removed outlier: 4.827A pdb=" N SER m 236 " --> pdb=" O ALA m 247 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL m 276 " --> pdb=" O ILE m 259 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N ILE m 259 " --> pdb=" O VAL m 276 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'T' and resid 143 through 154 removed outlier: 6.052A pdb=" N THR T 144 " --> pdb=" O LEU T 168 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LEU T 168 " --> pdb=" O THR T 144 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N SER T 146 " --> pdb=" O TYR T 166 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N TYR T 166 " --> pdb=" O SER T 146 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N VAL T 148 " --> pdb=" O VAL T 164 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N VAL T 164 " --> pdb=" O VAL T 148 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER T 150 " --> pdb=" O LYS T 162 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER T 158 " --> pdb=" O ASP T 154 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'T' and resid 194 through 198 Processing sheet with id=AM3, first strand: chain 'T' and resid 224 through 226 removed outlier: 3.864A pdb=" N GLU T 224 " --> pdb=" O LEU T 231 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'n' and resid 144 through 154 removed outlier: 6.786A pdb=" N LYS n 162 " --> pdb=" O GLY n 149 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N PHE n 151 " --> pdb=" O ALA n 160 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ALA n 160 " --> pdb=" O PHE n 151 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ARG n 153 " --> pdb=" O SER n 158 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N SER n 158 " --> pdb=" O ARG n 153 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'n' and resid 194 through 201 Processing sheet with id=AM6, first strand: chain 'n' and resid 224 through 226 removed outlier: 4.844A pdb=" N SER n 236 " --> pdb=" O ALA n 247 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL n 276 " --> pdb=" O ILE n 259 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N ILE n 259 " --> pdb=" O VAL n 276 " (cutoff:3.500A) Processing sheet with id=AM7, first strand: chain 'U' and resid 143 through 154 removed outlier: 6.077A pdb=" N THR U 144 " --> pdb=" O LEU U 168 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU U 168 " --> pdb=" O THR U 144 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N SER U 146 " --> pdb=" O TYR U 166 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N TYR U 166 " --> pdb=" O SER U 146 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N VAL U 148 " --> pdb=" O VAL U 164 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N VAL U 164 " --> pdb=" O VAL U 148 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER U 150 " --> pdb=" O LYS U 162 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER U 158 " --> pdb=" O ASP U 154 " (cutoff:3.500A) Processing sheet with id=AM8, first strand: chain 'U' and resid 194 through 198 Processing sheet with id=AM9, first strand: chain 'U' and resid 224 through 226 removed outlier: 3.861A pdb=" N GLU U 224 " --> pdb=" O LEU U 231 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N SER U 236 " --> pdb=" O ALA U 247 " (cutoff:3.500A) Processing sheet with id=AN1, first strand: chain 'o' and resid 144 through 154 removed outlier: 6.797A pdb=" N LYS o 162 " --> pdb=" O GLY o 149 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N PHE o 151 " --> pdb=" O ALA o 160 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ALA o 160 " --> pdb=" O PHE o 151 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ARG o 153 " --> pdb=" O SER o 158 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N SER o 158 " --> pdb=" O ARG o 153 " (cutoff:3.500A) Processing sheet with id=AN2, first strand: chain 'o' and resid 194 through 201 Processing sheet with id=AN3, first strand: chain 'o' and resid 224 through 226 removed outlier: 5.034A pdb=" N SER o 236 " --> pdb=" O ALA o 247 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL o 276 " --> pdb=" O ILE o 259 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N ILE o 259 " --> pdb=" O VAL o 276 " (cutoff:3.500A) Processing sheet with id=AN4, first strand: chain 'V' and resid 143 through 154 removed outlier: 6.029A pdb=" N THR V 144 " --> pdb=" O LEU V 168 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N LEU V 168 " --> pdb=" O THR V 144 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N SER V 146 " --> pdb=" O TYR V 166 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N TYR V 166 " --> pdb=" O SER V 146 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N VAL V 148 " --> pdb=" O VAL V 164 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N VAL V 164 " --> pdb=" O VAL V 148 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER V 150 " --> pdb=" O LYS V 162 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER V 158 " --> pdb=" O ASP V 154 " (cutoff:3.500A) Processing sheet with id=AN5, first strand: chain 'V' and resid 194 through 198 Processing sheet with id=AN6, first strand: chain 'V' and resid 224 through 226 removed outlier: 3.839A pdb=" N GLU V 224 " --> pdb=" O LEU V 231 " (cutoff:3.500A) Processing sheet with id=AN7, first strand: chain 'p' and resid 144 through 154 removed outlier: 6.810A pdb=" N LYS p 162 " --> pdb=" O GLY p 149 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N PHE p 151 " --> pdb=" O ALA p 160 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ALA p 160 " --> pdb=" O PHE p 151 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ARG p 153 " --> pdb=" O SER p 158 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N SER p 158 " --> pdb=" O ARG p 153 " (cutoff:3.500A) Processing sheet with id=AN8, first strand: chain 'p' and resid 194 through 201 Processing sheet with id=AN9, first strand: chain 'p' and resid 224 through 226 removed outlier: 4.908A pdb=" N SER p 236 " --> pdb=" O ALA p 247 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL p 276 " --> pdb=" O ILE p 259 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N ILE p 259 " --> pdb=" O VAL p 276 " (cutoff:3.500A) 8326 hydrogen bonds defined for protein. 24228 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: 60.20 Time building geometry restraints manager: 40.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 41532 1.34 - 1.46: 20627 1.46 - 1.58: 57331 1.58 - 1.70: 0 1.70 - 1.82: 588 Bond restraints: 120078 Sorted by residual: bond pdb=" CG1 ILE B 112 " pdb=" CD1 ILE B 112 " ideal model delta sigma weight residual 1.513 1.457 0.056 3.90e-02 6.57e+02 2.08e+00 bond pdb=" CG1 ILE H 112 " pdb=" CD1 ILE H 112 " ideal model delta sigma weight residual 1.513 1.458 0.055 3.90e-02 6.57e+02 2.01e+00 bond pdb=" CG1 ILE D 112 " pdb=" CD1 ILE D 112 " ideal model delta sigma weight residual 1.513 1.458 0.055 3.90e-02 6.57e+02 2.01e+00 bond pdb=" CG1 ILE S 112 " pdb=" CD1 ILE S 112 " ideal model delta sigma weight residual 1.513 1.462 0.051 3.90e-02 6.57e+02 1.72e+00 bond pdb=" CG ARG O 30 " pdb=" CD ARG O 30 " ideal model delta sigma weight residual 1.520 1.486 0.034 3.00e-02 1.11e+03 1.32e+00 ... (remaining 120073 not shown) Histogram of bond angle deviations from ideal: 98.15 - 105.32: 400 105.32 - 112.48: 65500 112.48 - 119.65: 38006 119.65 - 126.82: 58639 126.82 - 133.99: 625 Bond angle restraints: 163170 Sorted by residual: angle pdb=" N GLU O 110 " pdb=" CA GLU O 110 " pdb=" CB GLU O 110 " ideal model delta sigma weight residual 110.28 116.70 -6.42 1.55e+00 4.16e-01 1.72e+01 angle pdb=" N GLU T 110 " pdb=" CA GLU T 110 " pdb=" CB GLU T 110 " ideal model delta sigma weight residual 110.28 116.70 -6.42 1.55e+00 4.16e-01 1.71e+01 angle pdb=" C GLN g 109 " pdb=" N GLU g 110 " pdb=" CA GLU g 110 " ideal model delta sigma weight residual 120.31 115.27 5.04 1.52e+00 4.33e-01 1.10e+01 angle pdb=" C GLN l 109 " pdb=" N GLU l 110 " pdb=" CA GLU l 110 " ideal model delta sigma weight residual 120.31 115.28 5.03 1.52e+00 4.33e-01 1.10e+01 angle pdb=" C GLN O 109 " pdb=" N GLU O 110 " pdb=" CA GLU O 110 " ideal model delta sigma weight residual 120.31 115.29 5.02 1.52e+00 4.33e-01 1.09e+01 ... (remaining 163165 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 66421 17.55 - 35.09: 4750 35.09 - 52.64: 809 52.64 - 70.18: 237 70.18 - 87.73: 107 Dihedral angle restraints: 72324 sinusoidal: 25032 harmonic: 47292 Sorted by residual: dihedral pdb=" CA ASP P 358 " pdb=" C ASP P 358 " pdb=" N MET P 359 " pdb=" CA MET P 359 " ideal model delta harmonic sigma weight residual -180.00 -161.87 -18.13 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA ASP a 358 " pdb=" C ASP a 358 " pdb=" N MET a 359 " pdb=" CA MET a 359 " ideal model delta harmonic sigma weight residual -180.00 -162.74 -17.26 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA ASP d 358 " pdb=" C ASP d 358 " pdb=" N MET d 359 " pdb=" CA MET d 359 " ideal model delta harmonic sigma weight residual -180.00 -162.86 -17.14 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 72321 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 13593 0.028 - 0.057: 4154 0.057 - 0.085: 1578 0.085 - 0.114: 768 0.114 - 0.142: 109 Chirality restraints: 20202 Sorted by residual: chirality pdb=" CA ASN J 43 " pdb=" N ASN J 43 " pdb=" C ASN J 43 " pdb=" CB ASN J 43 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.07e-01 chirality pdb=" CA ASN M 43 " pdb=" N ASN M 43 " pdb=" C ASN M 43 " pdb=" CB ASN M 43 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.01e-01 chirality pdb=" CA ASN G 43 " pdb=" N ASN G 43 " pdb=" C ASN G 43 " pdb=" CB ASN G 43 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.00e-01 ... (remaining 20199 not shown) Planarity restraints: 21336 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN H 294 " 0.011 2.00e-02 2.50e+03 2.15e-02 4.63e+00 pdb=" C ASN H 294 " -0.037 2.00e-02 2.50e+03 pdb=" O ASN H 294 " 0.014 2.00e-02 2.50e+03 pdb=" N ILE H 295 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP J 185 " 0.010 2.00e-02 2.50e+03 2.08e-02 4.32e+00 pdb=" CG ASP J 185 " -0.036 2.00e-02 2.50e+03 pdb=" OD1 ASP J 185 " 0.013 2.00e-02 2.50e+03 pdb=" OD2 ASP J 185 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP N 185 " -0.010 2.00e-02 2.50e+03 2.02e-02 4.09e+00 pdb=" CG ASP N 185 " 0.035 2.00e-02 2.50e+03 pdb=" OD1 ASP N 185 " -0.013 2.00e-02 2.50e+03 pdb=" OD2 ASP N 185 " -0.012 2.00e-02 2.50e+03 ... (remaining 21333 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 2429 2.69 - 3.24: 126176 3.24 - 3.79: 189551 3.79 - 4.35: 228397 4.35 - 4.90: 391229 Nonbonded interactions: 937782 Sorted by model distance: nonbonded pdb=" OG SER d 191 " pdb=" OG SER d 194 " model vdw 2.135 2.440 nonbonded pdb=" OG SER h 191 " pdb=" OG SER h 194 " model vdw 2.141 2.440 nonbonded pdb=" OG SER m 191 " pdb=" OG SER m 194 " model vdw 2.141 2.440 nonbonded pdb=" OG SER p 191 " pdb=" OG SER p 194 " model vdw 2.145 2.440 nonbonded pdb=" OG SER Y 191 " pdb=" OG SER Y 194 " model vdw 2.147 2.440 ... (remaining 937777 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' } 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: 3.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.100 Extract box with map and model: 15.790 Check model and map are aligned: 1.320 Set scattering table: 0.830 Process input model: 249.920 Find NCS groups from input model: 6.690 Set up NCS constraints: 1.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 281.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 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 : 0.002 0.056 120078 Z= 0.143 Angle : 0.525 10.195 163170 Z= 0.294 Chirality : 0.036 0.142 20202 Planarity : 0.003 0.043 21336 Dihedral : 13.549 87.729 41832 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 0.20 % Allowed : 0.07 % Favored : 99.73 % 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: 2.56 (0.07), residues: 16464 helix: 4.55 (0.05), residues: 8148 sheet: 1.46 (0.12), residues: 1617 loop : -2.22 (0.06), residues: 6699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP Q 47 HIS 0.001 0.000 HIS E 208 PHE 0.008 0.001 PHE g 175 TYR 0.021 0.001 TYR j 78 ARG 0.010 0.001 ARG k 18 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 32928 Ramachandran restraints generated. 16464 Oldfield, 0 Emsley, 16464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 32928 Ramachandran restraints generated. 16464 Oldfield, 0 Emsley, 16464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1984 residues out of total 12768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 1958 time to evaluate : 9.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 269 ILE cc_start: 0.8636 (mm) cc_final: 0.8372 (mt) REVERT: W 269 ILE cc_start: 0.8598 (mm) cc_final: 0.8304 (mt) REVERT: C 111 GLU cc_start: 0.8731 (mt-10) cc_final: 0.8475 (mt-10) REVERT: C 300 MET cc_start: 0.7399 (mmm) cc_final: 0.7128 (tpt) REVERT: C 356 ASP cc_start: 0.7940 (m-30) cc_final: 0.7556 (m-30) REVERT: X 294 ASN cc_start: 0.8611 (m-40) cc_final: 0.8143 (t0) REVERT: X 356 ASP cc_start: 0.7826 (m-30) cc_final: 0.7625 (m-30) REVERT: D 53 MET cc_start: 0.9222 (mmp) cc_final: 0.8816 (mmp) REVERT: D 356 ASP cc_start: 0.8162 (m-30) cc_final: 0.7698 (m-30) REVERT: Y 11 MET cc_start: 0.9073 (mtp) cc_final: 0.8830 (mtt) REVERT: Y 20 ILE cc_start: 0.9259 (mt) cc_final: 0.9027 (mm) REVERT: E 356 ASP cc_start: 0.8243 (m-30) cc_final: 0.7890 (m-30) REVERT: Z 294 ASN cc_start: 0.8631 (m-40) cc_final: 0.8109 (t0) REVERT: F 356 ASP cc_start: 0.8090 (m-30) cc_final: 0.7709 (m-30) REVERT: a 205 GLU cc_start: 0.8041 (mp0) cc_final: 0.7837 (mp0) REVERT: G 294 ASN cc_start: 0.8498 (t0) cc_final: 0.8005 (t0) REVERT: G 300 MET cc_start: 0.7641 (tpp) cc_final: 0.7393 (tpt) REVERT: G 356 ASP cc_start: 0.8109 (m-30) cc_final: 0.7725 (m-30) REVERT: G 361 GLU cc_start: 0.7360 (tm-30) cc_final: 0.6954 (tm-30) REVERT: b 30 ARG cc_start: 0.8919 (tpp80) cc_final: 0.8336 (ttm-80) REVERT: b 111 GLU cc_start: 0.8731 (mm-30) cc_final: 0.8513 (mm-30) REVERT: H 356 ASP cc_start: 0.8009 (m-30) cc_final: 0.7509 (m-30) REVERT: c 269 ILE cc_start: 0.8695 (mm) cc_final: 0.8471 (mt) REVERT: I 294 ASN cc_start: 0.8487 (t0) cc_final: 0.7993 (t0) REVERT: I 356 ASP cc_start: 0.8038 (m-30) cc_final: 0.7693 (m-30) REVERT: J 356 ASP cc_start: 0.8042 (m-30) cc_final: 0.7626 (m-30) REVERT: J 384 ASN cc_start: 0.8743 (m110) cc_final: 0.8342 (m110) REVERT: e 30 ARG cc_start: 0.9064 (tpp80) cc_final: 0.8849 (ttm-80) REVERT: e 269 ILE cc_start: 0.8754 (mm) cc_final: 0.8405 (mt) REVERT: e 294 ASN cc_start: 0.8544 (m-40) cc_final: 0.8085 (t0) REVERT: e 313 ASP cc_start: 0.9037 (t70) cc_final: 0.8807 (t0) REVERT: K 3 SER cc_start: 0.8734 (p) cc_final: 0.8423 (p) REVERT: K 356 ASP cc_start: 0.8121 (m-30) cc_final: 0.7695 (m-30) REVERT: f 30 ARG cc_start: 0.8974 (tpp80) cc_final: 0.8570 (tpp80) REVERT: f 205 GLU cc_start: 0.8131 (mp0) cc_final: 0.7813 (mp0) REVERT: f 269 ILE cc_start: 0.8650 (mm) cc_final: 0.8355 (mt) REVERT: f 313 ASP cc_start: 0.8890 (t70) cc_final: 0.8594 (t0) REVERT: L 359 MET cc_start: 0.8711 (mmt) cc_final: 0.8482 (mmt) REVERT: M 348 GLU cc_start: 0.8859 (tm-30) cc_final: 0.8643 (tm-30) REVERT: M 356 ASP cc_start: 0.8165 (m-30) cc_final: 0.7818 (m-30) REVERT: M 361 GLU cc_start: 0.7192 (tm-30) cc_final: 0.6867 (tm-30) REVERT: M 365 ARG cc_start: 0.9134 (mtp85) cc_final: 0.8831 (mmm-85) REVERT: h 75 ASP cc_start: 0.9130 (m-30) cc_final: 0.8836 (m-30) REVERT: h 78 TYR cc_start: 0.8979 (t80) cc_final: 0.8687 (t80) REVERT: N 111 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7784 (tt0) REVERT: N 356 ASP cc_start: 0.8020 (m-30) cc_final: 0.7691 (m-30) REVERT: i 269 ILE cc_start: 0.8717 (mm) cc_final: 0.8434 (mt) REVERT: O 356 ASP cc_start: 0.8001 (m-30) cc_final: 0.7462 (m-30) REVERT: O 359 MET cc_start: 0.8941 (mmm) cc_final: 0.8619 (mmm) REVERT: j 269 ILE cc_start: 0.8645 (mm) cc_final: 0.8320 (mt) REVERT: j 313 ASP cc_start: 0.8931 (t70) cc_final: 0.8489 (t0) REVERT: Q 356 ASP cc_start: 0.8077 (m-30) cc_final: 0.7876 (m-30) REVERT: Q 359 MET cc_start: 0.8554 (mmt) cc_final: 0.8051 (mmt) REVERT: k 30 ARG cc_start: 0.8997 (tpp80) cc_final: 0.8458 (ttm-80) REVERT: R 294 ASN cc_start: 0.8426 (OUTLIER) cc_final: 0.8209 (t0) REVERT: R 356 ASP cc_start: 0.7987 (m-30) cc_final: 0.7643 (m-30) REVERT: R 359 MET cc_start: 0.8703 (mmt) cc_final: 0.8475 (mmt) REVERT: R 361 GLU cc_start: 0.7032 (tm-30) cc_final: 0.6807 (tm-30) REVERT: l 269 ILE cc_start: 0.8794 (mm) cc_final: 0.8519 (mt) REVERT: S 294 ASN cc_start: 0.8400 (OUTLIER) cc_final: 0.8111 (t0) REVERT: S 348 GLU cc_start: 0.8905 (tm-30) cc_final: 0.8380 (tm-30) REVERT: S 356 ASP cc_start: 0.8091 (m-30) cc_final: 0.7636 (m-30) REVERT: S 361 GLU cc_start: 0.7413 (tm-30) cc_final: 0.7011 (tm-30) REVERT: m 269 ILE cc_start: 0.8748 (mm) cc_final: 0.8390 (mt) REVERT: T 3 SER cc_start: 0.8884 (p) cc_final: 0.8470 (p) REVERT: T 11 MET cc_start: 0.9203 (mtm) cc_final: 0.8997 (mtm) REVERT: T 90 GLU cc_start: 0.9296 (tp30) cc_final: 0.9093 (tp30) REVERT: T 356 ASP cc_start: 0.7493 (m-30) cc_final: 0.7038 (m-30) REVERT: n 11 MET cc_start: 0.9399 (mtt) cc_final: 0.9168 (mtt) REVERT: n 78 TYR cc_start: 0.9257 (t80) cc_final: 0.9047 (t80) REVERT: U 294 ASN cc_start: 0.8525 (t0) cc_final: 0.8181 (t0) REVERT: o 30 ARG cc_start: 0.9054 (ttm-80) cc_final: 0.8802 (tpp80) REVERT: p 78 TYR cc_start: 0.9149 (t80) cc_final: 0.8900 (t80) REVERT: p 356 ASP cc_start: 0.7744 (m-30) cc_final: 0.7495 (m-30) outliers start: 26 outliers final: 1 residues processed: 1978 average time/residue: 0.9505 time to fit residues: 3308.5792 Evaluate side-chains 1373 residues out of total 12768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1370 time to evaluate : 9.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 294 ASN Chi-restraints excluded: chain R residue 294 ASN Chi-restraints excluded: chain S residue 294 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1638 random chunks: chunk 1383 optimal weight: 7.9990 chunk 1241 optimal weight: 10.0000 chunk 688 optimal weight: 6.9990 chunk 424 optimal weight: 3.9990 chunk 837 optimal weight: 9.9990 chunk 663 optimal weight: 2.9990 chunk 1283 optimal weight: 10.0000 chunk 496 optimal weight: 7.9990 chunk 780 optimal weight: 9.9990 chunk 955 optimal weight: 5.9990 chunk 1487 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 64 GLN W 118 GLN ** C 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 ASN Y 64 GLN E 242 ASN Z 28 GLN Z 64 GLN ** Z 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 336 GLN a 64 GLN ** a 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 336 GLN b 28 GLN b 64 GLN ** b 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 242 ASN c 64 GLN ** c 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 242 ASN I 336 GLN I 384 ASN d 64 GLN ** d 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 64 GLN ** e 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 64 GLN f 118 GLN ** f 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 242 ASN M 242 ASN h 64 GLN ** h 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 242 ASN i 118 GLN ** i 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 64 GLN j 118 GLN ** j 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 336 GLN R 242 ASN R 384 ASN S 28 GLN S 336 GLN ** T 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 242 ASN T 294 ASN T 336 GLN U 242 ASN U 336 GLN ** o 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 242 ASN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 120078 Z= 0.320 Angle : 0.563 7.682 163170 Z= 0.315 Chirality : 0.038 0.313 20202 Planarity : 0.003 0.046 21336 Dihedral : 5.083 57.847 17268 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 1.67 % Allowed : 6.76 % Favored : 91.57 % 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: 2.24 (0.07), residues: 16464 helix: 4.25 (0.05), residues: 8274 sheet: 0.82 (0.12), residues: 1638 loop : -2.31 (0.06), residues: 6552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP O 47 HIS 0.004 0.001 HIS n 208 PHE 0.025 0.002 PHE N 339 TYR 0.020 0.002 TYR i 78 ARG 0.016 0.001 ARG J 36 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 32928 Ramachandran restraints generated. 16464 Oldfield, 0 Emsley, 16464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 32928 Ramachandran restraints generated. 16464 Oldfield, 0 Emsley, 16464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1596 residues out of total 12768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 1383 time to evaluate : 9.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.9159 (mtp-110) cc_final: 0.8956 (ttp-110) REVERT: A 345 ASP cc_start: 0.8915 (OUTLIER) cc_final: 0.8545 (t0) REVERT: P 28 GLN cc_start: 0.8383 (tt0) cc_final: 0.8150 (mt0) REVERT: B 348 GLU cc_start: 0.9073 (tm-30) cc_final: 0.8762 (tm-30) REVERT: B 360 ASN cc_start: 0.8901 (OUTLIER) cc_final: 0.8624 (m-40) REVERT: C 82 GLU cc_start: 0.8983 (tt0) cc_final: 0.8364 (mt-10) REVERT: C 356 ASP cc_start: 0.8371 (m-30) cc_final: 0.8002 (m-30) REVERT: C 365 ARG cc_start: 0.9192 (mtp85) cc_final: 0.8972 (mtp180) REVERT: D 53 MET cc_start: 0.9222 (mmp) cc_final: 0.8812 (mmp) REVERT: D 319 MET cc_start: 0.9413 (mtm) cc_final: 0.9144 (mtm) REVERT: D 356 ASP cc_start: 0.8299 (m-30) cc_final: 0.8037 (m-30) REVERT: Y 30 ARG cc_start: 0.8925 (tpp80) cc_final: 0.8560 (tpp80) REVERT: E 356 ASP cc_start: 0.8506 (m-30) cc_final: 0.8296 (m-30) REVERT: E 361 GLU cc_start: 0.8151 (tm-30) cc_final: 0.7578 (tm-30) REVERT: F 229 TYR cc_start: 0.8456 (t80) cc_final: 0.8225 (t80) REVERT: F 300 MET cc_start: 0.7834 (mmm) cc_final: 0.7625 (tmm) REVERT: G 294 ASN cc_start: 0.8564 (t0) cc_final: 0.8104 (t0) REVERT: G 300 MET cc_start: 0.8019 (tpp) cc_final: 0.7678 (tpt) REVERT: G 348 GLU cc_start: 0.8939 (tm-30) cc_final: 0.8708 (tm-30) REVERT: G 361 GLU cc_start: 0.7784 (tm-30) cc_final: 0.7421 (tm-30) REVERT: c 269 ILE cc_start: 0.8728 (mm) cc_final: 0.8470 (mt) REVERT: I 294 ASN cc_start: 0.8575 (t0) cc_final: 0.8073 (t0) REVERT: I 300 MET cc_start: 0.7422 (mmm) cc_final: 0.6512 (tpt) REVERT: J 30 ARG cc_start: 0.8826 (mtp85) cc_final: 0.8608 (ttm-80) REVERT: J 90 GLU cc_start: 0.9096 (tp30) cc_final: 0.8848 (tp30) REVERT: J 338 GLU cc_start: 0.8528 (tm-30) cc_final: 0.8200 (tm-30) REVERT: e 81 MET cc_start: 0.9553 (tpp) cc_final: 0.9309 (mmt) REVERT: e 269 ILE cc_start: 0.8824 (mm) cc_final: 0.8466 (mt) REVERT: e 294 ASN cc_start: 0.8563 (m-40) cc_final: 0.8071 (t0) REVERT: e 313 ASP cc_start: 0.9134 (t70) cc_final: 0.8878 (t0) REVERT: K 90 GLU cc_start: 0.9019 (tp30) cc_final: 0.8712 (tp30) REVERT: K 356 ASP cc_start: 0.8469 (m-30) cc_final: 0.8218 (m-30) REVERT: f 30 ARG cc_start: 0.8886 (tpp80) cc_final: 0.8304 (ttm-80) REVERT: f 205 GLU cc_start: 0.8269 (mp0) cc_final: 0.8030 (mp0) REVERT: f 269 ILE cc_start: 0.8638 (mm) cc_final: 0.8313 (mt) REVERT: f 313 ASP cc_start: 0.9049 (t70) cc_final: 0.8677 (t0) REVERT: L 361 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7674 (tm-30) REVERT: g 67 LEU cc_start: 0.9395 (OUTLIER) cc_final: 0.9184 (mm) REVERT: M 348 GLU cc_start: 0.8874 (tm-30) cc_final: 0.8631 (tm-30) REVERT: M 361 GLU cc_start: 0.7493 (tm-30) cc_final: 0.6969 (tm-30) REVERT: h 81 MET cc_start: 0.9498 (tpp) cc_final: 0.9280 (tpt) REVERT: h 300 MET cc_start: 0.7800 (mmm) cc_final: 0.7572 (mtp) REVERT: N 82 GLU cc_start: 0.9001 (tt0) cc_final: 0.8540 (mt-10) REVERT: N 111 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7891 (tt0) REVERT: N 356 ASP cc_start: 0.8323 (m-30) cc_final: 0.8053 (m-30) REVERT: i 269 ILE cc_start: 0.8797 (mm) cc_final: 0.8496 (mt) REVERT: i 300 MET cc_start: 0.7386 (mtp) cc_final: 0.7066 (mtp) REVERT: O 53 MET cc_start: 0.8986 (mmm) cc_final: 0.8643 (mmp) REVERT: O 90 GLU cc_start: 0.9076 (tp30) cc_final: 0.8744 (tp30) REVERT: O 111 GLU cc_start: 0.7716 (mt-10) cc_final: 0.7289 (tt0) REVERT: O 356 ASP cc_start: 0.8256 (m-30) cc_final: 0.7975 (m-30) REVERT: j 30 ARG cc_start: 0.8885 (tpp80) cc_final: 0.8547 (tpp80) REVERT: j 78 TYR cc_start: 0.9075 (t80) cc_final: 0.8840 (t80) REVERT: j 269 ILE cc_start: 0.8689 (mm) cc_final: 0.8336 (mt) REVERT: j 313 ASP cc_start: 0.9008 (t70) cc_final: 0.8612 (t0) REVERT: R 361 GLU cc_start: 0.7484 (tm-30) cc_final: 0.7174 (tm-30) REVERT: l 300 MET cc_start: 0.8022 (mmm) cc_final: 0.7718 (mtp) REVERT: S 294 ASN cc_start: 0.8605 (t0) cc_final: 0.8258 (t0) REVERT: S 361 GLU cc_start: 0.7622 (tm-30) cc_final: 0.7270 (tm-30) REVERT: m 81 MET cc_start: 0.9485 (tpp) cc_final: 0.9257 (tpt) REVERT: m 269 ILE cc_start: 0.8808 (mm) cc_final: 0.8446 (mt) REVERT: T 3 SER cc_start: 0.8877 (p) cc_final: 0.8595 (t) REVERT: T 90 GLU cc_start: 0.9288 (tp30) cc_final: 0.8995 (tp30) REVERT: T 111 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7566 (tt0) REVERT: T 356 ASP cc_start: 0.8582 (m-30) cc_final: 0.8207 (m-30) REVERT: T 378 GLN cc_start: 0.9234 (mm-40) cc_final: 0.8830 (mm-40) REVERT: n 53 MET cc_start: 0.9312 (mmm) cc_final: 0.9100 (mmp) REVERT: U 111 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7972 (tt0) REVERT: U 294 ASN cc_start: 0.8624 (t0) cc_final: 0.8249 (t0) REVERT: o 30 ARG cc_start: 0.9098 (ttm-80) cc_final: 0.8884 (tpp80) REVERT: o 78 TYR cc_start: 0.9269 (t80) cc_final: 0.9010 (t80) outliers start: 213 outliers final: 148 residues processed: 1518 average time/residue: 1.0046 time to fit residues: 2645.9681 Evaluate side-chains 1336 residues out of total 12768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 1185 time to evaluate : 9.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain P residue 37 VAL Chi-restraints excluded: chain P residue 249 THR Chi-restraints excluded: chain B residue 8 ASN Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain W residue 243 VAL Chi-restraints excluded: chain W residue 249 THR Chi-restraints excluded: chain W residue 345 ASP Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain X residue 31 ILE Chi-restraints excluded: chain X residue 165 ASP Chi-restraints excluded: chain X residue 243 VAL Chi-restraints excluded: chain X residue 249 THR Chi-restraints excluded: chain X residue 391 LEU Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain Y residue 8 ASN Chi-restraints excluded: chain Y residue 31 ILE Chi-restraints excluded: chain Y residue 35 LEU Chi-restraints excluded: chain Y residue 67 LEU Chi-restraints excluded: chain Y residue 249 THR Chi-restraints excluded: chain E residue 8 ASN Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 270 THR Chi-restraints excluded: chain E residue 297 ILE Chi-restraints excluded: chain E residue 319 MET Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain Z residue 8 ASN Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 243 VAL Chi-restraints excluded: chain F residue 8 ASN Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain a residue 31 ILE Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 204 VAL Chi-restraints excluded: chain G residue 270 THR Chi-restraints excluded: chain b residue 28 GLN Chi-restraints excluded: chain b residue 249 THR Chi-restraints excluded: chain b residue 329 ILE Chi-restraints excluded: chain H residue 8 ASN Chi-restraints excluded: chain H residue 35 LEU Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 242 ASN Chi-restraints excluded: chain H residue 270 THR Chi-restraints excluded: chain H residue 358 ASP Chi-restraints excluded: chain c residue 75 ASP Chi-restraints excluded: chain c residue 249 THR Chi-restraints excluded: chain c residue 359 MET Chi-restraints excluded: chain I residue 8 ASN Chi-restraints excluded: chain I residue 204 VAL Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 360 ASN Chi-restraints excluded: chain d residue 243 VAL Chi-restraints excluded: chain d residue 249 THR Chi-restraints excluded: chain J residue 3 SER Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain J residue 56 ASP Chi-restraints excluded: chain J residue 270 THR Chi-restraints excluded: chain J residue 360 ASN Chi-restraints excluded: chain J residue 387 SER Chi-restraints excluded: chain e residue 8 ASN Chi-restraints excluded: chain e residue 31 ILE Chi-restraints excluded: chain e residue 249 THR Chi-restraints excluded: chain e residue 319 MET Chi-restraints excluded: chain K residue 8 ASN Chi-restraints excluded: chain K residue 35 LEU Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 270 THR Chi-restraints excluded: chain K residue 360 ASN Chi-restraints excluded: chain f residue 60 LEU Chi-restraints excluded: chain f residue 111 GLU Chi-restraints excluded: chain f residue 249 THR Chi-restraints excluded: chain L residue 8 ASN Chi-restraints excluded: chain L residue 270 THR Chi-restraints excluded: chain L residue 358 ASP Chi-restraints excluded: chain g residue 8 ASN Chi-restraints excluded: chain g residue 67 LEU Chi-restraints excluded: chain g residue 249 THR Chi-restraints excluded: chain M residue 3 SER Chi-restraints excluded: chain M residue 8 ASN Chi-restraints excluded: chain M residue 35 LEU Chi-restraints excluded: chain M residue 270 THR Chi-restraints excluded: chain M residue 297 ILE Chi-restraints excluded: chain h residue 249 THR Chi-restraints excluded: chain N residue 8 ASN Chi-restraints excluded: chain N residue 35 LEU Chi-restraints excluded: chain N residue 242 ASN Chi-restraints excluded: chain N residue 270 THR Chi-restraints excluded: chain N residue 360 ASN Chi-restraints excluded: chain i residue 29 SER Chi-restraints excluded: chain i residue 243 VAL Chi-restraints excluded: chain i residue 249 THR Chi-restraints excluded: chain i residue 329 ILE Chi-restraints excluded: chain O residue 3 SER Chi-restraints excluded: chain O residue 37 VAL Chi-restraints excluded: chain O residue 204 VAL Chi-restraints excluded: chain O residue 270 THR Chi-restraints excluded: chain O residue 358 ASP Chi-restraints excluded: chain O residue 387 SER Chi-restraints excluded: chain j residue 8 ASN Chi-restraints excluded: chain j residue 29 SER Chi-restraints excluded: chain j residue 249 THR Chi-restraints excluded: chain Q residue 8 ASN Chi-restraints excluded: chain Q residue 35 LEU Chi-restraints excluded: chain Q residue 37 VAL Chi-restraints excluded: chain Q residue 91 ILE Chi-restraints excluded: chain Q residue 204 VAL Chi-restraints excluded: chain Q residue 270 THR Chi-restraints excluded: chain Q residue 358 ASP Chi-restraints excluded: chain k residue 249 THR Chi-restraints excluded: chain R residue 8 ASN Chi-restraints excluded: chain R residue 29 SER Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 270 THR Chi-restraints excluded: chain l residue 243 VAL Chi-restraints excluded: chain l residue 249 THR Chi-restraints excluded: chain S residue 8 ASN Chi-restraints excluded: chain S residue 35 LEU Chi-restraints excluded: chain S residue 270 THR Chi-restraints excluded: chain S residue 360 ASN Chi-restraints excluded: chain m residue 8 ASN Chi-restraints excluded: chain m residue 249 THR Chi-restraints excluded: chain T residue 8 ASN Chi-restraints excluded: chain T residue 35 LEU Chi-restraints excluded: chain T residue 270 THR Chi-restraints excluded: chain T residue 297 ILE Chi-restraints excluded: chain n residue 37 VAL Chi-restraints excluded: chain n residue 249 THR Chi-restraints excluded: chain U residue 35 LEU Chi-restraints excluded: chain U residue 204 VAL Chi-restraints excluded: chain U residue 242 ASN Chi-restraints excluded: chain U residue 270 THR Chi-restraints excluded: chain U residue 360 ASN Chi-restraints excluded: chain o residue 60 LEU Chi-restraints excluded: chain o residue 243 VAL Chi-restraints excluded: chain V residue 3 SER Chi-restraints excluded: chain V residue 35 LEU Chi-restraints excluded: chain V residue 270 THR Chi-restraints excluded: chain V residue 387 SER Chi-restraints excluded: chain p residue 37 VAL Chi-restraints excluded: chain p residue 249 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1638 random chunks: chunk 826 optimal weight: 0.8980 chunk 461 optimal weight: 0.9980 chunk 1238 optimal weight: 6.9990 chunk 1012 optimal weight: 0.9990 chunk 410 optimal weight: 10.0000 chunk 1490 optimal weight: 0.9990 chunk 1609 optimal weight: 5.9990 chunk 1327 optimal weight: 6.9990 chunk 1477 optimal weight: 5.9990 chunk 508 optimal weight: 5.9990 chunk 1195 optimal weight: 20.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 118 GLN W 118 GLN D 28 GLN D 242 ASN D 294 ASN Y 118 GLN ** Z 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 336 GLN ** a 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 336 GLN ** b 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 242 ASN I 336 GLN d 118 GLN ** d 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 118 GLN ** f 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 242 ASN h 118 GLN ** h 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 118 GLN ** i 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 336 GLN S 336 GLN T 336 GLN ** o 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 120078 Z= 0.153 Angle : 0.455 9.262 163170 Z= 0.257 Chirality : 0.036 0.208 20202 Planarity : 0.003 0.033 21336 Dihedral : 4.815 54.900 17262 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 1.59 % Allowed : 8.38 % Favored : 90.03 % 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: 2.30 (0.07), residues: 16464 helix: 4.30 (0.05), residues: 8316 sheet: 0.95 (0.12), residues: 1722 loop : -2.40 (0.06), residues: 6426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 47 HIS 0.001 0.000 HIS n 208 PHE 0.015 0.001 PHE i 394 TYR 0.022 0.001 TYR T 229 ARG 0.007 0.001 ARG H 365 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 32928 Ramachandran restraints generated. 16464 Oldfield, 0 Emsley, 16464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 32928 Ramachandran restraints generated. 16464 Oldfield, 0 Emsley, 16464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1665 residues out of total 12768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 1462 time to evaluate : 9.951 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: A 18 ARG cc_start: 0.9113 (mtp-110) cc_final: 0.8912 (ttp-110) REVERT: P 111 GLU cc_start: 0.8737 (mm-30) cc_final: 0.8497 (mm-30) REVERT: P 269 ILE cc_start: 0.8623 (mm) cc_final: 0.8357 (mt) REVERT: B 111 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8380 (mt-10) REVERT: W 269 ILE cc_start: 0.8666 (mm) cc_final: 0.8352 (mt) REVERT: C 82 GLU cc_start: 0.8949 (tt0) cc_final: 0.8392 (mt-10) REVERT: C 356 ASP cc_start: 0.8376 (m-30) cc_final: 0.8172 (m-30) REVERT: C 361 GLU cc_start: 0.7798 (tm-30) cc_final: 0.7285 (tm-30) REVERT: C 365 ARG cc_start: 0.9169 (mtp85) cc_final: 0.8868 (mtp180) REVERT: X 30 ARG cc_start: 0.8794 (tpp80) cc_final: 0.8205 (ttm-80) REVERT: Y 30 ARG cc_start: 0.8894 (tpp80) cc_final: 0.8635 (tpp80) REVERT: E 361 GLU cc_start: 0.8139 (tm-30) cc_final: 0.7672 (tm-30) REVERT: Z 30 ARG cc_start: 0.8984 (tpp80) cc_final: 0.8666 (ttm-80) REVERT: Z 78 TYR cc_start: 0.8997 (t80) cc_final: 0.8762 (t80) REVERT: a 30 ARG cc_start: 0.8906 (tpp80) cc_final: 0.8703 (ttm-80) REVERT: G 18 ARG cc_start: 0.9020 (ttp-110) cc_final: 0.8752 (mtp-110) REVERT: G 82 GLU cc_start: 0.8846 (tp30) cc_final: 0.8625 (tp30) REVERT: G 294 ASN cc_start: 0.8427 (t0) cc_final: 0.7904 (t0) REVERT: G 300 MET cc_start: 0.7999 (tpp) cc_final: 0.7622 (tpt) REVERT: G 361 GLU cc_start: 0.7721 (tm-30) cc_final: 0.7330 (tm-30) REVERT: H 348 GLU cc_start: 0.9113 (tp30) cc_final: 0.8884 (tp30) REVERT: c 269 ILE cc_start: 0.8740 (mm) cc_final: 0.8508 (mt) REVERT: I 20 ILE cc_start: 0.9317 (mm) cc_final: 0.9072 (tp) REVERT: I 90 GLU cc_start: 0.9026 (tp30) cc_final: 0.8792 (tp30) REVERT: I 294 ASN cc_start: 0.8489 (t0) cc_final: 0.7913 (t0) REVERT: I 359 MET cc_start: 0.9195 (mmm) cc_final: 0.8899 (mmm) REVERT: I 361 GLU cc_start: 0.7636 (tm-30) cc_final: 0.7101 (tm-30) REVERT: J 338 GLU cc_start: 0.8451 (tm-30) cc_final: 0.8147 (tm-30) REVERT: e 30 ARG cc_start: 0.9005 (ttm-80) cc_final: 0.8704 (tpp80) REVERT: e 269 ILE cc_start: 0.8768 (mm) cc_final: 0.8431 (mt) REVERT: K 90 GLU cc_start: 0.8998 (tp30) cc_final: 0.8672 (tp30) REVERT: K 356 ASP cc_start: 0.8215 (m-30) cc_final: 0.7865 (m-30) REVERT: f 205 GLU cc_start: 0.8247 (mp0) cc_final: 0.7986 (mp0) REVERT: f 269 ILE cc_start: 0.8624 (mm) cc_final: 0.8308 (mt) REVERT: f 313 ASP cc_start: 0.9016 (t70) cc_final: 0.8593 (t0) REVERT: L 361 GLU cc_start: 0.8191 (tm-30) cc_final: 0.7659 (tm-30) REVERT: g 67 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.9029 (mm) REVERT: M 111 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8329 (mt-10) REVERT: M 348 GLU cc_start: 0.8892 (tm-30) cc_final: 0.8670 (tm-30) REVERT: M 361 GLU cc_start: 0.7538 (tm-30) cc_final: 0.6983 (tm-30) REVERT: h 30 ARG cc_start: 0.9046 (tpp80) cc_final: 0.8727 (tpp80) REVERT: h 81 MET cc_start: 0.9486 (tpp) cc_final: 0.9241 (tpt) REVERT: N 82 GLU cc_start: 0.8968 (tt0) cc_final: 0.8498 (mt-10) REVERT: N 111 GLU cc_start: 0.7650 (mt-10) cc_final: 0.7100 (tt0) REVERT: i 269 ILE cc_start: 0.8763 (mm) cc_final: 0.8475 (mt) REVERT: O 53 MET cc_start: 0.9187 (mmm) cc_final: 0.8598 (mmp) REVERT: O 90 GLU cc_start: 0.9077 (tp30) cc_final: 0.8810 (tp30) REVERT: O 213 TYR cc_start: 0.8948 (m-80) cc_final: 0.8536 (m-80) REVERT: O 356 ASP cc_start: 0.8353 (m-30) cc_final: 0.7937 (m-30) REVERT: j 11 MET cc_start: 0.9332 (mtm) cc_final: 0.9106 (mtp) REVERT: j 30 ARG cc_start: 0.8947 (tpp80) cc_final: 0.8707 (tpp80) REVERT: j 269 ILE cc_start: 0.8637 (mm) cc_final: 0.8330 (mt) REVERT: j 313 ASP cc_start: 0.8997 (t70) cc_final: 0.8557 (t0) REVERT: Q 361 GLU cc_start: 0.8156 (tm-30) cc_final: 0.7573 (tm-30) REVERT: R 361 GLU cc_start: 0.7417 (tm-30) cc_final: 0.6988 (tm-30) REVERT: l 118 GLN cc_start: 0.9205 (tp-100) cc_final: 0.8729 (tp-100) REVERT: l 269 ILE cc_start: 0.8865 (mm) cc_final: 0.8565 (mt) REVERT: S 294 ASN cc_start: 0.8609 (t0) cc_final: 0.8306 (t0) REVERT: S 361 GLU cc_start: 0.7560 (tm-30) cc_final: 0.7095 (tm-30) REVERT: m 81 MET cc_start: 0.9506 (tpp) cc_final: 0.9278 (tpt) REVERT: m 269 ILE cc_start: 0.8769 (mm) cc_final: 0.8402 (mt) REVERT: T 82 GLU cc_start: 0.8984 (tt0) cc_final: 0.8610 (mt-10) REVERT: T 90 GLU cc_start: 0.9262 (tp30) cc_final: 0.8917 (tp30) REVERT: T 110 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8288 (tm-30) REVERT: T 111 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7554 (tt0) REVERT: T 378 GLN cc_start: 0.9172 (mm-40) cc_final: 0.8886 (tp40) REVERT: n 30 ARG cc_start: 0.8998 (ttm-80) cc_final: 0.8765 (tpp80) REVERT: U 213 TYR cc_start: 0.8989 (m-80) cc_final: 0.8446 (m-80) REVERT: U 294 ASN cc_start: 0.8501 (t0) cc_final: 0.8117 (t0) REVERT: U 361 GLU cc_start: 0.7779 (tm-30) cc_final: 0.7288 (tm-30) REVERT: o 78 TYR cc_start: 0.9177 (t80) cc_final: 0.8808 (t80) REVERT: p 28 GLN cc_start: 0.8165 (tt0) cc_final: 0.7900 (tt0) outliers start: 203 outliers final: 128 residues processed: 1587 average time/residue: 0.9973 time to fit residues: 2736.5833 Evaluate side-chains 1403 residues out of total 12768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 1273 time to evaluate : 8.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain P residue 8 ASN Chi-restraints excluded: chain P residue 37 VAL Chi-restraints excluded: chain P residue 110 GLU Chi-restraints excluded: chain B residue 8 ASN Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain W residue 8 ASN Chi-restraints excluded: chain W residue 110 GLU Chi-restraints excluded: chain W residue 345 ASP Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain X residue 35 LEU Chi-restraints excluded: chain X residue 110 GLU Chi-restraints excluded: chain X residue 165 ASP Chi-restraints excluded: chain D residue 242 ASN Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain Y residue 67 LEU Chi-restraints excluded: chain Y residue 111 GLU Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 270 THR Chi-restraints excluded: chain E residue 360 ASN Chi-restraints excluded: chain Z residue 8 ASN Chi-restraints excluded: chain Z residue 110 GLU Chi-restraints excluded: chain Z residue 243 VAL Chi-restraints excluded: chain F residue 8 ASN Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain a residue 110 GLU Chi-restraints excluded: chain a residue 356 ASP Chi-restraints excluded: chain G residue 8 ASN Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 204 VAL Chi-restraints excluded: chain G residue 270 THR Chi-restraints excluded: chain G residue 360 ASN Chi-restraints excluded: chain b residue 110 GLU Chi-restraints excluded: chain b residue 249 THR Chi-restraints excluded: chain b residue 329 ILE Chi-restraints excluded: chain H residue 8 ASN Chi-restraints excluded: chain H residue 35 LEU Chi-restraints excluded: chain H residue 270 THR Chi-restraints excluded: chain H residue 360 ASN Chi-restraints excluded: chain H residue 387 SER Chi-restraints excluded: chain c residue 359 MET Chi-restraints excluded: chain I residue 204 VAL Chi-restraints excluded: chain I residue 242 ASN Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 360 ASN Chi-restraints excluded: chain d residue 110 GLU Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain J residue 56 ASP Chi-restraints excluded: chain J residue 360 ASN Chi-restraints excluded: chain e residue 31 ILE Chi-restraints excluded: chain e residue 110 GLU Chi-restraints excluded: chain K residue 8 ASN Chi-restraints excluded: chain K residue 35 LEU Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 270 THR Chi-restraints excluded: chain K residue 360 ASN Chi-restraints excluded: chain f residue 110 GLU Chi-restraints excluded: chain L residue 8 ASN Chi-restraints excluded: chain L residue 270 THR Chi-restraints excluded: chain L residue 360 ASN Chi-restraints excluded: chain g residue 8 ASN Chi-restraints excluded: chain g residue 67 LEU Chi-restraints excluded: chain M residue 3 SER Chi-restraints excluded: chain M residue 8 ASN Chi-restraints excluded: chain M residue 35 LEU Chi-restraints excluded: chain M residue 270 THR Chi-restraints excluded: chain M residue 297 ILE Chi-restraints excluded: chain h residue 110 GLU Chi-restraints excluded: chain N residue 8 ASN Chi-restraints excluded: chain N residue 35 LEU Chi-restraints excluded: chain N residue 270 THR Chi-restraints excluded: chain N residue 360 ASN Chi-restraints excluded: chain i residue 110 GLU Chi-restraints excluded: chain i residue 329 ILE Chi-restraints excluded: chain O residue 3 SER Chi-restraints excluded: chain O residue 8 ASN Chi-restraints excluded: chain O residue 37 VAL Chi-restraints excluded: chain O residue 204 VAL Chi-restraints excluded: chain O residue 270 THR Chi-restraints excluded: chain j residue 8 ASN Chi-restraints excluded: chain j residue 35 LEU Chi-restraints excluded: chain j residue 110 GLU Chi-restraints excluded: chain Q residue 8 ASN Chi-restraints excluded: chain Q residue 35 LEU Chi-restraints excluded: chain Q residue 37 VAL Chi-restraints excluded: chain Q residue 270 THR Chi-restraints excluded: chain Q residue 360 ASN Chi-restraints excluded: chain R residue 8 ASN Chi-restraints excluded: chain R residue 270 THR Chi-restraints excluded: chain R residue 360 ASN Chi-restraints excluded: chain S residue 3 SER Chi-restraints excluded: chain S residue 8 ASN Chi-restraints excluded: chain S residue 35 LEU Chi-restraints excluded: chain S residue 270 THR Chi-restraints excluded: chain S residue 360 ASN Chi-restraints excluded: chain m residue 8 ASN Chi-restraints excluded: chain m residue 75 ASP Chi-restraints excluded: chain T residue 8 ASN Chi-restraints excluded: chain T residue 35 LEU Chi-restraints excluded: chain T residue 110 GLU Chi-restraints excluded: chain T residue 270 THR Chi-restraints excluded: chain T residue 360 ASN Chi-restraints excluded: chain n residue 37 VAL Chi-restraints excluded: chain n residue 67 LEU Chi-restraints excluded: chain U residue 8 ASN Chi-restraints excluded: chain U residue 35 LEU Chi-restraints excluded: chain U residue 204 VAL Chi-restraints excluded: chain U residue 270 THR Chi-restraints excluded: chain U residue 360 ASN Chi-restraints excluded: chain o residue 243 VAL Chi-restraints excluded: chain o residue 249 THR Chi-restraints excluded: chain o residue 333 ILE Chi-restraints excluded: chain V residue 3 SER Chi-restraints excluded: chain V residue 35 LEU Chi-restraints excluded: chain V residue 270 THR Chi-restraints excluded: chain V residue 360 ASN Chi-restraints excluded: chain p residue 37 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1638 random chunks: chunk 1472 optimal weight: 0.0370 chunk 1120 optimal weight: 3.9990 chunk 773 optimal weight: 10.0000 chunk 164 optimal weight: 5.9990 chunk 711 optimal weight: 8.9990 chunk 1000 optimal weight: 6.9990 chunk 1495 optimal weight: 0.0170 chunk 1583 optimal weight: 7.9990 chunk 781 optimal weight: 9.9990 chunk 1417 optimal weight: 10.0000 chunk 426 optimal weight: 5.9990 overall best weight: 3.2102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 118 GLN W 118 GLN Y 118 GLN E 28 GLN E 242 ASN ** Z 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 336 GLN ** a 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 336 GLN ** b 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 336 GLN ** d 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 118 GLN ** f 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 242 ASN h 118 GLN ** h 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 118 GLN ** i 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 336 GLN S 336 GLN T 336 GLN U 242 ASN ** o 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 120078 Z= 0.201 Angle : 0.472 8.621 163170 Z= 0.266 Chirality : 0.036 0.294 20202 Planarity : 0.003 0.045 21336 Dihedral : 4.785 54.691 17262 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 2.40 % Allowed : 9.93 % Favored : 87.66 % 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: 2.25 (0.07), residues: 16464 helix: 4.27 (0.05), residues: 8316 sheet: 0.70 (0.12), residues: 1848 loop : -2.45 (0.06), residues: 6300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 47 HIS 0.002 0.001 HIS n 208 PHE 0.012 0.002 PHE g 175 TYR 0.022 0.001 TYR d 78 ARG 0.008 0.001 ARG J 30 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 32928 Ramachandran restraints generated. 16464 Oldfield, 0 Emsley, 16464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 32928 Ramachandran restraints generated. 16464 Oldfield, 0 Emsley, 16464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1684 residues out of total 12768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 307 poor density : 1377 time to evaluate : 9.677 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: P 111 GLU cc_start: 0.8736 (mm-30) cc_final: 0.8457 (mm-30) REVERT: P 269 ILE cc_start: 0.8619 (mm) cc_final: 0.8351 (mt) REVERT: B 18 ARG cc_start: 0.8991 (ttp-110) cc_final: 0.8766 (mtm110) REVERT: B 95 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8616 (tt) REVERT: B 111 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8406 (mt-10) REVERT: W 82 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8560 (mt-10) REVERT: W 269 ILE cc_start: 0.8657 (mm) cc_final: 0.8350 (mt) REVERT: C 82 GLU cc_start: 0.8986 (tt0) cc_final: 0.8390 (mt-10) REVERT: C 361 GLU cc_start: 0.7829 (tm-30) cc_final: 0.7295 (tm-30) REVERT: C 365 ARG cc_start: 0.9180 (mtp85) cc_final: 0.8893 (mtp180) REVERT: X 78 TYR cc_start: 0.8962 (t80) cc_final: 0.8486 (t80) REVERT: D 356 ASP cc_start: 0.8331 (m-30) cc_final: 0.8027 (m-30) REVERT: Y 30 ARG cc_start: 0.8866 (tpp80) cc_final: 0.8577 (tpp80) REVERT: E 95 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8734 (tt) REVERT: E 361 GLU cc_start: 0.8145 (tm-30) cc_final: 0.7621 (tm-30) REVERT: Z 216 GLU cc_start: 0.8887 (mm-30) cc_final: 0.8583 (tm-30) REVERT: F 300 MET cc_start: 0.8117 (tpp) cc_final: 0.7894 (mmm) REVERT: a 30 ARG cc_start: 0.8911 (tpp80) cc_final: 0.8693 (ttm-80) REVERT: G 18 ARG cc_start: 0.9003 (ttp-110) cc_final: 0.8766 (mtp-110) REVERT: G 82 GLU cc_start: 0.8853 (tp30) cc_final: 0.8628 (tp30) REVERT: G 294 ASN cc_start: 0.8499 (t0) cc_final: 0.8000 (t0) REVERT: G 300 MET cc_start: 0.8120 (tpp) cc_final: 0.7726 (tpt) REVERT: G 359 MET cc_start: 0.8846 (mmt) cc_final: 0.8427 (mmt) REVERT: G 361 GLU cc_start: 0.7759 (tm-30) cc_final: 0.7355 (tm-30) REVERT: b 11 MET cc_start: 0.9311 (mtm) cc_final: 0.9101 (mtm) REVERT: H 20 ILE cc_start: 0.9376 (OUTLIER) cc_final: 0.8997 (tp) REVERT: c 269 ILE cc_start: 0.8743 (mm) cc_final: 0.8522 (mt) REVERT: I 90 GLU cc_start: 0.9010 (tp30) cc_final: 0.8718 (tp30) REVERT: I 95 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8636 (tt) REVERT: I 294 ASN cc_start: 0.8520 (t0) cc_final: 0.7936 (t0) REVERT: I 300 MET cc_start: 0.7577 (mmm) cc_final: 0.6910 (tpt) REVERT: I 359 MET cc_start: 0.9217 (mmm) cc_final: 0.8952 (mmm) REVERT: I 361 GLU cc_start: 0.7667 (tm-30) cc_final: 0.7136 (tm-30) REVERT: J 338 GLU cc_start: 0.8477 (tm-30) cc_final: 0.8197 (tm-30) REVERT: e 81 MET cc_start: 0.9571 (tpp) cc_final: 0.9329 (tpp) REVERT: e 269 ILE cc_start: 0.8795 (mm) cc_final: 0.8451 (mt) REVERT: e 313 ASP cc_start: 0.9131 (t0) cc_final: 0.8922 (t0) REVERT: K 90 GLU cc_start: 0.9017 (tp30) cc_final: 0.8703 (tp30) REVERT: K 356 ASP cc_start: 0.8345 (m-30) cc_final: 0.8027 (m-30) REVERT: f 205 GLU cc_start: 0.8258 (mp0) cc_final: 0.7997 (mp0) REVERT: f 269 ILE cc_start: 0.8616 (mm) cc_final: 0.8297 (mt) REVERT: f 313 ASP cc_start: 0.9025 (t70) cc_final: 0.8591 (t0) REVERT: L 361 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7675 (tm-30) REVERT: g 67 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.9058 (mm) REVERT: g 300 MET cc_start: 0.8477 (tpt) cc_final: 0.8247 (tpt) REVERT: M 111 GLU cc_start: 0.8572 (mt-10) cc_final: 0.8353 (mt-10) REVERT: M 361 GLU cc_start: 0.7538 (tm-30) cc_final: 0.6961 (tm-30) REVERT: h 81 MET cc_start: 0.9481 (tpp) cc_final: 0.9240 (tpt) REVERT: N 82 GLU cc_start: 0.8977 (tt0) cc_final: 0.8493 (mt-10) REVERT: N 111 GLU cc_start: 0.7547 (mt-10) cc_final: 0.7057 (tt0) REVERT: i 269 ILE cc_start: 0.8742 (mm) cc_final: 0.8473 (mt) REVERT: O 90 GLU cc_start: 0.9080 (tp30) cc_final: 0.8837 (tp30) REVERT: O 213 TYR cc_start: 0.8982 (m-80) cc_final: 0.8581 (m-80) REVERT: O 300 MET cc_start: 0.8196 (tpp) cc_final: 0.7816 (tpt) REVERT: O 356 ASP cc_start: 0.8218 (m-30) cc_final: 0.7902 (m-30) REVERT: O 359 MET cc_start: 0.9097 (mmm) cc_final: 0.8853 (mmm) REVERT: j 30 ARG cc_start: 0.8924 (tpp80) cc_final: 0.8694 (tpp80) REVERT: j 269 ILE cc_start: 0.8669 (mm) cc_final: 0.8362 (mt) REVERT: j 313 ASP cc_start: 0.9001 (t70) cc_final: 0.8604 (t0) REVERT: Q 82 GLU cc_start: 0.8816 (tt0) cc_final: 0.8515 (tt0) REVERT: Q 361 GLU cc_start: 0.8182 (tm-30) cc_final: 0.7591 (tm-30) REVERT: R 361 GLU cc_start: 0.7550 (tm-30) cc_final: 0.7092 (tm-30) REVERT: l 118 GLN cc_start: 0.9219 (tp-100) cc_final: 0.8748 (tp-100) REVERT: l 269 ILE cc_start: 0.8871 (mm) cc_final: 0.8573 (mt) REVERT: S 294 ASN cc_start: 0.8654 (t0) cc_final: 0.8309 (t0) REVERT: m 81 MET cc_start: 0.9514 (tpp) cc_final: 0.9254 (tpt) REVERT: m 269 ILE cc_start: 0.8766 (mm) cc_final: 0.8399 (mt) REVERT: T 82 GLU cc_start: 0.8988 (tt0) cc_final: 0.8607 (mt-10) REVERT: T 90 GLU cc_start: 0.9265 (tp30) cc_final: 0.8923 (tp30) REVERT: T 110 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8251 (tm-30) REVERT: T 111 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7444 (tt0) REVERT: T 240 VAL cc_start: 0.9052 (OUTLIER) cc_final: 0.8828 (p) REVERT: n 30 ARG cc_start: 0.8973 (ttm-80) cc_final: 0.8657 (tpp80) REVERT: U 95 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8615 (tt) REVERT: U 213 TYR cc_start: 0.9043 (m-80) cc_final: 0.8520 (m-80) REVERT: U 294 ASN cc_start: 0.8567 (t0) cc_final: 0.8185 (t0) REVERT: U 361 GLU cc_start: 0.7846 (tm-30) cc_final: 0.7352 (tm-30) REVERT: o 30 ARG cc_start: 0.9104 (tpp80) cc_final: 0.8861 (ttm-80) REVERT: V 361 GLU cc_start: 0.7873 (tm-30) cc_final: 0.7383 (tm-30) outliers start: 307 outliers final: 194 residues processed: 1589 average time/residue: 0.9907 time to fit residues: 2745.6960 Evaluate side-chains 1460 residues out of total 12768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 1258 time to evaluate : 9.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain P residue 8 ASN Chi-restraints excluded: chain P residue 110 GLU Chi-restraints excluded: chain P residue 249 THR Chi-restraints excluded: chain P residue 375 LEU Chi-restraints excluded: chain B residue 8 ASN Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain W residue 8 ASN Chi-restraints excluded: chain W residue 110 GLU Chi-restraints excluded: chain W residue 111 GLU Chi-restraints excluded: chain W residue 243 VAL Chi-restraints excluded: chain W residue 249 THR Chi-restraints excluded: chain W residue 319 MET Chi-restraints excluded: chain W residue 345 ASP Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain X residue 35 LEU Chi-restraints excluded: chain X residue 110 GLU Chi-restraints excluded: chain X residue 165 ASP Chi-restraints excluded: chain X residue 249 THR Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain Y residue 8 ASN Chi-restraints excluded: chain Y residue 67 LEU Chi-restraints excluded: chain Y residue 111 GLU Chi-restraints excluded: chain Y residue 249 THR Chi-restraints excluded: chain Y residue 356 ASP Chi-restraints excluded: chain E residue 3 SER Chi-restraints excluded: chain E residue 8 ASN Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 242 ASN Chi-restraints excluded: chain E residue 270 THR Chi-restraints excluded: chain E residue 297 ILE Chi-restraints excluded: chain E residue 360 ASN Chi-restraints excluded: chain Z residue 8 ASN Chi-restraints excluded: chain Z residue 110 GLU Chi-restraints excluded: chain Z residue 243 VAL Chi-restraints excluded: chain F residue 8 ASN Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 56 ASP Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 387 SER Chi-restraints excluded: chain a residue 31 ILE Chi-restraints excluded: chain a residue 110 GLU Chi-restraints excluded: chain a residue 356 ASP Chi-restraints excluded: chain a residue 375 LEU Chi-restraints excluded: chain G residue 8 ASN Chi-restraints excluded: chain G residue 204 VAL Chi-restraints excluded: chain G residue 270 THR Chi-restraints excluded: chain G residue 360 ASN Chi-restraints excluded: chain b residue 28 GLN Chi-restraints excluded: chain b residue 75 ASP Chi-restraints excluded: chain b residue 110 GLU Chi-restraints excluded: chain b residue 249 THR Chi-restraints excluded: chain b residue 329 ILE Chi-restraints excluded: chain H residue 3 SER Chi-restraints excluded: chain H residue 8 ASN Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 25 GLU Chi-restraints excluded: chain H residue 35 LEU Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 270 THR Chi-restraints excluded: chain H residue 387 SER Chi-restraints excluded: chain c residue 67 LEU Chi-restraints excluded: chain c residue 75 ASP Chi-restraints excluded: chain c residue 249 THR Chi-restraints excluded: chain c residue 359 MET Chi-restraints excluded: chain I residue 8 ASN Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain I residue 204 VAL Chi-restraints excluded: chain I residue 241 GLU Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 360 ASN Chi-restraints excluded: chain d residue 110 GLU Chi-restraints excluded: chain d residue 243 VAL Chi-restraints excluded: chain d residue 249 THR Chi-restraints excluded: chain J residue 3 SER Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 56 ASP Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain J residue 270 THR Chi-restraints excluded: chain J residue 360 ASN Chi-restraints excluded: chain e residue 31 ILE Chi-restraints excluded: chain e residue 110 GLU Chi-restraints excluded: chain e residue 111 GLU Chi-restraints excluded: chain e residue 249 THR Chi-restraints excluded: chain e residue 375 LEU Chi-restraints excluded: chain K residue 8 ASN Chi-restraints excluded: chain K residue 35 LEU Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 270 THR Chi-restraints excluded: chain K residue 360 ASN Chi-restraints excluded: chain f residue 110 GLU Chi-restraints excluded: chain f residue 249 THR Chi-restraints excluded: chain L residue 8 ASN Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain L residue 270 THR Chi-restraints excluded: chain L residue 292 VAL Chi-restraints excluded: chain L residue 347 ILE Chi-restraints excluded: chain L residue 360 ASN Chi-restraints excluded: chain g residue 8 ASN Chi-restraints excluded: chain g residue 28 GLN Chi-restraints excluded: chain g residue 67 LEU Chi-restraints excluded: chain g residue 75 ASP Chi-restraints excluded: chain g residue 249 THR Chi-restraints excluded: chain M residue 3 SER Chi-restraints excluded: chain M residue 8 ASN Chi-restraints excluded: chain M residue 35 LEU Chi-restraints excluded: chain M residue 270 THR Chi-restraints excluded: chain M residue 297 ILE Chi-restraints excluded: chain h residue 8 ASN Chi-restraints excluded: chain h residue 35 LEU Chi-restraints excluded: chain h residue 110 GLU Chi-restraints excluded: chain h residue 111 GLU Chi-restraints excluded: chain h residue 243 VAL Chi-restraints excluded: chain N residue 8 ASN Chi-restraints excluded: chain N residue 35 LEU Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain N residue 270 THR Chi-restraints excluded: chain N residue 360 ASN Chi-restraints excluded: chain i residue 110 GLU Chi-restraints excluded: chain i residue 243 VAL Chi-restraints excluded: chain i residue 249 THR Chi-restraints excluded: chain i residue 329 ILE Chi-restraints excluded: chain O residue 3 SER Chi-restraints excluded: chain O residue 8 ASN Chi-restraints excluded: chain O residue 204 VAL Chi-restraints excluded: chain O residue 270 THR Chi-restraints excluded: chain O residue 387 SER Chi-restraints excluded: chain j residue 8 ASN Chi-restraints excluded: chain j residue 35 LEU Chi-restraints excluded: chain j residue 110 GLU Chi-restraints excluded: chain j residue 375 LEU Chi-restraints excluded: chain Q residue 8 ASN Chi-restraints excluded: chain Q residue 35 LEU Chi-restraints excluded: chain Q residue 37 VAL Chi-restraints excluded: chain Q residue 91 ILE Chi-restraints excluded: chain Q residue 270 THR Chi-restraints excluded: chain Q residue 360 ASN Chi-restraints excluded: chain k residue 249 THR Chi-restraints excluded: chain R residue 8 ASN Chi-restraints excluded: chain R residue 270 THR Chi-restraints excluded: chain R residue 360 ASN Chi-restraints excluded: chain l residue 75 ASP Chi-restraints excluded: chain l residue 110 GLU Chi-restraints excluded: chain l residue 243 VAL Chi-restraints excluded: chain l residue 249 THR Chi-restraints excluded: chain S residue 3 SER Chi-restraints excluded: chain S residue 8 ASN Chi-restraints excluded: chain S residue 35 LEU Chi-restraints excluded: chain S residue 270 THR Chi-restraints excluded: chain S residue 360 ASN Chi-restraints excluded: chain m residue 8 ASN Chi-restraints excluded: chain m residue 35 LEU Chi-restraints excluded: chain m residue 75 ASP Chi-restraints excluded: chain m residue 110 GLU Chi-restraints excluded: chain m residue 249 THR Chi-restraints excluded: chain m residue 375 LEU Chi-restraints excluded: chain T residue 8 ASN Chi-restraints excluded: chain T residue 35 LEU Chi-restraints excluded: chain T residue 110 GLU Chi-restraints excluded: chain T residue 240 VAL Chi-restraints excluded: chain T residue 270 THR Chi-restraints excluded: chain n residue 35 LEU Chi-restraints excluded: chain n residue 37 VAL Chi-restraints excluded: chain n residue 67 LEU Chi-restraints excluded: chain n residue 249 THR Chi-restraints excluded: chain U residue 8 ASN Chi-restraints excluded: chain U residue 35 LEU Chi-restraints excluded: chain U residue 95 LEU Chi-restraints excluded: chain U residue 204 VAL Chi-restraints excluded: chain U residue 242 ASN Chi-restraints excluded: chain U residue 270 THR Chi-restraints excluded: chain U residue 360 ASN Chi-restraints excluded: chain U residue 387 SER Chi-restraints excluded: chain o residue 60 LEU Chi-restraints excluded: chain o residue 110 GLU Chi-restraints excluded: chain o residue 243 VAL Chi-restraints excluded: chain o residue 249 THR Chi-restraints excluded: chain o residue 333 ILE Chi-restraints excluded: chain V residue 3 SER Chi-restraints excluded: chain V residue 35 LEU Chi-restraints excluded: chain V residue 37 VAL Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 270 THR Chi-restraints excluded: chain V residue 375 LEU Chi-restraints excluded: chain p residue 37 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1638 random chunks: chunk 1318 optimal weight: 5.9990 chunk 898 optimal weight: 8.9990 chunk 23 optimal weight: 10.0000 chunk 1178 optimal weight: 1.9990 chunk 653 optimal weight: 0.8980 chunk 1351 optimal weight: 5.9990 chunk 1094 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 808 optimal weight: 9.9990 chunk 1421 optimal weight: 8.9990 chunk 399 optimal weight: 9.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 64 GLN D 294 ASN E 384 ASN ** Z 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 242 ASN F 384 ASN ** a 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 384 ASN ** c 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 336 GLN ** e 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 242 ASN ** h 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 242 ASN U 242 ASN U 384 ASN ** o 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 120078 Z= 0.247 Angle : 0.500 11.470 163170 Z= 0.280 Chirality : 0.036 0.209 20202 Planarity : 0.003 0.044 21336 Dihedral : 4.869 56.952 17262 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 2.41 % Allowed : 11.00 % Favored : 86.59 % 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: 2.29 (0.07), residues: 16464 helix: 4.36 (0.05), residues: 8148 sheet: 0.74 (0.12), residues: 1638 loop : -2.23 (0.06), residues: 6678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 133 HIS 0.002 0.001 HIS n 208 PHE 0.012 0.002 PHE g 175 TYR 0.029 0.001 TYR Z 78 ARG 0.008 0.001 ARG J 18 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 32928 Ramachandran restraints generated. 16464 Oldfield, 0 Emsley, 16464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 32928 Ramachandran restraints generated. 16464 Oldfield, 0 Emsley, 16464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1616 residues out of total 12768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 308 poor density : 1308 time to evaluate : 9.719 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: A 82 GLU cc_start: 0.8667 (mt-10) cc_final: 0.8387 (mt-10) REVERT: P 111 GLU cc_start: 0.8786 (mm-30) cc_final: 0.8501 (mm-30) REVERT: B 18 ARG cc_start: 0.9038 (ttp-110) cc_final: 0.8687 (mtp-110) REVERT: B 95 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8658 (tt) REVERT: B 111 GLU cc_start: 0.8716 (mt-10) cc_final: 0.8283 (mt-10) REVERT: W 78 TYR cc_start: 0.9170 (t80) cc_final: 0.8811 (t80) REVERT: W 269 ILE cc_start: 0.8649 (mm) cc_final: 0.8337 (mt) REVERT: C 18 ARG cc_start: 0.9125 (ttp-110) cc_final: 0.8894 (mtm110) REVERT: C 82 GLU cc_start: 0.8993 (tt0) cc_final: 0.8390 (mt-10) REVERT: C 361 GLU cc_start: 0.7880 (tm-30) cc_final: 0.7370 (tm-30) REVERT: C 365 ARG cc_start: 0.9213 (mtp85) cc_final: 0.8979 (mtp180) REVERT: X 30 ARG cc_start: 0.8836 (tpp80) cc_final: 0.8225 (ttm-80) REVERT: D 20 ILE cc_start: 0.9306 (mm) cc_final: 0.9001 (tp) REVERT: D 356 ASP cc_start: 0.8234 (m-30) cc_final: 0.8003 (m-30) REVERT: Y 30 ARG cc_start: 0.8850 (tpp80) cc_final: 0.8545 (tpp80) REVERT: E 95 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8752 (tt) REVERT: E 361 GLU cc_start: 0.8206 (tm-30) cc_final: 0.7680 (tm-30) REVERT: Z 30 ARG cc_start: 0.9015 (tpp80) cc_final: 0.8673 (tpp80) REVERT: Z 216 GLU cc_start: 0.8900 (mm-30) cc_final: 0.8627 (tm-30) REVERT: F 300 MET cc_start: 0.8275 (tpp) cc_final: 0.7893 (mmm) REVERT: G 18 ARG cc_start: 0.9018 (ttp-110) cc_final: 0.8776 (mtp-110) REVERT: G 82 GLU cc_start: 0.8864 (tp30) cc_final: 0.8628 (tp30) REVERT: G 294 ASN cc_start: 0.8549 (t0) cc_final: 0.8055 (t0) REVERT: G 300 MET cc_start: 0.8248 (tpp) cc_final: 0.7858 (tpt) REVERT: G 361 GLU cc_start: 0.7863 (tm-30) cc_final: 0.7432 (tm-30) REVERT: H 20 ILE cc_start: 0.9412 (OUTLIER) cc_final: 0.9063 (tp) REVERT: c 269 ILE cc_start: 0.8746 (mm) cc_final: 0.8520 (mt) REVERT: I 53 MET cc_start: 0.9202 (mmt) cc_final: 0.8675 (mmt) REVERT: I 90 GLU cc_start: 0.9023 (tp30) cc_final: 0.8743 (tp30) REVERT: I 95 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8645 (tt) REVERT: I 294 ASN cc_start: 0.8573 (t0) cc_final: 0.8067 (t0) REVERT: I 300 MET cc_start: 0.7623 (mmm) cc_final: 0.7078 (tpt) REVERT: I 361 GLU cc_start: 0.7788 (tm-30) cc_final: 0.7234 (tm-30) REVERT: J 18 ARG cc_start: 0.8603 (ttp-110) cc_final: 0.8401 (ttp-110) REVERT: J 338 GLU cc_start: 0.8520 (tm-30) cc_final: 0.8226 (tm-30) REVERT: e 30 ARG cc_start: 0.9013 (ttm-80) cc_final: 0.8624 (tpp80) REVERT: e 269 ILE cc_start: 0.8810 (mm) cc_final: 0.8466 (mt) REVERT: e 313 ASP cc_start: 0.9144 (t0) cc_final: 0.8908 (t0) REVERT: K 46 TYR cc_start: 0.9097 (m-80) cc_final: 0.8890 (m-80) REVERT: K 356 ASP cc_start: 0.8399 (m-30) cc_final: 0.8138 (m-30) REVERT: f 8 ASN cc_start: 0.9061 (OUTLIER) cc_final: 0.8787 (m-40) REVERT: f 269 ILE cc_start: 0.8606 (mm) cc_final: 0.8292 (mt) REVERT: f 313 ASP cc_start: 0.9021 (t70) cc_final: 0.8615 (t0) REVERT: L 361 GLU cc_start: 0.8250 (tm-30) cc_final: 0.7708 (tm-30) REVERT: g 67 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.9050 (mm) REVERT: M 361 GLU cc_start: 0.7649 (tm-30) cc_final: 0.7046 (tm-30) REVERT: h 81 MET cc_start: 0.9469 (tpp) cc_final: 0.9205 (tpt) REVERT: N 82 GLU cc_start: 0.8992 (tt0) cc_final: 0.8503 (mt-10) REVERT: N 111 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7006 (tt0) REVERT: i 269 ILE cc_start: 0.8784 (mm) cc_final: 0.8517 (mt) REVERT: O 213 TYR cc_start: 0.9017 (m-80) cc_final: 0.8596 (m-80) REVERT: O 241 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8287 (pm20) REVERT: O 300 MET cc_start: 0.8315 (tpp) cc_final: 0.8033 (tpt) REVERT: O 356 ASP cc_start: 0.8204 (m-30) cc_final: 0.7955 (m-30) REVERT: j 30 ARG cc_start: 0.8913 (tpp80) cc_final: 0.8674 (tpp80) REVERT: j 269 ILE cc_start: 0.8684 (mm) cc_final: 0.8362 (mt) REVERT: Q 82 GLU cc_start: 0.8828 (tt0) cc_final: 0.8512 (tt0) REVERT: Q 95 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8725 (tt) REVERT: Q 361 GLU cc_start: 0.8213 (tm-30) cc_final: 0.7615 (tm-30) REVERT: R 361 GLU cc_start: 0.7653 (tm-30) cc_final: 0.7112 (tm-30) REVERT: l 78 TYR cc_start: 0.8997 (t80) cc_final: 0.8796 (t80) REVERT: l 118 GLN cc_start: 0.9244 (tp-100) cc_final: 0.8779 (tp-100) REVERT: l 269 ILE cc_start: 0.8891 (mm) cc_final: 0.8580 (mt) REVERT: S 229 TYR cc_start: 0.8375 (t80) cc_final: 0.8155 (t80) REVERT: S 294 ASN cc_start: 0.8680 (t0) cc_final: 0.8197 (t0) REVERT: S 361 GLU cc_start: 0.7481 (tm-30) cc_final: 0.7147 (tm-30) REVERT: m 53 MET cc_start: 0.9336 (mmp) cc_final: 0.9111 (mmt) REVERT: m 81 MET cc_start: 0.9499 (tpp) cc_final: 0.9262 (tpt) REVERT: m 269 ILE cc_start: 0.8758 (mm) cc_final: 0.8393 (mt) REVERT: m 386 ASP cc_start: 0.8609 (p0) cc_final: 0.8390 (p0) REVERT: T 90 GLU cc_start: 0.9261 (tp30) cc_final: 0.8924 (tp30) REVERT: T 110 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8264 (tm-30) REVERT: T 111 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7482 (tt0) REVERT: U 95 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8565 (tt) REVERT: U 213 TYR cc_start: 0.9067 (m-80) cc_final: 0.8549 (m-80) REVERT: U 294 ASN cc_start: 0.8584 (t0) cc_final: 0.8213 (t0) REVERT: U 361 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7378 (tm-30) REVERT: o 30 ARG cc_start: 0.9087 (tpp80) cc_final: 0.8850 (tpp80) REVERT: V 361 GLU cc_start: 0.7919 (tm-30) cc_final: 0.7446 (tm-30) outliers start: 308 outliers final: 232 residues processed: 1519 average time/residue: 0.9854 time to fit residues: 2609.5496 Evaluate side-chains 1468 residues out of total 12768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 242 poor density : 1226 time to evaluate : 9.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain P residue 8 ASN Chi-restraints excluded: chain P residue 110 GLU Chi-restraints excluded: chain P residue 249 THR Chi-restraints excluded: chain P residue 375 LEU Chi-restraints excluded: chain B residue 8 ASN Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain W residue 8 ASN Chi-restraints excluded: chain W residue 110 GLU Chi-restraints excluded: chain W residue 111 GLU Chi-restraints excluded: chain W residue 165 ASP Chi-restraints excluded: chain W residue 243 VAL Chi-restraints excluded: chain W residue 249 THR Chi-restraints excluded: chain W residue 319 MET Chi-restraints excluded: chain W residue 345 ASP Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain X residue 110 GLU Chi-restraints excluded: chain X residue 249 THR Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain Y residue 8 ASN Chi-restraints excluded: chain Y residue 67 LEU Chi-restraints excluded: chain Y residue 110 GLU Chi-restraints excluded: chain Y residue 111 GLU Chi-restraints excluded: chain Y residue 249 THR Chi-restraints excluded: chain Y residue 356 ASP Chi-restraints excluded: chain E residue 3 SER Chi-restraints excluded: chain E residue 8 ASN Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 270 THR Chi-restraints excluded: chain E residue 297 ILE Chi-restraints excluded: chain E residue 360 ASN Chi-restraints excluded: chain Z residue 8 ASN Chi-restraints excluded: chain Z residue 110 GLU Chi-restraints excluded: chain Z residue 243 VAL Chi-restraints excluded: chain Z residue 333 ILE Chi-restraints excluded: chain F residue 8 ASN Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 56 ASP Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 356 ASP Chi-restraints excluded: chain F residue 387 SER Chi-restraints excluded: chain a residue 31 ILE Chi-restraints excluded: chain a residue 110 GLU Chi-restraints excluded: chain a residue 356 ASP Chi-restraints excluded: chain a residue 375 LEU Chi-restraints excluded: chain G residue 8 ASN Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 204 VAL Chi-restraints excluded: chain G residue 270 THR Chi-restraints excluded: chain b residue 75 ASP Chi-restraints excluded: chain b residue 110 GLU Chi-restraints excluded: chain b residue 249 THR Chi-restraints excluded: chain b residue 329 ILE Chi-restraints excluded: chain H residue 3 SER Chi-restraints excluded: chain H residue 8 ASN Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 25 GLU Chi-restraints excluded: chain H residue 35 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 270 THR Chi-restraints excluded: chain H residue 387 SER Chi-restraints excluded: chain c residue 75 ASP Chi-restraints excluded: chain c residue 249 THR Chi-restraints excluded: chain c residue 359 MET Chi-restraints excluded: chain I residue 8 ASN Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain I residue 204 VAL Chi-restraints excluded: chain I residue 241 GLU Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 360 ASN Chi-restraints excluded: chain d residue 67 LEU Chi-restraints excluded: chain d residue 110 GLU Chi-restraints excluded: chain d residue 243 VAL Chi-restraints excluded: chain d residue 249 THR Chi-restraints excluded: chain J residue 3 SER Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 42 ASP Chi-restraints excluded: chain J residue 56 ASP Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain J residue 270 THR Chi-restraints excluded: chain J residue 360 ASN Chi-restraints excluded: chain J residue 387 SER Chi-restraints excluded: chain e residue 8 ASN Chi-restraints excluded: chain e residue 31 ILE Chi-restraints excluded: chain e residue 110 GLU Chi-restraints excluded: chain e residue 111 GLU Chi-restraints excluded: chain e residue 249 THR Chi-restraints excluded: chain e residue 375 LEU Chi-restraints excluded: chain K residue 8 ASN Chi-restraints excluded: chain K residue 35 LEU Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 270 THR Chi-restraints excluded: chain K residue 360 ASN Chi-restraints excluded: chain f residue 8 ASN Chi-restraints excluded: chain f residue 60 LEU Chi-restraints excluded: chain f residue 110 GLU Chi-restraints excluded: chain f residue 249 THR Chi-restraints excluded: chain f residue 375 LEU Chi-restraints excluded: chain L residue 8 ASN Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain L residue 270 THR Chi-restraints excluded: chain L residue 292 VAL Chi-restraints excluded: chain L residue 345 ASP Chi-restraints excluded: chain L residue 347 ILE Chi-restraints excluded: chain L residue 360 ASN Chi-restraints excluded: chain g residue 8 ASN Chi-restraints excluded: chain g residue 28 GLN Chi-restraints excluded: chain g residue 67 LEU Chi-restraints excluded: chain g residue 75 ASP Chi-restraints excluded: chain g residue 249 THR Chi-restraints excluded: chain M residue 3 SER Chi-restraints excluded: chain M residue 8 ASN Chi-restraints excluded: chain M residue 35 LEU Chi-restraints excluded: chain M residue 42 ASP Chi-restraints excluded: chain M residue 270 THR Chi-restraints excluded: chain M residue 297 ILE Chi-restraints excluded: chain h residue 35 LEU Chi-restraints excluded: chain h residue 63 VAL Chi-restraints excluded: chain h residue 67 LEU Chi-restraints excluded: chain h residue 110 GLU Chi-restraints excluded: chain h residue 111 GLU Chi-restraints excluded: chain h residue 243 VAL Chi-restraints excluded: chain h residue 249 THR Chi-restraints excluded: chain N residue 8 ASN Chi-restraints excluded: chain N residue 35 LEU Chi-restraints excluded: chain N residue 42 ASP Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain N residue 270 THR Chi-restraints excluded: chain N residue 360 ASN Chi-restraints excluded: chain i residue 29 SER Chi-restraints excluded: chain i residue 110 GLU Chi-restraints excluded: chain i residue 243 VAL Chi-restraints excluded: chain i residue 249 THR Chi-restraints excluded: chain i residue 329 ILE Chi-restraints excluded: chain O residue 3 SER Chi-restraints excluded: chain O residue 8 ASN Chi-restraints excluded: chain O residue 35 LEU Chi-restraints excluded: chain O residue 56 ASP Chi-restraints excluded: chain O residue 95 LEU Chi-restraints excluded: chain O residue 204 VAL Chi-restraints excluded: chain O residue 241 GLU Chi-restraints excluded: chain O residue 270 THR Chi-restraints excluded: chain O residue 387 SER Chi-restraints excluded: chain j residue 8 ASN Chi-restraints excluded: chain j residue 35 LEU Chi-restraints excluded: chain j residue 67 LEU Chi-restraints excluded: chain j residue 110 GLU Chi-restraints excluded: chain j residue 249 THR Chi-restraints excluded: chain j residue 319 MET Chi-restraints excluded: chain j residue 375 LEU Chi-restraints excluded: chain Q residue 8 ASN Chi-restraints excluded: chain Q residue 35 LEU Chi-restraints excluded: chain Q residue 37 VAL Chi-restraints excluded: chain Q residue 91 ILE Chi-restraints excluded: chain Q residue 95 LEU Chi-restraints excluded: chain Q residue 270 THR Chi-restraints excluded: chain Q residue 360 ASN Chi-restraints excluded: chain k residue 35 LEU Chi-restraints excluded: chain k residue 249 THR Chi-restraints excluded: chain R residue 8 ASN Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 42 ASP Chi-restraints excluded: chain R residue 270 THR Chi-restraints excluded: chain R residue 360 ASN Chi-restraints excluded: chain l residue 75 ASP Chi-restraints excluded: chain l residue 110 GLU Chi-restraints excluded: chain l residue 243 VAL Chi-restraints excluded: chain l residue 249 THR Chi-restraints excluded: chain l residue 333 ILE Chi-restraints excluded: chain S residue 3 SER Chi-restraints excluded: chain S residue 8 ASN Chi-restraints excluded: chain S residue 35 LEU Chi-restraints excluded: chain S residue 37 VAL Chi-restraints excluded: chain S residue 270 THR Chi-restraints excluded: chain S residue 297 ILE Chi-restraints excluded: chain S residue 360 ASN Chi-restraints excluded: chain m residue 8 ASN Chi-restraints excluded: chain m residue 29 SER Chi-restraints excluded: chain m residue 35 LEU Chi-restraints excluded: chain m residue 110 GLU Chi-restraints excluded: chain m residue 165 ASP Chi-restraints excluded: chain m residue 249 THR Chi-restraints excluded: chain m residue 375 LEU Chi-restraints excluded: chain T residue 3 SER Chi-restraints excluded: chain T residue 8 ASN Chi-restraints excluded: chain T residue 35 LEU Chi-restraints excluded: chain T residue 37 VAL Chi-restraints excluded: chain T residue 110 GLU Chi-restraints excluded: chain T residue 270 THR Chi-restraints excluded: chain T residue 297 ILE Chi-restraints excluded: chain T residue 360 ASN Chi-restraints excluded: chain n residue 35 LEU Chi-restraints excluded: chain n residue 37 VAL Chi-restraints excluded: chain n residue 249 THR Chi-restraints excluded: chain U residue 8 ASN Chi-restraints excluded: chain U residue 37 VAL Chi-restraints excluded: chain U residue 63 VAL Chi-restraints excluded: chain U residue 95 LEU Chi-restraints excluded: chain U residue 204 VAL Chi-restraints excluded: chain U residue 242 ASN Chi-restraints excluded: chain U residue 270 THR Chi-restraints excluded: chain U residue 360 ASN Chi-restraints excluded: chain U residue 387 SER Chi-restraints excluded: chain o residue 60 LEU Chi-restraints excluded: chain o residue 110 GLU Chi-restraints excluded: chain o residue 243 VAL Chi-restraints excluded: chain o residue 249 THR Chi-restraints excluded: chain o residue 333 ILE Chi-restraints excluded: chain V residue 3 SER Chi-restraints excluded: chain V residue 8 ASN Chi-restraints excluded: chain V residue 35 LEU Chi-restraints excluded: chain V residue 37 VAL Chi-restraints excluded: chain V residue 42 ASP Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 270 THR Chi-restraints excluded: chain V residue 375 LEU Chi-restraints excluded: chain p residue 29 SER Chi-restraints excluded: chain p residue 249 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1638 random chunks: chunk 532 optimal weight: 1.9990 chunk 1425 optimal weight: 7.9990 chunk 312 optimal weight: 10.0000 chunk 929 optimal weight: 4.9990 chunk 390 optimal weight: 0.0870 chunk 1584 optimal weight: 20.0000 chunk 1315 optimal weight: 4.9990 chunk 733 optimal weight: 1.9990 chunk 131 optimal weight: 5.9990 chunk 524 optimal weight: 9.9990 chunk 832 optimal weight: 5.9990 overall best weight: 2.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 294 ASN ** Z 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 28 GLN ** b 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 232 GLN ** e 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 384 ASN g 64 GLN ** h 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 64 GLN ** i 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 242 ASN ** o 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 120078 Z= 0.187 Angle : 0.473 12.682 163170 Z= 0.265 Chirality : 0.036 0.259 20202 Planarity : 0.003 0.048 21336 Dihedral : 4.773 55.988 17262 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 2.33 % Allowed : 11.87 % Favored : 85.79 % 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: 2.34 (0.07), residues: 16464 helix: 4.41 (0.05), residues: 8148 sheet: 0.77 (0.12), residues: 1638 loop : -2.22 (0.06), residues: 6678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 133 HIS 0.001 0.000 HIS n 208 PHE 0.011 0.001 PHE Y 339 TYR 0.028 0.001 TYR J 229 ARG 0.008 0.001 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 32928 Ramachandran restraints generated. 16464 Oldfield, 0 Emsley, 16464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 32928 Ramachandran restraints generated. 16464 Oldfield, 0 Emsley, 16464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1661 residues out of total 12768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 298 poor density : 1363 time to evaluate : 9.702 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: A 82 GLU cc_start: 0.8631 (mt-10) cc_final: 0.8353 (mt-10) REVERT: P 111 GLU cc_start: 0.8752 (mm-30) cc_final: 0.8508 (mt-10) REVERT: P 269 ILE cc_start: 0.8585 (mm) cc_final: 0.8323 (mt) REVERT: P 334 ASP cc_start: 0.9004 (t0) cc_final: 0.8793 (t0) REVERT: B 18 ARG cc_start: 0.9043 (ttp-110) cc_final: 0.8703 (mtp-110) REVERT: B 95 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8640 (tt) REVERT: B 111 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8261 (mt-10) REVERT: B 361 GLU cc_start: 0.8272 (tm-30) cc_final: 0.7837 (tm-30) REVERT: W 269 ILE cc_start: 0.8646 (mm) cc_final: 0.8334 (mt) REVERT: C 82 GLU cc_start: 0.8983 (tt0) cc_final: 0.8385 (mt-10) REVERT: C 361 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7356 (tm-30) REVERT: D 241 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8360 (pm20) REVERT: D 356 ASP cc_start: 0.8173 (m-30) cc_final: 0.7902 (m-30) REVERT: Y 30 ARG cc_start: 0.8863 (tpp80) cc_final: 0.8655 (tpp80) REVERT: Y 110 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8199 (pm20) REVERT: E 95 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8691 (tt) REVERT: E 361 GLU cc_start: 0.8199 (tm-30) cc_final: 0.7673 (tm-30) REVERT: Z 30 ARG cc_start: 0.9011 (tpp80) cc_final: 0.8682 (tpp80) REVERT: Z 216 GLU cc_start: 0.8920 (mm-30) cc_final: 0.8641 (tm-30) REVERT: F 241 GLU cc_start: 0.8183 (pm20) cc_final: 0.7925 (pm20) REVERT: F 300 MET cc_start: 0.8295 (tpp) cc_final: 0.7912 (mmm) REVERT: G 18 ARG cc_start: 0.9023 (ttp-110) cc_final: 0.8774 (mtp-110) REVERT: G 82 GLU cc_start: 0.8824 (tp30) cc_final: 0.8573 (tp30) REVERT: G 294 ASN cc_start: 0.8498 (t0) cc_final: 0.8005 (t0) REVERT: G 300 MET cc_start: 0.8223 (tpp) cc_final: 0.7858 (tpt) REVERT: G 361 GLU cc_start: 0.7842 (tm-30) cc_final: 0.7401 (tm-30) REVERT: H 348 GLU cc_start: 0.9139 (tp30) cc_final: 0.8864 (tp30) REVERT: c 269 ILE cc_start: 0.8747 (mm) cc_final: 0.8529 (mt) REVERT: I 53 MET cc_start: 0.9191 (mmt) cc_final: 0.8695 (mmt) REVERT: I 90 GLU cc_start: 0.9012 (tp30) cc_final: 0.8770 (tp30) REVERT: I 95 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8645 (tt) REVERT: I 294 ASN cc_start: 0.8535 (t0) cc_final: 0.8020 (t0) REVERT: I 300 MET cc_start: 0.7522 (mmm) cc_final: 0.7007 (tpt) REVERT: I 361 GLU cc_start: 0.7856 (tm-30) cc_final: 0.7368 (tm-30) REVERT: J 338 GLU cc_start: 0.8514 (tm-30) cc_final: 0.8206 (tm-30) REVERT: e 269 ILE cc_start: 0.8794 (mm) cc_final: 0.8441 (mt) REVERT: e 313 ASP cc_start: 0.9138 (t0) cc_final: 0.8922 (t0) REVERT: K 46 TYR cc_start: 0.9057 (m-80) cc_final: 0.8814 (m-80) REVERT: K 356 ASP cc_start: 0.8339 (m-30) cc_final: 0.8062 (m-30) REVERT: f 313 ASP cc_start: 0.9004 (t70) cc_final: 0.8785 (t0) REVERT: L 361 GLU cc_start: 0.8242 (tm-30) cc_final: 0.7726 (tm-30) REVERT: g 67 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.9039 (mm) REVERT: g 110 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8263 (pm20) REVERT: M 361 GLU cc_start: 0.7703 (tm-30) cc_final: 0.7101 (tm-30) REVERT: h 30 ARG cc_start: 0.9017 (tpp80) cc_final: 0.8753 (mmt90) REVERT: h 359 MET cc_start: 0.8777 (mmm) cc_final: 0.8450 (mmm) REVERT: N 82 GLU cc_start: 0.8986 (tt0) cc_final: 0.8496 (mt-10) REVERT: N 111 GLU cc_start: 0.7569 (mt-10) cc_final: 0.7046 (tt0) REVERT: i 269 ILE cc_start: 0.8725 (mm) cc_final: 0.8468 (mt) REVERT: O 213 TYR cc_start: 0.9027 (m-80) cc_final: 0.8600 (m-80) REVERT: O 241 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.8261 (pm20) REVERT: O 294 ASN cc_start: 0.8343 (m-40) cc_final: 0.7882 (t0) REVERT: O 300 MET cc_start: 0.8234 (tpp) cc_final: 0.7865 (tpt) REVERT: O 356 ASP cc_start: 0.8216 (m-30) cc_final: 0.7924 (m-30) REVERT: j 30 ARG cc_start: 0.8906 (tpp80) cc_final: 0.8675 (tpp80) REVERT: j 269 ILE cc_start: 0.8636 (mm) cc_final: 0.8338 (mt) REVERT: j 300 MET cc_start: 0.8254 (tpp) cc_final: 0.7959 (tpt) REVERT: Q 82 GLU cc_start: 0.8842 (tt0) cc_final: 0.8505 (tt0) REVERT: Q 95 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8730 (tt) REVERT: Q 229 TYR cc_start: 0.8567 (t80) cc_final: 0.8279 (t80) REVERT: Q 300 MET cc_start: 0.7467 (tpp) cc_final: 0.7252 (mmm) REVERT: Q 359 MET cc_start: 0.8947 (mmt) cc_final: 0.8110 (mmt) REVERT: Q 361 GLU cc_start: 0.8177 (tm-30) cc_final: 0.7581 (tm-30) REVERT: l 118 GLN cc_start: 0.9097 (tp-100) cc_final: 0.8635 (tp-100) REVERT: l 269 ILE cc_start: 0.8871 (mm) cc_final: 0.8567 (mt) REVERT: S 229 TYR cc_start: 0.8446 (t80) cc_final: 0.8206 (t80) REVERT: S 294 ASN cc_start: 0.8659 (t0) cc_final: 0.8168 (t0) REVERT: S 361 GLU cc_start: 0.7402 (tm-30) cc_final: 0.7006 (tm-30) REVERT: m 53 MET cc_start: 0.9336 (mmp) cc_final: 0.9066 (mmt) REVERT: m 81 MET cc_start: 0.9509 (tpp) cc_final: 0.9255 (tpt) REVERT: m 269 ILE cc_start: 0.8735 (mm) cc_final: 0.8376 (mt) REVERT: T 82 GLU cc_start: 0.8987 (tt0) cc_final: 0.8652 (mt-10) REVERT: T 90 GLU cc_start: 0.9241 (tp30) cc_final: 0.8904 (tp30) REVERT: T 110 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8341 (tm-30) REVERT: T 111 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7477 (tt0) REVERT: U 95 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8615 (tt) REVERT: U 213 TYR cc_start: 0.9068 (m-80) cc_final: 0.8567 (m-80) REVERT: U 294 ASN cc_start: 0.8572 (t0) cc_final: 0.8197 (t0) REVERT: U 361 GLU cc_start: 0.7889 (tm-30) cc_final: 0.7384 (tm-30) REVERT: o 30 ARG cc_start: 0.9046 (tpp80) cc_final: 0.8654 (tpp80) REVERT: o 300 MET cc_start: 0.7985 (mmm) cc_final: 0.7772 (mmm) REVERT: V 361 GLU cc_start: 0.7884 (tm-30) cc_final: 0.7413 (tm-30) outliers start: 298 outliers final: 223 residues processed: 1567 average time/residue: 0.9696 time to fit residues: 2645.1201 Evaluate side-chains 1481 residues out of total 12768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 234 poor density : 1247 time to evaluate : 9.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain P residue 8 ASN Chi-restraints excluded: chain P residue 110 GLU Chi-restraints excluded: chain P residue 249 THR Chi-restraints excluded: chain P residue 375 LEU Chi-restraints excluded: chain B residue 8 ASN Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain W residue 8 ASN Chi-restraints excluded: chain W residue 110 GLU Chi-restraints excluded: chain W residue 165 ASP Chi-restraints excluded: chain W residue 243 VAL Chi-restraints excluded: chain W residue 249 THR Chi-restraints excluded: chain W residue 319 MET Chi-restraints excluded: chain W residue 345 ASP Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain X residue 29 SER Chi-restraints excluded: chain X residue 110 GLU Chi-restraints excluded: chain X residue 165 ASP Chi-restraints excluded: chain X residue 188 TYR Chi-restraints excluded: chain X residue 249 THR Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain Y residue 8 ASN Chi-restraints excluded: chain Y residue 67 LEU Chi-restraints excluded: chain Y residue 110 GLU Chi-restraints excluded: chain Y residue 111 GLU Chi-restraints excluded: chain Y residue 198 THR Chi-restraints excluded: chain Y residue 249 THR Chi-restraints excluded: chain E residue 3 SER Chi-restraints excluded: chain E residue 8 ASN Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 270 THR Chi-restraints excluded: chain E residue 297 ILE Chi-restraints excluded: chain E residue 360 ASN Chi-restraints excluded: chain Z residue 8 ASN Chi-restraints excluded: chain Z residue 28 GLN Chi-restraints excluded: chain Z residue 110 GLU Chi-restraints excluded: chain Z residue 243 VAL Chi-restraints excluded: chain F residue 8 ASN Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 56 ASP Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain a residue 31 ILE Chi-restraints excluded: chain a residue 110 GLU Chi-restraints excluded: chain a residue 375 LEU Chi-restraints excluded: chain G residue 8 ASN Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 204 VAL Chi-restraints excluded: chain G residue 270 THR Chi-restraints excluded: chain G residue 360 ASN Chi-restraints excluded: chain b residue 28 GLN Chi-restraints excluded: chain b residue 110 GLU Chi-restraints excluded: chain b residue 249 THR Chi-restraints excluded: chain b residue 329 ILE Chi-restraints excluded: chain H residue 3 SER Chi-restraints excluded: chain H residue 8 ASN Chi-restraints excluded: chain H residue 25 GLU Chi-restraints excluded: chain H residue 35 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 270 THR Chi-restraints excluded: chain c residue 35 LEU Chi-restraints excluded: chain c residue 67 LEU Chi-restraints excluded: chain c residue 75 ASP Chi-restraints excluded: chain c residue 249 THR Chi-restraints excluded: chain c residue 359 MET Chi-restraints excluded: chain I residue 8 ASN Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain I residue 204 VAL Chi-restraints excluded: chain I residue 241 GLU Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 360 ASN Chi-restraints excluded: chain d residue 110 GLU Chi-restraints excluded: chain d residue 243 VAL Chi-restraints excluded: chain d residue 249 THR Chi-restraints excluded: chain J residue 8 ASN Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 56 ASP Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain J residue 270 THR Chi-restraints excluded: chain J residue 347 ILE Chi-restraints excluded: chain J residue 360 ASN Chi-restraints excluded: chain J residue 387 SER Chi-restraints excluded: chain e residue 8 ASN Chi-restraints excluded: chain e residue 31 ILE Chi-restraints excluded: chain e residue 110 GLU Chi-restraints excluded: chain e residue 375 LEU Chi-restraints excluded: chain K residue 8 ASN Chi-restraints excluded: chain K residue 35 LEU Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 270 THR Chi-restraints excluded: chain K residue 360 ASN Chi-restraints excluded: chain f residue 110 GLU Chi-restraints excluded: chain f residue 249 THR Chi-restraints excluded: chain f residue 375 LEU Chi-restraints excluded: chain L residue 8 ASN Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain L residue 270 THR Chi-restraints excluded: chain L residue 292 VAL Chi-restraints excluded: chain L residue 345 ASP Chi-restraints excluded: chain L residue 347 ILE Chi-restraints excluded: chain L residue 360 ASN Chi-restraints excluded: chain g residue 8 ASN Chi-restraints excluded: chain g residue 28 GLN Chi-restraints excluded: chain g residue 64 GLN Chi-restraints excluded: chain g residue 67 LEU Chi-restraints excluded: chain g residue 75 ASP Chi-restraints excluded: chain g residue 110 GLU Chi-restraints excluded: chain g residue 249 THR Chi-restraints excluded: chain M residue 3 SER Chi-restraints excluded: chain M residue 8 ASN Chi-restraints excluded: chain M residue 35 LEU Chi-restraints excluded: chain M residue 42 ASP Chi-restraints excluded: chain M residue 270 THR Chi-restraints excluded: chain M residue 297 ILE Chi-restraints excluded: chain h residue 8 ASN Chi-restraints excluded: chain h residue 35 LEU Chi-restraints excluded: chain h residue 63 VAL Chi-restraints excluded: chain h residue 110 GLU Chi-restraints excluded: chain h residue 243 VAL Chi-restraints excluded: chain h residue 249 THR Chi-restraints excluded: chain N residue 8 ASN Chi-restraints excluded: chain N residue 35 LEU Chi-restraints excluded: chain N residue 42 ASP Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain N residue 228 ASN Chi-restraints excluded: chain N residue 270 THR Chi-restraints excluded: chain N residue 360 ASN Chi-restraints excluded: chain i residue 110 GLU Chi-restraints excluded: chain i residue 240 VAL Chi-restraints excluded: chain i residue 243 VAL Chi-restraints excluded: chain i residue 249 THR Chi-restraints excluded: chain i residue 329 ILE Chi-restraints excluded: chain O residue 3 SER Chi-restraints excluded: chain O residue 8 ASN Chi-restraints excluded: chain O residue 35 LEU Chi-restraints excluded: chain O residue 56 ASP Chi-restraints excluded: chain O residue 204 VAL Chi-restraints excluded: chain O residue 241 GLU Chi-restraints excluded: chain O residue 270 THR Chi-restraints excluded: chain O residue 387 SER Chi-restraints excluded: chain j residue 8 ASN Chi-restraints excluded: chain j residue 35 LEU Chi-restraints excluded: chain j residue 110 GLU Chi-restraints excluded: chain j residue 249 THR Chi-restraints excluded: chain j residue 319 MET Chi-restraints excluded: chain j residue 375 LEU Chi-restraints excluded: chain Q residue 3 SER Chi-restraints excluded: chain Q residue 8 ASN Chi-restraints excluded: chain Q residue 35 LEU Chi-restraints excluded: chain Q residue 37 VAL Chi-restraints excluded: chain Q residue 91 ILE Chi-restraints excluded: chain Q residue 95 LEU Chi-restraints excluded: chain Q residue 270 THR Chi-restraints excluded: chain Q residue 360 ASN Chi-restraints excluded: chain k residue 35 LEU Chi-restraints excluded: chain k residue 249 THR Chi-restraints excluded: chain k residue 319 MET Chi-restraints excluded: chain R residue 8 ASN Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 183 ILE Chi-restraints excluded: chain R residue 270 THR Chi-restraints excluded: chain R residue 360 ASN Chi-restraints excluded: chain l residue 75 ASP Chi-restraints excluded: chain l residue 110 GLU Chi-restraints excluded: chain l residue 243 VAL Chi-restraints excluded: chain l residue 249 THR Chi-restraints excluded: chain l residue 333 ILE Chi-restraints excluded: chain S residue 3 SER Chi-restraints excluded: chain S residue 8 ASN Chi-restraints excluded: chain S residue 35 LEU Chi-restraints excluded: chain S residue 37 VAL Chi-restraints excluded: chain S residue 241 GLU Chi-restraints excluded: chain S residue 270 THR Chi-restraints excluded: chain S residue 360 ASN Chi-restraints excluded: chain m residue 8 ASN Chi-restraints excluded: chain m residue 35 LEU Chi-restraints excluded: chain m residue 110 GLU Chi-restraints excluded: chain m residue 165 ASP Chi-restraints excluded: chain m residue 249 THR Chi-restraints excluded: chain m residue 375 LEU Chi-restraints excluded: chain T residue 8 ASN Chi-restraints excluded: chain T residue 35 LEU Chi-restraints excluded: chain T residue 37 VAL Chi-restraints excluded: chain T residue 110 GLU Chi-restraints excluded: chain T residue 270 THR Chi-restraints excluded: chain T residue 360 ASN Chi-restraints excluded: chain n residue 67 LEU Chi-restraints excluded: chain n residue 249 THR Chi-restraints excluded: chain U residue 4 ILE Chi-restraints excluded: chain U residue 8 ASN Chi-restraints excluded: chain U residue 37 VAL Chi-restraints excluded: chain U residue 95 LEU Chi-restraints excluded: chain U residue 270 THR Chi-restraints excluded: chain U residue 360 ASN Chi-restraints excluded: chain o residue 60 LEU Chi-restraints excluded: chain o residue 110 GLU Chi-restraints excluded: chain o residue 243 VAL Chi-restraints excluded: chain o residue 249 THR Chi-restraints excluded: chain o residue 333 ILE Chi-restraints excluded: chain V residue 3 SER Chi-restraints excluded: chain V residue 8 ASN Chi-restraints excluded: chain V residue 35 LEU Chi-restraints excluded: chain V residue 37 VAL Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 270 THR Chi-restraints excluded: chain V residue 375 LEU Chi-restraints excluded: chain p residue 29 SER Chi-restraints excluded: chain p residue 249 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1638 random chunks: chunk 1527 optimal weight: 9.9990 chunk 178 optimal weight: 4.9990 chunk 902 optimal weight: 2.9990 chunk 1157 optimal weight: 9.9990 chunk 896 optimal weight: 0.1980 chunk 1334 optimal weight: 4.9990 chunk 884 optimal weight: 30.0000 chunk 1578 optimal weight: 0.0170 chunk 988 optimal weight: 10.0000 chunk 962 optimal weight: 20.0000 chunk 728 optimal weight: 7.9990 overall best weight: 2.6424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 294 ASN ** Z 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 28 GLN ** b 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 118 GLN ** d 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 64 GLN ** h 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 336 GLN ** i 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 384 ASN ** j 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 242 ASN T 384 ASN ** o 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 120078 Z= 0.186 Angle : 0.481 13.301 163170 Z= 0.268 Chirality : 0.036 0.347 20202 Planarity : 0.003 0.055 21336 Dihedral : 4.700 54.470 17262 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 2.42 % Allowed : 12.59 % Favored : 84.99 % 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: 2.33 (0.07), residues: 16464 helix: 4.39 (0.05), residues: 8148 sheet: 0.79 (0.12), residues: 1638 loop : -2.22 (0.06), residues: 6678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP N 133 HIS 0.001 0.000 HIS n 208 PHE 0.010 0.001 PHE g 175 TYR 0.020 0.001 TYR p 78 ARG 0.012 0.001 ARG J 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 32928 Ramachandran restraints generated. 16464 Oldfield, 0 Emsley, 16464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 32928 Ramachandran restraints generated. 16464 Oldfield, 0 Emsley, 16464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1649 residues out of total 12768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 309 poor density : 1340 time to evaluate : 9.603 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: A 82 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8334 (mt-10) REVERT: P 28 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7701 (mt0) REVERT: P 111 GLU cc_start: 0.8753 (mm-30) cc_final: 0.8460 (mt-10) REVERT: P 269 ILE cc_start: 0.8600 (mm) cc_final: 0.8347 (mt) REVERT: P 334 ASP cc_start: 0.8968 (t0) cc_final: 0.8766 (t0) REVERT: B 18 ARG cc_start: 0.9039 (ttp-110) cc_final: 0.8696 (mtp-110) REVERT: B 95 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8643 (tt) REVERT: B 111 GLU cc_start: 0.8683 (mt-10) cc_final: 0.8248 (mt-10) REVERT: B 361 GLU cc_start: 0.8328 (tm-30) cc_final: 0.7825 (tm-30) REVERT: W 269 ILE cc_start: 0.8641 (mm) cc_final: 0.8336 (mt) REVERT: C 82 GLU cc_start: 0.8980 (tt0) cc_final: 0.8369 (mt-10) REVERT: C 86 GLU cc_start: 0.8952 (mm-30) cc_final: 0.8704 (mm-30) REVERT: C 361 GLU cc_start: 0.7866 (tm-30) cc_final: 0.7351 (tm-30) REVERT: C 386 ASP cc_start: 0.8741 (t0) cc_final: 0.8468 (m-30) REVERT: D 20 ILE cc_start: 0.9267 (mm) cc_final: 0.8994 (tp) REVERT: D 356 ASP cc_start: 0.8266 (m-30) cc_final: 0.7962 (m-30) REVERT: D 359 MET cc_start: 0.8938 (mmm) cc_final: 0.8467 (mmt) REVERT: Y 110 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8200 (pm20) REVERT: E 95 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8706 (tt) REVERT: E 361 GLU cc_start: 0.8206 (tm-30) cc_final: 0.7682 (tm-30) REVERT: Z 30 ARG cc_start: 0.9016 (tpp80) cc_final: 0.8705 (tpp80) REVERT: Z 216 GLU cc_start: 0.8920 (mm-30) cc_final: 0.8656 (tm-30) REVERT: F 241 GLU cc_start: 0.8157 (pm20) cc_final: 0.7924 (pm20) REVERT: G 18 ARG cc_start: 0.9014 (ttp-110) cc_final: 0.8772 (mtp-110) REVERT: G 82 GLU cc_start: 0.8808 (tp30) cc_final: 0.8553 (tp30) REVERT: G 294 ASN cc_start: 0.8496 (t0) cc_final: 0.8028 (t0) REVERT: G 300 MET cc_start: 0.8219 (tpp) cc_final: 0.7866 (tpt) REVERT: G 361 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7398 (tm-30) REVERT: c 269 ILE cc_start: 0.8740 (mm) cc_final: 0.8529 (mt) REVERT: c 300 MET cc_start: 0.8495 (tpt) cc_final: 0.8029 (tpt) REVERT: I 53 MET cc_start: 0.9185 (mmt) cc_final: 0.8825 (mmt) REVERT: I 90 GLU cc_start: 0.8973 (tp30) cc_final: 0.8730 (tp30) REVERT: I 294 ASN cc_start: 0.8518 (t0) cc_final: 0.8006 (t0) REVERT: I 300 MET cc_start: 0.7592 (mmm) cc_final: 0.7071 (tpt) REVERT: I 361 GLU cc_start: 0.7850 (tm-30) cc_final: 0.7450 (tm-30) REVERT: J 338 GLU cc_start: 0.8511 (tm-30) cc_final: 0.8202 (tm-30) REVERT: e 313 ASP cc_start: 0.9133 (t0) cc_final: 0.8919 (t0) REVERT: K 356 ASP cc_start: 0.8327 (m-30) cc_final: 0.8045 (m-30) REVERT: f 8 ASN cc_start: 0.9019 (OUTLIER) cc_final: 0.8774 (m-40) REVERT: f 205 GLU cc_start: 0.8237 (mp0) cc_final: 0.7985 (mp0) REVERT: f 313 ASP cc_start: 0.9002 (t70) cc_final: 0.8783 (t0) REVERT: L 18 ARG cc_start: 0.8650 (ttp-110) cc_final: 0.8444 (ttp-110) REVERT: L 361 GLU cc_start: 0.8239 (tm-30) cc_final: 0.7696 (tm-30) REVERT: g 67 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.9024 (mm) REVERT: g 110 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8288 (pm20) REVERT: h 30 ARG cc_start: 0.9050 (tpp80) cc_final: 0.8774 (mmt90) REVERT: h 359 MET cc_start: 0.8759 (mmm) cc_final: 0.8436 (mmm) REVERT: N 53 MET cc_start: 0.9206 (mmt) cc_final: 0.8972 (mmt) REVERT: N 82 GLU cc_start: 0.8976 (tt0) cc_final: 0.8476 (mt-10) REVERT: N 111 GLU cc_start: 0.7644 (mt-10) cc_final: 0.7055 (tt0) REVERT: i 269 ILE cc_start: 0.8724 (mm) cc_final: 0.8471 (mt) REVERT: O 213 TYR cc_start: 0.9048 (m-80) cc_final: 0.8631 (m-80) REVERT: O 241 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.8266 (pm20) REVERT: O 294 ASN cc_start: 0.8357 (m-40) cc_final: 0.7908 (t0) REVERT: O 300 MET cc_start: 0.8202 (tpp) cc_final: 0.7866 (tpt) REVERT: O 356 ASP cc_start: 0.8187 (m-30) cc_final: 0.7869 (m-30) REVERT: O 359 MET cc_start: 0.9083 (mmm) cc_final: 0.8808 (mmm) REVERT: j 30 ARG cc_start: 0.8915 (tpp80) cc_final: 0.8691 (tpp80) REVERT: j 269 ILE cc_start: 0.8635 (mm) cc_final: 0.8340 (mt) REVERT: j 300 MET cc_start: 0.8466 (tpp) cc_final: 0.8033 (tpt) REVERT: Q 82 GLU cc_start: 0.8808 (tt0) cc_final: 0.8467 (tt0) REVERT: Q 95 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8760 (tt) REVERT: Q 229 TYR cc_start: 0.8578 (t80) cc_final: 0.8291 (t80) REVERT: Q 300 MET cc_start: 0.7633 (tpp) cc_final: 0.7379 (mmm) REVERT: Q 359 MET cc_start: 0.8904 (mmt) cc_final: 0.8093 (mmt) REVERT: Q 361 GLU cc_start: 0.8142 (tm-30) cc_final: 0.7538 (tm-30) REVERT: k 198 THR cc_start: 0.9638 (OUTLIER) cc_final: 0.8510 (t) REVERT: l 118 GLN cc_start: 0.9067 (tp-100) cc_final: 0.8622 (tp-100) REVERT: l 269 ILE cc_start: 0.8864 (mm) cc_final: 0.8571 (mt) REVERT: S 82 GLU cc_start: 0.8965 (tt0) cc_final: 0.8606 (tt0) REVERT: S 229 TYR cc_start: 0.8414 (t80) cc_final: 0.8168 (t80) REVERT: S 294 ASN cc_start: 0.8663 (t0) cc_final: 0.8324 (t0) REVERT: S 361 GLU cc_start: 0.7322 (tm-30) cc_final: 0.6953 (tm-30) REVERT: m 81 MET cc_start: 0.9516 (tpp) cc_final: 0.9264 (tpt) REVERT: m 269 ILE cc_start: 0.8736 (mm) cc_final: 0.8381 (mt) REVERT: T 82 GLU cc_start: 0.8980 (tt0) cc_final: 0.8645 (mt-10) REVERT: T 90 GLU cc_start: 0.9245 (tp30) cc_final: 0.8910 (tp30) REVERT: T 111 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7626 (tt0) REVERT: n 30 ARG cc_start: 0.9002 (ttm-80) cc_final: 0.8602 (tpp80) REVERT: U 30 ARG cc_start: 0.9177 (mmm-85) cc_final: 0.8944 (mmm-85) REVERT: U 95 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8567 (tt) REVERT: U 213 TYR cc_start: 0.9077 (m-80) cc_final: 0.8590 (m-80) REVERT: U 294 ASN cc_start: 0.8570 (t0) cc_final: 0.8196 (t0) REVERT: U 361 GLU cc_start: 0.7884 (tm-30) cc_final: 0.7374 (tm-30) REVERT: o 11 MET cc_start: 0.9160 (mtt) cc_final: 0.8847 (mtp) REVERT: o 30 ARG cc_start: 0.9045 (tpp80) cc_final: 0.8678 (tpp80) REVERT: V 361 GLU cc_start: 0.7879 (tm-30) cc_final: 0.7399 (tm-30) REVERT: p 78 TYR cc_start: 0.8935 (t80) cc_final: 0.8664 (t80) REVERT: p 118 GLN cc_start: 0.8824 (tp-100) cc_final: 0.8130 (mm-40) outliers start: 309 outliers final: 233 residues processed: 1552 average time/residue: 0.9872 time to fit residues: 2669.0300 Evaluate side-chains 1507 residues out of total 12768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 244 poor density : 1263 time to evaluate : 9.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain P residue 8 ASN Chi-restraints excluded: chain P residue 28 GLN Chi-restraints excluded: chain P residue 110 GLU Chi-restraints excluded: chain P residue 249 THR Chi-restraints excluded: chain P residue 375 LEU Chi-restraints excluded: chain B residue 8 ASN Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain W residue 8 ASN Chi-restraints excluded: chain W residue 110 GLU Chi-restraints excluded: chain W residue 111 GLU Chi-restraints excluded: chain W residue 165 ASP Chi-restraints excluded: chain W residue 243 VAL Chi-restraints excluded: chain W residue 249 THR Chi-restraints excluded: chain W residue 319 MET Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain X residue 29 SER Chi-restraints excluded: chain X residue 110 GLU Chi-restraints excluded: chain X residue 249 THR Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain Y residue 67 LEU Chi-restraints excluded: chain Y residue 110 GLU Chi-restraints excluded: chain Y residue 111 GLU Chi-restraints excluded: chain Y residue 198 THR Chi-restraints excluded: chain Y residue 249 THR Chi-restraints excluded: chain E residue 3 SER Chi-restraints excluded: chain E residue 8 ASN Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 270 THR Chi-restraints excluded: chain E residue 297 ILE Chi-restraints excluded: chain E residue 360 ASN Chi-restraints excluded: chain Z residue 8 ASN Chi-restraints excluded: chain Z residue 28 GLN Chi-restraints excluded: chain Z residue 110 GLU Chi-restraints excluded: chain Z residue 243 VAL Chi-restraints excluded: chain Z residue 333 ILE Chi-restraints excluded: chain F residue 8 ASN Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 56 ASP Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain a residue 31 ILE Chi-restraints excluded: chain a residue 110 GLU Chi-restraints excluded: chain a residue 356 ASP Chi-restraints excluded: chain a residue 375 LEU Chi-restraints excluded: chain G residue 8 ASN Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 204 VAL Chi-restraints excluded: chain G residue 270 THR Chi-restraints excluded: chain G residue 360 ASN Chi-restraints excluded: chain b residue 28 GLN Chi-restraints excluded: chain b residue 110 GLU Chi-restraints excluded: chain b residue 198 THR Chi-restraints excluded: chain b residue 249 THR Chi-restraints excluded: chain b residue 329 ILE Chi-restraints excluded: chain b residue 358 ASP Chi-restraints excluded: chain H residue 3 SER Chi-restraints excluded: chain H residue 8 ASN Chi-restraints excluded: chain H residue 25 GLU Chi-restraints excluded: chain H residue 35 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 228 ASN Chi-restraints excluded: chain H residue 270 THR Chi-restraints excluded: chain H residue 387 SER Chi-restraints excluded: chain c residue 75 ASP Chi-restraints excluded: chain c residue 249 THR Chi-restraints excluded: chain I residue 8 ASN Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 183 ILE Chi-restraints excluded: chain I residue 204 VAL Chi-restraints excluded: chain I residue 241 GLU Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 360 ASN Chi-restraints excluded: chain d residue 110 GLU Chi-restraints excluded: chain d residue 243 VAL Chi-restraints excluded: chain d residue 249 THR Chi-restraints excluded: chain J residue 3 SER Chi-restraints excluded: chain J residue 8 ASN Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 56 ASP Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain J residue 270 THR Chi-restraints excluded: chain J residue 347 ILE Chi-restraints excluded: chain J residue 360 ASN Chi-restraints excluded: chain e residue 8 ASN Chi-restraints excluded: chain e residue 31 ILE Chi-restraints excluded: chain e residue 110 GLU Chi-restraints excluded: chain e residue 249 THR Chi-restraints excluded: chain e residue 375 LEU Chi-restraints excluded: chain K residue 8 ASN Chi-restraints excluded: chain K residue 35 LEU Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 270 THR Chi-restraints excluded: chain K residue 360 ASN Chi-restraints excluded: chain f residue 8 ASN Chi-restraints excluded: chain f residue 110 GLU Chi-restraints excluded: chain f residue 249 THR Chi-restraints excluded: chain f residue 358 ASP Chi-restraints excluded: chain f residue 375 LEU Chi-restraints excluded: chain L residue 8 ASN Chi-restraints excluded: chain L residue 42 ASP Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain L residue 270 THR Chi-restraints excluded: chain L residue 292 VAL Chi-restraints excluded: chain L residue 345 ASP Chi-restraints excluded: chain L residue 360 ASN Chi-restraints excluded: chain g residue 8 ASN Chi-restraints excluded: chain g residue 28 GLN Chi-restraints excluded: chain g residue 64 GLN Chi-restraints excluded: chain g residue 67 LEU Chi-restraints excluded: chain g residue 75 ASP Chi-restraints excluded: chain g residue 110 GLU Chi-restraints excluded: chain g residue 249 THR Chi-restraints excluded: chain M residue 3 SER Chi-restraints excluded: chain M residue 8 ASN Chi-restraints excluded: chain M residue 35 LEU Chi-restraints excluded: chain M residue 42 ASP Chi-restraints excluded: chain M residue 95 LEU Chi-restraints excluded: chain M residue 270 THR Chi-restraints excluded: chain M residue 297 ILE Chi-restraints excluded: chain h residue 8 ASN Chi-restraints excluded: chain h residue 35 LEU Chi-restraints excluded: chain h residue 63 VAL Chi-restraints excluded: chain h residue 110 GLU Chi-restraints excluded: chain h residue 111 GLU Chi-restraints excluded: chain h residue 243 VAL Chi-restraints excluded: chain h residue 249 THR Chi-restraints excluded: chain N residue 8 ASN Chi-restraints excluded: chain N residue 35 LEU Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain N residue 228 ASN Chi-restraints excluded: chain N residue 270 THR Chi-restraints excluded: chain N residue 345 ASP Chi-restraints excluded: chain N residue 360 ASN Chi-restraints excluded: chain i residue 110 GLU Chi-restraints excluded: chain i residue 240 VAL Chi-restraints excluded: chain i residue 243 VAL Chi-restraints excluded: chain i residue 249 THR Chi-restraints excluded: chain i residue 329 ILE Chi-restraints excluded: chain O residue 3 SER Chi-restraints excluded: chain O residue 8 ASN Chi-restraints excluded: chain O residue 35 LEU Chi-restraints excluded: chain O residue 56 ASP Chi-restraints excluded: chain O residue 95 LEU Chi-restraints excluded: chain O residue 204 VAL Chi-restraints excluded: chain O residue 241 GLU Chi-restraints excluded: chain O residue 270 THR Chi-restraints excluded: chain O residue 387 SER Chi-restraints excluded: chain j residue 8 ASN Chi-restraints excluded: chain j residue 35 LEU Chi-restraints excluded: chain j residue 110 GLU Chi-restraints excluded: chain j residue 243 VAL Chi-restraints excluded: chain j residue 249 THR Chi-restraints excluded: chain j residue 319 MET Chi-restraints excluded: chain j residue 375 LEU Chi-restraints excluded: chain Q residue 3 SER Chi-restraints excluded: chain Q residue 8 ASN Chi-restraints excluded: chain Q residue 35 LEU Chi-restraints excluded: chain Q residue 37 VAL Chi-restraints excluded: chain Q residue 91 ILE Chi-restraints excluded: chain Q residue 95 LEU Chi-restraints excluded: chain Q residue 270 THR Chi-restraints excluded: chain Q residue 360 ASN Chi-restraints excluded: chain k residue 198 THR Chi-restraints excluded: chain k residue 249 THR Chi-restraints excluded: chain k residue 319 MET Chi-restraints excluded: chain R residue 8 ASN Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 183 ILE Chi-restraints excluded: chain R residue 270 THR Chi-restraints excluded: chain R residue 360 ASN Chi-restraints excluded: chain l residue 75 ASP Chi-restraints excluded: chain l residue 110 GLU Chi-restraints excluded: chain l residue 243 VAL Chi-restraints excluded: chain l residue 249 THR Chi-restraints excluded: chain l residue 333 ILE Chi-restraints excluded: chain S residue 3 SER Chi-restraints excluded: chain S residue 8 ASN Chi-restraints excluded: chain S residue 35 LEU Chi-restraints excluded: chain S residue 241 GLU Chi-restraints excluded: chain S residue 270 THR Chi-restraints excluded: chain S residue 356 ASP Chi-restraints excluded: chain S residue 360 ASN Chi-restraints excluded: chain m residue 8 ASN Chi-restraints excluded: chain m residue 35 LEU Chi-restraints excluded: chain m residue 110 GLU Chi-restraints excluded: chain m residue 165 ASP Chi-restraints excluded: chain m residue 249 THR Chi-restraints excluded: chain T residue 3 SER Chi-restraints excluded: chain T residue 8 ASN Chi-restraints excluded: chain T residue 35 LEU Chi-restraints excluded: chain T residue 37 VAL Chi-restraints excluded: chain T residue 270 THR Chi-restraints excluded: chain n residue 35 LEU Chi-restraints excluded: chain n residue 37 VAL Chi-restraints excluded: chain n residue 67 LEU Chi-restraints excluded: chain n residue 249 THR Chi-restraints excluded: chain U residue 8 ASN Chi-restraints excluded: chain U residue 37 VAL Chi-restraints excluded: chain U residue 95 LEU Chi-restraints excluded: chain U residue 204 VAL Chi-restraints excluded: chain U residue 270 THR Chi-restraints excluded: chain U residue 360 ASN Chi-restraints excluded: chain o residue 60 LEU Chi-restraints excluded: chain o residue 110 GLU Chi-restraints excluded: chain o residue 198 THR Chi-restraints excluded: chain o residue 243 VAL Chi-restraints excluded: chain o residue 249 THR Chi-restraints excluded: chain o residue 333 ILE Chi-restraints excluded: chain V residue 3 SER Chi-restraints excluded: chain V residue 8 ASN Chi-restraints excluded: chain V residue 37 VAL Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 270 THR Chi-restraints excluded: chain V residue 375 LEU Chi-restraints excluded: chain p residue 29 SER Chi-restraints excluded: chain p residue 249 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1638 random chunks: chunk 976 optimal weight: 8.9990 chunk 630 optimal weight: 5.9990 chunk 942 optimal weight: 9.9990 chunk 475 optimal weight: 0.9990 chunk 310 optimal weight: 3.9990 chunk 305 optimal weight: 7.9990 chunk 1003 optimal weight: 0.9990 chunk 1075 optimal weight: 20.0000 chunk 780 optimal weight: 5.9990 chunk 147 optimal weight: 5.9990 chunk 1240 optimal weight: 0.9980 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 64 GLN ** C 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 ASN ** Z 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 118 GLN ** d 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 336 GLN ** i 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 242 ASN ** o 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 120078 Z= 0.184 Angle : 0.486 13.962 163170 Z= 0.270 Chirality : 0.036 0.280 20202 Planarity : 0.003 0.042 21336 Dihedral : 4.645 52.424 17262 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 2.37 % Allowed : 13.10 % Favored : 84.54 % 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: 2.22 (0.07), residues: 16464 helix: 4.24 (0.05), residues: 8316 sheet: 0.81 (0.12), residues: 1638 loop : -2.38 (0.06), residues: 6510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP N 133 HIS 0.001 0.000 HIS n 208 PHE 0.027 0.001 PHE i 394 TYR 0.020 0.001 TYR g 78 ARG 0.010 0.001 ARG J 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 32928 Ramachandran restraints generated. 16464 Oldfield, 0 Emsley, 16464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 32928 Ramachandran restraints generated. 16464 Oldfield, 0 Emsley, 16464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1624 residues out of total 12768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 302 poor density : 1322 time to evaluate : 9.793 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: A 82 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8326 (mt-10) REVERT: P 28 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.7754 (mt0) REVERT: P 111 GLU cc_start: 0.8737 (mm-30) cc_final: 0.8490 (mm-30) REVERT: P 269 ILE cc_start: 0.8599 (mm) cc_final: 0.8346 (mt) REVERT: B 18 ARG cc_start: 0.9038 (ttp-110) cc_final: 0.8691 (mtp-110) REVERT: B 95 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8662 (tt) REVERT: B 111 GLU cc_start: 0.8667 (mt-10) cc_final: 0.8361 (mt-10) REVERT: W 269 ILE cc_start: 0.8637 (mm) cc_final: 0.8334 (mt) REVERT: C 82 GLU cc_start: 0.8968 (tt0) cc_final: 0.8358 (mt-10) REVERT: C 361 GLU cc_start: 0.7847 (tm-30) cc_final: 0.7345 (tm-30) REVERT: D 241 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8328 (pm20) REVERT: D 356 ASP cc_start: 0.8174 (m-30) cc_final: 0.7968 (m-30) REVERT: D 359 MET cc_start: 0.8962 (mmm) cc_final: 0.8560 (mmt) REVERT: Y 30 ARG cc_start: 0.9017 (tpp80) cc_final: 0.8742 (tpp80) REVERT: Y 110 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.8202 (pm20) REVERT: E 95 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8683 (tt) REVERT: E 359 MET cc_start: 0.8862 (mmt) cc_final: 0.8074 (mmt) REVERT: E 361 GLU cc_start: 0.8205 (tm-30) cc_final: 0.7687 (tm-30) REVERT: Z 216 GLU cc_start: 0.8921 (mm-30) cc_final: 0.8655 (tm-30) REVERT: F 241 GLU cc_start: 0.8175 (pm20) cc_final: 0.7951 (pm20) REVERT: G 18 ARG cc_start: 0.9013 (ttp-110) cc_final: 0.8765 (mtp-110) REVERT: G 82 GLU cc_start: 0.8804 (tp30) cc_final: 0.8547 (tp30) REVERT: G 294 ASN cc_start: 0.8506 (t0) cc_final: 0.8039 (t0) REVERT: G 300 MET cc_start: 0.8150 (tpp) cc_final: 0.7792 (tpt) REVERT: G 361 GLU cc_start: 0.7858 (tm-30) cc_final: 0.7408 (tm-30) REVERT: c 269 ILE cc_start: 0.8741 (mm) cc_final: 0.8533 (mt) REVERT: I 53 MET cc_start: 0.9184 (mmt) cc_final: 0.8849 (mmt) REVERT: I 90 GLU cc_start: 0.8978 (tp30) cc_final: 0.8751 (tp30) REVERT: I 294 ASN cc_start: 0.8567 (t0) cc_final: 0.8065 (t0) REVERT: I 300 MET cc_start: 0.7576 (mmm) cc_final: 0.7066 (tpt) REVERT: I 361 GLU cc_start: 0.7838 (tm-30) cc_final: 0.7421 (tm-30) REVERT: J 213 TYR cc_start: 0.9141 (m-80) cc_final: 0.8723 (m-80) REVERT: J 338 GLU cc_start: 0.8509 (tm-30) cc_final: 0.8211 (tm-30) REVERT: e 313 ASP cc_start: 0.9132 (t0) cc_final: 0.8916 (t0) REVERT: K 356 ASP cc_start: 0.8291 (m-30) cc_final: 0.8002 (m-30) REVERT: f 8 ASN cc_start: 0.8995 (OUTLIER) cc_final: 0.8740 (m-40) REVERT: f 205 GLU cc_start: 0.8236 (mp0) cc_final: 0.7967 (mp0) REVERT: f 313 ASP cc_start: 0.8994 (t70) cc_final: 0.8699 (t0) REVERT: L 361 GLU cc_start: 0.8232 (tm-30) cc_final: 0.7712 (tm-30) REVERT: g 67 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.8973 (mm) REVERT: g 110 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8288 (pm20) REVERT: h 30 ARG cc_start: 0.9056 (tpp80) cc_final: 0.8742 (mmt90) REVERT: h 359 MET cc_start: 0.8753 (mmm) cc_final: 0.8463 (mmm) REVERT: N 82 GLU cc_start: 0.8967 (tt0) cc_final: 0.8466 (mt-10) REVERT: N 111 GLU cc_start: 0.7644 (mt-10) cc_final: 0.7052 (tt0) REVERT: i 269 ILE cc_start: 0.8723 (mm) cc_final: 0.8474 (mt) REVERT: O 53 MET cc_start: 0.9287 (mmp) cc_final: 0.8951 (mmp) REVERT: O 213 TYR cc_start: 0.9054 (m-80) cc_final: 0.8643 (m-80) REVERT: O 241 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.8271 (pm20) REVERT: O 294 ASN cc_start: 0.8353 (m-40) cc_final: 0.7901 (t0) REVERT: O 300 MET cc_start: 0.8124 (tpp) cc_final: 0.7834 (tpt) REVERT: O 356 ASP cc_start: 0.8120 (m-30) cc_final: 0.7852 (m-30) REVERT: O 359 MET cc_start: 0.9113 (mmm) cc_final: 0.8854 (mmm) REVERT: j 30 ARG cc_start: 0.8924 (tpp80) cc_final: 0.8704 (tpp80) REVERT: j 269 ILE cc_start: 0.8641 (mm) cc_final: 0.8355 (mt) REVERT: j 300 MET cc_start: 0.8450 (tpp) cc_final: 0.8037 (tpt) REVERT: Q 82 GLU cc_start: 0.8808 (tt0) cc_final: 0.8468 (tt0) REVERT: Q 95 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8775 (tt) REVERT: Q 229 TYR cc_start: 0.8538 (t80) cc_final: 0.8264 (t80) REVERT: Q 300 MET cc_start: 0.7851 (tpp) cc_final: 0.7494 (mmm) REVERT: Q 359 MET cc_start: 0.8856 (mmt) cc_final: 0.8085 (mmt) REVERT: Q 361 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7556 (tm-30) REVERT: R 300 MET cc_start: 0.8090 (tpp) cc_final: 0.7665 (mmm) REVERT: R 365 ARG cc_start: 0.9099 (mtp85) cc_final: 0.8855 (mtp85) REVERT: l 118 GLN cc_start: 0.9047 (tp-100) cc_final: 0.8605 (tp-100) REVERT: l 300 MET cc_start: 0.8314 (mmt) cc_final: 0.7823 (tpt) REVERT: S 82 GLU cc_start: 0.8944 (tt0) cc_final: 0.8592 (tt0) REVERT: S 229 TYR cc_start: 0.8416 (t80) cc_final: 0.8160 (t80) REVERT: S 294 ASN cc_start: 0.8659 (t0) cc_final: 0.8159 (t0) REVERT: S 361 GLU cc_start: 0.7288 (tm-30) cc_final: 0.6944 (tm-30) REVERT: m 81 MET cc_start: 0.9534 (tpp) cc_final: 0.9275 (tpt) REVERT: m 269 ILE cc_start: 0.8775 (mm) cc_final: 0.8432 (mt) REVERT: T 82 GLU cc_start: 0.8977 (tt0) cc_final: 0.8642 (mt-10) REVERT: T 90 GLU cc_start: 0.9237 (tp30) cc_final: 0.8892 (tp30) REVERT: T 111 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7564 (tt0) REVERT: U 95 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8572 (tt) REVERT: U 213 TYR cc_start: 0.9085 (m-80) cc_final: 0.8607 (m-80) REVERT: U 294 ASN cc_start: 0.8591 (t0) cc_final: 0.8222 (t0) REVERT: U 361 GLU cc_start: 0.7879 (tm-30) cc_final: 0.7440 (tm-30) REVERT: o 30 ARG cc_start: 0.9033 (tpp80) cc_final: 0.8676 (tpp80) REVERT: o 353 ARG cc_start: 0.9117 (ttm-80) cc_final: 0.8917 (ttm-80) REVERT: V 361 GLU cc_start: 0.7879 (tm-30) cc_final: 0.7382 (tm-30) REVERT: p 118 GLN cc_start: 0.8818 (tp-100) cc_final: 0.8132 (mm-40) REVERT: p 362 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8256 (mm-30) outliers start: 302 outliers final: 243 residues processed: 1536 average time/residue: 0.9716 time to fit residues: 2608.4717 Evaluate side-chains 1510 residues out of total 12768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 255 poor density : 1255 time to evaluate : 9.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain P residue 8 ASN Chi-restraints excluded: chain P residue 28 GLN Chi-restraints excluded: chain P residue 110 GLU Chi-restraints excluded: chain P residue 249 THR Chi-restraints excluded: chain P residue 375 LEU Chi-restraints excluded: chain B residue 8 ASN Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain W residue 8 ASN Chi-restraints excluded: chain W residue 110 GLU Chi-restraints excluded: chain W residue 165 ASP Chi-restraints excluded: chain W residue 243 VAL Chi-restraints excluded: chain W residue 249 THR Chi-restraints excluded: chain W residue 319 MET Chi-restraints excluded: chain W residue 345 ASP Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain X residue 110 GLU Chi-restraints excluded: chain X residue 165 ASP Chi-restraints excluded: chain X residue 188 TYR Chi-restraints excluded: chain X residue 249 THR Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain Y residue 8 ASN Chi-restraints excluded: chain Y residue 67 LEU Chi-restraints excluded: chain Y residue 110 GLU Chi-restraints excluded: chain Y residue 111 GLU Chi-restraints excluded: chain Y residue 198 THR Chi-restraints excluded: chain Y residue 249 THR Chi-restraints excluded: chain E residue 3 SER Chi-restraints excluded: chain E residue 8 ASN Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 270 THR Chi-restraints excluded: chain E residue 297 ILE Chi-restraints excluded: chain E residue 360 ASN Chi-restraints excluded: chain Z residue 8 ASN Chi-restraints excluded: chain Z residue 28 GLN Chi-restraints excluded: chain Z residue 110 GLU Chi-restraints excluded: chain Z residue 243 VAL Chi-restraints excluded: chain F residue 8 ASN Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 56 ASP Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain a residue 31 ILE Chi-restraints excluded: chain a residue 110 GLU Chi-restraints excluded: chain a residue 356 ASP Chi-restraints excluded: chain a residue 375 LEU Chi-restraints excluded: chain G residue 8 ASN Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 204 VAL Chi-restraints excluded: chain G residue 270 THR Chi-restraints excluded: chain G residue 360 ASN Chi-restraints excluded: chain b residue 28 GLN Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain b residue 75 ASP Chi-restraints excluded: chain b residue 110 GLU Chi-restraints excluded: chain b residue 198 THR Chi-restraints excluded: chain b residue 249 THR Chi-restraints excluded: chain b residue 329 ILE Chi-restraints excluded: chain b residue 358 ASP Chi-restraints excluded: chain H residue 3 SER Chi-restraints excluded: chain H residue 8 ASN Chi-restraints excluded: chain H residue 25 GLU Chi-restraints excluded: chain H residue 35 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 228 ASN Chi-restraints excluded: chain H residue 270 THR Chi-restraints excluded: chain H residue 387 SER Chi-restraints excluded: chain c residue 75 ASP Chi-restraints excluded: chain c residue 249 THR Chi-restraints excluded: chain I residue 8 ASN Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain I residue 183 ILE Chi-restraints excluded: chain I residue 204 VAL Chi-restraints excluded: chain I residue 241 GLU Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 360 ASN Chi-restraints excluded: chain d residue 110 GLU Chi-restraints excluded: chain d residue 243 VAL Chi-restraints excluded: chain d residue 249 THR Chi-restraints excluded: chain J residue 3 SER Chi-restraints excluded: chain J residue 8 ASN Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 56 ASP Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain J residue 270 THR Chi-restraints excluded: chain J residue 347 ILE Chi-restraints excluded: chain J residue 360 ASN Chi-restraints excluded: chain e residue 31 ILE Chi-restraints excluded: chain e residue 110 GLU Chi-restraints excluded: chain e residue 249 THR Chi-restraints excluded: chain e residue 375 LEU Chi-restraints excluded: chain K residue 8 ASN Chi-restraints excluded: chain K residue 35 LEU Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 270 THR Chi-restraints excluded: chain K residue 360 ASN Chi-restraints excluded: chain f residue 8 ASN Chi-restraints excluded: chain f residue 110 GLU Chi-restraints excluded: chain f residue 249 THR Chi-restraints excluded: chain f residue 358 ASP Chi-restraints excluded: chain f residue 375 LEU Chi-restraints excluded: chain L residue 8 ASN Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain L residue 270 THR Chi-restraints excluded: chain L residue 292 VAL Chi-restraints excluded: chain L residue 360 ASN Chi-restraints excluded: chain g residue 8 ASN Chi-restraints excluded: chain g residue 28 GLN Chi-restraints excluded: chain g residue 67 LEU Chi-restraints excluded: chain g residue 110 GLU Chi-restraints excluded: chain g residue 249 THR Chi-restraints excluded: chain g residue 319 MET Chi-restraints excluded: chain M residue 3 SER Chi-restraints excluded: chain M residue 8 ASN Chi-restraints excluded: chain M residue 35 LEU Chi-restraints excluded: chain M residue 42 ASP Chi-restraints excluded: chain M residue 95 LEU Chi-restraints excluded: chain M residue 270 THR Chi-restraints excluded: chain M residue 297 ILE Chi-restraints excluded: chain h residue 8 ASN Chi-restraints excluded: chain h residue 35 LEU Chi-restraints excluded: chain h residue 63 VAL Chi-restraints excluded: chain h residue 110 GLU Chi-restraints excluded: chain h residue 111 GLU Chi-restraints excluded: chain h residue 243 VAL Chi-restraints excluded: chain N residue 8 ASN Chi-restraints excluded: chain N residue 35 LEU Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain N residue 228 ASN Chi-restraints excluded: chain N residue 270 THR Chi-restraints excluded: chain N residue 345 ASP Chi-restraints excluded: chain N residue 360 ASN Chi-restraints excluded: chain i residue 110 GLU Chi-restraints excluded: chain i residue 240 VAL Chi-restraints excluded: chain i residue 243 VAL Chi-restraints excluded: chain i residue 249 THR Chi-restraints excluded: chain i residue 329 ILE Chi-restraints excluded: chain O residue 3 SER Chi-restraints excluded: chain O residue 8 ASN Chi-restraints excluded: chain O residue 35 LEU Chi-restraints excluded: chain O residue 42 ASP Chi-restraints excluded: chain O residue 56 ASP Chi-restraints excluded: chain O residue 95 LEU Chi-restraints excluded: chain O residue 204 VAL Chi-restraints excluded: chain O residue 241 GLU Chi-restraints excluded: chain O residue 270 THR Chi-restraints excluded: chain O residue 387 SER Chi-restraints excluded: chain j residue 8 ASN Chi-restraints excluded: chain j residue 35 LEU Chi-restraints excluded: chain j residue 110 GLU Chi-restraints excluded: chain j residue 198 THR Chi-restraints excluded: chain j residue 243 VAL Chi-restraints excluded: chain j residue 249 THR Chi-restraints excluded: chain j residue 319 MET Chi-restraints excluded: chain j residue 375 LEU Chi-restraints excluded: chain Q residue 3 SER Chi-restraints excluded: chain Q residue 8 ASN Chi-restraints excluded: chain Q residue 35 LEU Chi-restraints excluded: chain Q residue 37 VAL Chi-restraints excluded: chain Q residue 91 ILE Chi-restraints excluded: chain Q residue 95 LEU Chi-restraints excluded: chain Q residue 270 THR Chi-restraints excluded: chain Q residue 360 ASN Chi-restraints excluded: chain k residue 198 THR Chi-restraints excluded: chain k residue 249 THR Chi-restraints excluded: chain k residue 319 MET Chi-restraints excluded: chain R residue 8 ASN Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 42 ASP Chi-restraints excluded: chain R residue 161 VAL Chi-restraints excluded: chain R residue 183 ILE Chi-restraints excluded: chain R residue 270 THR Chi-restraints excluded: chain R residue 292 VAL Chi-restraints excluded: chain R residue 360 ASN Chi-restraints excluded: chain l residue 75 ASP Chi-restraints excluded: chain l residue 243 VAL Chi-restraints excluded: chain l residue 249 THR Chi-restraints excluded: chain l residue 333 ILE Chi-restraints excluded: chain S residue 3 SER Chi-restraints excluded: chain S residue 8 ASN Chi-restraints excluded: chain S residue 35 LEU Chi-restraints excluded: chain S residue 95 LEU Chi-restraints excluded: chain S residue 241 GLU Chi-restraints excluded: chain S residue 270 THR Chi-restraints excluded: chain S residue 356 ASP Chi-restraints excluded: chain S residue 360 ASN Chi-restraints excluded: chain m residue 8 ASN Chi-restraints excluded: chain m residue 29 SER Chi-restraints excluded: chain m residue 35 LEU Chi-restraints excluded: chain m residue 110 GLU Chi-restraints excluded: chain m residue 165 ASP Chi-restraints excluded: chain m residue 249 THR Chi-restraints excluded: chain T residue 3 SER Chi-restraints excluded: chain T residue 8 ASN Chi-restraints excluded: chain T residue 35 LEU Chi-restraints excluded: chain T residue 37 VAL Chi-restraints excluded: chain T residue 95 LEU Chi-restraints excluded: chain T residue 270 THR Chi-restraints excluded: chain n residue 37 VAL Chi-restraints excluded: chain n residue 67 LEU Chi-restraints excluded: chain n residue 249 THR Chi-restraints excluded: chain U residue 8 ASN Chi-restraints excluded: chain U residue 37 VAL Chi-restraints excluded: chain U residue 95 LEU Chi-restraints excluded: chain U residue 204 VAL Chi-restraints excluded: chain U residue 270 THR Chi-restraints excluded: chain U residue 360 ASN Chi-restraints excluded: chain o residue 60 LEU Chi-restraints excluded: chain o residue 110 GLU Chi-restraints excluded: chain o residue 198 THR Chi-restraints excluded: chain o residue 243 VAL Chi-restraints excluded: chain o residue 249 THR Chi-restraints excluded: chain o residue 333 ILE Chi-restraints excluded: chain V residue 3 SER Chi-restraints excluded: chain V residue 8 ASN Chi-restraints excluded: chain V residue 37 VAL Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 270 THR Chi-restraints excluded: chain V residue 375 LEU Chi-restraints excluded: chain p residue 249 THR Chi-restraints excluded: chain p residue 362 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1638 random chunks: chunk 1436 optimal weight: 5.9990 chunk 1512 optimal weight: 9.9990 chunk 1379 optimal weight: 20.0000 chunk 1471 optimal weight: 10.0000 chunk 885 optimal weight: 9.9990 chunk 640 optimal weight: 7.9990 chunk 1155 optimal weight: 0.6980 chunk 451 optimal weight: 0.0040 chunk 1329 optimal weight: 10.0000 chunk 1391 optimal weight: 3.9990 chunk 1466 optimal weight: 2.9990 overall best weight: 2.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 ASN ** Z 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 118 GLN ** d 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 336 GLN ** i 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 28 GLN R 336 GLN ** o 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 120078 Z= 0.194 Angle : 0.502 13.904 163170 Z= 0.276 Chirality : 0.037 0.365 20202 Planarity : 0.003 0.057 21336 Dihedral : 4.612 50.527 17262 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 2.29 % Allowed : 13.52 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.07), residues: 16464 helix: 4.21 (0.05), residues: 8316 sheet: 0.80 (0.12), residues: 1638 loop : -2.38 (0.06), residues: 6510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP N 133 HIS 0.001 0.000 HIS W 208 PHE 0.014 0.001 PHE i 394 TYR 0.040 0.001 TYR X 78 ARG 0.012 0.001 ARG J 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 32928 Ramachandran restraints generated. 16464 Oldfield, 0 Emsley, 16464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 32928 Ramachandran restraints generated. 16464 Oldfield, 0 Emsley, 16464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1595 residues out of total 12768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 292 poor density : 1303 time to evaluate : 9.638 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: A 82 GLU cc_start: 0.8632 (mt-10) cc_final: 0.8334 (mt-10) REVERT: P 28 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7828 (mt0) REVERT: P 111 GLU cc_start: 0.8767 (mm-30) cc_final: 0.8529 (mm-30) REVERT: P 269 ILE cc_start: 0.8603 (mm) cc_final: 0.8349 (mt) REVERT: B 18 ARG cc_start: 0.9039 (ttp-110) cc_final: 0.8689 (mtp-110) REVERT: B 95 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8658 (tt) REVERT: B 111 GLU cc_start: 0.8658 (mt-10) cc_final: 0.8356 (mt-10) REVERT: W 269 ILE cc_start: 0.8647 (mm) cc_final: 0.8351 (mt) REVERT: C 82 GLU cc_start: 0.8987 (tt0) cc_final: 0.8381 (mt-10) REVERT: C 361 GLU cc_start: 0.7847 (tm-30) cc_final: 0.7343 (tm-30) REVERT: X 20 ILE cc_start: 0.9407 (mt) cc_final: 0.9200 (mm) REVERT: D 356 ASP cc_start: 0.8292 (m-30) cc_final: 0.8066 (m-30) REVERT: D 359 MET cc_start: 0.8926 (mmm) cc_final: 0.8560 (mmt) REVERT: Y 30 ARG cc_start: 0.9013 (tpp80) cc_final: 0.8740 (tpp80) REVERT: Y 110 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.8210 (pm20) REVERT: E 95 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8688 (tt) REVERT: E 359 MET cc_start: 0.8866 (mmt) cc_final: 0.8071 (mmt) REVERT: E 361 GLU cc_start: 0.8221 (tm-30) cc_final: 0.7705 (tm-30) REVERT: Z 216 GLU cc_start: 0.8925 (mm-30) cc_final: 0.8646 (tm-30) REVERT: F 229 TYR cc_start: 0.8462 (t80) cc_final: 0.7954 (t80) REVERT: F 241 GLU cc_start: 0.8159 (pm20) cc_final: 0.7947 (pm20) REVERT: a 78 TYR cc_start: 0.9117 (t80) cc_final: 0.8870 (t80) REVERT: G 18 ARG cc_start: 0.9013 (ttp-110) cc_final: 0.8763 (mtp-110) REVERT: G 82 GLU cc_start: 0.8812 (tp30) cc_final: 0.8551 (tp30) REVERT: G 294 ASN cc_start: 0.8512 (t0) cc_final: 0.8046 (t0) REVERT: G 300 MET cc_start: 0.8152 (tpp) cc_final: 0.7802 (tpt) REVERT: G 361 GLU cc_start: 0.7857 (tm-30) cc_final: 0.7396 (tm-30) REVERT: c 269 ILE cc_start: 0.8742 (mm) cc_final: 0.8534 (mt) REVERT: c 300 MET cc_start: 0.8348 (tpt) cc_final: 0.7757 (tpt) REVERT: I 53 MET cc_start: 0.9184 (mmt) cc_final: 0.8845 (mmt) REVERT: I 90 GLU cc_start: 0.8982 (tp30) cc_final: 0.8754 (tp30) REVERT: I 294 ASN cc_start: 0.8575 (t0) cc_final: 0.8075 (t0) REVERT: I 300 MET cc_start: 0.7580 (mmm) cc_final: 0.7076 (tpt) REVERT: I 361 GLU cc_start: 0.7878 (tm-30) cc_final: 0.7466 (tm-30) REVERT: d 30 ARG cc_start: 0.9154 (tpp80) cc_final: 0.8632 (mmt90) REVERT: J 213 TYR cc_start: 0.9141 (m-80) cc_final: 0.8734 (m-80) REVERT: J 338 GLU cc_start: 0.8526 (tm-30) cc_final: 0.8246 (tm-30) REVERT: e 313 ASP cc_start: 0.9136 (t0) cc_final: 0.8921 (t0) REVERT: K 356 ASP cc_start: 0.8284 (m-30) cc_final: 0.7992 (m-30) REVERT: f 8 ASN cc_start: 0.9001 (OUTLIER) cc_final: 0.8749 (m-40) REVERT: f 205 GLU cc_start: 0.8237 (mp0) cc_final: 0.7982 (mp0) REVERT: f 313 ASP cc_start: 0.8990 (t70) cc_final: 0.8775 (t0) REVERT: L 18 ARG cc_start: 0.8662 (ttp-110) cc_final: 0.8350 (ttp-110) REVERT: L 361 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7687 (tm-30) REVERT: g 67 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.9005 (mm) REVERT: g 110 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8287 (pm20) REVERT: M 81 MET cc_start: 0.9332 (tpp) cc_final: 0.8931 (tpp) REVERT: h 30 ARG cc_start: 0.9051 (tpp80) cc_final: 0.8757 (mmt90) REVERT: h 359 MET cc_start: 0.8745 (mmm) cc_final: 0.8457 (mmm) REVERT: N 82 GLU cc_start: 0.8974 (tt0) cc_final: 0.8476 (mt-10) REVERT: N 111 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7056 (tt0) REVERT: i 269 ILE cc_start: 0.8732 (mm) cc_final: 0.8489 (mt) REVERT: O 53 MET cc_start: 0.9286 (mmp) cc_final: 0.9027 (mmp) REVERT: O 213 TYR cc_start: 0.9061 (m-80) cc_final: 0.8655 (m-80) REVERT: O 241 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8248 (pm20) REVERT: O 294 ASN cc_start: 0.8361 (m-40) cc_final: 0.7923 (t0) REVERT: O 300 MET cc_start: 0.8123 (tpp) cc_final: 0.7827 (tpt) REVERT: O 356 ASP cc_start: 0.8106 (m-30) cc_final: 0.7853 (m-30) REVERT: O 359 MET cc_start: 0.9126 (mmm) cc_final: 0.8876 (mmm) REVERT: j 30 ARG cc_start: 0.8934 (tpp80) cc_final: 0.8715 (tpp80) REVERT: j 269 ILE cc_start: 0.8642 (mm) cc_final: 0.8358 (mt) REVERT: j 300 MET cc_start: 0.8442 (tpp) cc_final: 0.8069 (tpt) REVERT: Q 82 GLU cc_start: 0.8809 (tt0) cc_final: 0.8458 (tt0) REVERT: Q 95 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8775 (tt) REVERT: Q 300 MET cc_start: 0.7934 (tpp) cc_final: 0.7540 (mmm) REVERT: Q 359 MET cc_start: 0.8842 (mmt) cc_final: 0.8066 (mmt) REVERT: Q 361 GLU cc_start: 0.8174 (tm-30) cc_final: 0.7588 (tm-30) REVERT: R 300 MET cc_start: 0.8111 (tpp) cc_final: 0.7635 (mmm) REVERT: R 365 ARG cc_start: 0.9121 (mtp85) cc_final: 0.8880 (mtp85) REVERT: l 86 GLU cc_start: 0.8968 (mm-30) cc_final: 0.8750 (mm-30) REVERT: l 118 GLN cc_start: 0.9054 (tp-100) cc_final: 0.8611 (tp-100) REVERT: l 300 MET cc_start: 0.8371 (OUTLIER) cc_final: 0.7892 (tpt) REVERT: l 362 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8313 (mm-30) REVERT: S 82 GLU cc_start: 0.8938 (tt0) cc_final: 0.8597 (tt0) REVERT: S 229 TYR cc_start: 0.8426 (t80) cc_final: 0.8160 (t80) REVERT: S 294 ASN cc_start: 0.8663 (t0) cc_final: 0.8163 (t0) REVERT: S 361 GLU cc_start: 0.7302 (tm-30) cc_final: 0.6936 (tm-30) REVERT: m 81 MET cc_start: 0.9539 (tpp) cc_final: 0.9280 (tpt) REVERT: m 269 ILE cc_start: 0.8747 (mm) cc_final: 0.8397 (mt) REVERT: T 82 GLU cc_start: 0.8978 (tt0) cc_final: 0.8641 (mt-10) REVERT: T 90 GLU cc_start: 0.9240 (tp30) cc_final: 0.8898 (tp30) REVERT: T 111 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7606 (tt0) REVERT: n 30 ARG cc_start: 0.8942 (ttm110) cc_final: 0.8702 (tpp80) REVERT: U 95 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8577 (tt) REVERT: U 213 TYR cc_start: 0.9109 (m-80) cc_final: 0.8643 (m-80) REVERT: U 294 ASN cc_start: 0.8592 (t0) cc_final: 0.8225 (t0) REVERT: U 361 GLU cc_start: 0.7889 (tm-30) cc_final: 0.7398 (tm-30) REVERT: o 11 MET cc_start: 0.9090 (mtp) cc_final: 0.8799 (mtp) REVERT: o 30 ARG cc_start: 0.9045 (tpp80) cc_final: 0.8693 (tpp80) REVERT: V 361 GLU cc_start: 0.7881 (tm-30) cc_final: 0.7389 (tm-30) REVERT: p 118 GLN cc_start: 0.8817 (tp-100) cc_final: 0.8132 (mm-40) REVERT: p 362 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8248 (mm-30) outliers start: 292 outliers final: 248 residues processed: 1504 average time/residue: 1.0549 time to fit residues: 2796.7339 Evaluate side-chains 1513 residues out of total 12768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 261 poor density : 1252 time to evaluate : 9.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain P residue 8 ASN Chi-restraints excluded: chain P residue 28 GLN Chi-restraints excluded: chain P residue 110 GLU Chi-restraints excluded: chain P residue 249 THR Chi-restraints excluded: chain P residue 375 LEU Chi-restraints excluded: chain B residue 8 ASN Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain W residue 8 ASN Chi-restraints excluded: chain W residue 35 LEU Chi-restraints excluded: chain W residue 110 GLU Chi-restraints excluded: chain W residue 165 ASP Chi-restraints excluded: chain W residue 243 VAL Chi-restraints excluded: chain W residue 249 THR Chi-restraints excluded: chain W residue 345 ASP Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain X residue 29 SER Chi-restraints excluded: chain X residue 110 GLU Chi-restraints excluded: chain X residue 165 ASP Chi-restraints excluded: chain X residue 188 TYR Chi-restraints excluded: chain X residue 249 THR Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain Y residue 8 ASN Chi-restraints excluded: chain Y residue 67 LEU Chi-restraints excluded: chain Y residue 110 GLU Chi-restraints excluded: chain Y residue 111 GLU Chi-restraints excluded: chain Y residue 198 THR Chi-restraints excluded: chain Y residue 249 THR Chi-restraints excluded: chain E residue 3 SER Chi-restraints excluded: chain E residue 8 ASN Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 270 THR Chi-restraints excluded: chain E residue 297 ILE Chi-restraints excluded: chain E residue 360 ASN Chi-restraints excluded: chain Z residue 8 ASN Chi-restraints excluded: chain Z residue 110 GLU Chi-restraints excluded: chain Z residue 243 VAL Chi-restraints excluded: chain Z residue 333 ILE Chi-restraints excluded: chain F residue 8 ASN Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 56 ASP Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain a residue 31 ILE Chi-restraints excluded: chain a residue 110 GLU Chi-restraints excluded: chain a residue 356 ASP Chi-restraints excluded: chain a residue 375 LEU Chi-restraints excluded: chain G residue 8 ASN Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 204 VAL Chi-restraints excluded: chain G residue 270 THR Chi-restraints excluded: chain G residue 360 ASN Chi-restraints excluded: chain b residue 28 GLN Chi-restraints excluded: chain b residue 75 ASP Chi-restraints excluded: chain b residue 110 GLU Chi-restraints excluded: chain b residue 198 THR Chi-restraints excluded: chain b residue 249 THR Chi-restraints excluded: chain b residue 329 ILE Chi-restraints excluded: chain b residue 358 ASP Chi-restraints excluded: chain H residue 3 SER Chi-restraints excluded: chain H residue 8 ASN Chi-restraints excluded: chain H residue 25 GLU Chi-restraints excluded: chain H residue 35 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 228 ASN Chi-restraints excluded: chain H residue 270 THR Chi-restraints excluded: chain H residue 387 SER Chi-restraints excluded: chain c residue 75 ASP Chi-restraints excluded: chain c residue 249 THR Chi-restraints excluded: chain I residue 8 ASN Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain I residue 183 ILE Chi-restraints excluded: chain I residue 204 VAL Chi-restraints excluded: chain I residue 241 GLU Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 360 ASN Chi-restraints excluded: chain d residue 67 LEU Chi-restraints excluded: chain d residue 110 GLU Chi-restraints excluded: chain d residue 243 VAL Chi-restraints excluded: chain d residue 249 THR Chi-restraints excluded: chain J residue 3 SER Chi-restraints excluded: chain J residue 8 ASN Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 56 ASP Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain J residue 270 THR Chi-restraints excluded: chain J residue 347 ILE Chi-restraints excluded: chain J residue 360 ASN Chi-restraints excluded: chain e residue 31 ILE Chi-restraints excluded: chain e residue 110 GLU Chi-restraints excluded: chain e residue 249 THR Chi-restraints excluded: chain e residue 375 LEU Chi-restraints excluded: chain K residue 8 ASN Chi-restraints excluded: chain K residue 35 LEU Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 270 THR Chi-restraints excluded: chain K residue 360 ASN Chi-restraints excluded: chain f residue 8 ASN Chi-restraints excluded: chain f residue 60 LEU Chi-restraints excluded: chain f residue 110 GLU Chi-restraints excluded: chain f residue 249 THR Chi-restraints excluded: chain f residue 358 ASP Chi-restraints excluded: chain f residue 375 LEU Chi-restraints excluded: chain L residue 8 ASN Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain L residue 240 VAL Chi-restraints excluded: chain L residue 270 THR Chi-restraints excluded: chain L residue 292 VAL Chi-restraints excluded: chain L residue 360 ASN Chi-restraints excluded: chain g residue 8 ASN Chi-restraints excluded: chain g residue 28 GLN Chi-restraints excluded: chain g residue 67 LEU Chi-restraints excluded: chain g residue 110 GLU Chi-restraints excluded: chain g residue 249 THR Chi-restraints excluded: chain M residue 3 SER Chi-restraints excluded: chain M residue 8 ASN Chi-restraints excluded: chain M residue 35 LEU Chi-restraints excluded: chain M residue 37 VAL Chi-restraints excluded: chain M residue 42 ASP Chi-restraints excluded: chain M residue 95 LEU Chi-restraints excluded: chain M residue 270 THR Chi-restraints excluded: chain M residue 297 ILE Chi-restraints excluded: chain h residue 8 ASN Chi-restraints excluded: chain h residue 35 LEU Chi-restraints excluded: chain h residue 63 VAL Chi-restraints excluded: chain h residue 110 GLU Chi-restraints excluded: chain h residue 243 VAL Chi-restraints excluded: chain N residue 8 ASN Chi-restraints excluded: chain N residue 35 LEU Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain N residue 228 ASN Chi-restraints excluded: chain N residue 270 THR Chi-restraints excluded: chain N residue 345 ASP Chi-restraints excluded: chain N residue 360 ASN Chi-restraints excluded: chain i residue 110 GLU Chi-restraints excluded: chain i residue 240 VAL Chi-restraints excluded: chain i residue 243 VAL Chi-restraints excluded: chain i residue 249 THR Chi-restraints excluded: chain O residue 3 SER Chi-restraints excluded: chain O residue 8 ASN Chi-restraints excluded: chain O residue 35 LEU Chi-restraints excluded: chain O residue 42 ASP Chi-restraints excluded: chain O residue 56 ASP Chi-restraints excluded: chain O residue 95 LEU Chi-restraints excluded: chain O residue 204 VAL Chi-restraints excluded: chain O residue 241 GLU Chi-restraints excluded: chain O residue 270 THR Chi-restraints excluded: chain O residue 387 SER Chi-restraints excluded: chain j residue 8 ASN Chi-restraints excluded: chain j residue 35 LEU Chi-restraints excluded: chain j residue 110 GLU Chi-restraints excluded: chain j residue 198 THR Chi-restraints excluded: chain j residue 243 VAL Chi-restraints excluded: chain j residue 249 THR Chi-restraints excluded: chain j residue 319 MET Chi-restraints excluded: chain j residue 375 LEU Chi-restraints excluded: chain Q residue 3 SER Chi-restraints excluded: chain Q residue 8 ASN Chi-restraints excluded: chain Q residue 35 LEU Chi-restraints excluded: chain Q residue 37 VAL Chi-restraints excluded: chain Q residue 91 ILE Chi-restraints excluded: chain Q residue 95 LEU Chi-restraints excluded: chain Q residue 161 VAL Chi-restraints excluded: chain Q residue 270 THR Chi-restraints excluded: chain Q residue 360 ASN Chi-restraints excluded: chain k residue 28 GLN Chi-restraints excluded: chain k residue 29 SER Chi-restraints excluded: chain k residue 198 THR Chi-restraints excluded: chain k residue 249 THR Chi-restraints excluded: chain k residue 319 MET Chi-restraints excluded: chain R residue 8 ASN Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 161 VAL Chi-restraints excluded: chain R residue 183 ILE Chi-restraints excluded: chain R residue 270 THR Chi-restraints excluded: chain R residue 292 VAL Chi-restraints excluded: chain R residue 360 ASN Chi-restraints excluded: chain l residue 75 ASP Chi-restraints excluded: chain l residue 243 VAL Chi-restraints excluded: chain l residue 249 THR Chi-restraints excluded: chain l residue 300 MET Chi-restraints excluded: chain l residue 333 ILE Chi-restraints excluded: chain l residue 362 GLU Chi-restraints excluded: chain S residue 3 SER Chi-restraints excluded: chain S residue 8 ASN Chi-restraints excluded: chain S residue 35 LEU Chi-restraints excluded: chain S residue 95 LEU Chi-restraints excluded: chain S residue 241 GLU Chi-restraints excluded: chain S residue 270 THR Chi-restraints excluded: chain S residue 360 ASN Chi-restraints excluded: chain m residue 8 ASN Chi-restraints excluded: chain m residue 29 SER Chi-restraints excluded: chain m residue 35 LEU Chi-restraints excluded: chain m residue 110 GLU Chi-restraints excluded: chain m residue 165 ASP Chi-restraints excluded: chain m residue 249 THR Chi-restraints excluded: chain T residue 3 SER Chi-restraints excluded: chain T residue 8 ASN Chi-restraints excluded: chain T residue 35 LEU Chi-restraints excluded: chain T residue 37 VAL Chi-restraints excluded: chain T residue 95 LEU Chi-restraints excluded: chain T residue 270 THR Chi-restraints excluded: chain n residue 67 LEU Chi-restraints excluded: chain n residue 249 THR Chi-restraints excluded: chain U residue 8 ASN Chi-restraints excluded: chain U residue 37 VAL Chi-restraints excluded: chain U residue 95 LEU Chi-restraints excluded: chain U residue 204 VAL Chi-restraints excluded: chain U residue 270 THR Chi-restraints excluded: chain U residue 360 ASN Chi-restraints excluded: chain o residue 60 LEU Chi-restraints excluded: chain o residue 110 GLU Chi-restraints excluded: chain o residue 198 THR Chi-restraints excluded: chain o residue 243 VAL Chi-restraints excluded: chain o residue 249 THR Chi-restraints excluded: chain o residue 333 ILE Chi-restraints excluded: chain V residue 3 SER Chi-restraints excluded: chain V residue 8 ASN Chi-restraints excluded: chain V residue 37 VAL Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 270 THR Chi-restraints excluded: chain V residue 375 LEU Chi-restraints excluded: chain p residue 29 SER Chi-restraints excluded: chain p residue 249 THR Chi-restraints excluded: chain p residue 362 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1638 random chunks: chunk 966 optimal weight: 3.9990 chunk 1555 optimal weight: 3.9990 chunk 949 optimal weight: 1.9990 chunk 738 optimal weight: 4.9990 chunk 1081 optimal weight: 0.0470 chunk 1631 optimal weight: 9.9990 chunk 1501 optimal weight: 2.9990 chunk 1299 optimal weight: 6.9990 chunk 134 optimal weight: 5.9990 chunk 1003 optimal weight: 0.9980 chunk 796 optimal weight: 8.9990 overall best weight: 2.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 ASN ** Z 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 28 GLN ** b 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 384 ASN d 118 GLN ** d 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 28 GLN N 336 GLN ** i 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 28 GLN R 336 GLN ** o 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 120078 Z= 0.170 Angle : 0.501 14.807 163170 Z= 0.274 Chirality : 0.036 0.419 20202 Planarity : 0.003 0.069 21336 Dihedral : 4.527 46.630 17262 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 1.93 % Allowed : 13.98 % Favored : 84.09 % 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: 2.30 (0.07), residues: 16464 helix: 4.35 (0.05), residues: 8148 sheet: 0.73 (0.12), residues: 1848 loop : -2.27 (0.07), residues: 6468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP N 133 HIS 0.001 0.000 HIS n 208 PHE 0.022 0.001 PHE i 394 TYR 0.019 0.001 TYR g 78 ARG 0.010 0.001 ARG S 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 32928 Ramachandran restraints generated. 16464 Oldfield, 0 Emsley, 16464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 32928 Ramachandran restraints generated. 16464 Oldfield, 0 Emsley, 16464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1600 residues out of total 12768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 246 poor density : 1354 time to evaluate : 9.654 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: A 82 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8318 (mt-10) REVERT: A 369 LEU cc_start: 0.9619 (mt) cc_final: 0.9396 (mt) REVERT: P 28 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.7817 (mt0) REVERT: P 111 GLU cc_start: 0.8748 (mm-30) cc_final: 0.8512 (mm-30) REVERT: P 269 ILE cc_start: 0.8600 (mm) cc_final: 0.8353 (mt) REVERT: B 18 ARG cc_start: 0.9037 (ttp-110) cc_final: 0.8687 (mtp-110) REVERT: B 95 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8638 (tt) REVERT: W 269 ILE cc_start: 0.8618 (mm) cc_final: 0.8331 (mt) REVERT: C 18 ARG cc_start: 0.9084 (ttp-110) cc_final: 0.8871 (mtm110) REVERT: C 82 GLU cc_start: 0.8975 (tt0) cc_final: 0.8372 (mt-10) REVERT: C 361 GLU cc_start: 0.7831 (tm-30) cc_final: 0.7337 (tm-30) REVERT: X 20 ILE cc_start: 0.9399 (mt) cc_final: 0.9190 (mm) REVERT: D 241 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8288 (pm20) REVERT: D 319 MET cc_start: 0.9404 (mtm) cc_final: 0.9138 (mtm) REVERT: D 356 ASP cc_start: 0.8222 (m-30) cc_final: 0.7965 (m-30) REVERT: D 359 MET cc_start: 0.8964 (mmm) cc_final: 0.8566 (mmt) REVERT: Y 30 ARG cc_start: 0.9060 (tpp80) cc_final: 0.8781 (tpp80) REVERT: Y 110 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.8179 (pm20) REVERT: E 95 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8723 (tt) REVERT: E 361 GLU cc_start: 0.8213 (tm-30) cc_final: 0.7695 (tm-30) REVERT: Z 28 GLN cc_start: 0.8670 (tp-100) cc_final: 0.8303 (mm-40) REVERT: Z 216 GLU cc_start: 0.8919 (mm-30) cc_final: 0.8651 (tm-30) REVERT: F 229 TYR cc_start: 0.8451 (t80) cc_final: 0.7943 (t80) REVERT: a 78 TYR cc_start: 0.9052 (t80) cc_final: 0.8735 (t80) REVERT: G 18 ARG cc_start: 0.8997 (ttp-110) cc_final: 0.8746 (mtp-110) REVERT: G 82 GLU cc_start: 0.8773 (tp30) cc_final: 0.8511 (tp30) REVERT: G 294 ASN cc_start: 0.8488 (t0) cc_final: 0.8020 (t0) REVERT: G 300 MET cc_start: 0.8135 (tpp) cc_final: 0.7747 (tpt) REVERT: G 361 GLU cc_start: 0.7843 (tm-30) cc_final: 0.7375 (tm-30) REVERT: H 82 GLU cc_start: 0.8943 (tt0) cc_final: 0.8594 (mt-10) REVERT: c 188 TYR cc_start: 0.8351 (m-10) cc_final: 0.8030 (m-10) REVERT: c 269 ILE cc_start: 0.8729 (mm) cc_final: 0.8525 (mt) REVERT: c 300 MET cc_start: 0.8299 (tpt) cc_final: 0.7692 (tpt) REVERT: I 53 MET cc_start: 0.9183 (mmt) cc_final: 0.8839 (mmt) REVERT: I 90 GLU cc_start: 0.8973 (tp30) cc_final: 0.8743 (tp30) REVERT: I 294 ASN cc_start: 0.8542 (t0) cc_final: 0.8037 (t0) REVERT: I 300 MET cc_start: 0.7540 (mmm) cc_final: 0.7030 (tpt) REVERT: I 361 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7439 (tm-30) REVERT: d 30 ARG cc_start: 0.9161 (tpp80) cc_final: 0.8672 (mmt90) REVERT: J 213 TYR cc_start: 0.9153 (m-80) cc_final: 0.8771 (m-80) REVERT: J 229 TYR cc_start: 0.8636 (t80) cc_final: 0.8154 (t80) REVERT: J 338 GLU cc_start: 0.8532 (tm-30) cc_final: 0.8288 (tm-30) REVERT: e 269 ILE cc_start: 0.8756 (mm) cc_final: 0.8420 (mt) REVERT: e 313 ASP cc_start: 0.9130 (t0) cc_final: 0.8917 (t0) REVERT: K 90 GLU cc_start: 0.8991 (tp30) cc_final: 0.8695 (tp30) REVERT: K 356 ASP cc_start: 0.8156 (m-30) cc_final: 0.7857 (m-30) REVERT: f 8 ASN cc_start: 0.9002 (OUTLIER) cc_final: 0.8733 (m-40) REVERT: f 30 ARG cc_start: 0.9122 (tpp80) cc_final: 0.8850 (mmt90) REVERT: f 205 GLU cc_start: 0.8224 (mp0) cc_final: 0.7967 (mp0) REVERT: f 313 ASP cc_start: 0.8963 (t70) cc_final: 0.8675 (t0) REVERT: L 18 ARG cc_start: 0.8622 (ttp-110) cc_final: 0.8322 (ttp-110) REVERT: L 359 MET cc_start: 0.8834 (mmt) cc_final: 0.8612 (mmt) REVERT: L 361 GLU cc_start: 0.8180 (tm-30) cc_final: 0.7648 (tm-30) REVERT: g 67 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8998 (mm) REVERT: g 110 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8269 (pm20) REVERT: M 81 MET cc_start: 0.9399 (tpp) cc_final: 0.9044 (tpp) REVERT: h 30 ARG cc_start: 0.9060 (tpp80) cc_final: 0.8766 (mmt90) REVERT: N 82 GLU cc_start: 0.8963 (tt0) cc_final: 0.8460 (mt-10) REVERT: N 111 GLU cc_start: 0.7632 (mt-10) cc_final: 0.7045 (tt0) REVERT: i 30 ARG cc_start: 0.9058 (tpp80) cc_final: 0.8847 (tpp80) REVERT: i 269 ILE cc_start: 0.8729 (mm) cc_final: 0.8495 (mt) REVERT: O 135 GLN cc_start: 0.8665 (mt0) cc_final: 0.8409 (mt0) REVERT: O 213 TYR cc_start: 0.9048 (m-80) cc_final: 0.8659 (m-80) REVERT: O 241 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.8242 (pm20) REVERT: O 294 ASN cc_start: 0.8335 (m-40) cc_final: 0.7906 (t0) REVERT: O 300 MET cc_start: 0.8054 (tpp) cc_final: 0.7783 (tpt) REVERT: O 356 ASP cc_start: 0.8101 (m-30) cc_final: 0.7895 (m-30) REVERT: O 359 MET cc_start: 0.9135 (mmm) cc_final: 0.8891 (mmm) REVERT: j 30 ARG cc_start: 0.8936 (tpp80) cc_final: 0.8724 (tpp80) REVERT: j 269 ILE cc_start: 0.8641 (mm) cc_final: 0.8366 (mt) REVERT: j 300 MET cc_start: 0.8404 (tpp) cc_final: 0.8059 (tpt) REVERT: Q 95 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8796 (tt) REVERT: Q 229 TYR cc_start: 0.8596 (t80) cc_final: 0.8334 (t80) REVERT: Q 300 MET cc_start: 0.8019 (tpp) cc_final: 0.7588 (mmm) REVERT: Q 359 MET cc_start: 0.8769 (mmt) cc_final: 0.8067 (mmt) REVERT: Q 361 GLU cc_start: 0.8142 (tm-30) cc_final: 0.7564 (tm-30) REVERT: R 294 ASN cc_start: 0.8361 (m-40) cc_final: 0.8054 (t0) REVERT: R 300 MET cc_start: 0.8094 (tpp) cc_final: 0.7648 (mmm) REVERT: R 365 ARG cc_start: 0.9119 (mtp85) cc_final: 0.8880 (mtp85) REVERT: l 118 GLN cc_start: 0.9040 (tp-100) cc_final: 0.8173 (mm-40) REVERT: l 300 MET cc_start: 0.8352 (mmt) cc_final: 0.7797 (tpt) REVERT: l 362 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8346 (mm-30) REVERT: S 82 GLU cc_start: 0.8945 (tt0) cc_final: 0.8602 (tt0) REVERT: S 229 TYR cc_start: 0.8421 (t80) cc_final: 0.8147 (t80) REVERT: S 294 ASN cc_start: 0.8635 (t0) cc_final: 0.8122 (t0) REVERT: S 361 GLU cc_start: 0.7261 (tm-30) cc_final: 0.6891 (tm-30) REVERT: m 269 ILE cc_start: 0.8761 (mm) cc_final: 0.8437 (mt) REVERT: m 334 ASP cc_start: 0.8947 (t0) cc_final: 0.8712 (t0) REVERT: T 82 GLU cc_start: 0.8968 (tt0) cc_final: 0.8714 (mt-10) REVERT: T 90 GLU cc_start: 0.9242 (tp30) cc_final: 0.8898 (tp30) REVERT: T 111 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7612 (tt0) REVERT: n 53 MET cc_start: 0.9299 (mmm) cc_final: 0.9054 (mmp) REVERT: U 95 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8561 (tt) REVERT: U 213 TYR cc_start: 0.9108 (m-80) cc_final: 0.8656 (m-80) REVERT: U 294 ASN cc_start: 0.8576 (t0) cc_final: 0.8198 (t0) REVERT: U 361 GLU cc_start: 0.7866 (tm-30) cc_final: 0.7376 (tm-30) REVERT: o 11 MET cc_start: 0.9104 (mtp) cc_final: 0.8771 (mtp) REVERT: o 30 ARG cc_start: 0.9036 (tpp80) cc_final: 0.8702 (tpp80) REVERT: V 361 GLU cc_start: 0.7829 (tm-30) cc_final: 0.7348 (tm-30) REVERT: p 28 GLN cc_start: 0.8169 (tt0) cc_final: 0.7872 (tt0) REVERT: p 118 GLN cc_start: 0.8798 (tp-100) cc_final: 0.8201 (mm-40) REVERT: p 362 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8167 (mm-30) outliers start: 246 outliers final: 211 residues processed: 1521 average time/residue: 1.0214 time to fit residues: 2722.7479 Evaluate side-chains 1497 residues out of total 12768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 1273 time to evaluate : 9.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain P residue 8 ASN Chi-restraints excluded: chain P residue 28 GLN Chi-restraints excluded: chain P residue 110 GLU Chi-restraints excluded: chain B residue 8 ASN Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain W residue 8 ASN Chi-restraints excluded: chain W residue 110 GLU Chi-restraints excluded: chain W residue 165 ASP Chi-restraints excluded: chain W residue 243 VAL Chi-restraints excluded: chain W residue 249 THR Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain X residue 110 GLU Chi-restraints excluded: chain X residue 165 ASP Chi-restraints excluded: chain X residue 188 TYR Chi-restraints excluded: chain X residue 249 THR Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain Y residue 8 ASN Chi-restraints excluded: chain Y residue 67 LEU Chi-restraints excluded: chain Y residue 110 GLU Chi-restraints excluded: chain Y residue 111 GLU Chi-restraints excluded: chain Y residue 198 THR Chi-restraints excluded: chain E residue 3 SER Chi-restraints excluded: chain E residue 8 ASN Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 270 THR Chi-restraints excluded: chain E residue 297 ILE Chi-restraints excluded: chain E residue 360 ASN Chi-restraints excluded: chain Z residue 8 ASN Chi-restraints excluded: chain Z residue 110 GLU Chi-restraints excluded: chain Z residue 243 VAL Chi-restraints excluded: chain F residue 8 ASN Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain a residue 31 ILE Chi-restraints excluded: chain a residue 110 GLU Chi-restraints excluded: chain a residue 375 LEU Chi-restraints excluded: chain G residue 8 ASN Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 204 VAL Chi-restraints excluded: chain G residue 270 THR Chi-restraints excluded: chain G residue 360 ASN Chi-restraints excluded: chain b residue 28 GLN Chi-restraints excluded: chain b residue 110 GLU Chi-restraints excluded: chain b residue 198 THR Chi-restraints excluded: chain b residue 329 ILE Chi-restraints excluded: chain b residue 358 ASP Chi-restraints excluded: chain H residue 8 ASN Chi-restraints excluded: chain H residue 25 GLU Chi-restraints excluded: chain H residue 35 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 228 ASN Chi-restraints excluded: chain H residue 270 THR Chi-restraints excluded: chain H residue 387 SER Chi-restraints excluded: chain c residue 35 LEU Chi-restraints excluded: chain I residue 8 ASN Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain I residue 204 VAL Chi-restraints excluded: chain I residue 241 GLU Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 360 ASN Chi-restraints excluded: chain d residue 67 LEU Chi-restraints excluded: chain d residue 110 GLU Chi-restraints excluded: chain d residue 243 VAL Chi-restraints excluded: chain d residue 249 THR Chi-restraints excluded: chain J residue 3 SER Chi-restraints excluded: chain J residue 8 ASN Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 56 ASP Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain J residue 270 THR Chi-restraints excluded: chain J residue 347 ILE Chi-restraints excluded: chain J residue 360 ASN Chi-restraints excluded: chain e residue 31 ILE Chi-restraints excluded: chain e residue 110 GLU Chi-restraints excluded: chain e residue 249 THR Chi-restraints excluded: chain e residue 375 LEU Chi-restraints excluded: chain K residue 8 ASN Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 270 THR Chi-restraints excluded: chain K residue 360 ASN Chi-restraints excluded: chain f residue 8 ASN Chi-restraints excluded: chain f residue 110 GLU Chi-restraints excluded: chain f residue 249 THR Chi-restraints excluded: chain f residue 358 ASP Chi-restraints excluded: chain f residue 375 LEU Chi-restraints excluded: chain L residue 8 ASN Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain L residue 270 THR Chi-restraints excluded: chain L residue 360 ASN Chi-restraints excluded: chain g residue 8 ASN Chi-restraints excluded: chain g residue 28 GLN Chi-restraints excluded: chain g residue 67 LEU Chi-restraints excluded: chain g residue 75 ASP Chi-restraints excluded: chain g residue 110 GLU Chi-restraints excluded: chain g residue 319 MET Chi-restraints excluded: chain M residue 3 SER Chi-restraints excluded: chain M residue 8 ASN Chi-restraints excluded: chain M residue 35 LEU Chi-restraints excluded: chain M residue 37 VAL Chi-restraints excluded: chain M residue 270 THR Chi-restraints excluded: chain M residue 297 ILE Chi-restraints excluded: chain h residue 8 ASN Chi-restraints excluded: chain h residue 35 LEU Chi-restraints excluded: chain h residue 63 VAL Chi-restraints excluded: chain h residue 110 GLU Chi-restraints excluded: chain h residue 243 VAL Chi-restraints excluded: chain N residue 8 ASN Chi-restraints excluded: chain N residue 35 LEU Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain N residue 228 ASN Chi-restraints excluded: chain N residue 270 THR Chi-restraints excluded: chain N residue 345 ASP Chi-restraints excluded: chain N residue 360 ASN Chi-restraints excluded: chain i residue 110 GLU Chi-restraints excluded: chain i residue 240 VAL Chi-restraints excluded: chain i residue 243 VAL Chi-restraints excluded: chain i residue 249 THR Chi-restraints excluded: chain O residue 3 SER Chi-restraints excluded: chain O residue 8 ASN Chi-restraints excluded: chain O residue 35 LEU Chi-restraints excluded: chain O residue 56 ASP Chi-restraints excluded: chain O residue 95 LEU Chi-restraints excluded: chain O residue 204 VAL Chi-restraints excluded: chain O residue 241 GLU Chi-restraints excluded: chain O residue 270 THR Chi-restraints excluded: chain O residue 387 SER Chi-restraints excluded: chain j residue 8 ASN Chi-restraints excluded: chain j residue 35 LEU Chi-restraints excluded: chain j residue 110 GLU Chi-restraints excluded: chain j residue 198 THR Chi-restraints excluded: chain j residue 243 VAL Chi-restraints excluded: chain j residue 319 MET Chi-restraints excluded: chain j residue 375 LEU Chi-restraints excluded: chain Q residue 3 SER Chi-restraints excluded: chain Q residue 8 ASN Chi-restraints excluded: chain Q residue 35 LEU Chi-restraints excluded: chain Q residue 37 VAL Chi-restraints excluded: chain Q residue 91 ILE Chi-restraints excluded: chain Q residue 95 LEU Chi-restraints excluded: chain Q residue 161 VAL Chi-restraints excluded: chain Q residue 270 THR Chi-restraints excluded: chain Q residue 360 ASN Chi-restraints excluded: chain k residue 198 THR Chi-restraints excluded: chain R residue 8 ASN Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 183 ILE Chi-restraints excluded: chain R residue 270 THR Chi-restraints excluded: chain R residue 360 ASN Chi-restraints excluded: chain l residue 75 ASP Chi-restraints excluded: chain l residue 243 VAL Chi-restraints excluded: chain l residue 249 THR Chi-restraints excluded: chain l residue 333 ILE Chi-restraints excluded: chain l residue 362 GLU Chi-restraints excluded: chain S residue 3 SER Chi-restraints excluded: chain S residue 8 ASN Chi-restraints excluded: chain S residue 35 LEU Chi-restraints excluded: chain S residue 95 LEU Chi-restraints excluded: chain S residue 241 GLU Chi-restraints excluded: chain S residue 270 THR Chi-restraints excluded: chain S residue 360 ASN Chi-restraints excluded: chain m residue 8 ASN Chi-restraints excluded: chain m residue 110 GLU Chi-restraints excluded: chain m residue 165 ASP Chi-restraints excluded: chain T residue 3 SER Chi-restraints excluded: chain T residue 8 ASN Chi-restraints excluded: chain T residue 35 LEU Chi-restraints excluded: chain T residue 37 VAL Chi-restraints excluded: chain T residue 95 LEU Chi-restraints excluded: chain T residue 270 THR Chi-restraints excluded: chain n residue 67 LEU Chi-restraints excluded: chain n residue 249 THR Chi-restraints excluded: chain U residue 8 ASN Chi-restraints excluded: chain U residue 37 VAL Chi-restraints excluded: chain U residue 95 LEU Chi-restraints excluded: chain U residue 204 VAL Chi-restraints excluded: chain U residue 270 THR Chi-restraints excluded: chain U residue 360 ASN Chi-restraints excluded: chain o residue 60 LEU Chi-restraints excluded: chain o residue 110 GLU Chi-restraints excluded: chain o residue 198 THR Chi-restraints excluded: chain o residue 243 VAL Chi-restraints excluded: chain o residue 249 THR Chi-restraints excluded: chain o residue 333 ILE Chi-restraints excluded: chain V residue 3 SER Chi-restraints excluded: chain V residue 8 ASN Chi-restraints excluded: chain V residue 37 VAL Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 270 THR Chi-restraints excluded: chain V residue 375 LEU Chi-restraints excluded: chain p residue 249 THR Chi-restraints excluded: chain p residue 362 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1638 random chunks: chunk 1032 optimal weight: 7.9990 chunk 1384 optimal weight: 0.6980 chunk 398 optimal weight: 3.9990 chunk 1198 optimal weight: 0.7980 chunk 191 optimal weight: 6.9990 chunk 361 optimal weight: 5.9990 chunk 1301 optimal weight: 10.0000 chunk 544 optimal weight: 5.9990 chunk 1336 optimal weight: 6.9990 chunk 164 optimal weight: 5.9990 chunk 239 optimal weight: 10.0000 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 ASN ** Z 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 171 ASN b 28 GLN ** b 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 257 GLN ** c 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 118 GLN ** d 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 336 GLN ** i 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 257 GLN ** j 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 171 ASN ** m 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.068066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.058302 restraints weight = 389310.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.060213 restraints weight = 188358.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.061523 restraints weight = 112254.297| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 120078 Z= 0.227 Angle : 0.531 14.311 163170 Z= 0.291 Chirality : 0.037 0.383 20202 Planarity : 0.003 0.063 21336 Dihedral : 4.602 46.577 17262 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 2.07 % Allowed : 14.20 % Favored : 83.73 % 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: 2.21 (0.07), residues: 16464 helix: 4.24 (0.05), residues: 8253 sheet: 0.77 (0.12), residues: 1638 loop : -2.32 (0.06), residues: 6573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP N 133 HIS 0.001 0.000 HIS n 208 PHE 0.015 0.002 PHE i 394 TYR 0.029 0.001 TYR Z 78 ARG 0.013 0.001 ARG J 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 35145.07 seconds wall clock time: 611 minutes 59.93 seconds (36719.93 seconds total)