Starting phenix.real_space_refine on Mon Mar 25 21:10:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dde_30652/03_2024/7dde_30652.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dde_30652/03_2024/7dde_30652.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dde_30652/03_2024/7dde_30652.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dde_30652/03_2024/7dde_30652.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dde_30652/03_2024/7dde_30652.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dde_30652/03_2024/7dde_30652.pdb" } resolution = 2.26 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= 0.055 sd= 1.605 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: 5 Type Number sf(0) Gaussians Zn 48 6.06 5 S 336 5.16 5 C 31176 2.51 5 N 8352 2.21 5 O 11259 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 138": "NH1" <-> "NH2" Residue "A ASP 170": "OD1" <-> "OD2" Residue "A TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 296": "OD1" <-> "OD2" Residue "A TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 425": "NH1" <-> "NH2" Residue "A PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 449": "OE1" <-> "OE2" Residue "A PHE 1074": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1086": "NH1" <-> "NH2" Residue "C TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 138": "NH1" <-> "NH2" Residue "C ASP 170": "OD1" <-> "OD2" Residue "C TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 296": "OD1" <-> "OD2" Residue "C TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 425": "NH1" <-> "NH2" Residue "C PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 449": "OE1" <-> "OE2" Residue "C PHE 1074": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1086": "NH1" <-> "NH2" Residue "E TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 138": "NH1" <-> "NH2" Residue "E ASP 170": "OD1" <-> "OD2" Residue "E TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 296": "OD1" <-> "OD2" Residue "E TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 425": "NH1" <-> "NH2" Residue "E PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 449": "OE1" <-> "OE2" Residue "E PHE 1074": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 1086": "NH1" <-> "NH2" Residue "G TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 138": "NH1" <-> "NH2" Residue "G ASP 170": "OD1" <-> "OD2" Residue "G TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 296": "OD1" <-> "OD2" Residue "G TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 425": "NH1" <-> "NH2" Residue "G PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 449": "OE1" <-> "OE2" Residue "G PHE 1074": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 1086": "NH1" <-> "NH2" Residue "I TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 138": "NH1" <-> "NH2" Residue "I ASP 170": "OD1" <-> "OD2" Residue "I TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 262": "OD1" <-> "OD2" Residue "I PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 296": "OD1" <-> "OD2" Residue "I TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 425": "NH1" <-> "NH2" Residue "I PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 449": "OE1" <-> "OE2" Residue "I PHE 1074": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 1086": "NH1" <-> "NH2" Residue "K TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 138": "NH1" <-> "NH2" Residue "K ASP 170": "OD1" <-> "OD2" Residue "K TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 296": "OD1" <-> "OD2" Residue "K TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 425": "NH1" <-> "NH2" Residue "K PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 449": "OE1" <-> "OE2" Residue "K PHE 1074": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 1086": "NH1" <-> "NH2" Residue "M TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 138": "NH1" <-> "NH2" Residue "M ASP 170": "OD1" <-> "OD2" Residue "M TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 296": "OD1" <-> "OD2" Residue "M TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 425": "NH1" <-> "NH2" Residue "M PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 449": "OE1" <-> "OE2" Residue "M PHE 1074": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 1086": "NH1" <-> "NH2" Residue "O TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 138": "NH1" <-> "NH2" Residue "O ASP 170": "OD1" <-> "OD2" Residue "O TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 296": "OD1" <-> "OD2" Residue "O TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 425": "NH1" <-> "NH2" Residue "O PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 449": "OE1" <-> "OE2" Residue "O PHE 1074": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 1086": "NH1" <-> "NH2" Residue "Q TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 138": "NH1" <-> "NH2" Residue "Q ASP 170": "OD1" <-> "OD2" Residue "Q TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 296": "OD1" <-> "OD2" Residue "Q TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 425": "NH1" <-> "NH2" Residue "Q PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 449": "OE1" <-> "OE2" Residue "Q PHE 1074": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 1086": "NH1" <-> "NH2" Residue "S TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 138": "NH1" <-> "NH2" Residue "S ASP 170": "OD1" <-> "OD2" Residue "S TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 296": "OD1" <-> "OD2" Residue "S TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 425": "NH1" <-> "NH2" Residue "S PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 449": "OE1" <-> "OE2" Residue "S PHE 1074": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 1086": "NH1" <-> "NH2" Residue "V TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 138": "NH1" <-> "NH2" Residue "V ASP 170": "OD1" <-> "OD2" Residue "V TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 296": "OD1" <-> "OD2" Residue "V GLU 298": "OE1" <-> "OE2" Residue "V TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 425": "NH1" <-> "NH2" Residue "V PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 449": "OE1" <-> "OE2" Residue "V PHE 1074": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 1086": "NH1" <-> "NH2" Residue "X TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 138": "NH1" <-> "NH2" Residue "X ASP 170": "OD1" <-> "OD2" Residue "X TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 296": "OD1" <-> "OD2" Residue "X TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 425": "NH1" <-> "NH2" Residue "X PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 449": "OE1" <-> "OE2" Residue "X PHE 1074": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 1086": "NH1" <-> "NH2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 51171 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 4101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4101 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 24, 'TRANS': 500} Chain breaks: 1 Chain: "C" Number of atoms: 4101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4101 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 24, 'TRANS': 500} Chain breaks: 1 Chain: "E" Number of atoms: 4101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4101 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 24, 'TRANS': 500} Chain breaks: 1 Chain: "G" Number of atoms: 4101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4101 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 24, 'TRANS': 500} Chain breaks: 1 Chain: "I" Number of atoms: 4101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4101 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 24, 'TRANS': 500} Chain breaks: 1 Chain: "K" Number of atoms: 4101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4101 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 24, 'TRANS': 500} Chain breaks: 1 Chain: "M" Number of atoms: 4101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4101 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 24, 'TRANS': 500} Chain breaks: 1 Chain: "O" Number of atoms: 4101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4101 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 24, 'TRANS': 500} Chain breaks: 1 Chain: "Q" Number of atoms: 4101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4101 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 24, 'TRANS': 500} Chain breaks: 1 Chain: "S" Number of atoms: 4101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4101 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 24, 'TRANS': 500} Chain breaks: 1 Chain: "V" Number of atoms: 4101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4101 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 24, 'TRANS': 500} Chain breaks: 1 Chain: "X" Number of atoms: 4101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4101 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 24, 'TRANS': 500} Chain breaks: 1 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "I" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "K" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "M" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "O" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "Q" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "S" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "V" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "X" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 166 Classifications: {'water': 166} Link IDs: {None: 165} Chain: "C" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 152 Classifications: {'water': 152} Link IDs: {None: 151} Chain: "E" Number of atoms: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 164 Classifications: {'water': 164} Link IDs: {None: 163} Chain: "G" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 151 Classifications: {'water': 151} Link IDs: {None: 150} Chain: "I" Number of atoms: 158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 158 Classifications: {'water': 158} Link IDs: {None: 157} Chain: "K" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 167 Classifications: {'water': 167} Link IDs: {None: 166} Chain: "M" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 162 Classifications: {'water': 162} Link IDs: {None: 161} Chain: "O" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Chain: "Q" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 153 Classifications: {'water': 153} Link IDs: {None: 152} Chain: "S" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 165 Classifications: {'water': 165} Link IDs: {None: 164} Chain: "V" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 151 Classifications: {'water': 151} Link IDs: {None: 150} Chain: "X" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 162 Classifications: {'water': 162} Link IDs: {None: 161} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3838 SG CYS A1076 71.475 28.884 39.942 1.00164.81 S ATOM 4018 SG CYS A1098 75.202 31.406 39.577 1.00176.31 S ATOM 3724 SG CYS A1062 61.474 32.628 33.683 1.00166.84 S ATOM 3745 SG CYS A1065 58.651 33.306 31.239 1.00167.25 S ATOM 3911 SG CYS A1085 59.233 29.764 32.345 1.00165.22 S ATOM 3936 SG CYS A1088 61.435 31.339 29.869 1.00165.90 S ATOM 7939 SG CYS C1076 84.401 25.879 44.239 1.00166.33 S ATOM 8119 SG CYS C1098 80.697 26.382 46.771 1.00177.41 S ATOM 7825 SG CYS C1062 94.478 21.320 49.795 1.00170.64 S ATOM 7846 SG CYS C1065 97.324 19.267 51.239 1.00172.29 S ATOM 8012 SG CYS C1085 96.707 19.094 47.538 1.00166.36 S ATOM 8037 SG CYS C1088 94.536 17.296 49.886 1.00166.92 S ATOM 12040 SG CYS E1076 29.525 50.056 112.781 1.00155.08 S ATOM 12220 SG CYS E1098 33.584 50.329 114.739 1.00164.66 S ATOM 11926 SG CYS E1062 27.694 40.756 104.821 1.00162.48 S ATOM 11947 SG CYS E1065 26.850 37.551 102.973 1.00164.00 S ATOM 12113 SG CYS E1085 24.089 39.337 104.787 1.00159.46 S ATOM 12138 SG CYS E1088 26.558 37.344 106.629 1.00160.67 S ATOM 16141 SG CYS G1076 119.955 53.767 123.148 1.00163.40 S ATOM 16321 SG CYS G1098 119.581 51.923 119.044 1.00173.54 S ATOM 16027 SG CYS G1062 111.818 50.144 131.742 1.00170.57 S ATOM 16048 SG CYS G1065 109.854 48.546 134.569 1.00170.41 S ATOM 16214 SG CYS G1085 113.224 50.009 135.351 1.00164.27 S ATOM 16239 SG CYS G1088 112.936 46.775 133.642 1.00164.38 S ATOM 20242 SG CYS I1076 126.300 101.772 40.078 1.00170.04 S ATOM 20422 SG CYS I1098 122.236 103.702 39.704 1.00184.53 S ATOM 20128 SG CYS I1062 128.171 91.260 33.818 1.00175.33 S ATOM 20149 SG CYS I1065 129.026 88.485 31.375 1.00176.94 S ATOM 20315 SG CYS I1085 131.779 90.784 32.489 1.00171.68 S ATOM 20340 SG CYS I1088 129.310 91.883 30.008 1.00172.46 S ATOM 24343 SG CYS K1076 122.674 114.239 44.176 1.00169.25 S ATOM 24523 SG CYS K1098 124.115 110.750 46.651 1.00181.81 S ATOM 24229 SG CYS K1062 121.551 125.157 49.897 1.00171.88 S ATOM 24250 SG CYS K1065 121.894 128.628 51.391 1.00172.94 S ATOM 24416 SG CYS K1085 122.343 128.237 47.683 1.00169.85 S ATOM 24441 SG CYS K1088 124.998 127.234 50.007 1.00172.17 S ATOM 28444 SG CYS M1076 128.850 54.586 112.836 1.00163.99 S ATOM 28624 SG CYS M1098 126.532 57.923 114.805 1.00176.03 S ATOM 28330 SG CYS M1062 137.817 57.817 104.940 1.00168.46 S ATOM 28351 SG CYS M1065 141.012 58.741 103.113 1.00170.10 S ATOM 28517 SG CYS M1085 140.880 55.443 104.905 1.00165.87 S ATOM 28542 SG CYS M1088 141.323 58.572 106.769 1.00170.02 S ATOM 32545 SG CYS O1076 80.543 131.006 123.170 1.00163.66 S ATOM 32725 SG CYS O1098 82.344 131.606 119.074 1.00173.46 S ATOM 32431 SG CYS O1062 87.688 125.698 131.771 1.00167.17 S ATOM 32452 SG CYS O1065 90.038 124.772 134.602 1.00166.48 S ATOM 32618 SG CYS O1085 87.098 126.974 135.382 1.00166.22 S ATOM 32643 SG CYS O1088 90.056 128.329 133.687 1.00167.54 S ATOM 36646 SG CYS Q1076 36.044 112.656 40.062 1.00160.21 S ATOM 36826 SG CYS Q1098 36.398 108.167 39.733 1.00175.33 S ATOM 36532 SG CYS Q1062 44.299 119.456 33.832 1.00165.18 S ATOM 36553 SG CYS Q1065 46.306 121.558 31.392 1.00166.72 S ATOM 36719 SG CYS Q1085 42.929 122.810 32.457 1.00162.61 S ATOM 36744 SG CYS Q1088 43.234 120.099 30.004 1.00164.22 S ATOM 40747 SG CYS S1076 26.892 103.150 44.196 1.00167.47 S ATOM 40927 SG CYS S1098 29.172 106.134 46.702 1.00176.93 S ATOM 40633 SG CYS S1062 17.954 96.694 49.821 1.00169.02 S ATOM 40654 SG CYS S1065 14.765 95.249 51.284 1.00169.24 S ATOM 40820 SG CYS S1085 14.909 95.848 47.579 1.00166.12 S ATOM 40845 SG CYS S1088 14.431 98.640 49.911 1.00169.71 S ATOM 44848 SG CYS V1076 75.545 138.366 112.826 1.00166.92 S ATOM 45028 SG CYS V1098 73.779 134.709 114.798 1.00173.39 S ATOM 44734 SG CYS V1062 68.264 144.681 105.061 1.00173.75 S ATOM 44755 SG CYS V1065 65.881 147.036 103.278 1.00174.56 S ATOM 44921 SG CYS V1085 68.852 148.511 105.040 1.00170.89 S ATOM 44946 SG CYS V1088 65.926 147.369 106.936 1.00170.21 S ATOM 48949 SG CYS X1076 33.370 58.377 123.135 1.00153.13 S ATOM 49129 SG CYS X1098 31.949 59.627 119.036 1.00161.79 S ATOM 48835 SG CYS X1062 34.478 67.253 131.690 1.00160.32 S ATOM 48856 SG CYS X1065 34.129 69.767 134.510 1.00159.36 S ATOM 49022 SG CYS X1085 33.669 66.127 135.309 1.00153.84 S ATOM 49047 SG CYS X1088 31.025 68.021 133.611 1.00153.68 S Time building chain proxies: 26.17, per 1000 atoms: 0.51 Number of scatterers: 51171 At special positions: 0 Unit cell: (157.04, 161.2, 151.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 48 29.99 S 336 16.00 O 11259 8.00 N 8352 7.00 C 31176 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: 22.44 Conformation dependent library (CDL) restraints added in 8.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1501 " pdb="ZN ZN A1501 " - pdb=" NE2 HIS A 437 " pdb="ZN ZN A1501 " - pdb="ZN ZN A1502 " pdb=" ZN A1502 " pdb="ZN ZN A1502 " - pdb=" NE2 HIS A 93 " pdb=" ZN A1503 " pdb="ZN ZN A1503 " - pdb=" SG CYS A1076 " pdb="ZN ZN A1503 " - pdb=" SG CYS A1098 " pdb="ZN ZN A1503 " - pdb=" NE2 HIS A1096 " pdb=" ZN A1504 " pdb="ZN ZN A1504 " - pdb=" SG CYS A1065 " pdb="ZN ZN A1504 " - pdb=" SG CYS A1085 " pdb="ZN ZN A1504 " - pdb=" SG CYS A1088 " pdb="ZN ZN A1504 " - pdb=" SG CYS A1062 " pdb=" ZN C1501 " pdb="ZN ZN C1501 " - pdb=" NE2 HIS C 437 " pdb="ZN ZN C1501 " - pdb="ZN ZN C1502 " pdb=" ZN C1502 " pdb="ZN ZN C1502 " - pdb=" NE2 HIS C 93 " pdb=" ZN C1503 " pdb="ZN ZN C1503 " - pdb=" SG CYS C1076 " pdb="ZN ZN C1503 " - pdb=" SG CYS C1098 " pdb="ZN ZN C1503 " - pdb=" NE2 HIS C1096 " pdb=" ZN C1504 " pdb="ZN ZN C1504 " - pdb=" SG CYS C1065 " pdb="ZN ZN C1504 " - pdb=" SG CYS C1085 " pdb="ZN ZN C1504 " - pdb=" SG CYS C1088 " pdb="ZN ZN C1504 " - pdb=" SG CYS C1062 " pdb=" ZN E1501 " pdb="ZN ZN E1501 " - pdb=" NE2 HIS E 437 " pdb="ZN ZN E1501 " - pdb="ZN ZN E1502 " pdb=" ZN E1502 " pdb="ZN ZN E1502 " - pdb=" NE2 HIS E 93 " pdb=" ZN E1503 " pdb="ZN ZN E1503 " - pdb=" SG CYS E1076 " pdb="ZN ZN E1503 " - pdb=" SG CYS E1098 " pdb="ZN ZN E1503 " - pdb=" NE2 HIS E1096 " pdb=" ZN E1504 " pdb="ZN ZN E1504 " - pdb=" SG CYS E1065 " pdb="ZN ZN E1504 " - pdb=" SG CYS E1085 " pdb="ZN ZN E1504 " - pdb=" SG CYS E1088 " pdb="ZN ZN E1504 " - pdb=" SG CYS E1062 " pdb=" ZN G1501 " pdb="ZN ZN G1501 " - pdb=" NE2 HIS G 437 " pdb="ZN ZN G1501 " - pdb="ZN ZN G1502 " pdb=" ZN G1502 " pdb="ZN ZN G1502 " - pdb=" NE2 HIS G 93 " pdb=" ZN G1503 " pdb="ZN ZN G1503 " - pdb=" SG CYS G1076 " pdb="ZN ZN G1503 " - pdb=" SG CYS G1098 " pdb="ZN ZN G1503 " - pdb=" NE2 HIS G1096 " pdb=" ZN G1504 " pdb="ZN ZN G1504 " - pdb=" SG CYS G1065 " pdb="ZN ZN G1504 " - pdb=" SG CYS G1085 " pdb="ZN ZN G1504 " - pdb=" SG CYS G1088 " pdb="ZN ZN G1504 " - pdb=" SG CYS G1062 " pdb=" ZN I1501 " pdb="ZN ZN I1501 " - pdb=" NE2 HIS I 437 " pdb="ZN ZN I1501 " - pdb="ZN ZN I1502 " pdb=" ZN I1502 " pdb="ZN ZN I1502 " - pdb=" NE2 HIS I 93 " pdb=" ZN I1503 " pdb="ZN ZN I1503 " - pdb=" SG CYS I1076 " pdb="ZN ZN I1503 " - pdb=" SG CYS I1098 " pdb="ZN ZN I1503 " - pdb=" NE2 HIS I1096 " pdb=" ZN I1504 " pdb="ZN ZN I1504 " - pdb=" SG CYS I1065 " pdb="ZN ZN I1504 " - pdb=" SG CYS I1085 " pdb="ZN ZN I1504 " - pdb=" SG CYS I1088 " pdb="ZN ZN I1504 " - pdb=" SG CYS I1062 " pdb=" ZN K1501 " pdb="ZN ZN K1501 " - pdb=" NE2 HIS K 437 " pdb="ZN ZN K1501 " - pdb="ZN ZN K1502 " pdb=" ZN K1502 " pdb="ZN ZN K1502 " - pdb=" NE2 HIS K 93 " pdb=" ZN K1503 " pdb="ZN ZN K1503 " - pdb=" SG CYS K1076 " pdb="ZN ZN K1503 " - pdb=" SG CYS K1098 " pdb="ZN ZN K1503 " - pdb=" NE2 HIS K1096 " pdb=" ZN K1504 " pdb="ZN ZN K1504 " - pdb=" SG CYS K1065 " pdb="ZN ZN K1504 " - pdb=" SG CYS K1085 " pdb="ZN ZN K1504 " - pdb=" SG CYS K1088 " pdb="ZN ZN K1504 " - pdb=" SG CYS K1062 " pdb=" ZN M1501 " pdb="ZN ZN M1501 " - pdb=" NE2 HIS M 437 " pdb="ZN ZN M1501 " - pdb="ZN ZN M1502 " pdb=" ZN M1502 " pdb="ZN ZN M1502 " - pdb=" NE2 HIS M 93 " pdb=" ZN M1503 " pdb="ZN ZN M1503 " - pdb=" SG CYS M1076 " pdb="ZN ZN M1503 " - pdb=" SG CYS M1098 " pdb="ZN ZN M1503 " - pdb=" NE2 HIS M1096 " pdb=" ZN M1504 " pdb="ZN ZN M1504 " - pdb=" SG CYS M1065 " pdb="ZN ZN M1504 " - pdb=" SG CYS M1085 " pdb="ZN ZN M1504 " - pdb=" SG CYS M1088 " pdb="ZN ZN M1504 " - pdb=" SG CYS M1062 " pdb=" ZN O1501 " pdb="ZN ZN O1501 " - pdb=" NE2 HIS O 437 " pdb="ZN ZN O1501 " - pdb="ZN ZN O1502 " pdb=" ZN O1502 " pdb="ZN ZN O1502 " - pdb=" NE2 HIS O 93 " pdb=" ZN O1503 " pdb="ZN ZN O1503 " - pdb=" SG CYS O1076 " pdb="ZN ZN O1503 " - pdb=" SG CYS O1098 " pdb="ZN ZN O1503 " - pdb=" NE2 HIS O1096 " pdb=" ZN O1504 " pdb="ZN ZN O1504 " - pdb=" SG CYS O1065 " pdb="ZN ZN O1504 " - pdb=" SG CYS O1085 " pdb="ZN ZN O1504 " - pdb=" SG CYS O1088 " pdb="ZN ZN O1504 " - pdb=" SG CYS O1062 " pdb=" ZN Q1501 " pdb="ZN ZN Q1501 " - pdb=" NE2 HIS Q 437 " pdb="ZN ZN Q1501 " - pdb="ZN ZN Q1502 " pdb=" ZN Q1502 " pdb="ZN ZN Q1502 " - pdb=" NE2 HIS Q 93 " pdb=" ZN Q1503 " pdb="ZN ZN Q1503 " - pdb=" SG CYS Q1076 " pdb="ZN ZN Q1503 " - pdb=" SG CYS Q1098 " pdb="ZN ZN Q1503 " - pdb=" NE2 HIS Q1096 " pdb=" ZN Q1504 " pdb="ZN ZN Q1504 " - pdb=" SG CYS Q1065 " pdb="ZN ZN Q1504 " - pdb=" SG CYS Q1085 " pdb="ZN ZN Q1504 " - pdb=" SG CYS Q1088 " pdb="ZN ZN Q1504 " - pdb=" SG CYS Q1062 " pdb=" ZN S1501 " pdb="ZN ZN S1501 " - pdb=" NE2 HIS S 437 " pdb="ZN ZN S1501 " - pdb="ZN ZN S1502 " pdb=" ZN S1502 " pdb="ZN ZN S1502 " - pdb=" NE2 HIS S 93 " pdb=" ZN S1503 " pdb="ZN ZN S1503 " - pdb=" SG CYS S1076 " pdb="ZN ZN S1503 " - pdb=" SG CYS S1098 " pdb="ZN ZN S1503 " - pdb=" NE2 HIS S1096 " pdb=" ZN S1504 " pdb="ZN ZN S1504 " - pdb=" SG CYS S1065 " pdb="ZN ZN S1504 " - pdb=" SG CYS S1085 " pdb="ZN ZN S1504 " - pdb=" SG CYS S1088 " pdb="ZN ZN S1504 " - pdb=" SG CYS S1062 " pdb=" ZN V1501 " pdb="ZN ZN V1501 " - pdb=" NE2 HIS V 437 " pdb="ZN ZN V1501 " - pdb="ZN ZN V1502 " pdb=" ZN V1502 " pdb="ZN ZN V1502 " - pdb=" NE2 HIS V 93 " pdb=" ZN V1503 " pdb="ZN ZN V1503 " - pdb=" SG CYS V1076 " pdb="ZN ZN V1503 " - pdb=" SG CYS V1098 " pdb="ZN ZN V1503 " - pdb=" NE2 HIS V1096 " pdb=" ZN V1504 " pdb="ZN ZN V1504 " - pdb=" SG CYS V1065 " pdb="ZN ZN V1504 " - pdb=" SG CYS V1085 " pdb="ZN ZN V1504 " - pdb=" SG CYS V1088 " pdb="ZN ZN V1504 " - pdb=" SG CYS V1062 " pdb=" ZN X1501 " pdb="ZN ZN X1501 " - pdb=" NE2 HIS X 437 " pdb="ZN ZN X1501 " - pdb="ZN ZN X1502 " pdb=" ZN X1502 " pdb="ZN ZN X1502 " - pdb=" NE2 HIS X 93 " pdb=" ZN X1503 " pdb="ZN ZN X1503 " - pdb=" SG CYS X1076 " pdb="ZN ZN X1503 " - pdb=" SG CYS X1098 " pdb="ZN ZN X1503 " - pdb=" NE2 HIS X1096 " pdb=" ZN X1504 " pdb="ZN ZN X1504 " - pdb=" SG CYS X1065 " pdb="ZN ZN X1504 " - pdb=" SG CYS X1085 " pdb="ZN ZN X1504 " - pdb=" SG CYS X1088 " pdb="ZN ZN X1504 " - pdb=" SG CYS X1062 " Number of angles added : 72 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11880 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 48 sheets defined 31.5% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.60 Creating SS restraints... Processing helix chain 'A' and resid 10 through 24 Processing helix chain 'A' and resid 27 through 42 Processing helix chain 'A' and resid 124 through 129 Processing helix chain 'A' and resid 170 through 174 removed outlier: 3.563A pdb=" N ASN A 174 " --> pdb=" O PRO A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 195 No H-bonds generated for 'chain 'A' and resid 193 through 195' Processing helix chain 'A' and resid 209 through 222 Processing helix chain 'A' and resid 229 through 231 No H-bonds generated for 'chain 'A' and resid 229 through 231' Processing helix chain 'A' and resid 263 through 277 Processing helix chain 'A' and resid 311 through 322 Processing helix chain 'A' and resid 328 through 336 removed outlier: 3.843A pdb=" N VAL A 335 " --> pdb=" O SER A 331 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS A 336 " --> pdb=" O ILE A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 356 removed outlier: 4.198A pdb=" N SER A 353 " --> pdb=" O PRO A 350 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N SER A 354 " --> pdb=" O ASN A 351 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR A 356 " --> pdb=" O SER A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 396 removed outlier: 3.616A pdb=" N LEU A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 423 Processing helix chain 'A' and resid 445 through 461 removed outlier: 4.471A pdb=" N GLU A 449 " --> pdb=" O SER A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 466 Processing helix chain 'A' and resid 1085 through 1092 removed outlier: 3.718A pdb=" N ALA A1090 " --> pdb=" O ARG A1086 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 24 Processing helix chain 'C' and resid 27 through 42 Processing helix chain 'C' and resid 124 through 129 Processing helix chain 'C' and resid 170 through 174 removed outlier: 3.562A pdb=" N ASN C 174 " --> pdb=" O PRO C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 195 No H-bonds generated for 'chain 'C' and resid 193 through 195' Processing helix chain 'C' and resid 209 through 222 Processing helix chain 'C' and resid 229 through 231 No H-bonds generated for 'chain 'C' and resid 229 through 231' Processing helix chain 'C' and resid 260 through 277 removed outlier: 3.584A pdb=" N LEU C 264 " --> pdb=" O ARG C 260 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY C 265 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N MET C 266 " --> pdb=" O ASP C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 322 Processing helix chain 'C' and resid 328 through 336 removed outlier: 3.843A pdb=" N VAL C 335 " --> pdb=" O SER C 331 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS C 336 " --> pdb=" O ILE C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 356 removed outlier: 4.199A pdb=" N SER C 353 " --> pdb=" O PRO C 350 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N SER C 354 " --> pdb=" O ASN C 351 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR C 356 " --> pdb=" O SER C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 396 removed outlier: 3.617A pdb=" N LEU C 387 " --> pdb=" O ALA C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 423 Processing helix chain 'C' and resid 445 through 461 removed outlier: 4.472A pdb=" N GLU C 449 " --> pdb=" O SER C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 467 removed outlier: 4.118A pdb=" N GLU C 467 " --> pdb=" O ALA C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 1085 through 1092 removed outlier: 3.718A pdb=" N ALA C1090 " --> pdb=" O ARG C1086 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 24 Processing helix chain 'E' and resid 27 through 42 Processing helix chain 'E' and resid 124 through 129 Processing helix chain 'E' and resid 170 through 174 removed outlier: 3.563A pdb=" N ASN E 174 " --> pdb=" O PRO E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 195 No H-bonds generated for 'chain 'E' and resid 193 through 195' Processing helix chain 'E' and resid 209 through 222 Processing helix chain 'E' and resid 229 through 231 No H-bonds generated for 'chain 'E' and resid 229 through 231' Processing helix chain 'E' and resid 260 through 277 removed outlier: 4.179A pdb=" N LEU E 264 " --> pdb=" O ARG E 260 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY E 265 " --> pdb=" O LEU E 261 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N MET E 266 " --> pdb=" O ASP E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 322 Processing helix chain 'E' and resid 328 through 336 removed outlier: 3.843A pdb=" N VAL E 335 " --> pdb=" O SER E 331 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS E 336 " --> pdb=" O ILE E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 356 removed outlier: 4.199A pdb=" N SER E 353 " --> pdb=" O PRO E 350 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N SER E 354 " --> pdb=" O ASN E 351 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR E 356 " --> pdb=" O SER E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 381 through 396 removed outlier: 3.616A pdb=" N LEU E 387 " --> pdb=" O ALA E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 423 Processing helix chain 'E' and resid 445 through 461 removed outlier: 4.472A pdb=" N GLU E 449 " --> pdb=" O SER E 445 " (cutoff:3.500A) Processing helix chain 'E' and resid 461 through 467 removed outlier: 4.117A pdb=" N GLU E 467 " --> pdb=" O ALA E 463 " (cutoff:3.500A) Processing helix chain 'E' and resid 1085 through 1092 removed outlier: 3.718A pdb=" N ALA E1090 " --> pdb=" O ARG E1086 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 24 Processing helix chain 'G' and resid 27 through 42 Processing helix chain 'G' and resid 124 through 129 Processing helix chain 'G' and resid 170 through 174 removed outlier: 3.563A pdb=" N ASN G 174 " --> pdb=" O PRO G 171 " (cutoff:3.500A) Processing helix chain 'G' and resid 193 through 195 No H-bonds generated for 'chain 'G' and resid 193 through 195' Processing helix chain 'G' and resid 209 through 222 Processing helix chain 'G' and resid 229 through 231 No H-bonds generated for 'chain 'G' and resid 229 through 231' Processing helix chain 'G' and resid 260 through 277 removed outlier: 3.831A pdb=" N LEU G 264 " --> pdb=" O ARG G 260 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY G 265 " --> pdb=" O LEU G 261 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N MET G 266 " --> pdb=" O ASP G 262 " (cutoff:3.500A) Processing helix chain 'G' and resid 311 through 322 Processing helix chain 'G' and resid 328 through 336 removed outlier: 3.842A pdb=" N VAL G 335 " --> pdb=" O SER G 331 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS G 336 " --> pdb=" O ILE G 332 " (cutoff:3.500A) Processing helix chain 'G' and resid 349 through 356 removed outlier: 4.199A pdb=" N SER G 353 " --> pdb=" O PRO G 350 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N SER G 354 " --> pdb=" O ASN G 351 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR G 356 " --> pdb=" O SER G 353 " (cutoff:3.500A) Processing helix chain 'G' and resid 381 through 396 removed outlier: 3.617A pdb=" N LEU G 387 " --> pdb=" O ALA G 383 " (cutoff:3.500A) Processing helix chain 'G' and resid 414 through 423 Processing helix chain 'G' and resid 445 through 461 removed outlier: 4.471A pdb=" N GLU G 449 " --> pdb=" O SER G 445 " (cutoff:3.500A) Processing helix chain 'G' and resid 461 through 467 removed outlier: 4.117A pdb=" N GLU G 467 " --> pdb=" O ALA G 463 " (cutoff:3.500A) Processing helix chain 'G' and resid 1085 through 1092 removed outlier: 3.718A pdb=" N ALA G1090 " --> pdb=" O ARG G1086 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 24 Processing helix chain 'I' and resid 27 through 42 Processing helix chain 'I' and resid 124 through 129 Processing helix chain 'I' and resid 170 through 174 removed outlier: 3.563A pdb=" N ASN I 174 " --> pdb=" O PRO I 171 " (cutoff:3.500A) Processing helix chain 'I' and resid 193 through 195 No H-bonds generated for 'chain 'I' and resid 193 through 195' Processing helix chain 'I' and resid 209 through 222 Processing helix chain 'I' and resid 229 through 231 No H-bonds generated for 'chain 'I' and resid 229 through 231' Processing helix chain 'I' and resid 260 through 277 removed outlier: 3.750A pdb=" N LEU I 264 " --> pdb=" O ARG I 260 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY I 265 " --> pdb=" O LEU I 261 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N MET I 266 " --> pdb=" O ASP I 262 " (cutoff:3.500A) Processing helix chain 'I' and resid 311 through 322 Processing helix chain 'I' and resid 328 through 336 removed outlier: 3.843A pdb=" N VAL I 335 " --> pdb=" O SER I 331 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS I 336 " --> pdb=" O ILE I 332 " (cutoff:3.500A) Processing helix chain 'I' and resid 349 through 356 removed outlier: 4.197A pdb=" N SER I 353 " --> pdb=" O PRO I 350 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N SER I 354 " --> pdb=" O ASN I 351 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR I 356 " --> pdb=" O SER I 353 " (cutoff:3.500A) Processing helix chain 'I' and resid 381 through 396 removed outlier: 3.617A pdb=" N LEU I 387 " --> pdb=" O ALA I 383 " (cutoff:3.500A) Processing helix chain 'I' and resid 414 through 423 Processing helix chain 'I' and resid 445 through 461 removed outlier: 4.471A pdb=" N GLU I 449 " --> pdb=" O SER I 445 " (cutoff:3.500A) Processing helix chain 'I' and resid 461 through 467 removed outlier: 4.118A pdb=" N GLU I 467 " --> pdb=" O ALA I 463 " (cutoff:3.500A) Processing helix chain 'I' and resid 1085 through 1092 removed outlier: 3.717A pdb=" N ALA I1090 " --> pdb=" O ARG I1086 " (cutoff:3.500A) Processing helix chain 'K' and resid 10 through 24 Processing helix chain 'K' and resid 27 through 42 Processing helix chain 'K' and resid 124 through 129 Processing helix chain 'K' and resid 170 through 174 removed outlier: 3.563A pdb=" N ASN K 174 " --> pdb=" O PRO K 171 " (cutoff:3.500A) Processing helix chain 'K' and resid 193 through 195 No H-bonds generated for 'chain 'K' and resid 193 through 195' Processing helix chain 'K' and resid 209 through 222 Processing helix chain 'K' and resid 229 through 231 No H-bonds generated for 'chain 'K' and resid 229 through 231' Processing helix chain 'K' and resid 260 through 277 removed outlier: 3.787A pdb=" N LEU K 264 " --> pdb=" O ARG K 260 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLY K 265 " --> pdb=" O LEU K 261 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N MET K 266 " --> pdb=" O ASP K 262 " (cutoff:3.500A) Processing helix chain 'K' and resid 311 through 322 Processing helix chain 'K' and resid 328 through 336 removed outlier: 3.842A pdb=" N VAL K 335 " --> pdb=" O SER K 331 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS K 336 " --> pdb=" O ILE K 332 " (cutoff:3.500A) Processing helix chain 'K' and resid 349 through 356 removed outlier: 4.198A pdb=" N SER K 353 " --> pdb=" O PRO K 350 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N SER K 354 " --> pdb=" O ASN K 351 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR K 356 " --> pdb=" O SER K 353 " (cutoff:3.500A) Processing helix chain 'K' and resid 381 through 396 removed outlier: 3.617A pdb=" N LEU K 387 " --> pdb=" O ALA K 383 " (cutoff:3.500A) Processing helix chain 'K' and resid 414 through 423 Processing helix chain 'K' and resid 445 through 461 removed outlier: 4.471A pdb=" N GLU K 449 " --> pdb=" O SER K 445 " (cutoff:3.500A) Processing helix chain 'K' and resid 461 through 467 removed outlier: 4.118A pdb=" N GLU K 467 " --> pdb=" O ALA K 463 " (cutoff:3.500A) Processing helix chain 'K' and resid 1085 through 1092 removed outlier: 3.718A pdb=" N ALA K1090 " --> pdb=" O ARG K1086 " (cutoff:3.500A) Processing helix chain 'M' and resid 10 through 24 Processing helix chain 'M' and resid 27 through 42 Processing helix chain 'M' and resid 124 through 129 Processing helix chain 'M' and resid 170 through 174 removed outlier: 3.562A pdb=" N ASN M 174 " --> pdb=" O PRO M 171 " (cutoff:3.500A) Processing helix chain 'M' and resid 193 through 195 No H-bonds generated for 'chain 'M' and resid 193 through 195' Processing helix chain 'M' and resid 209 through 222 Processing helix chain 'M' and resid 229 through 231 No H-bonds generated for 'chain 'M' and resid 229 through 231' Processing helix chain 'M' and resid 260 through 277 removed outlier: 3.706A pdb=" N LEU M 264 " --> pdb=" O ARG M 260 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLY M 265 " --> pdb=" O LEU M 261 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N MET M 266 " --> pdb=" O ASP M 262 " (cutoff:3.500A) Processing helix chain 'M' and resid 311 through 322 Processing helix chain 'M' and resid 328 through 336 removed outlier: 3.843A pdb=" N VAL M 335 " --> pdb=" O SER M 331 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS M 336 " --> pdb=" O ILE M 332 " (cutoff:3.500A) Processing helix chain 'M' and resid 349 through 356 removed outlier: 4.199A pdb=" N SER M 353 " --> pdb=" O PRO M 350 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N SER M 354 " --> pdb=" O ASN M 351 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR M 356 " --> pdb=" O SER M 353 " (cutoff:3.500A) Processing helix chain 'M' and resid 381 through 396 removed outlier: 3.617A pdb=" N LEU M 387 " --> pdb=" O ALA M 383 " (cutoff:3.500A) Processing helix chain 'M' and resid 414 through 423 Processing helix chain 'M' and resid 445 through 461 removed outlier: 4.472A pdb=" N GLU M 449 " --> pdb=" O SER M 445 " (cutoff:3.500A) Processing helix chain 'M' and resid 461 through 467 removed outlier: 4.118A pdb=" N GLU M 467 " --> pdb=" O ALA M 463 " (cutoff:3.500A) Processing helix chain 'M' and resid 1085 through 1092 removed outlier: 3.717A pdb=" N ALA M1090 " --> pdb=" O ARG M1086 " (cutoff:3.500A) Processing helix chain 'O' and resid 10 through 24 Processing helix chain 'O' and resid 27 through 42 Processing helix chain 'O' and resid 124 through 129 Processing helix chain 'O' and resid 170 through 174 removed outlier: 3.563A pdb=" N ASN O 174 " --> pdb=" O PRO O 171 " (cutoff:3.500A) Processing helix chain 'O' and resid 193 through 195 No H-bonds generated for 'chain 'O' and resid 193 through 195' Processing helix chain 'O' and resid 209 through 222 Processing helix chain 'O' and resid 229 through 231 No H-bonds generated for 'chain 'O' and resid 229 through 231' Processing helix chain 'O' and resid 260 through 277 removed outlier: 3.660A pdb=" N LEU O 264 " --> pdb=" O ARG O 260 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY O 265 " --> pdb=" O LEU O 261 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N MET O 266 " --> pdb=" O ASP O 262 " (cutoff:3.500A) Processing helix chain 'O' and resid 311 through 322 Processing helix chain 'O' and resid 328 through 336 removed outlier: 3.843A pdb=" N VAL O 335 " --> pdb=" O SER O 331 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS O 336 " --> pdb=" O ILE O 332 " (cutoff:3.500A) Processing helix chain 'O' and resid 349 through 356 removed outlier: 4.197A pdb=" N SER O 353 " --> pdb=" O PRO O 350 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N SER O 354 " --> pdb=" O ASN O 351 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR O 356 " --> pdb=" O SER O 353 " (cutoff:3.500A) Processing helix chain 'O' and resid 381 through 396 removed outlier: 3.616A pdb=" N LEU O 387 " --> pdb=" O ALA O 383 " (cutoff:3.500A) Processing helix chain 'O' and resid 414 through 423 Processing helix chain 'O' and resid 445 through 461 removed outlier: 4.470A pdb=" N GLU O 449 " --> pdb=" O SER O 445 " (cutoff:3.500A) Processing helix chain 'O' and resid 461 through 467 removed outlier: 4.118A pdb=" N GLU O 467 " --> pdb=" O ALA O 463 " (cutoff:3.500A) Processing helix chain 'O' and resid 1085 through 1092 removed outlier: 3.718A pdb=" N ALA O1090 " --> pdb=" O ARG O1086 " (cutoff:3.500A) Processing helix chain 'Q' and resid 10 through 24 Processing helix chain 'Q' and resid 27 through 42 Processing helix chain 'Q' and resid 124 through 129 Processing helix chain 'Q' and resid 170 through 174 removed outlier: 3.563A pdb=" N ASN Q 174 " --> pdb=" O PRO Q 171 " (cutoff:3.500A) Processing helix chain 'Q' and resid 193 through 195 No H-bonds generated for 'chain 'Q' and resid 193 through 195' Processing helix chain 'Q' and resid 209 through 222 Processing helix chain 'Q' and resid 229 through 231 No H-bonds generated for 'chain 'Q' and resid 229 through 231' Processing helix chain 'Q' and resid 264 through 277 Processing helix chain 'Q' and resid 311 through 322 Processing helix chain 'Q' and resid 328 through 336 removed outlier: 3.842A pdb=" N VAL Q 335 " --> pdb=" O SER Q 331 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS Q 336 " --> pdb=" O ILE Q 332 " (cutoff:3.500A) Processing helix chain 'Q' and resid 349 through 356 removed outlier: 4.198A pdb=" N SER Q 353 " --> pdb=" O PRO Q 350 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N SER Q 354 " --> pdb=" O ASN Q 351 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR Q 356 " --> pdb=" O SER Q 353 " (cutoff:3.500A) Processing helix chain 'Q' and resid 381 through 396 removed outlier: 3.616A pdb=" N LEU Q 387 " --> pdb=" O ALA Q 383 " (cutoff:3.500A) Processing helix chain 'Q' and resid 414 through 423 Processing helix chain 'Q' and resid 445 through 461 removed outlier: 4.471A pdb=" N GLU Q 449 " --> pdb=" O SER Q 445 " (cutoff:3.500A) Processing helix chain 'Q' and resid 461 through 467 removed outlier: 4.118A pdb=" N GLU Q 467 " --> pdb=" O ALA Q 463 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1085 through 1092 removed outlier: 3.718A pdb=" N ALA Q1090 " --> pdb=" O ARG Q1086 " (cutoff:3.500A) Processing helix chain 'S' and resid 10 through 24 Processing helix chain 'S' and resid 27 through 42 Processing helix chain 'S' and resid 124 through 129 Processing helix chain 'S' and resid 170 through 174 removed outlier: 3.563A pdb=" N ASN S 174 " --> pdb=" O PRO S 171 " (cutoff:3.500A) Processing helix chain 'S' and resid 193 through 195 No H-bonds generated for 'chain 'S' and resid 193 through 195' Processing helix chain 'S' and resid 209 through 222 Processing helix chain 'S' and resid 229 through 231 No H-bonds generated for 'chain 'S' and resid 229 through 231' Processing helix chain 'S' and resid 264 through 277 Processing helix chain 'S' and resid 311 through 322 Processing helix chain 'S' and resid 328 through 336 removed outlier: 3.843A pdb=" N VAL S 335 " --> pdb=" O SER S 331 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS S 336 " --> pdb=" O ILE S 332 " (cutoff:3.500A) Processing helix chain 'S' and resid 349 through 356 removed outlier: 4.198A pdb=" N SER S 353 " --> pdb=" O PRO S 350 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N SER S 354 " --> pdb=" O ASN S 351 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR S 356 " --> pdb=" O SER S 353 " (cutoff:3.500A) Processing helix chain 'S' and resid 381 through 396 removed outlier: 3.617A pdb=" N LEU S 387 " --> pdb=" O ALA S 383 " (cutoff:3.500A) Processing helix chain 'S' and resid 414 through 423 Processing helix chain 'S' and resid 445 through 461 removed outlier: 4.471A pdb=" N GLU S 449 " --> pdb=" O SER S 445 " (cutoff:3.500A) Processing helix chain 'S' and resid 461 through 467 removed outlier: 4.118A pdb=" N GLU S 467 " --> pdb=" O ALA S 463 " (cutoff:3.500A) Processing helix chain 'S' and resid 1085 through 1092 removed outlier: 3.718A pdb=" N ALA S1090 " --> pdb=" O ARG S1086 " (cutoff:3.500A) Processing helix chain 'V' and resid 10 through 24 Processing helix chain 'V' and resid 27 through 42 Processing helix chain 'V' and resid 124 through 129 Processing helix chain 'V' and resid 170 through 174 removed outlier: 3.563A pdb=" N ASN V 174 " --> pdb=" O PRO V 171 " (cutoff:3.500A) Processing helix chain 'V' and resid 193 through 195 No H-bonds generated for 'chain 'V' and resid 193 through 195' Processing helix chain 'V' and resid 209 through 222 Processing helix chain 'V' and resid 229 through 231 No H-bonds generated for 'chain 'V' and resid 229 through 231' Processing helix chain 'V' and resid 264 through 277 Processing helix chain 'V' and resid 311 through 322 Processing helix chain 'V' and resid 328 through 336 removed outlier: 3.843A pdb=" N VAL V 335 " --> pdb=" O SER V 331 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS V 336 " --> pdb=" O ILE V 332 " (cutoff:3.500A) Processing helix chain 'V' and resid 349 through 356 removed outlier: 4.198A pdb=" N SER V 353 " --> pdb=" O PRO V 350 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N SER V 354 " --> pdb=" O ASN V 351 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR V 356 " --> pdb=" O SER V 353 " (cutoff:3.500A) Processing helix chain 'V' and resid 381 through 396 removed outlier: 3.617A pdb=" N LEU V 387 " --> pdb=" O ALA V 383 " (cutoff:3.500A) Processing helix chain 'V' and resid 414 through 423 Processing helix chain 'V' and resid 445 through 461 removed outlier: 4.470A pdb=" N GLU V 449 " --> pdb=" O SER V 445 " (cutoff:3.500A) Processing helix chain 'V' and resid 461 through 467 removed outlier: 4.118A pdb=" N GLU V 467 " --> pdb=" O ALA V 463 " (cutoff:3.500A) Processing helix chain 'V' and resid 1085 through 1092 removed outlier: 3.718A pdb=" N ALA V1090 " --> pdb=" O ARG V1086 " (cutoff:3.500A) Processing helix chain 'X' and resid 10 through 24 Processing helix chain 'X' and resid 27 through 42 Processing helix chain 'X' and resid 124 through 129 Processing helix chain 'X' and resid 170 through 174 removed outlier: 3.564A pdb=" N ASN X 174 " --> pdb=" O PRO X 171 " (cutoff:3.500A) Processing helix chain 'X' and resid 193 through 195 No H-bonds generated for 'chain 'X' and resid 193 through 195' Processing helix chain 'X' and resid 209 through 222 Processing helix chain 'X' and resid 229 through 231 No H-bonds generated for 'chain 'X' and resid 229 through 231' Processing helix chain 'X' and resid 265 through 277 Processing helix chain 'X' and resid 311 through 322 Processing helix chain 'X' and resid 328 through 336 removed outlier: 3.842A pdb=" N VAL X 335 " --> pdb=" O SER X 331 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS X 336 " --> pdb=" O ILE X 332 " (cutoff:3.500A) Processing helix chain 'X' and resid 349 through 356 removed outlier: 4.198A pdb=" N SER X 353 " --> pdb=" O PRO X 350 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N SER X 354 " --> pdb=" O ASN X 351 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR X 356 " --> pdb=" O SER X 353 " (cutoff:3.500A) Processing helix chain 'X' and resid 381 through 396 removed outlier: 3.616A pdb=" N LEU X 387 " --> pdb=" O ALA X 383 " (cutoff:3.500A) Processing helix chain 'X' and resid 414 through 423 Processing helix chain 'X' and resid 445 through 461 removed outlier: 4.471A pdb=" N GLU X 449 " --> pdb=" O SER X 445 " (cutoff:3.500A) Processing helix chain 'X' and resid 461 through 467 removed outlier: 4.117A pdb=" N GLU X 467 " --> pdb=" O ALA X 463 " (cutoff:3.500A) Processing helix chain 'X' and resid 1085 through 1092 removed outlier: 3.718A pdb=" N ALA X1090 " --> pdb=" O ARG X1086 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 47 removed outlier: 6.051A pdb=" N GLN A 45 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N THR A 66 " --> pdb=" O GLN A 45 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N LEU A 47 " --> pdb=" O THR A 66 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N HIS A 93 " --> pdb=" O ALA A 342 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ASP A 428 " --> pdb=" O LYS A 371 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 188 through 191 removed outlier: 6.102A pdb=" N LEU A 188 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL A 115 " --> pdb=" O LEU A 188 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N SER A 105 " --> pdb=" O GLY A 116 " (cutoff:3.500A) removed outlier: 11.045A pdb=" N GLU A 118 " --> pdb=" O PRO A 103 " (cutoff:3.500A) removed outlier: 9.800A pdb=" N TYR A 120 " --> pdb=" O LEU A 101 " (cutoff:3.500A) removed outlier: 10.713A pdb=" N LEU A 101 " --> pdb=" O TYR A 120 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU A 99 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N LEU A 238 " --> pdb=" O LEU A 101 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N PHE A 236 " --> pdb=" O PRO A 103 " (cutoff:3.500A) removed outlier: 10.616A pdb=" N SER A 105 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 15.420A pdb=" N VAL A 234 " --> pdb=" O SER A 105 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ILE A 233 " --> pdb=" O GLU A 142 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N GLU A 142 " --> pdb=" O ILE A 233 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASP A 235 " --> pdb=" O MET A 140 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N LEU A 133 " --> pdb=" O ARG A 157 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ARG A 157 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU A 135 " --> pdb=" O ILE A 155 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL A 148 " --> pdb=" O ILE I 470 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 247 through 249 removed outlier: 4.298A pdb=" N GLY A 444 " --> pdb=" O PRO A 432 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ALA A 345 " --> pdb=" O MET A 433 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 469 through 470 removed outlier: 3.763A pdb=" N GLN Q 150 " --> pdb=" O ILE A 470 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU Q 135 " --> pdb=" O ILE Q 155 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ARG Q 157 " --> pdb=" O LEU Q 133 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N LEU Q 133 " --> pdb=" O ARG Q 157 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASP Q 235 " --> pdb=" O MET Q 140 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N GLU Q 142 " --> pdb=" O ILE Q 233 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ILE Q 233 " --> pdb=" O GLU Q 142 " (cutoff:3.500A) removed outlier: 15.421A pdb=" N VAL Q 234 " --> pdb=" O SER Q 105 " (cutoff:3.500A) removed outlier: 10.617A pdb=" N SER Q 105 " --> pdb=" O VAL Q 234 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N PHE Q 236 " --> pdb=" O PRO Q 103 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N LEU Q 238 " --> pdb=" O LEU Q 101 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU Q 99 " --> pdb=" O LEU Q 240 " (cutoff:3.500A) removed outlier: 10.713A pdb=" N LEU Q 101 " --> pdb=" O TYR Q 120 " (cutoff:3.500A) removed outlier: 9.800A pdb=" N TYR Q 120 " --> pdb=" O LEU Q 101 " (cutoff:3.500A) removed outlier: 11.045A pdb=" N GLU Q 118 " --> pdb=" O PRO Q 103 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N SER Q 105 " --> pdb=" O GLY Q 116 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL Q 115 " --> pdb=" O LEU Q 188 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LEU Q 188 " --> pdb=" O VAL Q 115 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1073 through 1076 Processing sheet with id=AA6, first strand: chain 'C' and resid 45 through 47 removed outlier: 6.051A pdb=" N GLN C 45 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N THR C 66 " --> pdb=" O GLN C 45 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N LEU C 47 " --> pdb=" O THR C 66 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N HIS C 93 " --> pdb=" O ALA C 342 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ASP C 428 " --> pdb=" O LYS C 371 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 188 through 191 removed outlier: 6.102A pdb=" N LEU C 188 " --> pdb=" O VAL C 115 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL C 115 " --> pdb=" O LEU C 188 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N SER C 105 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 11.045A pdb=" N GLU C 118 " --> pdb=" O PRO C 103 " (cutoff:3.500A) removed outlier: 9.799A pdb=" N TYR C 120 " --> pdb=" O LEU C 101 " (cutoff:3.500A) removed outlier: 10.712A pdb=" N LEU C 101 " --> pdb=" O TYR C 120 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU C 99 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N LEU C 238 " --> pdb=" O LEU C 101 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N PHE C 236 " --> pdb=" O PRO C 103 " (cutoff:3.500A) removed outlier: 10.616A pdb=" N SER C 105 " --> pdb=" O VAL C 234 " (cutoff:3.500A) removed outlier: 15.421A pdb=" N VAL C 234 " --> pdb=" O SER C 105 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ILE C 233 " --> pdb=" O GLU C 142 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N GLU C 142 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASP C 235 " --> pdb=" O MET C 140 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N LEU C 133 " --> pdb=" O ARG C 157 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ARG C 157 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU C 135 " --> pdb=" O ILE C 155 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL C 148 " --> pdb=" O ILE E 470 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 247 through 249 removed outlier: 4.298A pdb=" N GLY C 444 " --> pdb=" O PRO C 432 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ALA C 345 " --> pdb=" O MET C 433 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 469 through 470 removed outlier: 3.795A pdb=" N GLN G 150 " --> pdb=" O ILE C 470 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU G 135 " --> pdb=" O ILE G 155 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ARG G 157 " --> pdb=" O LEU G 133 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N LEU G 133 " --> pdb=" O ARG G 157 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASP G 235 " --> pdb=" O MET G 140 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N GLU G 142 " --> pdb=" O ILE G 233 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ILE G 233 " --> pdb=" O GLU G 142 " (cutoff:3.500A) removed outlier: 15.421A pdb=" N VAL G 234 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 10.616A pdb=" N SER G 105 " --> pdb=" O VAL G 234 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N PHE G 236 " --> pdb=" O PRO G 103 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N LEU G 238 " --> pdb=" O LEU G 101 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU G 99 " --> pdb=" O LEU G 240 " (cutoff:3.500A) removed outlier: 10.712A pdb=" N LEU G 101 " --> pdb=" O TYR G 120 " (cutoff:3.500A) removed outlier: 9.799A pdb=" N TYR G 120 " --> pdb=" O LEU G 101 " (cutoff:3.500A) removed outlier: 11.045A pdb=" N GLU G 118 " --> pdb=" O PRO G 103 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N SER G 105 " --> pdb=" O GLY G 116 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL G 115 " --> pdb=" O LEU G 188 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LEU G 188 " --> pdb=" O VAL G 115 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 1073 through 1076 Processing sheet with id=AB2, first strand: chain 'E' and resid 45 through 47 removed outlier: 6.051A pdb=" N GLN E 45 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N THR E 66 " --> pdb=" O GLN E 45 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N LEU E 47 " --> pdb=" O THR E 66 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N HIS E 93 " --> pdb=" O ALA E 342 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ASP E 428 " --> pdb=" O LYS E 371 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 188 through 191 removed outlier: 6.102A pdb=" N LEU E 188 " --> pdb=" O VAL E 115 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL E 115 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N SER E 105 " --> pdb=" O GLY E 116 " (cutoff:3.500A) removed outlier: 11.045A pdb=" N GLU E 118 " --> pdb=" O PRO E 103 " (cutoff:3.500A) removed outlier: 9.800A pdb=" N TYR E 120 " --> pdb=" O LEU E 101 " (cutoff:3.500A) removed outlier: 10.712A pdb=" N LEU E 101 " --> pdb=" O TYR E 120 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU E 99 " --> pdb=" O LEU E 240 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N LEU E 238 " --> pdb=" O LEU E 101 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N PHE E 236 " --> pdb=" O PRO E 103 " (cutoff:3.500A) removed outlier: 10.616A pdb=" N SER E 105 " --> pdb=" O VAL E 234 " (cutoff:3.500A) removed outlier: 15.421A pdb=" N VAL E 234 " --> pdb=" O SER E 105 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ILE E 233 " --> pdb=" O GLU E 142 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N GLU E 142 " --> pdb=" O ILE E 233 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASP E 235 " --> pdb=" O MET E 140 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N LEU E 133 " --> pdb=" O ARG E 157 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ARG E 157 " --> pdb=" O LEU E 133 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU E 135 " --> pdb=" O ILE E 155 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N VAL E 148 " --> pdb=" O ILE G 470 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 247 through 249 removed outlier: 4.298A pdb=" N GLY E 444 " --> pdb=" O PRO E 432 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ALA E 345 " --> pdb=" O MET E 433 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 1073 through 1076 Processing sheet with id=AB6, first strand: chain 'G' and resid 45 through 47 removed outlier: 6.050A pdb=" N GLN G 45 " --> pdb=" O PHE G 64 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N THR G 66 " --> pdb=" O GLN G 45 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N LEU G 47 " --> pdb=" O THR G 66 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N HIS G 93 " --> pdb=" O ALA G 342 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ASP G 428 " --> pdb=" O LYS G 371 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 247 through 249 removed outlier: 4.298A pdb=" N GLY G 444 " --> pdb=" O PRO G 432 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N ALA G 345 " --> pdb=" O MET G 433 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 1073 through 1076 Processing sheet with id=AB9, first strand: chain 'I' and resid 45 through 47 removed outlier: 6.050A pdb=" N GLN I 45 " --> pdb=" O PHE I 64 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N THR I 66 " --> pdb=" O GLN I 45 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N LEU I 47 " --> pdb=" O THR I 66 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N HIS I 93 " --> pdb=" O ALA I 342 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ASP I 428 " --> pdb=" O LYS I 371 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 188 through 191 removed outlier: 6.102A pdb=" N LEU I 188 " --> pdb=" O VAL I 115 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL I 115 " --> pdb=" O LEU I 188 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N SER I 105 " --> pdb=" O GLY I 116 " (cutoff:3.500A) removed outlier: 11.045A pdb=" N GLU I 118 " --> pdb=" O PRO I 103 " (cutoff:3.500A) removed outlier: 9.799A pdb=" N TYR I 120 " --> pdb=" O LEU I 101 " (cutoff:3.500A) removed outlier: 10.712A pdb=" N LEU I 101 " --> pdb=" O TYR I 120 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU I 99 " --> pdb=" O LEU I 240 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N LEU I 238 " --> pdb=" O LEU I 101 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N PHE I 236 " --> pdb=" O PRO I 103 " (cutoff:3.500A) removed outlier: 10.616A pdb=" N SER I 105 " --> pdb=" O VAL I 234 " (cutoff:3.500A) removed outlier: 15.420A pdb=" N VAL I 234 " --> pdb=" O SER I 105 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ILE I 233 " --> pdb=" O GLU I 142 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N GLU I 142 " --> pdb=" O ILE I 233 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASP I 235 " --> pdb=" O MET I 140 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N LEU I 133 " --> pdb=" O ARG I 157 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ARG I 157 " --> pdb=" O LEU I 133 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU I 135 " --> pdb=" O ILE I 155 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL I 148 " --> pdb=" O ILE Q 470 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 247 through 249 removed outlier: 4.297A pdb=" N GLY I 444 " --> pdb=" O PRO I 432 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ALA I 345 " --> pdb=" O MET I 433 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 1073 through 1076 Processing sheet with id=AC4, first strand: chain 'K' and resid 45 through 47 removed outlier: 6.051A pdb=" N GLN K 45 " --> pdb=" O PHE K 64 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N THR K 66 " --> pdb=" O GLN K 45 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N LEU K 47 " --> pdb=" O THR K 66 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N HIS K 93 " --> pdb=" O ALA K 342 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ASP K 428 " --> pdb=" O LYS K 371 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 188 through 191 removed outlier: 6.103A pdb=" N LEU K 188 " --> pdb=" O VAL K 115 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL K 115 " --> pdb=" O LEU K 188 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N SER K 105 " --> pdb=" O GLY K 116 " (cutoff:3.500A) removed outlier: 11.044A pdb=" N GLU K 118 " --> pdb=" O PRO K 103 " (cutoff:3.500A) removed outlier: 9.800A pdb=" N TYR K 120 " --> pdb=" O LEU K 101 " (cutoff:3.500A) removed outlier: 10.713A pdb=" N LEU K 101 " --> pdb=" O TYR K 120 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU K 99 " --> pdb=" O LEU K 240 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N LEU K 238 " --> pdb=" O LEU K 101 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N PHE K 236 " --> pdb=" O PRO K 103 " (cutoff:3.500A) removed outlier: 10.616A pdb=" N SER K 105 " --> pdb=" O VAL K 234 " (cutoff:3.500A) removed outlier: 15.420A pdb=" N VAL K 234 " --> pdb=" O SER K 105 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ILE K 233 " --> pdb=" O GLU K 142 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N GLU K 142 " --> pdb=" O ILE K 233 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASP K 235 " --> pdb=" O MET K 140 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N LEU K 133 " --> pdb=" O ARG K 157 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ARG K 157 " --> pdb=" O LEU K 133 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU K 135 " --> pdb=" O ILE K 155 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N VAL K 148 " --> pdb=" O ILE M 470 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 247 through 249 removed outlier: 4.298A pdb=" N GLY K 444 " --> pdb=" O PRO K 432 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ALA K 345 " --> pdb=" O MET K 433 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 469 through 470 removed outlier: 3.749A pdb=" N GLN O 150 " --> pdb=" O ILE K 470 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU O 135 " --> pdb=" O ILE O 155 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ARG O 157 " --> pdb=" O LEU O 133 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N LEU O 133 " --> pdb=" O ARG O 157 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASP O 235 " --> pdb=" O MET O 140 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N GLU O 142 " --> pdb=" O ILE O 233 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ILE O 233 " --> pdb=" O GLU O 142 " (cutoff:3.500A) removed outlier: 15.421A pdb=" N VAL O 234 " --> pdb=" O SER O 105 " (cutoff:3.500A) removed outlier: 10.616A pdb=" N SER O 105 " --> pdb=" O VAL O 234 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N PHE O 236 " --> pdb=" O PRO O 103 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N LEU O 238 " --> pdb=" O LEU O 101 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU O 99 " --> pdb=" O LEU O 240 " (cutoff:3.500A) removed outlier: 10.712A pdb=" N LEU O 101 " --> pdb=" O TYR O 120 " (cutoff:3.500A) removed outlier: 9.800A pdb=" N TYR O 120 " --> pdb=" O LEU O 101 " (cutoff:3.500A) removed outlier: 11.045A pdb=" N GLU O 118 " --> pdb=" O PRO O 103 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N SER O 105 " --> pdb=" O GLY O 116 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL O 115 " --> pdb=" O LEU O 188 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LEU O 188 " --> pdb=" O VAL O 115 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 1073 through 1076 Processing sheet with id=AC9, first strand: chain 'M' and resid 45 through 47 removed outlier: 6.050A pdb=" N GLN M 45 " --> pdb=" O PHE M 64 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N THR M 66 " --> pdb=" O GLN M 45 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N LEU M 47 " --> pdb=" O THR M 66 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N HIS M 93 " --> pdb=" O ALA M 342 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ASP M 428 " --> pdb=" O LYS M 371 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 188 through 191 removed outlier: 6.102A pdb=" N LEU M 188 " --> pdb=" O VAL M 115 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL M 115 " --> pdb=" O LEU M 188 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N SER M 105 " --> pdb=" O GLY M 116 " (cutoff:3.500A) removed outlier: 11.045A pdb=" N GLU M 118 " --> pdb=" O PRO M 103 " (cutoff:3.500A) removed outlier: 9.800A pdb=" N TYR M 120 " --> pdb=" O LEU M 101 " (cutoff:3.500A) removed outlier: 10.712A pdb=" N LEU M 101 " --> pdb=" O TYR M 120 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU M 99 " --> pdb=" O LEU M 240 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N LEU M 238 " --> pdb=" O LEU M 101 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N PHE M 236 " --> pdb=" O PRO M 103 " (cutoff:3.500A) removed outlier: 10.615A pdb=" N SER M 105 " --> pdb=" O VAL M 234 " (cutoff:3.500A) removed outlier: 15.420A pdb=" N VAL M 234 " --> pdb=" O SER M 105 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ILE M 233 " --> pdb=" O GLU M 142 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N GLU M 142 " --> pdb=" O ILE M 233 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASP M 235 " --> pdb=" O MET M 140 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N LEU M 133 " --> pdb=" O ARG M 157 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ARG M 157 " --> pdb=" O LEU M 133 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU M 135 " --> pdb=" O ILE M 155 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL M 148 " --> pdb=" O ILE O 470 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'M' and resid 247 through 249 removed outlier: 4.298A pdb=" N GLY M 444 " --> pdb=" O PRO M 432 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ALA M 345 " --> pdb=" O MET M 433 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 1073 through 1076 Processing sheet with id=AD4, first strand: chain 'O' and resid 45 through 47 removed outlier: 6.050A pdb=" N GLN O 45 " --> pdb=" O PHE O 64 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N THR O 66 " --> pdb=" O GLN O 45 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N LEU O 47 " --> pdb=" O THR O 66 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N HIS O 93 " --> pdb=" O ALA O 342 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ASP O 428 " --> pdb=" O LYS O 371 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'O' and resid 247 through 249 removed outlier: 4.297A pdb=" N GLY O 444 " --> pdb=" O PRO O 432 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ALA O 345 " --> pdb=" O MET O 433 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'O' and resid 1073 through 1076 Processing sheet with id=AD7, first strand: chain 'Q' and resid 45 through 47 removed outlier: 6.050A pdb=" N GLN Q 45 " --> pdb=" O PHE Q 64 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N THR Q 66 " --> pdb=" O GLN Q 45 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N LEU Q 47 " --> pdb=" O THR Q 66 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N HIS Q 93 " --> pdb=" O ALA Q 342 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ASP Q 428 " --> pdb=" O LYS Q 371 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'Q' and resid 247 through 249 removed outlier: 4.297A pdb=" N GLY Q 444 " --> pdb=" O PRO Q 432 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ALA Q 345 " --> pdb=" O MET Q 433 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'Q' and resid 1073 through 1076 Processing sheet with id=AE1, first strand: chain 'S' and resid 45 through 47 removed outlier: 6.050A pdb=" N GLN S 45 " --> pdb=" O PHE S 64 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N THR S 66 " --> pdb=" O GLN S 45 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N LEU S 47 " --> pdb=" O THR S 66 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N HIS S 93 " --> pdb=" O ALA S 342 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ASP S 428 " --> pdb=" O LYS S 371 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'S' and resid 188 through 191 removed outlier: 6.102A pdb=" N LEU S 188 " --> pdb=" O VAL S 115 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL S 115 " --> pdb=" O LEU S 188 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N SER S 105 " --> pdb=" O GLY S 116 " (cutoff:3.500A) removed outlier: 11.045A pdb=" N GLU S 118 " --> pdb=" O PRO S 103 " (cutoff:3.500A) removed outlier: 9.799A pdb=" N TYR S 120 " --> pdb=" O LEU S 101 " (cutoff:3.500A) removed outlier: 10.712A pdb=" N LEU S 101 " --> pdb=" O TYR S 120 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU S 99 " --> pdb=" O LEU S 240 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N LEU S 238 " --> pdb=" O LEU S 101 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N PHE S 236 " --> pdb=" O PRO S 103 " (cutoff:3.500A) removed outlier: 10.616A pdb=" N SER S 105 " --> pdb=" O VAL S 234 " (cutoff:3.500A) removed outlier: 15.421A pdb=" N VAL S 234 " --> pdb=" O SER S 105 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ILE S 233 " --> pdb=" O GLU S 142 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N GLU S 142 " --> pdb=" O ILE S 233 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASP S 235 " --> pdb=" O MET S 140 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N LEU S 133 " --> pdb=" O ARG S 157 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ARG S 157 " --> pdb=" O LEU S 133 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU S 135 " --> pdb=" O ILE S 155 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL S 148 " --> pdb=" O ILE V 470 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'S' and resid 247 through 249 removed outlier: 4.297A pdb=" N GLY S 444 " --> pdb=" O PRO S 432 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ALA S 345 " --> pdb=" O MET S 433 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'S' and resid 469 through 470 removed outlier: 3.612A pdb=" N GLN X 150 " --> pdb=" O ILE S 470 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU X 135 " --> pdb=" O ILE X 155 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ARG X 157 " --> pdb=" O LEU X 133 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N LEU X 133 " --> pdb=" O ARG X 157 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASP X 235 " --> pdb=" O MET X 140 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N GLU X 142 " --> pdb=" O ILE X 233 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ILE X 233 " --> pdb=" O GLU X 142 " (cutoff:3.500A) removed outlier: 15.421A pdb=" N VAL X 234 " --> pdb=" O SER X 105 " (cutoff:3.500A) removed outlier: 10.616A pdb=" N SER X 105 " --> pdb=" O VAL X 234 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N PHE X 236 " --> pdb=" O PRO X 103 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N LEU X 238 " --> pdb=" O LEU X 101 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU X 99 " --> pdb=" O LEU X 240 " (cutoff:3.500A) removed outlier: 10.712A pdb=" N LEU X 101 " --> pdb=" O TYR X 120 " (cutoff:3.500A) removed outlier: 9.800A pdb=" N TYR X 120 " --> pdb=" O LEU X 101 " (cutoff:3.500A) removed outlier: 11.045A pdb=" N GLU X 118 " --> pdb=" O PRO X 103 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N SER X 105 " --> pdb=" O GLY X 116 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL X 115 " --> pdb=" O LEU X 188 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LEU X 188 " --> pdb=" O VAL X 115 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'S' and resid 1073 through 1076 Processing sheet with id=AE6, first strand: chain 'V' and resid 45 through 47 removed outlier: 6.050A pdb=" N GLN V 45 " --> pdb=" O PHE V 64 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N THR V 66 " --> pdb=" O GLN V 45 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N LEU V 47 " --> pdb=" O THR V 66 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N HIS V 93 " --> pdb=" O ALA V 342 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ASP V 428 " --> pdb=" O LYS V 371 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'V' and resid 188 through 191 removed outlier: 6.102A pdb=" N LEU V 188 " --> pdb=" O VAL V 115 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL V 115 " --> pdb=" O LEU V 188 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N SER V 105 " --> pdb=" O GLY V 116 " (cutoff:3.500A) removed outlier: 11.045A pdb=" N GLU V 118 " --> pdb=" O PRO V 103 " (cutoff:3.500A) removed outlier: 9.800A pdb=" N TYR V 120 " --> pdb=" O LEU V 101 " (cutoff:3.500A) removed outlier: 10.713A pdb=" N LEU V 101 " --> pdb=" O TYR V 120 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU V 99 " --> pdb=" O LEU V 240 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N LEU V 238 " --> pdb=" O LEU V 101 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N PHE V 236 " --> pdb=" O PRO V 103 " (cutoff:3.500A) removed outlier: 10.616A pdb=" N SER V 105 " --> pdb=" O VAL V 234 " (cutoff:3.500A) removed outlier: 15.420A pdb=" N VAL V 234 " --> pdb=" O SER V 105 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ILE V 233 " --> pdb=" O GLU V 142 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N GLU V 142 " --> pdb=" O ILE V 233 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASP V 235 " --> pdb=" O MET V 140 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N LEU V 133 " --> pdb=" O ARG V 157 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ARG V 157 " --> pdb=" O LEU V 133 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU V 135 " --> pdb=" O ILE V 155 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL V 148 " --> pdb=" O ILE X 470 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'V' and resid 247 through 249 removed outlier: 4.298A pdb=" N GLY V 444 " --> pdb=" O PRO V 432 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ALA V 345 " --> pdb=" O MET V 433 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'V' and resid 1073 through 1076 Processing sheet with id=AF1, first strand: chain 'X' and resid 45 through 47 removed outlier: 6.050A pdb=" N GLN X 45 " --> pdb=" O PHE X 64 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N THR X 66 " --> pdb=" O GLN X 45 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N LEU X 47 " --> pdb=" O THR X 66 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N HIS X 93 " --> pdb=" O ALA X 342 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ASP X 428 " --> pdb=" O LYS X 371 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'X' and resid 247 through 249 removed outlier: 4.298A pdb=" N GLY X 444 " --> pdb=" O PRO X 432 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ALA X 345 " --> pdb=" O MET X 433 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'X' and resid 1073 through 1076 1967 hydrogen bonds defined for protein. 5433 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: 25.58 Time building geometry restraints manager: 23.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 8244 1.30 - 1.43: 13353 1.43 - 1.56: 28226 1.56 - 1.69: 1 1.69 - 1.81: 504 Bond restraints: 50328 Sorted by residual: bond pdb=" C ASN E 263 " pdb=" O ASN E 263 " ideal model delta sigma weight residual 1.235 1.177 0.058 1.26e-02 6.30e+03 2.15e+01 bond pdb=" CA LEU Q 264 " pdb=" C LEU Q 264 " ideal model delta sigma weight residual 1.522 1.563 -0.041 1.31e-02 5.83e+03 9.66e+00 bond pdb=" CG1 ILE M 300 " pdb=" CD1 ILE M 300 " ideal model delta sigma weight residual 1.513 1.396 0.117 3.90e-02 6.57e+02 9.07e+00 bond pdb=" CG1 ILE X 300 " pdb=" CD1 ILE X 300 " ideal model delta sigma weight residual 1.513 1.396 0.117 3.90e-02 6.57e+02 9.06e+00 bond pdb=" CG1 ILE K 300 " pdb=" CD1 ILE K 300 " ideal model delta sigma weight residual 1.513 1.396 0.117 3.90e-02 6.57e+02 8.96e+00 ... (remaining 50323 not shown) Histogram of bond angle deviations from ideal: 95.73 - 103.44: 691 103.44 - 111.15: 19326 111.15 - 118.86: 20839 118.86 - 126.57: 26504 126.57 - 134.28: 728 Bond angle restraints: 68088 Sorted by residual: angle pdb=" N LEU V 264 " pdb=" CA LEU V 264 " pdb=" C LEU V 264 " ideal model delta sigma weight residual 114.56 98.73 15.83 1.27e+00 6.20e-01 1.55e+02 angle pdb=" N LEU Q 264 " pdb=" CA LEU Q 264 " pdb=" C LEU Q 264 " ideal model delta sigma weight residual 113.12 97.90 15.22 1.25e+00 6.40e-01 1.48e+02 angle pdb=" N LEU X 264 " pdb=" CA LEU X 264 " pdb=" C LEU X 264 " ideal model delta sigma weight residual 114.12 98.04 16.08 1.39e+00 5.18e-01 1.34e+02 angle pdb=" N LEU G 264 " pdb=" CA LEU G 264 " pdb=" C LEU G 264 " ideal model delta sigma weight residual 113.38 101.18 12.20 1.23e+00 6.61e-01 9.84e+01 angle pdb=" N LEU S 264 " pdb=" CA LEU S 264 " pdb=" C LEU S 264 " ideal model delta sigma weight residual 111.69 100.54 11.15 1.23e+00 6.61e-01 8.22e+01 ... (remaining 68083 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 27462 17.54 - 35.07: 2181 35.07 - 52.61: 496 52.61 - 70.15: 77 70.15 - 87.69: 84 Dihedral angle restraints: 30300 sinusoidal: 11976 harmonic: 18324 Sorted by residual: dihedral pdb=" N ASN K 263 " pdb=" C ASN K 263 " pdb=" CA ASN K 263 " pdb=" CB ASN K 263 " ideal model delta harmonic sigma weight residual 122.80 140.78 -17.98 0 2.50e+00 1.60e-01 5.17e+01 dihedral pdb=" C ASN O 263 " pdb=" N ASN O 263 " pdb=" CA ASN O 263 " pdb=" CB ASN O 263 " ideal model delta harmonic sigma weight residual -122.60 -140.09 17.49 0 2.50e+00 1.60e-01 4.90e+01 dihedral pdb=" N ASN O 263 " pdb=" C ASN O 263 " pdb=" CA ASN O 263 " pdb=" CB ASN O 263 " ideal model delta harmonic sigma weight residual 122.80 139.82 -17.02 0 2.50e+00 1.60e-01 4.64e+01 ... (remaining 30297 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.161: 7348 0.161 - 0.321: 176 0.321 - 0.482: 25 0.482 - 0.642: 6 0.642 - 0.803: 5 Chirality restraints: 7560 Sorted by residual: chirality pdb=" CA ASN O 263 " pdb=" N ASN O 263 " pdb=" C ASN O 263 " pdb=" CB ASN O 263 " both_signs ideal model delta sigma weight residual False 2.51 1.71 0.80 2.00e-01 2.50e+01 1.61e+01 chirality pdb=" CA ASN K 263 " pdb=" N ASN K 263 " pdb=" C ASN K 263 " pdb=" CB ASN K 263 " both_signs ideal model delta sigma weight residual False 2.51 1.71 0.80 2.00e-01 2.50e+01 1.60e+01 chirality pdb=" CA ASN I 263 " pdb=" N ASN I 263 " pdb=" C ASN I 263 " pdb=" CB ASN I 263 " both_signs ideal model delta sigma weight residual False 2.51 1.77 0.74 2.00e-01 2.50e+01 1.36e+01 ... (remaining 7557 not shown) Planarity restraints: 8820 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP X 262 " -0.018 2.00e-02 2.50e+03 3.90e-02 1.52e+01 pdb=" C ASP X 262 " 0.067 2.00e-02 2.50e+03 pdb=" O ASP X 262 " -0.027 2.00e-02 2.50e+03 pdb=" N ASN X 263 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR O 356 " 0.024 2.00e-02 2.50e+03 2.50e-02 1.25e+01 pdb=" CG TYR O 356 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 TYR O 356 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR O 356 " 0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR O 356 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 TYR O 356 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR O 356 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR O 356 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 356 " 0.024 2.00e-02 2.50e+03 2.49e-02 1.24e+01 pdb=" CG TYR G 356 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 TYR G 356 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR G 356 " 0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR G 356 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR G 356 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR G 356 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR G 356 " 0.002 2.00e-02 2.50e+03 ... (remaining 8817 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 1452 2.61 - 3.19: 44355 3.19 - 3.76: 91759 3.76 - 4.33: 128844 4.33 - 4.90: 205301 Nonbonded interactions: 471711 Sorted by model distance: nonbonded pdb=" OE2 GLU V 298 " pdb="ZN ZN V1502 " model vdw 2.042 2.230 nonbonded pdb=" OD2 ASP Q 262 " pdb="ZN ZN Q1501 " model vdw 2.053 2.230 nonbonded pdb=" OD2 ASP G 262 " pdb="ZN ZN G1501 " model vdw 2.053 2.230 nonbonded pdb=" OD2 ASP V 262 " pdb="ZN ZN V1501 " model vdw 2.054 2.230 nonbonded pdb=" OD2 ASP O 262 " pdb="ZN ZN O1501 " model vdw 2.054 2.230 ... (remaining 471706 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 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'V' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 9.900 Check model and map are aligned: 0.760 Set scattering table: 0.480 Process input model: 147.100 Find NCS groups from input model: 3.470 Set up NCS constraints: 0.460 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:16.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 180.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.117 50328 Z= 0.581 Angle : 1.136 16.079 68088 Z= 0.633 Chirality : 0.072 0.803 7560 Planarity : 0.008 0.068 8820 Dihedral : 14.343 87.687 18420 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.04 % Favored : 94.95 % Rotamer: Outliers : 1.16 % Allowed : 2.55 % Favored : 96.29 % Cbeta Deviations : 0.17 % 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: -2.84 (0.09), residues: 6252 helix: -2.45 (0.08), residues: 1572 sheet: -0.65 (0.14), residues: 1344 loop : -2.13 (0.08), residues: 3336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP M 128 HIS 0.018 0.002 HIS Q 154 PHE 0.033 0.003 PHE K1082 TYR 0.058 0.006 TYR O 356 ARG 0.018 0.002 ARG S1107 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1058 residues out of total 5520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 994 time to evaluate : 5.859 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: A 1 MET cc_start: 0.6278 (ttp) cc_final: 0.5869 (ttt) REVERT: A 17 ASP cc_start: 0.8611 (m-30) cc_final: 0.8359 (m-30) REVERT: A 235 ASP cc_start: 0.7996 (t70) cc_final: 0.7734 (t70) REVERT: A 266 MET cc_start: 0.9205 (mmm) cc_final: 0.8998 (mmp) REVERT: C 348 MET cc_start: 0.8921 (tpt) cc_final: 0.8701 (tpp) REVERT: C 1103 PHE cc_start: 0.8722 (m-80) cc_final: 0.8495 (m-80) REVERT: E 29 TYR cc_start: 0.9422 (m-80) cc_final: 0.9201 (m-80) REVERT: E 192 GLU cc_start: 0.8292 (pt0) cc_final: 0.7903 (pt0) REVERT: E 1107 ARG cc_start: 0.7422 (OUTLIER) cc_final: 0.7116 (mmt180) REVERT: G 1 MET cc_start: 0.6884 (ttp) cc_final: 0.6491 (ttm) REVERT: G 130 ASP cc_start: 0.8564 (m-30) cc_final: 0.8286 (m-30) REVERT: G 266 MET cc_start: 0.9251 (mmm) cc_final: 0.8935 (mmp) REVERT: G 341 SER cc_start: 0.8899 (t) cc_final: 0.8247 (p) REVERT: G 357 GLU cc_start: 0.7211 (tm-30) cc_final: 0.6904 (tm-30) REVERT: G 360 ASN cc_start: 0.8966 (m-40) cc_final: 0.8614 (m110) REVERT: G 428 ASP cc_start: 0.8500 (m-30) cc_final: 0.7643 (m-30) REVERT: G 1103 PHE cc_start: 0.8521 (m-80) cc_final: 0.8080 (m-80) REVERT: I 263 ASN cc_start: 0.8232 (OUTLIER) cc_final: 0.7943 (m-40) REVERT: I 341 SER cc_start: 0.8675 (t) cc_final: 0.8019 (p) REVERT: I 360 ASN cc_start: 0.9416 (m-40) cc_final: 0.8871 (m110) REVERT: I 428 ASP cc_start: 0.8630 (m-30) cc_final: 0.8400 (m-30) REVERT: K 1 MET cc_start: 0.6390 (ttp) cc_final: 0.6169 (ttp) REVERT: K 7 MET cc_start: 0.5453 (mmm) cc_final: 0.4909 (mtt) REVERT: K 40 MET cc_start: 0.8854 (mtp) cc_final: 0.8603 (mtp) REVERT: K 194 GLU cc_start: 0.8026 (pp20) cc_final: 0.7790 (pp20) REVERT: K 207 TYR cc_start: 0.8627 (m-80) cc_final: 0.8306 (m-80) REVERT: K 286 GLU cc_start: 0.8335 (tp30) cc_final: 0.8078 (tp30) REVERT: K 288 CYS cc_start: 0.8790 (m) cc_final: 0.8517 (m) REVERT: K 318 GLN cc_start: 0.8502 (mt0) cc_final: 0.8095 (mt0) REVERT: K 348 MET cc_start: 0.8983 (tpt) cc_final: 0.8585 (tpp) REVERT: K 357 GLU cc_start: 0.7268 (tm-30) cc_final: 0.6379 (tm-30) REVERT: K 360 ASN cc_start: 0.9222 (m-40) cc_final: 0.8759 (m110) REVERT: K 1070 ARG cc_start: 0.7413 (OUTLIER) cc_final: 0.6918 (mtt90) REVERT: K 1103 PHE cc_start: 0.8478 (m-80) cc_final: 0.8188 (m-10) REVERT: M 107 LYS cc_start: 0.9017 (mtpp) cc_final: 0.8712 (mtpm) REVERT: M 245 LYS cc_start: 0.8799 (mmtt) cc_final: 0.8244 (mmpt) REVERT: M 341 SER cc_start: 0.8015 (t) cc_final: 0.7703 (p) REVERT: M 358 ASN cc_start: 0.8903 (p0) cc_final: 0.8699 (p0) REVERT: M 428 ASP cc_start: 0.8560 (m-30) cc_final: 0.8055 (m-30) REVERT: O 357 GLU cc_start: 0.7388 (tm-30) cc_final: 0.7159 (tm-30) REVERT: O 446 LYS cc_start: 0.8938 (mttp) cc_final: 0.8719 (mtpp) REVERT: O 1070 ARG cc_start: 0.7322 (OUTLIER) cc_final: 0.7105 (mtp-110) REVERT: Q 68 ASN cc_start: 0.9328 (t0) cc_final: 0.9076 (t0) REVERT: Q 266 MET cc_start: 0.9104 (mmm) cc_final: 0.8856 (mmp) REVERT: Q 341 SER cc_start: 0.8545 (t) cc_final: 0.7884 (p) REVERT: Q 428 ASP cc_start: 0.8735 (m-30) cc_final: 0.8100 (m-30) REVERT: Q 431 ASN cc_start: 0.8357 (m110) cc_final: 0.8134 (m110) REVERT: Q 446 LYS cc_start: 0.8646 (mttp) cc_final: 0.8302 (mtpp) REVERT: Q 1070 ARG cc_start: 0.7405 (OUTLIER) cc_final: 0.7073 (mtt90) REVERT: Q 1103 PHE cc_start: 0.8509 (m-80) cc_final: 0.8193 (m-80) REVERT: S 1 MET cc_start: 0.6454 (ttp) cc_final: 0.5997 (ttp) REVERT: S 334 MET cc_start: 0.9195 (mmp) cc_final: 0.8626 (mmp) REVERT: S 433 MET cc_start: 0.9118 (ptm) cc_final: 0.8801 (ptt) REVERT: S 1070 ARG cc_start: 0.7415 (OUTLIER) cc_final: 0.7144 (mtt90) REVERT: V 1 MET cc_start: 0.6558 (ttp) cc_final: 0.5920 (ttp) REVERT: V 192 GLU cc_start: 0.7846 (pt0) cc_final: 0.7489 (pt0) REVERT: V 357 GLU cc_start: 0.7484 (tm-30) cc_final: 0.7228 (tm-30) REVERT: V 358 ASN cc_start: 0.8900 (p0) cc_final: 0.8691 (p0) REVERT: V 1070 ARG cc_start: 0.7754 (OUTLIER) cc_final: 0.7467 (mtp-110) REVERT: V 1089 TYR cc_start: 0.8397 (t80) cc_final: 0.8016 (t80) REVERT: X 263 ASN cc_start: 0.8725 (m-40) cc_final: 0.8392 (m-40) REVERT: X 266 MET cc_start: 0.9145 (mmm) cc_final: 0.8565 (mmm) REVERT: X 357 GLU cc_start: 0.7001 (tm-30) cc_final: 0.6800 (tm-30) REVERT: X 431 ASN cc_start: 0.8347 (m110) cc_final: 0.8039 (m110) REVERT: X 446 LYS cc_start: 0.8865 (mttp) cc_final: 0.8483 (mtpm) REVERT: X 1070 ARG cc_start: 0.7262 (OUTLIER) cc_final: 0.6986 (mtt90) REVERT: X 1103 PHE cc_start: 0.8516 (m-80) cc_final: 0.8176 (m-80) outliers start: 64 outliers final: 4 residues processed: 1044 average time/residue: 1.6872 time to fit residues: 2218.8027 Evaluate side-chains 667 residues out of total 5520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 655 time to evaluate : 5.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1107 ARG Chi-restraints excluded: chain I residue 263 ASN Chi-restraints excluded: chain K residue 1070 ARG Chi-restraints excluded: chain O residue 1070 ARG Chi-restraints excluded: chain O residue 1107 ARG Chi-restraints excluded: chain Q residue 264 LEU Chi-restraints excluded: chain Q residue 1070 ARG Chi-restraints excluded: chain S residue 264 LEU Chi-restraints excluded: chain S residue 1070 ARG Chi-restraints excluded: chain S residue 1107 ARG Chi-restraints excluded: chain V residue 1070 ARG Chi-restraints excluded: chain X residue 1070 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 526 optimal weight: 0.9980 chunk 472 optimal weight: 3.9990 chunk 262 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 chunk 319 optimal weight: 3.9990 chunk 252 optimal weight: 0.7980 chunk 489 optimal weight: 0.9980 chunk 189 optimal weight: 0.9980 chunk 297 optimal weight: 0.6980 chunk 364 optimal weight: 30.0000 chunk 566 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 HIS C 346 HIS ** C1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1075 HIS G 68 ASN ** G1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1071 ASN M 431 ASN ** O 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 168 HIS ** O 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 346 HIS ** Q 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 4 HIS S 34 ASN S 431 ASN ** S1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 318 GLN ** X 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 50328 Z= 0.206 Angle : 0.620 10.609 68088 Z= 0.321 Chirality : 0.047 0.227 7560 Planarity : 0.005 0.053 8820 Dihedral : 5.895 56.941 6714 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.03 % Allowed : 8.99 % Favored : 88.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.09), residues: 6252 helix: 0.46 (0.12), residues: 1512 sheet: -0.70 (0.12), residues: 1476 loop : -1.85 (0.09), residues: 3264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP Q 128 HIS 0.011 0.001 HIS E 93 PHE 0.018 0.001 PHE I 18 TYR 0.015 0.001 TYR X 110 ARG 0.004 0.000 ARG G1086 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 893 residues out of total 5520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 781 time to evaluate : 5.635 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 1 MET cc_start: 0.5929 (ttp) cc_final: 0.5549 (ttp) REVERT: A 192 GLU cc_start: 0.8236 (pt0) cc_final: 0.7940 (pt0) REVERT: A 235 ASP cc_start: 0.7888 (t70) cc_final: 0.7558 (t70) REVERT: C 237 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8196 (mp0) REVERT: C 341 SER cc_start: 0.8200 (t) cc_final: 0.7802 (t) REVERT: C 357 GLU cc_start: 0.7222 (tm-30) cc_final: 0.6661 (tm-30) REVERT: C 360 ASN cc_start: 0.9148 (m-40) cc_final: 0.8882 (m110) REVERT: E 130 ASP cc_start: 0.8622 (m-30) cc_final: 0.7885 (m-30) REVERT: E 192 GLU cc_start: 0.8213 (pt0) cc_final: 0.7879 (pt0) REVERT: E 237 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.7575 (mp0) REVERT: G 1 MET cc_start: 0.6605 (ttp) cc_final: 0.6201 (ttm) REVERT: G 100 ARG cc_start: 0.9222 (OUTLIER) cc_final: 0.9022 (ttp80) REVERT: G 130 ASP cc_start: 0.8401 (m-30) cc_final: 0.8194 (m-30) REVERT: G 140 MET cc_start: 0.9538 (mmm) cc_final: 0.9329 (mmm) REVERT: G 237 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8327 (mp0) REVERT: G 244 GLU cc_start: 0.7403 (tp30) cc_final: 0.7078 (tp30) REVERT: G 341 SER cc_start: 0.8591 (t) cc_final: 0.7697 (p) REVERT: G 357 GLU cc_start: 0.7599 (tm-30) cc_final: 0.7363 (tm-30) REVERT: I 218 ASN cc_start: 0.8406 (t0) cc_final: 0.7996 (t0) REVERT: I 237 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.7395 (mp0) REVERT: I 357 GLU cc_start: 0.6797 (tm-30) cc_final: 0.6325 (tm-30) REVERT: I 360 ASN cc_start: 0.9142 (m-40) cc_final: 0.8620 (m110) REVERT: K 1 MET cc_start: 0.5956 (ttp) cc_final: 0.5485 (ttp) REVERT: K 40 MET cc_start: 0.8842 (mtp) cc_final: 0.8470 (mtp) REVERT: K 192 GLU cc_start: 0.8189 (pt0) cc_final: 0.7884 (pt0) REVERT: K 194 GLU cc_start: 0.7996 (pp20) cc_final: 0.7723 (pp20) REVERT: K 207 TYR cc_start: 0.8659 (m-80) cc_final: 0.8391 (m-80) REVERT: K 286 GLU cc_start: 0.8347 (tp30) cc_final: 0.8092 (tp30) REVERT: K 309 GLU cc_start: 0.8437 (tt0) cc_final: 0.8164 (mt-10) REVERT: K 357 GLU cc_start: 0.7117 (tm-30) cc_final: 0.6862 (tm-30) REVERT: K 449 GLU cc_start: 0.8572 (tp30) cc_final: 0.7955 (tp30) REVERT: M 107 LYS cc_start: 0.8974 (mtpp) cc_final: 0.8703 (mtpm) REVERT: M 237 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7242 (mt-10) REVERT: M 341 SER cc_start: 0.7998 (t) cc_final: 0.7586 (p) REVERT: M 428 ASP cc_start: 0.8804 (m-30) cc_final: 0.8086 (m-30) REVERT: O 207 TYR cc_start: 0.8674 (m-80) cc_final: 0.8362 (m-80) REVERT: Q 68 ASN cc_start: 0.9405 (t0) cc_final: 0.9158 (t0) REVERT: Q 244 GLU cc_start: 0.7677 (tp30) cc_final: 0.7368 (tp30) REVERT: S 1 MET cc_start: 0.6284 (ttp) cc_final: 0.5909 (ttp) REVERT: S 357 GLU cc_start: 0.7192 (tm-30) cc_final: 0.6975 (tm-30) REVERT: S 1072 ASP cc_start: 0.7702 (p0) cc_final: 0.7488 (p0) REVERT: V 1 MET cc_start: 0.6336 (ttp) cc_final: 0.5863 (ttp) REVERT: V 192 GLU cc_start: 0.7818 (pt0) cc_final: 0.7488 (pt0) REVERT: V 286 GLU cc_start: 0.8105 (tp30) cc_final: 0.7784 (tp30) REVERT: V 334 MET cc_start: 0.9441 (mmp) cc_final: 0.9034 (mmm) REVERT: V 341 SER cc_start: 0.8645 (t) cc_final: 0.8352 (t) REVERT: V 357 GLU cc_start: 0.7146 (tm-30) cc_final: 0.6811 (tm-30) REVERT: V 358 ASN cc_start: 0.8843 (p0) cc_final: 0.8569 (p0) REVERT: X 140 MET cc_start: 0.9561 (mmm) cc_final: 0.9218 (mmm) REVERT: X 357 GLU cc_start: 0.6623 (tm-30) cc_final: 0.6409 (tm-30) REVERT: X 401 SER cc_start: 0.9157 (p) cc_final: 0.8934 (m) REVERT: X 417 LYS cc_start: 0.8923 (tptp) cc_final: 0.8682 (tptp) REVERT: X 446 LYS cc_start: 0.8529 (mttp) cc_final: 0.8312 (mttp) REVERT: X 456 SER cc_start: 0.8997 (p) cc_final: 0.8740 (p) outliers start: 112 outliers final: 30 residues processed: 831 average time/residue: 1.5144 time to fit residues: 1601.9085 Evaluate side-chains 670 residues out of total 5520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 634 time to evaluate : 5.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 ASN Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain C residue 358 ASN Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 399 ILE Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 322 GLU Chi-restraints excluded: chain E residue 388 LEU Chi-restraints excluded: chain G residue 100 ARG Chi-restraints excluded: chain G residue 237 GLU Chi-restraints excluded: chain G residue 399 ILE Chi-restraints excluded: chain G residue 426 THR Chi-restraints excluded: chain I residue 143 GLU Chi-restraints excluded: chain I residue 195 LEU Chi-restraints excluded: chain I residue 237 GLU Chi-restraints excluded: chain I residue 263 ASN Chi-restraints excluded: chain I residue 388 LEU Chi-restraints excluded: chain K residue 329 LEU Chi-restraints excluded: chain K residue 399 ILE Chi-restraints excluded: chain M residue 237 GLU Chi-restraints excluded: chain O residue 358 ASN Chi-restraints excluded: chain O residue 388 LEU Chi-restraints excluded: chain Q residue 88 SER Chi-restraints excluded: chain Q residue 195 LEU Chi-restraints excluded: chain S residue 88 SER Chi-restraints excluded: chain S residue 195 LEU Chi-restraints excluded: chain S residue 239 ILE Chi-restraints excluded: chain V residue 195 LEU Chi-restraints excluded: chain V residue 258 SER Chi-restraints excluded: chain X residue 7 MET Chi-restraints excluded: chain X residue 96 SER Chi-restraints excluded: chain X residue 142 GLU Chi-restraints excluded: chain X residue 258 SER Chi-restraints excluded: chain X residue 358 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 314 optimal weight: 0.8980 chunk 175 optimal weight: 4.9990 chunk 471 optimal weight: 0.6980 chunk 385 optimal weight: 3.9990 chunk 156 optimal weight: 30.0000 chunk 567 optimal weight: 0.3980 chunk 613 optimal weight: 0.9990 chunk 505 optimal weight: 4.9990 chunk 562 optimal weight: 6.9990 chunk 193 optimal weight: 0.9990 chunk 455 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 HIS ** C 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1075 HIS ** G1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 34 ASN ** I 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1071 ASN ** M 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q1075 HIS S 34 ASN S 360 ASN S 431 ASN V 431 ASN ** V1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 126 HIS ** X 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 50328 Z= 0.176 Angle : 0.567 10.957 68088 Z= 0.289 Chirality : 0.045 0.190 7560 Planarity : 0.004 0.048 8820 Dihedral : 5.158 50.570 6674 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.05 % Allowed : 11.11 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.10), residues: 6252 helix: 1.48 (0.13), residues: 1536 sheet: -0.70 (0.13), residues: 1464 loop : -1.53 (0.10), residues: 3252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP V 125 HIS 0.009 0.001 HIS E 93 PHE 0.018 0.001 PHE I 18 TYR 0.013 0.001 TYR I 120 ARG 0.007 0.000 ARG I 319 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 836 residues out of total 5520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 723 time to evaluate : 6.258 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: A 1 MET cc_start: 0.5832 (ttp) cc_final: 0.5533 (ttp) REVERT: A 192 GLU cc_start: 0.8299 (pt0) cc_final: 0.8059 (pt0) REVERT: A 235 ASP cc_start: 0.7941 (t70) cc_final: 0.7629 (t70) REVERT: A 244 GLU cc_start: 0.7684 (tp30) cc_final: 0.7296 (tp30) REVERT: A 341 SER cc_start: 0.8326 (t) cc_final: 0.7996 (t) REVERT: C 192 GLU cc_start: 0.8285 (pt0) cc_final: 0.7826 (pt0) REVERT: C 263 ASN cc_start: 0.8198 (OUTLIER) cc_final: 0.7886 (m110) REVERT: C 341 SER cc_start: 0.8065 (t) cc_final: 0.7679 (t) REVERT: C 357 GLU cc_start: 0.7150 (tm-30) cc_final: 0.6423 (tm-30) REVERT: C 360 ASN cc_start: 0.9221 (m-40) cc_final: 0.8830 (m110) REVERT: E 206 LYS cc_start: 0.8098 (mmmt) cc_final: 0.7839 (mmmt) REVERT: E 244 GLU cc_start: 0.7904 (tp30) cc_final: 0.7672 (tp30) REVERT: E 286 GLU cc_start: 0.8356 (tp30) cc_final: 0.8018 (tp30) REVERT: E 288 CYS cc_start: 0.8488 (m) cc_final: 0.8288 (m) REVERT: G 100 ARG cc_start: 0.9182 (OUTLIER) cc_final: 0.8980 (ttp80) REVERT: G 140 MET cc_start: 0.9583 (mmm) cc_final: 0.9268 (mmm) REVERT: G 194 GLU cc_start: 0.7696 (pp20) cc_final: 0.7485 (pp20) REVERT: G 237 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8175 (mp0) REVERT: G 244 GLU cc_start: 0.7541 (tp30) cc_final: 0.7268 (tp30) REVERT: G 341 SER cc_start: 0.8649 (t) cc_final: 0.7772 (p) REVERT: I 247 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.7847 (ptt90) REVERT: I 357 GLU cc_start: 0.6938 (tm-30) cc_final: 0.6433 (tm-30) REVERT: I 360 ASN cc_start: 0.9157 (m-40) cc_final: 0.8748 (m110) REVERT: K 1 MET cc_start: 0.5839 (ttp) cc_final: 0.5438 (ttp) REVERT: K 40 MET cc_start: 0.8932 (mtp) cc_final: 0.8549 (mtp) REVERT: K 192 GLU cc_start: 0.8064 (pt0) cc_final: 0.7769 (pt0) REVERT: K 194 GLU cc_start: 0.8017 (pp20) cc_final: 0.7696 (pp20) REVERT: K 244 GLU cc_start: 0.7336 (tp30) cc_final: 0.6433 (tp30) REVERT: K 286 GLU cc_start: 0.8391 (tp30) cc_final: 0.8128 (tp30) REVERT: K 309 GLU cc_start: 0.8388 (tt0) cc_final: 0.8141 (mm-30) REVERT: K 357 GLU cc_start: 0.7043 (tm-30) cc_final: 0.6685 (tm-30) REVERT: K 449 GLU cc_start: 0.8591 (tp30) cc_final: 0.7937 (tp30) REVERT: M 192 GLU cc_start: 0.8364 (pt0) cc_final: 0.8113 (pt0) REVERT: M 286 GLU cc_start: 0.8427 (tp30) cc_final: 0.8197 (tp30) REVERT: M 341 SER cc_start: 0.8197 (t) cc_final: 0.7587 (p) REVERT: M 428 ASP cc_start: 0.8826 (m-30) cc_final: 0.8081 (m-30) REVERT: O 40 MET cc_start: 0.9022 (mtp) cc_final: 0.8816 (mtp) REVERT: O 207 TYR cc_start: 0.8669 (m-80) cc_final: 0.8382 (m-80) REVERT: O 341 SER cc_start: 0.8744 (t) cc_final: 0.8285 (t) REVERT: O 357 GLU cc_start: 0.7263 (tm-30) cc_final: 0.6336 (tm-30) REVERT: O 360 ASN cc_start: 0.9183 (m-40) cc_final: 0.8915 (m110) REVERT: O 428 ASP cc_start: 0.8758 (m-30) cc_final: 0.8416 (m-30) REVERT: Q 68 ASN cc_start: 0.9434 (t0) cc_final: 0.9223 (t0) REVERT: Q 334 MET cc_start: 0.9463 (mmp) cc_final: 0.9224 (mmm) REVERT: Q 341 SER cc_start: 0.8670 (t) cc_final: 0.8393 (t) REVERT: Q 1089 TYR cc_start: 0.8793 (t80) cc_final: 0.8355 (t80) REVERT: S 1 MET cc_start: 0.5813 (ttp) cc_final: 0.5481 (ttp) REVERT: S 235 ASP cc_start: 0.7800 (t70) cc_final: 0.7452 (t70) REVERT: S 348 MET cc_start: 0.9042 (tpt) cc_final: 0.8831 (tpp) REVERT: S 377 ARG cc_start: 0.9068 (mmp80) cc_final: 0.8688 (mmp-170) REVERT: S 1072 ASP cc_start: 0.7745 (p0) cc_final: 0.7530 (p0) REVERT: V 1 MET cc_start: 0.6268 (ttp) cc_final: 0.5705 (ttp) REVERT: V 192 GLU cc_start: 0.7990 (pt0) cc_final: 0.7716 (pt0) REVERT: V 237 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8219 (mp0) REVERT: V 286 GLU cc_start: 0.7994 (tp30) cc_final: 0.7775 (tp30) REVERT: V 334 MET cc_start: 0.9448 (mmp) cc_final: 0.9090 (mmm) REVERT: V 341 SER cc_start: 0.8751 (t) cc_final: 0.8485 (t) REVERT: V 1089 TYR cc_start: 0.8514 (t80) cc_final: 0.7942 (t80) REVERT: X 140 MET cc_start: 0.9603 (mmm) cc_final: 0.9231 (mmm) REVERT: X 237 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7212 (mt-10) REVERT: X 309 GLU cc_start: 0.8486 (tt0) cc_final: 0.7880 (mm-30) REVERT: X 436 MET cc_start: 0.8733 (ttp) cc_final: 0.8477 (ttm) REVERT: X 446 LYS cc_start: 0.8518 (mttp) cc_final: 0.8262 (mttp) REVERT: X 456 SER cc_start: 0.8965 (p) cc_final: 0.8729 (p) outliers start: 113 outliers final: 42 residues processed: 772 average time/residue: 1.4722 time to fit residues: 1466.8465 Evaluate side-chains 685 residues out of total 5520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 637 time to evaluate : 6.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 GLU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 263 ASN Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 424 MET Chi-restraints excluded: chain E residue 7 MET Chi-restraints excluded: chain E residue 322 GLU Chi-restraints excluded: chain E residue 426 THR Chi-restraints excluded: chain E residue 435 SER Chi-restraints excluded: chain G residue 100 ARG Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain G residue 237 GLU Chi-restraints excluded: chain G residue 399 ILE Chi-restraints excluded: chain G residue 426 THR Chi-restraints excluded: chain G residue 1104 VAL Chi-restraints excluded: chain I residue 143 GLU Chi-restraints excluded: chain I residue 195 LEU Chi-restraints excluded: chain I residue 247 ARG Chi-restraints excluded: chain I residue 263 ASN Chi-restraints excluded: chain I residue 264 LEU Chi-restraints excluded: chain I residue 358 ASN Chi-restraints excluded: chain I residue 388 LEU Chi-restraints excluded: chain I residue 399 ILE Chi-restraints excluded: chain K residue 399 ILE Chi-restraints excluded: chain M residue 165 LEU Chi-restraints excluded: chain M residue 195 LEU Chi-restraints excluded: chain M residue 237 GLU Chi-restraints excluded: chain M residue 435 SER Chi-restraints excluded: chain M residue 1104 VAL Chi-restraints excluded: chain O residue 195 LEU Chi-restraints excluded: chain O residue 322 GLU Chi-restraints excluded: chain O residue 332 ILE Chi-restraints excluded: chain O residue 358 ASN Chi-restraints excluded: chain O residue 388 LEU Chi-restraints excluded: chain Q residue 195 LEU Chi-restraints excluded: chain Q residue 388 LEU Chi-restraints excluded: chain S residue 88 SER Chi-restraints excluded: chain S residue 239 ILE Chi-restraints excluded: chain S residue 244 GLU Chi-restraints excluded: chain S residue 426 THR Chi-restraints excluded: chain V residue 7 MET Chi-restraints excluded: chain V residue 195 LEU Chi-restraints excluded: chain V residue 237 GLU Chi-restraints excluded: chain V residue 258 SER Chi-restraints excluded: chain X residue 96 SER Chi-restraints excluded: chain X residue 237 GLU Chi-restraints excluded: chain X residue 358 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 560 optimal weight: 0.1980 chunk 426 optimal weight: 0.4980 chunk 294 optimal weight: 8.9990 chunk 62 optimal weight: 2.9990 chunk 270 optimal weight: 0.8980 chunk 381 optimal weight: 0.6980 chunk 569 optimal weight: 8.9990 chunk 603 optimal weight: 0.8980 chunk 297 optimal weight: 1.9990 chunk 539 optimal weight: 6.9990 chunk 162 optimal weight: 5.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 HIS ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 ASN ** C 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1075 HIS ** G 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 34 ASN I 431 ASN I1075 HIS ** K 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1071 ASN ** M 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 346 HIS O 431 ASN Q1075 HIS S 34 ASN V1071 ASN X 168 HIS X 431 ASN ** X1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 50328 Z= 0.159 Angle : 0.545 9.904 68088 Z= 0.277 Chirality : 0.045 0.177 7560 Planarity : 0.004 0.044 8820 Dihedral : 4.904 37.749 6674 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 2.05 % Allowed : 12.57 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.10), residues: 6252 helix: 1.97 (0.14), residues: 1536 sheet: -0.80 (0.13), residues: 1488 loop : -1.38 (0.10), residues: 3228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.000 TRP O 125 HIS 0.008 0.001 HIS E 93 PHE 0.018 0.001 PHE K1094 TYR 0.011 0.001 TYR I 120 ARG 0.004 0.000 ARG Q 100 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 808 residues out of total 5520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 695 time to evaluate : 6.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5769 (ttp) cc_final: 0.5510 (ttt) REVERT: A 192 GLU cc_start: 0.8249 (pt0) cc_final: 0.7870 (pt0) REVERT: A 235 ASP cc_start: 0.7867 (t70) cc_final: 0.7558 (t70) REVERT: C 1 MET cc_start: 0.6129 (ttm) cc_final: 0.5905 (ttp) REVERT: C 192 GLU cc_start: 0.8162 (pt0) cc_final: 0.7538 (pt0) REVERT: C 263 ASN cc_start: 0.8156 (OUTLIER) cc_final: 0.7862 (m110) REVERT: C 341 SER cc_start: 0.7974 (t) cc_final: 0.7622 (t) REVERT: C 357 GLU cc_start: 0.7238 (tm-30) cc_final: 0.6878 (tm-30) REVERT: C 431 ASN cc_start: 0.9168 (m-40) cc_final: 0.8738 (m110) REVERT: E 192 GLU cc_start: 0.8487 (pt0) cc_final: 0.8198 (pt0) REVERT: E 286 GLU cc_start: 0.8350 (tp30) cc_final: 0.8096 (tp30) REVERT: E 357 GLU cc_start: 0.6885 (tm-30) cc_final: 0.6542 (tm-30) REVERT: G 17 ASP cc_start: 0.8785 (m-30) cc_final: 0.8555 (m-30) REVERT: G 140 MET cc_start: 0.9595 (mmm) cc_final: 0.9355 (mmm) REVERT: G 244 GLU cc_start: 0.7423 (tp30) cc_final: 0.7218 (tp30) REVERT: G 341 SER cc_start: 0.8632 (t) cc_final: 0.7760 (p) REVERT: I 142 GLU cc_start: 0.8053 (tt0) cc_final: 0.7792 (tt0) REVERT: I 237 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7423 (mt-10) REVERT: I 247 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.7762 (ptt90) REVERT: I 263 ASN cc_start: 0.8173 (OUTLIER) cc_final: 0.7958 (t0) REVERT: I 357 GLU cc_start: 0.7027 (tm-30) cc_final: 0.6720 (tm-30) REVERT: I 360 ASN cc_start: 0.9201 (m-40) cc_final: 0.8934 (m-40) REVERT: K 1 MET cc_start: 0.5897 (ttp) cc_final: 0.5510 (ttp) REVERT: K 40 MET cc_start: 0.8897 (mtp) cc_final: 0.8524 (mtp) REVERT: K 192 GLU cc_start: 0.8094 (pt0) cc_final: 0.7688 (pt0) REVERT: K 194 GLU cc_start: 0.7997 (pp20) cc_final: 0.7731 (pp20) REVERT: K 237 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.6929 (mt-10) REVERT: K 247 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.8263 (ptt90) REVERT: K 357 GLU cc_start: 0.6995 (tm-30) cc_final: 0.6580 (tm-30) REVERT: K 449 GLU cc_start: 0.8584 (tp30) cc_final: 0.7878 (tp30) REVERT: M 1 MET cc_start: 0.5868 (ttp) cc_final: 0.5425 (ttp) REVERT: M 192 GLU cc_start: 0.8334 (pt0) cc_final: 0.8132 (pt0) REVERT: M 247 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.8232 (ptt90) REVERT: M 341 SER cc_start: 0.8164 (t) cc_final: 0.7505 (p) REVERT: M 428 ASP cc_start: 0.8755 (m-30) cc_final: 0.7952 (m-30) REVERT: O 40 MET cc_start: 0.9014 (mtp) cc_final: 0.8733 (mtp) REVERT: O 194 GLU cc_start: 0.7420 (pp20) cc_final: 0.7209 (OUTLIER) REVERT: O 207 TYR cc_start: 0.8655 (m-80) cc_final: 0.8360 (m-10) REVERT: O 237 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8348 (mp0) REVERT: O 244 GLU cc_start: 0.7342 (tp30) cc_final: 0.6337 (tp30) REVERT: O 263 ASN cc_start: 0.8361 (OUTLIER) cc_final: 0.8100 (m-40) REVERT: O 357 GLU cc_start: 0.7191 (tm-30) cc_final: 0.6908 (tm-30) REVERT: Q 1 MET cc_start: 0.3389 (ttp) cc_final: 0.2716 (ttt) REVERT: Q 68 ASN cc_start: 0.9394 (t0) cc_final: 0.9165 (t0) REVERT: Q 244 GLU cc_start: 0.7770 (tp30) cc_final: 0.7415 (mm-30) REVERT: Q 247 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.8225 (ptt90) REVERT: Q 341 SER cc_start: 0.8768 (t) cc_final: 0.8352 (t) REVERT: Q 1072 ASP cc_start: 0.7924 (p0) cc_final: 0.7715 (p0) REVERT: Q 1089 TYR cc_start: 0.8752 (t80) cc_final: 0.8333 (t80) REVERT: Q 1103 PHE cc_start: 0.8678 (m-80) cc_final: 0.8412 (m-80) REVERT: S 1 MET cc_start: 0.5784 (ttp) cc_final: 0.5496 (ttp) REVERT: S 235 ASP cc_start: 0.7747 (t70) cc_final: 0.7373 (t70) REVERT: S 237 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.7327 (mt-10) REVERT: S 377 ARG cc_start: 0.9073 (mmp80) cc_final: 0.8713 (mmp-170) REVERT: S 1072 ASP cc_start: 0.7912 (p0) cc_final: 0.7395 (m-30) REVERT: S 1103 PHE cc_start: 0.8713 (m-80) cc_final: 0.8477 (m-80) REVERT: V 1 MET cc_start: 0.6204 (ttp) cc_final: 0.5639 (ttp) REVERT: V 192 GLU cc_start: 0.7999 (pt0) cc_final: 0.7746 (pt0) REVERT: V 237 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8148 (mp0) REVERT: V 309 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7880 (mm-30) REVERT: V 341 SER cc_start: 0.8746 (t) cc_final: 0.8488 (t) REVERT: V 1089 TYR cc_start: 0.8489 (t80) cc_final: 0.7791 (t80) REVERT: X 168 HIS cc_start: 0.8655 (m-70) cc_final: 0.8389 (m90) outliers start: 113 outliers final: 31 residues processed: 748 average time/residue: 1.4645 time to fit residues: 1407.7280 Evaluate side-chains 682 residues out of total 5520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 639 time to evaluate : 5.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain C residue 263 ASN Chi-restraints excluded: chain C residue 358 ASN Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 322 GLU Chi-restraints excluded: chain E residue 426 THR Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain G residue 399 ILE Chi-restraints excluded: chain G residue 426 THR Chi-restraints excluded: chain G residue 1104 VAL Chi-restraints excluded: chain I residue 143 GLU Chi-restraints excluded: chain I residue 195 LEU Chi-restraints excluded: chain I residue 237 GLU Chi-restraints excluded: chain I residue 247 ARG Chi-restraints excluded: chain I residue 263 ASN Chi-restraints excluded: chain I residue 358 ASN Chi-restraints excluded: chain I residue 388 LEU Chi-restraints excluded: chain K residue 237 GLU Chi-restraints excluded: chain K residue 247 ARG Chi-restraints excluded: chain K residue 329 LEU Chi-restraints excluded: chain K residue 399 ILE Chi-restraints excluded: chain M residue 165 LEU Chi-restraints excluded: chain M residue 247 ARG Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain O residue 96 SER Chi-restraints excluded: chain O residue 237 GLU Chi-restraints excluded: chain O residue 263 ASN Chi-restraints excluded: chain O residue 358 ASN Chi-restraints excluded: chain O residue 388 LEU Chi-restraints excluded: chain Q residue 195 LEU Chi-restraints excluded: chain Q residue 247 ARG Chi-restraints excluded: chain S residue 237 GLU Chi-restraints excluded: chain S residue 244 GLU Chi-restraints excluded: chain S residue 426 THR Chi-restraints excluded: chain V residue 195 LEU Chi-restraints excluded: chain V residue 237 GLU Chi-restraints excluded: chain V residue 258 SER Chi-restraints excluded: chain V residue 309 GLU Chi-restraints excluded: chain V residue 322 GLU Chi-restraints excluded: chain X residue 358 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 502 optimal weight: 10.0000 chunk 342 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 449 optimal weight: 0.9990 chunk 248 optimal weight: 0.6980 chunk 514 optimal weight: 4.9990 chunk 416 optimal weight: 30.0000 chunk 0 optimal weight: 30.0000 chunk 307 optimal weight: 4.9990 chunk 541 optimal weight: 3.9990 chunk 152 optimal weight: 5.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 HIS ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 431 ASN E1075 HIS ** G 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 126 HIS I1075 HIS ** M 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 126 HIS ** O 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 431 ASN Q 126 HIS Q1075 HIS S 360 ASN V 126 HIS ** V1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V1075 HIS X 431 ASN ** X1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 50328 Z= 0.246 Angle : 0.579 11.139 68088 Z= 0.293 Chirality : 0.046 0.185 7560 Planarity : 0.004 0.045 8820 Dihedral : 4.928 30.126 6674 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 1.96 % Allowed : 14.22 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.11), residues: 6252 helix: 2.13 (0.14), residues: 1536 sheet: -0.81 (0.13), residues: 1524 loop : -1.24 (0.10), residues: 3192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 125 HIS 0.010 0.001 HIS A 154 PHE 0.019 0.001 PHE S 18 TYR 0.012 0.001 TYR M 112 ARG 0.004 0.000 ARG K1107 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 755 residues out of total 5520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 647 time to evaluate : 6.295 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 1 MET cc_start: 0.5850 (ttp) cc_final: 0.5588 (ttt) REVERT: A 192 GLU cc_start: 0.8238 (pt0) cc_final: 0.7820 (pt0) REVERT: A 235 ASP cc_start: 0.7956 (t70) cc_final: 0.7639 (t70) REVERT: A 237 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7223 (mt-10) REVERT: A 244 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7842 (mm-30) REVERT: A 286 GLU cc_start: 0.8467 (tp30) cc_final: 0.8196 (tp30) REVERT: A 1072 ASP cc_start: 0.7851 (p0) cc_final: 0.7165 (m-30) REVERT: C 140 MET cc_start: 0.9464 (OUTLIER) cc_final: 0.8205 (mmm) REVERT: C 192 GLU cc_start: 0.8183 (pt0) cc_final: 0.7529 (pt0) REVERT: C 237 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.7253 (mp0) REVERT: C 263 ASN cc_start: 0.8133 (OUTLIER) cc_final: 0.7860 (m110) REVERT: C 341 SER cc_start: 0.8018 (t) cc_final: 0.7673 (t) REVERT: C 357 GLU cc_start: 0.7482 (tm-30) cc_final: 0.7063 (tm-30) REVERT: E 192 GLU cc_start: 0.8510 (pt0) cc_final: 0.8160 (pt0) REVERT: E 194 GLU cc_start: 0.7614 (pp20) cc_final: 0.7355 (pp20) REVERT: E 247 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.8003 (ptt90) REVERT: E 286 GLU cc_start: 0.8368 (tp30) cc_final: 0.8121 (tp30) REVERT: E 357 GLU cc_start: 0.7071 (tm-30) cc_final: 0.6797 (tm-30) REVERT: G 17 ASP cc_start: 0.8770 (m-30) cc_final: 0.8550 (m-30) REVERT: G 140 MET cc_start: 0.9564 (mmm) cc_final: 0.9261 (mmm) REVERT: G 341 SER cc_start: 0.8653 (t) cc_final: 0.7819 (p) REVERT: I 247 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.7801 (ptt90) REVERT: K 1 MET cc_start: 0.5822 (ttp) cc_final: 0.5528 (ttp) REVERT: K 40 MET cc_start: 0.8923 (mtp) cc_final: 0.8521 (mtp) REVERT: K 192 GLU cc_start: 0.8198 (pt0) cc_final: 0.7678 (pt0) REVERT: K 357 GLU cc_start: 0.7206 (tm-30) cc_final: 0.6661 (tm-30) REVERT: K 449 GLU cc_start: 0.8634 (tp30) cc_final: 0.7959 (tp30) REVERT: M 1 MET cc_start: 0.5959 (ttp) cc_final: 0.5485 (ttp) REVERT: M 237 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.7615 (mp0) REVERT: M 247 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.8262 (ptt90) REVERT: M 341 SER cc_start: 0.8426 (t) cc_final: 0.7572 (t) REVERT: O 40 MET cc_start: 0.8997 (mtp) cc_final: 0.8716 (mtp) REVERT: O 207 TYR cc_start: 0.8702 (m-80) cc_final: 0.8372 (m-80) REVERT: O 237 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8405 (mp0) REVERT: O 244 GLU cc_start: 0.7508 (tp30) cc_final: 0.6771 (mm-30) REVERT: O 341 SER cc_start: 0.8787 (t) cc_final: 0.8329 (t) REVERT: O 357 GLU cc_start: 0.7326 (tm-30) cc_final: 0.7113 (tm-30) REVERT: O 428 ASP cc_start: 0.8768 (m-30) cc_final: 0.8426 (m-30) REVERT: Q 1 MET cc_start: 0.3698 (ttp) cc_final: 0.3069 (ttt) REVERT: Q 68 ASN cc_start: 0.9418 (t0) cc_final: 0.9210 (t0) REVERT: Q 341 SER cc_start: 0.8880 (t) cc_final: 0.8469 (t) REVERT: Q 1072 ASP cc_start: 0.7962 (p0) cc_final: 0.7693 (p0) REVERT: S 1 MET cc_start: 0.5846 (ttp) cc_final: 0.5593 (ttp) REVERT: S 235 ASP cc_start: 0.7774 (t70) cc_final: 0.7370 (t70) REVERT: S 237 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.8226 (mp0) REVERT: S 377 ARG cc_start: 0.9117 (mmp80) cc_final: 0.8758 (mmp-170) REVERT: S 1072 ASP cc_start: 0.7923 (p0) cc_final: 0.7408 (m-30) REVERT: S 1103 PHE cc_start: 0.8578 (m-80) cc_final: 0.8241 (m-80) REVERT: V 1 MET cc_start: 0.6200 (ttp) cc_final: 0.5565 (ttp) REVERT: V 192 GLU cc_start: 0.8125 (pt0) cc_final: 0.7897 (pt0) REVERT: V 237 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.7194 (mp0) REVERT: V 309 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7903 (mm-30) REVERT: V 341 SER cc_start: 0.8814 (t) cc_final: 0.8548 (t) REVERT: V 1089 TYR cc_start: 0.8424 (t80) cc_final: 0.7702 (t80) REVERT: X 168 HIS cc_start: 0.8749 (m-70) cc_final: 0.8473 (m90) REVERT: X 309 GLU cc_start: 0.8344 (mt-10) cc_final: 0.7990 (mm-30) outliers start: 108 outliers final: 43 residues processed: 697 average time/residue: 1.4984 time to fit residues: 1332.6619 Evaluate side-chains 655 residues out of total 5520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 600 time to evaluate : 5.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain C residue 263 ASN Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 358 ASN Chi-restraints excluded: chain C residue 399 ILE Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 247 ARG Chi-restraints excluded: chain E residue 322 GLU Chi-restraints excluded: chain E residue 426 THR Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain G residue 388 LEU Chi-restraints excluded: chain G residue 399 ILE Chi-restraints excluded: chain G residue 426 THR Chi-restraints excluded: chain G residue 1104 VAL Chi-restraints excluded: chain G residue 1105 LEU Chi-restraints excluded: chain I residue 143 GLU Chi-restraints excluded: chain I residue 195 LEU Chi-restraints excluded: chain I residue 247 ARG Chi-restraints excluded: chain I residue 329 LEU Chi-restraints excluded: chain I residue 358 ASN Chi-restraints excluded: chain I residue 388 LEU Chi-restraints excluded: chain I residue 399 ILE Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 329 LEU Chi-restraints excluded: chain K residue 399 ILE Chi-restraints excluded: chain M residue 165 LEU Chi-restraints excluded: chain M residue 237 GLU Chi-restraints excluded: chain M residue 247 ARG Chi-restraints excluded: chain M residue 357 GLU Chi-restraints excluded: chain M residue 1104 VAL Chi-restraints excluded: chain O residue 96 SER Chi-restraints excluded: chain O residue 237 GLU Chi-restraints excluded: chain O residue 358 ASN Chi-restraints excluded: chain O residue 388 LEU Chi-restraints excluded: chain S residue 237 GLU Chi-restraints excluded: chain S residue 244 GLU Chi-restraints excluded: chain S residue 359 SER Chi-restraints excluded: chain S residue 426 THR Chi-restraints excluded: chain V residue 237 GLU Chi-restraints excluded: chain V residue 309 GLU Chi-restraints excluded: chain V residue 1105 LEU Chi-restraints excluded: chain X residue 96 SER Chi-restraints excluded: chain X residue 142 GLU Chi-restraints excluded: chain X residue 244 GLU Chi-restraints excluded: chain X residue 426 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 202 optimal weight: 4.9990 chunk 543 optimal weight: 5.9990 chunk 119 optimal weight: 0.6980 chunk 354 optimal weight: 0.9980 chunk 148 optimal weight: 0.8980 chunk 603 optimal weight: 0.9990 chunk 501 optimal weight: 4.9990 chunk 279 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 199 optimal weight: 3.9990 chunk 316 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 HIS A 168 HIS ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 34 ASN E1075 HIS ** G 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1075 HIS ** M 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 431 ASN Q1075 HIS ** V1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V1075 HIS X1071 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 50328 Z= 0.207 Angle : 0.569 12.114 68088 Z= 0.287 Chirality : 0.045 0.185 7560 Planarity : 0.004 0.045 8820 Dihedral : 4.831 29.191 6672 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 2.05 % Allowed : 14.93 % Favored : 83.03 % 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: -0.37 (0.11), residues: 6252 helix: 2.22 (0.14), residues: 1536 sheet: -0.79 (0.12), residues: 1572 loop : -1.22 (0.11), residues: 3144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 125 HIS 0.008 0.001 HIS A 154 PHE 0.019 0.001 PHE V1094 TYR 0.010 0.001 TYR M 112 ARG 0.004 0.000 ARG I 319 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 768 residues out of total 5520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 655 time to evaluate : 6.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5993 (ttp) cc_final: 0.5784 (ttt) REVERT: A 192 GLU cc_start: 0.8227 (pt0) cc_final: 0.7787 (pt0) REVERT: A 235 ASP cc_start: 0.7940 (t70) cc_final: 0.7608 (t70) REVERT: A 237 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7212 (mt-10) REVERT: A 244 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7849 (mm-30) REVERT: A 286 GLU cc_start: 0.8452 (tp30) cc_final: 0.8221 (tp30) REVERT: A 344 MET cc_start: 0.8932 (mmm) cc_final: 0.8713 (mmm) REVERT: A 1072 ASP cc_start: 0.7770 (p0) cc_final: 0.7074 (m-30) REVERT: C 192 GLU cc_start: 0.8161 (pt0) cc_final: 0.7533 (pt0) REVERT: C 263 ASN cc_start: 0.8173 (OUTLIER) cc_final: 0.7946 (m110) REVERT: C 341 SER cc_start: 0.8042 (t) cc_final: 0.7691 (t) REVERT: C 357 GLU cc_start: 0.7581 (tm-30) cc_final: 0.7117 (tm-30) REVERT: C 431 ASN cc_start: 0.9279 (m-40) cc_final: 0.8838 (m-40) REVERT: E 192 GLU cc_start: 0.8536 (pt0) cc_final: 0.8146 (pt0) REVERT: E 247 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.8004 (ptt90) REVERT: E 286 GLU cc_start: 0.8348 (tp30) cc_final: 0.8136 (tp30) REVERT: E 357 GLU cc_start: 0.7074 (tm-30) cc_final: 0.6778 (tm-30) REVERT: G 17 ASP cc_start: 0.8738 (m-30) cc_final: 0.8483 (m-30) REVERT: G 140 MET cc_start: 0.9571 (mmm) cc_final: 0.9259 (mmm) REVERT: G 341 SER cc_start: 0.8644 (t) cc_final: 0.7812 (p) REVERT: G 399 ILE cc_start: 0.9234 (OUTLIER) cc_final: 0.8995 (pp) REVERT: I 142 GLU cc_start: 0.8046 (tt0) cc_final: 0.7744 (tt0) REVERT: I 237 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7317 (mt-10) REVERT: I 247 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.7833 (ptt90) REVERT: I 357 GLU cc_start: 0.7328 (tm-30) cc_final: 0.6867 (tm-30) REVERT: K 1 MET cc_start: 0.5719 (ttp) cc_final: 0.5338 (ttp) REVERT: K 40 MET cc_start: 0.8916 (mtp) cc_final: 0.8538 (mtp) REVERT: K 192 GLU cc_start: 0.8202 (pt0) cc_final: 0.7659 (pt0) REVERT: K 237 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.6662 (mt-10) REVERT: M 192 GLU cc_start: 0.8203 (pt0) cc_final: 0.7935 (pt0) REVERT: M 235 ASP cc_start: 0.7875 (t70) cc_final: 0.7548 (t70) REVERT: M 237 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.7484 (mp0) REVERT: M 247 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.8235 (ptt90) REVERT: M 334 MET cc_start: 0.9491 (mmp) cc_final: 0.9174 (mmp) REVERT: M 341 SER cc_start: 0.8256 (t) cc_final: 0.7985 (t) REVERT: O 40 MET cc_start: 0.8998 (mtp) cc_final: 0.8682 (mtp) REVERT: O 207 TYR cc_start: 0.8691 (m-80) cc_final: 0.8327 (m-80) REVERT: O 237 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8400 (mp0) REVERT: O 244 GLU cc_start: 0.7758 (tp30) cc_final: 0.7004 (mm-30) REVERT: O 341 SER cc_start: 0.8887 (t) cc_final: 0.8580 (t) REVERT: O 357 GLU cc_start: 0.7296 (tm-30) cc_final: 0.6943 (tm-30) REVERT: Q 1 MET cc_start: 0.3500 (ttp) cc_final: 0.2893 (ttt) REVERT: Q 68 ASN cc_start: 0.9408 (t0) cc_final: 0.9196 (t0) REVERT: Q 88 SER cc_start: 0.9278 (OUTLIER) cc_final: 0.8937 (p) REVERT: Q 244 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7736 (mm-30) REVERT: Q 341 SER cc_start: 0.8877 (t) cc_final: 0.8457 (t) REVERT: Q 1072 ASP cc_start: 0.7942 (p0) cc_final: 0.7699 (p0) REVERT: S 1 MET cc_start: 0.5796 (ttp) cc_final: 0.5553 (ttp) REVERT: S 235 ASP cc_start: 0.7754 (t70) cc_final: 0.7328 (t70) REVERT: S 237 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8217 (mp0) REVERT: S 377 ARG cc_start: 0.9123 (mmp80) cc_final: 0.8753 (mmp-170) REVERT: S 1072 ASP cc_start: 0.7978 (p0) cc_final: 0.7414 (m-30) REVERT: S 1103 PHE cc_start: 0.8590 (m-80) cc_final: 0.8304 (m-80) REVERT: V 1 MET cc_start: 0.6114 (ttp) cc_final: 0.5580 (ttp) REVERT: V 194 GLU cc_start: 0.7247 (pp20) cc_final: 0.6788 (pp20) REVERT: V 237 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.7191 (mp0) REVERT: V 309 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7938 (mm-30) REVERT: V 341 SER cc_start: 0.8810 (t) cc_final: 0.8544 (t) REVERT: V 1089 TYR cc_start: 0.8409 (t80) cc_final: 0.7705 (t80) REVERT: X 168 HIS cc_start: 0.8757 (m-70) cc_final: 0.8441 (m90) REVERT: X 286 GLU cc_start: 0.8360 (tp30) cc_final: 0.8158 (tp30) REVERT: X 309 GLU cc_start: 0.8338 (mt-10) cc_final: 0.8045 (mm-30) outliers start: 113 outliers final: 48 residues processed: 714 average time/residue: 1.4937 time to fit residues: 1368.1503 Evaluate side-chains 668 residues out of total 5520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 606 time to evaluate : 5.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 263 ASN Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 358 ASN Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 247 ARG Chi-restraints excluded: chain E residue 322 GLU Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain E residue 426 THR Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain G residue 388 LEU Chi-restraints excluded: chain G residue 399 ILE Chi-restraints excluded: chain G residue 426 THR Chi-restraints excluded: chain G residue 1104 VAL Chi-restraints excluded: chain G residue 1105 LEU Chi-restraints excluded: chain I residue 143 GLU Chi-restraints excluded: chain I residue 195 LEU Chi-restraints excluded: chain I residue 237 GLU Chi-restraints excluded: chain I residue 247 ARG Chi-restraints excluded: chain I residue 329 LEU Chi-restraints excluded: chain I residue 358 ASN Chi-restraints excluded: chain I residue 388 LEU Chi-restraints excluded: chain I residue 399 ILE Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 237 GLU Chi-restraints excluded: chain K residue 329 LEU Chi-restraints excluded: chain K residue 399 ILE Chi-restraints excluded: chain M residue 57 ILE Chi-restraints excluded: chain M residue 165 LEU Chi-restraints excluded: chain M residue 237 GLU Chi-restraints excluded: chain M residue 247 ARG Chi-restraints excluded: chain M residue 357 GLU Chi-restraints excluded: chain M residue 1104 VAL Chi-restraints excluded: chain O residue 96 SER Chi-restraints excluded: chain O residue 237 GLU Chi-restraints excluded: chain O residue 358 ASN Chi-restraints excluded: chain O residue 388 LEU Chi-restraints excluded: chain Q residue 88 SER Chi-restraints excluded: chain Q residue 195 LEU Chi-restraints excluded: chain S residue 237 GLU Chi-restraints excluded: chain S residue 244 GLU Chi-restraints excluded: chain S residue 359 SER Chi-restraints excluded: chain S residue 426 THR Chi-restraints excluded: chain V residue 7 MET Chi-restraints excluded: chain V residue 237 GLU Chi-restraints excluded: chain V residue 258 SER Chi-restraints excluded: chain V residue 309 GLU Chi-restraints excluded: chain V residue 426 THR Chi-restraints excluded: chain X residue 96 SER Chi-restraints excluded: chain X residue 142 GLU Chi-restraints excluded: chain X residue 244 GLU Chi-restraints excluded: chain X residue 261 LEU Chi-restraints excluded: chain X residue 426 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 582 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 343 optimal weight: 0.4980 chunk 440 optimal weight: 2.9990 chunk 341 optimal weight: 1.9990 chunk 508 optimal weight: 0.9990 chunk 337 optimal weight: 0.6980 chunk 601 optimal weight: 5.9990 chunk 376 optimal weight: 1.9990 chunk 366 optimal weight: 3.9990 chunk 277 optimal weight: 6.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 346 HIS ** C1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1075 HIS ** G 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 34 ASN I1075 HIS K 346 HIS M 34 ASN ** M 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 431 ASN Q1075 HIS ** V1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V1075 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 50328 Z= 0.202 Angle : 0.570 12.779 68088 Z= 0.287 Chirality : 0.045 0.185 7560 Planarity : 0.004 0.044 8820 Dihedral : 4.783 28.937 6672 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 1.97 % Allowed : 15.29 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.11), residues: 6252 helix: 2.27 (0.14), residues: 1536 sheet: -0.73 (0.13), residues: 1500 loop : -1.15 (0.10), residues: 3216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 125 HIS 0.008 0.001 HIS Q 154 PHE 0.019 0.001 PHE V1094 TYR 0.010 0.001 TYR M 112 ARG 0.003 0.000 ARG I 319 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 761 residues out of total 5520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 652 time to evaluate : 5.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 GLU cc_start: 0.8246 (pt0) cc_final: 0.7700 (pt0) REVERT: A 235 ASP cc_start: 0.7978 (t70) cc_final: 0.7639 (t70) REVERT: A 244 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7762 (mm-30) REVERT: A 428 ASP cc_start: 0.8749 (m-30) cc_final: 0.8411 (m-30) REVERT: A 1072 ASP cc_start: 0.7747 (p0) cc_final: 0.7078 (m-30) REVERT: C 192 GLU cc_start: 0.8115 (pt0) cc_final: 0.7521 (pt0) REVERT: C 235 ASP cc_start: 0.8061 (t70) cc_final: 0.7830 (t70) REVERT: C 237 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7097 (mp0) REVERT: C 263 ASN cc_start: 0.8206 (OUTLIER) cc_final: 0.7996 (m110) REVERT: C 341 SER cc_start: 0.8041 (t) cc_final: 0.7692 (t) REVERT: C 357 GLU cc_start: 0.7599 (tm-30) cc_final: 0.7215 (tm-30) REVERT: C 379 THR cc_start: 0.8662 (OUTLIER) cc_final: 0.8462 (t) REVERT: E 192 GLU cc_start: 0.8501 (pt0) cc_final: 0.8221 (pt0) REVERT: E 244 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7843 (mm-30) REVERT: E 247 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.8008 (ptt90) REVERT: E 357 GLU cc_start: 0.7130 (tm-30) cc_final: 0.6831 (tm-30) REVERT: G 17 ASP cc_start: 0.8720 (m-30) cc_final: 0.8492 (m-30) REVERT: G 140 MET cc_start: 0.9577 (mmm) cc_final: 0.9227 (mmm) REVERT: G 341 SER cc_start: 0.8621 (t) cc_final: 0.7790 (p) REVERT: G 377 ARG cc_start: 0.9142 (mmp80) cc_final: 0.8842 (mmp80) REVERT: G 399 ILE cc_start: 0.9222 (OUTLIER) cc_final: 0.8989 (pp) REVERT: I 142 GLU cc_start: 0.8016 (tt0) cc_final: 0.7744 (tt0) REVERT: I 247 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.7838 (ptt90) REVERT: I 341 SER cc_start: 0.9004 (t) cc_final: 0.8750 (t) REVERT: I 357 GLU cc_start: 0.7268 (tm-30) cc_final: 0.6874 (tm-30) REVERT: K 1 MET cc_start: 0.5714 (ttp) cc_final: 0.5384 (ttp) REVERT: K 40 MET cc_start: 0.8912 (mtp) cc_final: 0.8523 (mtp) REVERT: K 192 GLU cc_start: 0.8203 (pt0) cc_final: 0.7813 (pt0) REVERT: M 192 GLU cc_start: 0.8376 (pt0) cc_final: 0.8117 (pt0) REVERT: M 235 ASP cc_start: 0.7878 (t70) cc_final: 0.7537 (t70) REVERT: M 247 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.8192 (ptt90) REVERT: M 334 MET cc_start: 0.9408 (mmp) cc_final: 0.9134 (mmp) REVERT: O 40 MET cc_start: 0.9000 (mtp) cc_final: 0.8700 (mtp) REVERT: O 207 TYR cc_start: 0.8690 (m-80) cc_final: 0.8276 (m-80) REVERT: O 237 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8454 (mp0) REVERT: O 244 GLU cc_start: 0.7818 (tp30) cc_final: 0.7014 (mm-30) REVERT: O 263 ASN cc_start: 0.8351 (m-40) cc_final: 0.7862 (m110) REVERT: O 341 SER cc_start: 0.8919 (t) cc_final: 0.8497 (t) REVERT: O 357 GLU cc_start: 0.7246 (tm-30) cc_final: 0.6876 (tm-30) REVERT: O 428 ASP cc_start: 0.8761 (m-30) cc_final: 0.8496 (m-30) REVERT: Q 1 MET cc_start: 0.3507 (ttp) cc_final: 0.2973 (ttt) REVERT: Q 68 ASN cc_start: 0.9399 (t0) cc_final: 0.9179 (t0) REVERT: Q 88 SER cc_start: 0.9281 (OUTLIER) cc_final: 0.8942 (p) REVERT: Q 244 GLU cc_start: 0.8281 (mm-30) cc_final: 0.7825 (mm-30) REVERT: Q 341 SER cc_start: 0.8901 (t) cc_final: 0.8493 (t) REVERT: Q 1072 ASP cc_start: 0.7906 (p0) cc_final: 0.7660 (p0) REVERT: S 1 MET cc_start: 0.5908 (ttp) cc_final: 0.5685 (ttp) REVERT: S 168 HIS cc_start: 0.8728 (m90) cc_final: 0.8383 (m90) REVERT: S 235 ASP cc_start: 0.7744 (t70) cc_final: 0.7334 (t70) REVERT: S 237 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.7455 (mt-10) REVERT: S 357 GLU cc_start: 0.7413 (tm-30) cc_final: 0.6995 (tm-30) REVERT: S 377 ARG cc_start: 0.9120 (mmp80) cc_final: 0.8754 (mmp-170) REVERT: S 1072 ASP cc_start: 0.7989 (p0) cc_final: 0.7424 (m-30) REVERT: S 1103 PHE cc_start: 0.8604 (m-80) cc_final: 0.8367 (m-80) REVERT: V 1 MET cc_start: 0.6143 (ttp) cc_final: 0.5647 (ttp) REVERT: V 192 GLU cc_start: 0.8085 (pt0) cc_final: 0.7704 (pt0) REVERT: V 194 GLU cc_start: 0.7254 (pp20) cc_final: 0.6664 (pp20) REVERT: V 237 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.7192 (mp0) REVERT: V 309 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7892 (mm-30) REVERT: V 341 SER cc_start: 0.8813 (t) cc_final: 0.8533 (t) REVERT: V 1089 TYR cc_start: 0.8447 (t80) cc_final: 0.7745 (t80) REVERT: X 168 HIS cc_start: 0.8784 (m-70) cc_final: 0.8441 (m90) outliers start: 109 outliers final: 47 residues processed: 713 average time/residue: 1.5307 time to fit residues: 1392.8788 Evaluate side-chains 673 residues out of total 5520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 614 time to evaluate : 6.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 263 ASN Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 247 ARG Chi-restraints excluded: chain E residue 322 GLU Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain E residue 426 THR Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain G residue 388 LEU Chi-restraints excluded: chain G residue 399 ILE Chi-restraints excluded: chain G residue 426 THR Chi-restraints excluded: chain G residue 1104 VAL Chi-restraints excluded: chain G residue 1105 LEU Chi-restraints excluded: chain I residue 143 GLU Chi-restraints excluded: chain I residue 195 LEU Chi-restraints excluded: chain I residue 247 ARG Chi-restraints excluded: chain I residue 329 LEU Chi-restraints excluded: chain I residue 358 ASN Chi-restraints excluded: chain I residue 388 LEU Chi-restraints excluded: chain I residue 399 ILE Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 399 ILE Chi-restraints excluded: chain M residue 57 ILE Chi-restraints excluded: chain M residue 165 LEU Chi-restraints excluded: chain M residue 247 ARG Chi-restraints excluded: chain M residue 357 GLU Chi-restraints excluded: chain M residue 1104 VAL Chi-restraints excluded: chain O residue 96 SER Chi-restraints excluded: chain O residue 237 GLU Chi-restraints excluded: chain O residue 264 LEU Chi-restraints excluded: chain O residue 358 ASN Chi-restraints excluded: chain O residue 388 LEU Chi-restraints excluded: chain Q residue 88 SER Chi-restraints excluded: chain Q residue 96 SER Chi-restraints excluded: chain Q residue 142 GLU Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 88 SER Chi-restraints excluded: chain S residue 237 GLU Chi-restraints excluded: chain S residue 244 GLU Chi-restraints excluded: chain S residue 359 SER Chi-restraints excluded: chain S residue 426 THR Chi-restraints excluded: chain V residue 237 GLU Chi-restraints excluded: chain V residue 309 GLU Chi-restraints excluded: chain V residue 426 THR Chi-restraints excluded: chain X residue 96 SER Chi-restraints excluded: chain X residue 142 GLU Chi-restraints excluded: chain X residue 244 GLU Chi-restraints excluded: chain X residue 261 LEU Chi-restraints excluded: chain X residue 388 LEU Chi-restraints excluded: chain X residue 426 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 372 optimal weight: 0.9990 chunk 240 optimal weight: 0.0170 chunk 359 optimal weight: 8.9990 chunk 181 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 116 optimal weight: 0.6980 chunk 382 optimal weight: 3.9990 chunk 409 optimal weight: 4.9990 chunk 297 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 472 optimal weight: 0.6980 overall best weight: 0.6822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1075 HIS ** G 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1075 HIS ** M 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 431 ASN O1092 GLN Q1075 HIS S 85 ASN V1071 ASN V1075 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 50328 Z= 0.169 Angle : 0.569 12.116 68088 Z= 0.285 Chirality : 0.045 0.204 7560 Planarity : 0.004 0.043 8820 Dihedral : 4.708 28.190 6672 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 1.76 % Allowed : 15.96 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.11), residues: 6252 helix: 2.12 (0.14), residues: 1620 sheet: -0.89 (0.12), residues: 1572 loop : -1.12 (0.11), residues: 3060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.000 TRP A 125 HIS 0.011 0.001 HIS E 346 PHE 0.020 0.001 PHE V1094 TYR 0.009 0.001 TYR M 112 ARG 0.003 0.000 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 760 residues out of total 5520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 663 time to evaluate : 5.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 GLU cc_start: 0.8132 (pt0) cc_final: 0.7703 (pt0) REVERT: A 235 ASP cc_start: 0.7911 (t70) cc_final: 0.7590 (t70) REVERT: A 428 ASP cc_start: 0.8727 (m-30) cc_final: 0.8387 (m-30) REVERT: A 1072 ASP cc_start: 0.7713 (p0) cc_final: 0.6988 (m-30) REVERT: C 192 GLU cc_start: 0.7987 (pt0) cc_final: 0.7419 (pt0) REVERT: C 235 ASP cc_start: 0.8008 (t70) cc_final: 0.7771 (t70) REVERT: C 237 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7100 (mp0) REVERT: C 341 SER cc_start: 0.8059 (t) cc_final: 0.7715 (t) REVERT: C 357 GLU cc_start: 0.7552 (tm-30) cc_final: 0.7172 (tm-30) REVERT: C 431 ASN cc_start: 0.9276 (m-40) cc_final: 0.8949 (m-40) REVERT: E 192 GLU cc_start: 0.8504 (pt0) cc_final: 0.8223 (pt0) REVERT: E 247 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.7993 (ptt90) REVERT: E 357 GLU cc_start: 0.7103 (tm-30) cc_final: 0.6807 (tm-30) REVERT: E 1103 PHE cc_start: 0.8567 (m-80) cc_final: 0.8259 (m-80) REVERT: G 17 ASP cc_start: 0.8724 (m-30) cc_final: 0.8463 (m-30) REVERT: G 140 MET cc_start: 0.9592 (mmm) cc_final: 0.9266 (mmm) REVERT: G 341 SER cc_start: 0.8609 (t) cc_final: 0.7751 (p) REVERT: G 377 ARG cc_start: 0.9135 (mmp80) cc_final: 0.8833 (mmp80) REVERT: G 399 ILE cc_start: 0.9187 (OUTLIER) cc_final: 0.8985 (pp) REVERT: I 142 GLU cc_start: 0.7967 (tt0) cc_final: 0.7698 (tt0) REVERT: I 247 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.7830 (ptt90) REVERT: I 341 SER cc_start: 0.8966 (t) cc_final: 0.8645 (t) REVERT: I 357 GLU cc_start: 0.7229 (tm-30) cc_final: 0.6915 (tm-30) REVERT: K 1 MET cc_start: 0.5640 (ttp) cc_final: 0.5362 (ttp) REVERT: K 40 MET cc_start: 0.8915 (mtp) cc_final: 0.8581 (mtp) REVERT: M 1 MET cc_start: 0.5261 (ttp) cc_final: 0.4926 (ttp) REVERT: M 235 ASP cc_start: 0.7846 (t70) cc_final: 0.7507 (t70) REVERT: M 247 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.8173 (ptt90) REVERT: O 40 MET cc_start: 0.8998 (mtp) cc_final: 0.8697 (mtp) REVERT: O 207 TYR cc_start: 0.8670 (m-80) cc_final: 0.8272 (m-80) REVERT: O 244 GLU cc_start: 0.7870 (tp30) cc_final: 0.7112 (mm-30) REVERT: O 263 ASN cc_start: 0.8412 (m-40) cc_final: 0.7946 (m110) REVERT: O 357 GLU cc_start: 0.7184 (tm-30) cc_final: 0.6825 (tm-30) REVERT: Q 68 ASN cc_start: 0.9373 (t0) cc_final: 0.8970 (t0) REVERT: Q 88 SER cc_start: 0.9299 (OUTLIER) cc_final: 0.8954 (p) REVERT: Q 192 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7862 (pt0) REVERT: Q 244 GLU cc_start: 0.8285 (mm-30) cc_final: 0.7817 (mm-30) REVERT: Q 341 SER cc_start: 0.8897 (t) cc_final: 0.8498 (t) REVERT: Q 1072 ASP cc_start: 0.7847 (p0) cc_final: 0.7620 (p0) REVERT: S 1 MET cc_start: 0.5861 (ttp) cc_final: 0.5586 (ttp) REVERT: S 168 HIS cc_start: 0.8728 (m90) cc_final: 0.8359 (m90) REVERT: S 194 GLU cc_start: 0.7580 (pp20) cc_final: 0.7068 (pp20) REVERT: S 235 ASP cc_start: 0.7712 (t70) cc_final: 0.7300 (t70) REVERT: S 237 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.7432 (mt-10) REVERT: S 377 ARG cc_start: 0.9112 (mmp80) cc_final: 0.8752 (mmp-170) REVERT: S 1072 ASP cc_start: 0.7914 (p0) cc_final: 0.7401 (m-30) REVERT: V 1 MET cc_start: 0.6082 (ttp) cc_final: 0.5611 (ttp) REVERT: V 235 ASP cc_start: 0.7947 (t70) cc_final: 0.7657 (t70) REVERT: V 237 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.7144 (mp0) REVERT: V 309 GLU cc_start: 0.8230 (tt0) cc_final: 0.7826 (mm-30) REVERT: V 334 MET cc_start: 0.9361 (mmp) cc_final: 0.8975 (mmm) REVERT: V 341 SER cc_start: 0.8890 (t) cc_final: 0.8652 (t) REVERT: V 1089 TYR cc_start: 0.8489 (t80) cc_final: 0.7786 (t80) REVERT: V 1103 PHE cc_start: 0.8694 (m-80) cc_final: 0.8400 (m-80) REVERT: X 168 HIS cc_start: 0.8776 (m-70) cc_final: 0.8478 (m90) REVERT: X 192 GLU cc_start: 0.8243 (pt0) cc_final: 0.7763 (pm20) outliers start: 97 outliers final: 36 residues processed: 713 average time/residue: 1.4286 time to fit residues: 1315.0138 Evaluate side-chains 672 residues out of total 5520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 627 time to evaluate : 5.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 247 ARG Chi-restraints excluded: chain E residue 322 GLU Chi-restraints excluded: chain E residue 426 THR Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain G residue 388 LEU Chi-restraints excluded: chain G residue 399 ILE Chi-restraints excluded: chain G residue 426 THR Chi-restraints excluded: chain G residue 1104 VAL Chi-restraints excluded: chain G residue 1105 LEU Chi-restraints excluded: chain I residue 143 GLU Chi-restraints excluded: chain I residue 247 ARG Chi-restraints excluded: chain I residue 329 LEU Chi-restraints excluded: chain I residue 358 ASN Chi-restraints excluded: chain I residue 388 LEU Chi-restraints excluded: chain I residue 399 ILE Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 399 ILE Chi-restraints excluded: chain M residue 165 LEU Chi-restraints excluded: chain M residue 247 ARG Chi-restraints excluded: chain M residue 357 GLU Chi-restraints excluded: chain M residue 379 THR Chi-restraints excluded: chain M residue 1104 VAL Chi-restraints excluded: chain O residue 358 ASN Chi-restraints excluded: chain O residue 388 LEU Chi-restraints excluded: chain Q residue 88 SER Chi-restraints excluded: chain Q residue 142 GLU Chi-restraints excluded: chain Q residue 192 GLU Chi-restraints excluded: chain Q residue 442 MET Chi-restraints excluded: chain S residue 237 GLU Chi-restraints excluded: chain S residue 426 THR Chi-restraints excluded: chain V residue 237 GLU Chi-restraints excluded: chain V residue 426 THR Chi-restraints excluded: chain X residue 96 SER Chi-restraints excluded: chain X residue 244 GLU Chi-restraints excluded: chain X residue 261 LEU Chi-restraints excluded: chain X residue 388 LEU Chi-restraints excluded: chain X residue 426 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 547 optimal weight: 0.9990 chunk 576 optimal weight: 2.9990 chunk 525 optimal weight: 0.0170 chunk 560 optimal weight: 0.9980 chunk 337 optimal weight: 0.8980 chunk 244 optimal weight: 0.5980 chunk 440 optimal weight: 0.8980 chunk 171 optimal weight: 3.9990 chunk 506 optimal weight: 0.9990 chunk 530 optimal weight: 0.9990 chunk 558 optimal weight: 5.9990 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 4 HIS E1075 HIS ** G 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1075 HIS ** M 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 431 ASN Q1075 HIS V 114 GLN V1071 ASN V1075 HIS X 431 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 50328 Z= 0.171 Angle : 0.571 12.725 68088 Z= 0.286 Chirality : 0.045 0.190 7560 Planarity : 0.004 0.044 8820 Dihedral : 4.676 27.757 6672 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 1.49 % Allowed : 16.70 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.11), residues: 6252 helix: 2.17 (0.14), residues: 1620 sheet: -0.81 (0.13), residues: 1548 loop : -1.13 (0.11), residues: 3084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.000 TRP I 125 HIS 0.007 0.001 HIS A 154 PHE 0.021 0.001 PHE V1094 TYR 0.012 0.001 TYR M 112 ARG 0.006 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 745 residues out of total 5520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 663 time to evaluate : 5.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 MET cc_start: 0.9296 (mmp) cc_final: 0.8946 (mmp) REVERT: A 192 GLU cc_start: 0.8156 (pt0) cc_final: 0.7727 (pt0) REVERT: A 235 ASP cc_start: 0.7899 (t70) cc_final: 0.7604 (t70) REVERT: A 286 GLU cc_start: 0.8427 (tp30) cc_final: 0.8215 (tp30) REVERT: A 428 ASP cc_start: 0.8683 (m-30) cc_final: 0.8255 (m-30) REVERT: C 192 GLU cc_start: 0.7913 (pt0) cc_final: 0.7491 (pt0) REVERT: C 235 ASP cc_start: 0.8015 (t70) cc_final: 0.7791 (t70) REVERT: C 237 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7082 (mp0) REVERT: C 341 SER cc_start: 0.8054 (t) cc_final: 0.7705 (t) REVERT: C 357 GLU cc_start: 0.7514 (tm-30) cc_final: 0.7136 (tm-30) REVERT: C 379 THR cc_start: 0.8633 (OUTLIER) cc_final: 0.8409 (t) REVERT: E 140 MET cc_start: 0.9506 (mmp) cc_final: 0.9216 (mmp) REVERT: E 192 GLU cc_start: 0.8529 (pt0) cc_final: 0.8294 (pt0) REVERT: E 247 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.7983 (ptt90) REVERT: E 357 GLU cc_start: 0.7129 (tm-30) cc_final: 0.6839 (tm-30) REVERT: E 1103 PHE cc_start: 0.8568 (m-80) cc_final: 0.8222 (m-80) REVERT: G 17 ASP cc_start: 0.8697 (m-30) cc_final: 0.8422 (m-30) REVERT: G 140 MET cc_start: 0.9598 (mmm) cc_final: 0.9279 (mmm) REVERT: G 244 GLU cc_start: 0.6753 (tp30) cc_final: 0.6229 (tt0) REVERT: G 263 ASN cc_start: 0.8538 (OUTLIER) cc_final: 0.7960 (OUTLIER) REVERT: G 341 SER cc_start: 0.8541 (t) cc_final: 0.7712 (p) REVERT: G 377 ARG cc_start: 0.9141 (mmp80) cc_final: 0.8840 (mmp80) REVERT: G 399 ILE cc_start: 0.9164 (OUTLIER) cc_final: 0.8960 (pp) REVERT: G 441 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7978 (mt-10) REVERT: I 142 GLU cc_start: 0.7953 (tt0) cc_final: 0.7679 (tt0) REVERT: I 247 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.7861 (ptt90) REVERT: I 341 SER cc_start: 0.8977 (t) cc_final: 0.8661 (t) REVERT: I 357 GLU cc_start: 0.7191 (tm-30) cc_final: 0.6897 (tm-30) REVERT: K 1 MET cc_start: 0.5734 (ttp) cc_final: 0.5465 (ttp) REVERT: K 40 MET cc_start: 0.8899 (mtp) cc_final: 0.8560 (mtp) REVERT: M 1 MET cc_start: 0.4993 (ttp) cc_final: 0.4785 (ttp) REVERT: M 235 ASP cc_start: 0.7841 (t70) cc_final: 0.7520 (t70) REVERT: M 237 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.7439 (mp0) REVERT: M 244 GLU cc_start: 0.6825 (tp30) cc_final: 0.5934 (mm-30) REVERT: M 247 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.8147 (ptt90) REVERT: O 40 MET cc_start: 0.9005 (mtp) cc_final: 0.8725 (mtp) REVERT: O 207 TYR cc_start: 0.8686 (m-80) cc_final: 0.8288 (m-80) REVERT: O 244 GLU cc_start: 0.7936 (tp30) cc_final: 0.7147 (mm-30) REVERT: O 263 ASN cc_start: 0.8390 (m-40) cc_final: 0.7912 (m110) REVERT: O 334 MET cc_start: 0.9282 (mmp) cc_final: 0.8734 (mmp) REVERT: O 357 GLU cc_start: 0.7141 (tm-30) cc_final: 0.6773 (tm-30) REVERT: Q 1 MET cc_start: 0.3324 (ttp) cc_final: 0.2886 (ttt) REVERT: Q 68 ASN cc_start: 0.9365 (t0) cc_final: 0.8947 (t0) REVERT: Q 88 SER cc_start: 0.9290 (OUTLIER) cc_final: 0.8948 (p) REVERT: Q 192 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7853 (pt0) REVERT: Q 237 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.7796 (mt-10) REVERT: Q 244 GLU cc_start: 0.8221 (mm-30) cc_final: 0.7732 (mm-30) REVERT: Q 341 SER cc_start: 0.8904 (t) cc_final: 0.8523 (t) REVERT: Q 1072 ASP cc_start: 0.7822 (p0) cc_final: 0.7617 (p0) REVERT: Q 1089 TYR cc_start: 0.8872 (t80) cc_final: 0.8469 (t80) REVERT: S 1 MET cc_start: 0.5753 (ttp) cc_final: 0.5497 (ttp) REVERT: S 168 HIS cc_start: 0.8734 (m90) cc_final: 0.8396 (m90) REVERT: S 192 GLU cc_start: 0.8436 (pt0) cc_final: 0.8101 (pm20) REVERT: S 235 ASP cc_start: 0.7688 (t70) cc_final: 0.7263 (t70) REVERT: S 237 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.7327 (mt-10) REVERT: S 348 MET cc_start: 0.9066 (tpt) cc_final: 0.8837 (tpp) REVERT: S 1072 ASP cc_start: 0.7853 (p0) cc_final: 0.7224 (m-30) REVERT: V 1 MET cc_start: 0.6062 (ttp) cc_final: 0.5492 (ttp) REVERT: V 235 ASP cc_start: 0.7944 (t70) cc_final: 0.7658 (t70) REVERT: V 237 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.7132 (mp0) REVERT: V 309 GLU cc_start: 0.8193 (tt0) cc_final: 0.7773 (mm-30) REVERT: V 334 MET cc_start: 0.9345 (mmp) cc_final: 0.9081 (mmp) REVERT: V 341 SER cc_start: 0.8864 (t) cc_final: 0.8624 (t) REVERT: V 357 GLU cc_start: 0.7314 (tm-30) cc_final: 0.7089 (tm-30) REVERT: V 1089 TYR cc_start: 0.8509 (t80) cc_final: 0.7803 (t80) REVERT: V 1103 PHE cc_start: 0.8721 (m-80) cc_final: 0.8450 (m-80) REVERT: X 192 GLU cc_start: 0.8234 (pt0) cc_final: 0.7748 (pm20) outliers start: 82 outliers final: 42 residues processed: 711 average time/residue: 1.4545 time to fit residues: 1329.3150 Evaluate side-chains 682 residues out of total 5520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 628 time to evaluate : 5.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 247 ARG Chi-restraints excluded: chain E residue 322 GLU Chi-restraints excluded: chain E residue 426 THR Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain G residue 263 ASN Chi-restraints excluded: chain G residue 388 LEU Chi-restraints excluded: chain G residue 399 ILE Chi-restraints excluded: chain G residue 426 THR Chi-restraints excluded: chain G residue 1104 VAL Chi-restraints excluded: chain G residue 1105 LEU Chi-restraints excluded: chain I residue 143 GLU Chi-restraints excluded: chain I residue 195 LEU Chi-restraints excluded: chain I residue 247 ARG Chi-restraints excluded: chain I residue 329 LEU Chi-restraints excluded: chain I residue 358 ASN Chi-restraints excluded: chain I residue 388 LEU Chi-restraints excluded: chain I residue 399 ILE Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 263 ASN Chi-restraints excluded: chain K residue 329 LEU Chi-restraints excluded: chain K residue 399 ILE Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 165 LEU Chi-restraints excluded: chain M residue 237 GLU Chi-restraints excluded: chain M residue 247 ARG Chi-restraints excluded: chain M residue 357 GLU Chi-restraints excluded: chain M residue 1104 VAL Chi-restraints excluded: chain O residue 264 LEU Chi-restraints excluded: chain O residue 358 ASN Chi-restraints excluded: chain O residue 388 LEU Chi-restraints excluded: chain Q residue 88 SER Chi-restraints excluded: chain Q residue 192 GLU Chi-restraints excluded: chain Q residue 237 GLU Chi-restraints excluded: chain Q residue 442 MET Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 237 GLU Chi-restraints excluded: chain S residue 426 THR Chi-restraints excluded: chain V residue 237 GLU Chi-restraints excluded: chain V residue 426 THR Chi-restraints excluded: chain X residue 244 GLU Chi-restraints excluded: chain X residue 261 LEU Chi-restraints excluded: chain X residue 388 LEU Chi-restraints excluded: chain X residue 426 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 368 optimal weight: 3.9990 chunk 592 optimal weight: 10.0000 chunk 361 optimal weight: 20.0000 chunk 281 optimal weight: 0.9980 chunk 411 optimal weight: 9.9990 chunk 621 optimal weight: 8.9990 chunk 572 optimal weight: 20.0000 chunk 495 optimal weight: 3.9990 chunk 51 optimal weight: 0.0000 chunk 382 optimal weight: 0.5980 chunk 303 optimal weight: 0.7980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1075 HIS ** G 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1075 HIS M 114 GLN ** M 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 431 ASN Q1075 HIS V 360 ASN ** V 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V1075 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 50328 Z= 0.234 Angle : 0.602 12.856 68088 Z= 0.302 Chirality : 0.046 0.184 7560 Planarity : 0.004 0.042 8820 Dihedral : 4.778 30.026 6672 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 1.30 % Allowed : 17.26 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.11), residues: 6252 helix: 2.15 (0.14), residues: 1620 sheet: -0.73 (0.13), residues: 1500 loop : -1.12 (0.11), residues: 3132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP O 125 HIS 0.009 0.001 HIS A 154 PHE 0.021 0.001 PHE O1094 TYR 0.013 0.001 TYR M 112 ARG 0.008 0.000 ARG A1086 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 699 residues out of total 5520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 627 time to evaluate : 5.805 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: A 140 MET cc_start: 0.9312 (mmp) cc_final: 0.9078 (mmp) REVERT: A 192 GLU cc_start: 0.8237 (pt0) cc_final: 0.7787 (pt0) REVERT: A 235 ASP cc_start: 0.7961 (t70) cc_final: 0.7659 (t70) REVERT: A 286 GLU cc_start: 0.8434 (tp30) cc_final: 0.8217 (tp30) REVERT: A 428 ASP cc_start: 0.8693 (m-30) cc_final: 0.8291 (m-30) REVERT: C 192 GLU cc_start: 0.7978 (pt0) cc_final: 0.7599 (pt0) REVERT: C 235 ASP cc_start: 0.8030 (t70) cc_final: 0.7797 (t70) REVERT: C 237 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7120 (mp0) REVERT: C 286 GLU cc_start: 0.7996 (tp30) cc_final: 0.7089 (tp30) REVERT: C 341 SER cc_start: 0.8121 (t) cc_final: 0.7792 (t) REVERT: C 357 GLU cc_start: 0.7559 (tm-30) cc_final: 0.7161 (tm-30) REVERT: E 1 MET cc_start: 0.3471 (ttp) cc_final: 0.3018 (ttp) REVERT: E 140 MET cc_start: 0.9518 (mmp) cc_final: 0.9222 (mmp) REVERT: E 247 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.7955 (ptt90) REVERT: E 357 GLU cc_start: 0.7254 (tm-30) cc_final: 0.6958 (tm-30) REVERT: G 17 ASP cc_start: 0.8734 (m-30) cc_final: 0.8467 (m-30) REVERT: G 140 MET cc_start: 0.9581 (mmm) cc_final: 0.9229 (mmm) REVERT: G 341 SER cc_start: 0.8604 (t) cc_final: 0.7322 (p) REVERT: G 377 ARG cc_start: 0.9149 (mmp80) cc_final: 0.8850 (mmp80) REVERT: G 399 ILE cc_start: 0.9234 (OUTLIER) cc_final: 0.9008 (pp) REVERT: G 417 LYS cc_start: 0.8670 (tptm) cc_final: 0.8470 (tptp) REVERT: G 428 ASP cc_start: 0.8787 (m-30) cc_final: 0.7687 (m-30) REVERT: I 142 GLU cc_start: 0.8024 (tt0) cc_final: 0.7732 (tt0) REVERT: I 247 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.7861 (ptt90) REVERT: I 357 GLU cc_start: 0.7278 (tm-30) cc_final: 0.6956 (tm-30) REVERT: K 1 MET cc_start: 0.5753 (ttp) cc_final: 0.5485 (ttp) REVERT: K 40 MET cc_start: 0.8891 (mtp) cc_final: 0.8587 (mtp) REVERT: M 235 ASP cc_start: 0.7889 (t70) cc_final: 0.7560 (t70) REVERT: M 237 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.7463 (mp0) REVERT: M 247 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.8249 (ptt90) REVERT: O 207 TYR cc_start: 0.8715 (m-80) cc_final: 0.8268 (m-80) REVERT: O 244 GLU cc_start: 0.7999 (tp30) cc_final: 0.7165 (mm-30) REVERT: O 263 ASN cc_start: 0.8413 (m-40) cc_final: 0.8008 (m110) REVERT: O 357 GLU cc_start: 0.7200 (tm-30) cc_final: 0.6841 (tm-30) REVERT: Q 68 ASN cc_start: 0.9400 (t0) cc_final: 0.9177 (t0) REVERT: Q 88 SER cc_start: 0.9289 (OUTLIER) cc_final: 0.8950 (p) REVERT: Q 237 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.7811 (mt-10) REVERT: Q 244 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7888 (mm-30) REVERT: Q 341 SER cc_start: 0.8975 (t) cc_final: 0.8608 (t) REVERT: Q 1072 ASP cc_start: 0.7852 (p0) cc_final: 0.7643 (p0) REVERT: S 168 HIS cc_start: 0.8768 (m90) cc_final: 0.8464 (m90) REVERT: S 235 ASP cc_start: 0.7755 (t70) cc_final: 0.7355 (t70) REVERT: S 237 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.7447 (mt-10) REVERT: S 348 MET cc_start: 0.9142 (tpt) cc_final: 0.8871 (tpp) REVERT: S 357 GLU cc_start: 0.7564 (tm-30) cc_final: 0.7304 (tm-30) REVERT: S 1072 ASP cc_start: 0.7913 (p0) cc_final: 0.7261 (m-30) REVERT: V 1 MET cc_start: 0.6096 (ttp) cc_final: 0.5529 (ttp) REVERT: V 235 ASP cc_start: 0.8022 (t70) cc_final: 0.7685 (t70) REVERT: V 237 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.7162 (mp0) REVERT: V 309 GLU cc_start: 0.8244 (tt0) cc_final: 0.7885 (mm-30) REVERT: V 334 MET cc_start: 0.9373 (mmp) cc_final: 0.9005 (mmm) REVERT: V 341 SER cc_start: 0.9192 (t) cc_final: 0.8988 (t) REVERT: V 344 MET cc_start: 0.9108 (mmm) cc_final: 0.8866 (mmm) REVERT: V 1089 TYR cc_start: 0.8528 (t80) cc_final: 0.7812 (t80) REVERT: V 1103 PHE cc_start: 0.8750 (m-80) cc_final: 0.8542 (m-80) outliers start: 72 outliers final: 42 residues processed: 672 average time/residue: 1.4546 time to fit residues: 1255.2054 Evaluate side-chains 663 residues out of total 5520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 611 time to evaluate : 4.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 358 ASN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 247 ARG Chi-restraints excluded: chain E residue 322 GLU Chi-restraints excluded: chain E residue 426 THR Chi-restraints excluded: chain E residue 1104 VAL Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain G residue 388 LEU Chi-restraints excluded: chain G residue 399 ILE Chi-restraints excluded: chain G residue 426 THR Chi-restraints excluded: chain G residue 1104 VAL Chi-restraints excluded: chain G residue 1105 LEU Chi-restraints excluded: chain I residue 143 GLU Chi-restraints excluded: chain I residue 247 ARG Chi-restraints excluded: chain I residue 329 LEU Chi-restraints excluded: chain I residue 358 ASN Chi-restraints excluded: chain I residue 388 LEU Chi-restraints excluded: chain I residue 399 ILE Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 329 LEU Chi-restraints excluded: chain K residue 399 ILE Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 165 LEU Chi-restraints excluded: chain M residue 237 GLU Chi-restraints excluded: chain M residue 247 ARG Chi-restraints excluded: chain M residue 357 GLU Chi-restraints excluded: chain M residue 379 THR Chi-restraints excluded: chain M residue 1104 VAL Chi-restraints excluded: chain O residue 96 SER Chi-restraints excluded: chain O residue 358 ASN Chi-restraints excluded: chain O residue 388 LEU Chi-restraints excluded: chain Q residue 88 SER Chi-restraints excluded: chain Q residue 237 GLU Chi-restraints excluded: chain Q residue 388 LEU Chi-restraints excluded: chain Q residue 426 THR Chi-restraints excluded: chain S residue 237 GLU Chi-restraints excluded: chain S residue 426 THR Chi-restraints excluded: chain V residue 237 GLU Chi-restraints excluded: chain V residue 426 THR Chi-restraints excluded: chain X residue 244 GLU Chi-restraints excluded: chain X residue 261 LEU Chi-restraints excluded: chain X residue 388 LEU Chi-restraints excluded: chain X residue 426 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 393 optimal weight: 3.9990 chunk 527 optimal weight: 0.9980 chunk 151 optimal weight: 6.9990 chunk 456 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 137 optimal weight: 0.9990 chunk 495 optimal weight: 0.9990 chunk 207 optimal weight: 0.0010 chunk 509 optimal weight: 0.0970 chunk 62 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1075 HIS ** G 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1075 HIS M 85 ASN M 114 GLN ** M 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 431 ASN Q1075 HIS ** V 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 431 ASN V1071 ASN V1075 HIS X 68 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.108217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.080827 restraints weight = 63361.654| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 2.25 r_work: 0.2814 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 50328 Z= 0.164 Angle : 0.580 13.470 68088 Z= 0.290 Chirality : 0.045 0.217 7560 Planarity : 0.004 0.044 8820 Dihedral : 4.678 28.069 6672 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 1.16 % Allowed : 17.61 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.11), residues: 6252 helix: 2.26 (0.14), residues: 1608 sheet: -0.87 (0.13), residues: 1572 loop : -1.10 (0.11), residues: 3072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.000 TRP O 125 HIS 0.006 0.001 HIS A 154 PHE 0.022 0.001 PHE O1094 TYR 0.010 0.001 TYR E 112 ARG 0.011 0.000 ARG A1086 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21234.54 seconds wall clock time: 376 minutes 8.83 seconds (22568.83 seconds total)