Starting phenix.real_space_refine on Sat Feb 24 06:02:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dop_30796/02_2024/7dop_30796_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dop_30796/02_2024/7dop_30796.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dop_30796/02_2024/7dop_30796.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dop_30796/02_2024/7dop_30796.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dop_30796/02_2024/7dop_30796_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dop_30796/02_2024/7dop_30796_neut.pdb" } resolution = 2.38 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= 0.001 sd= 0.069 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 12 6.06 5 S 348 5.16 5 C 26400 2.51 5 N 7200 2.21 5 O 7740 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 7": "OD1" <-> "OD2" Residue "A TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 54": "OE1" <-> "OE2" Residue "A ASP 58": "OD1" <-> "OD2" Residue "A ARG 76": "NH1" <-> "NH2" Residue "A ARG 85": "NH1" <-> "NH2" Residue "A GLU 129": "OE1" <-> "OE2" Residue "A TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 202": "OE1" <-> "OE2" Residue "A ARG 222": "NH1" <-> "NH2" Residue "A ARG 238": "NH1" <-> "NH2" Residue "A GLU 250": "OE1" <-> "OE2" Residue "A ARG 275": "NH1" <-> "NH2" Residue "A ASP 277": "OD1" <-> "OD2" Residue "A TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 289": "NH1" <-> "NH2" Residue "A ASP 310": "OD1" <-> "OD2" Residue "A PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 399": "NH1" <-> "NH2" Residue "A ASP 448": "OD1" <-> "OD2" Residue "B TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 7": "OD1" <-> "OD2" Residue "B TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 54": "OE1" <-> "OE2" Residue "B ASP 58": "OD1" <-> "OD2" Residue "B ARG 76": "NH1" <-> "NH2" Residue "B ARG 85": "NH1" <-> "NH2" Residue "B GLU 129": "OE1" <-> "OE2" Residue "B TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 202": "OE1" <-> "OE2" Residue "B ARG 222": "NH1" <-> "NH2" Residue "B ARG 238": "NH1" <-> "NH2" Residue "B GLU 250": "OE1" <-> "OE2" Residue "B ARG 275": "NH1" <-> "NH2" Residue "B ASP 277": "OD1" <-> "OD2" Residue "B TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 289": "NH1" <-> "NH2" Residue "B ASP 310": "OD1" <-> "OD2" Residue "B PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 399": "NH1" <-> "NH2" Residue "B ASP 448": "OD1" <-> "OD2" Residue "C TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 7": "OD1" <-> "OD2" Residue "C TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 54": "OE1" <-> "OE2" Residue "C ASP 58": "OD1" <-> "OD2" Residue "C ARG 76": "NH1" <-> "NH2" Residue "C ARG 85": "NH1" <-> "NH2" Residue "C GLU 129": "OE1" <-> "OE2" Residue "C TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 202": "OE1" <-> "OE2" Residue "C ARG 222": "NH1" <-> "NH2" Residue "C ARG 238": "NH1" <-> "NH2" Residue "C GLU 250": "OE1" <-> "OE2" Residue "C ARG 275": "NH1" <-> "NH2" Residue "C ASP 277": "OD1" <-> "OD2" Residue "C TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 289": "NH1" <-> "NH2" Residue "C ASP 310": "OD1" <-> "OD2" Residue "C PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 399": "NH1" <-> "NH2" Residue "C ASP 448": "OD1" <-> "OD2" Residue "D TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 7": "OD1" <-> "OD2" Residue "D TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 54": "OE1" <-> "OE2" Residue "D ASP 58": "OD1" <-> "OD2" Residue "D ARG 76": "NH1" <-> "NH2" Residue "D ARG 85": "NH1" <-> "NH2" Residue "D GLU 129": "OE1" <-> "OE2" Residue "D TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 202": "OE1" <-> "OE2" Residue "D ARG 222": "NH1" <-> "NH2" Residue "D ARG 238": "NH1" <-> "NH2" Residue "D GLU 250": "OE1" <-> "OE2" Residue "D ARG 275": "NH1" <-> "NH2" Residue "D ASP 277": "OD1" <-> "OD2" Residue "D TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 289": "NH1" <-> "NH2" Residue "D ASP 310": "OD1" <-> "OD2" Residue "D PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 399": "NH1" <-> "NH2" Residue "D ASP 448": "OD1" <-> "OD2" Residue "E TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 7": "OD1" <-> "OD2" Residue "E TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 54": "OE1" <-> "OE2" Residue "E ASP 58": "OD1" <-> "OD2" Residue "E ARG 76": "NH1" <-> "NH2" Residue "E ARG 85": "NH1" <-> "NH2" Residue "E GLU 129": "OE1" <-> "OE2" Residue "E TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 202": "OE1" <-> "OE2" Residue "E ARG 222": "NH1" <-> "NH2" Residue "E ARG 238": "NH1" <-> "NH2" Residue "E GLU 250": "OE1" <-> "OE2" Residue "E ARG 275": "NH1" <-> "NH2" Residue "E ASP 277": "OD1" <-> "OD2" Residue "E TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 289": "NH1" <-> "NH2" Residue "E ASP 310": "OD1" <-> "OD2" Residue "E PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 399": "NH1" <-> "NH2" Residue "E ASP 448": "OD1" <-> "OD2" Residue "F TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 7": "OD1" <-> "OD2" Residue "F TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 54": "OE1" <-> "OE2" Residue "F ASP 58": "OD1" <-> "OD2" Residue "F ARG 76": "NH1" <-> "NH2" Residue "F ARG 85": "NH1" <-> "NH2" Residue "F GLU 129": "OE1" <-> "OE2" Residue "F TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 202": "OE1" <-> "OE2" Residue "F ARG 222": "NH1" <-> "NH2" Residue "F ARG 238": "NH1" <-> "NH2" Residue "F GLU 250": "OE1" <-> "OE2" Residue "F ARG 275": "NH1" <-> "NH2" Residue "F ASP 277": "OD1" <-> "OD2" Residue "F TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 289": "NH1" <-> "NH2" Residue "F ASP 310": "OD1" <-> "OD2" Residue "F PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 399": "NH1" <-> "NH2" Residue "F ASP 448": "OD1" <-> "OD2" Residue "G TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 7": "OD1" <-> "OD2" Residue "G TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 54": "OE1" <-> "OE2" Residue "G ASP 58": "OD1" <-> "OD2" Residue "G ARG 76": "NH1" <-> "NH2" Residue "G ARG 85": "NH1" <-> "NH2" Residue "G GLU 129": "OE1" <-> "OE2" Residue "G TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 202": "OE1" <-> "OE2" Residue "G ARG 222": "NH1" <-> "NH2" Residue "G ARG 238": "NH1" <-> "NH2" Residue "G GLU 250": "OE1" <-> "OE2" Residue "G ARG 275": "NH1" <-> "NH2" Residue "G ASP 277": "OD1" <-> "OD2" Residue "G TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 289": "NH1" <-> "NH2" Residue "G ASP 310": "OD1" <-> "OD2" Residue "G PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 399": "NH1" <-> "NH2" Residue "G ASP 448": "OD1" <-> "OD2" Residue "H TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 7": "OD1" <-> "OD2" Residue "H TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 54": "OE1" <-> "OE2" Residue "H ASP 58": "OD1" <-> "OD2" Residue "H ARG 76": "NH1" <-> "NH2" Residue "H ARG 85": "NH1" <-> "NH2" Residue "H GLU 129": "OE1" <-> "OE2" Residue "H TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 202": "OE1" <-> "OE2" Residue "H ARG 222": "NH1" <-> "NH2" Residue "H ARG 238": "NH1" <-> "NH2" Residue "H GLU 250": "OE1" <-> "OE2" Residue "H ARG 275": "NH1" <-> "NH2" Residue "H ASP 277": "OD1" <-> "OD2" Residue "H TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 289": "NH1" <-> "NH2" Residue "H ASP 310": "OD1" <-> "OD2" Residue "H PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 399": "NH1" <-> "NH2" Residue "H ASP 448": "OD1" <-> "OD2" Residue "I TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 7": "OD1" <-> "OD2" Residue "I TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 54": "OE1" <-> "OE2" Residue "I ASP 58": "OD1" <-> "OD2" Residue "I ARG 76": "NH1" <-> "NH2" Residue "I ARG 85": "NH1" <-> "NH2" Residue "I GLU 129": "OE1" <-> "OE2" Residue "I TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 202": "OE1" <-> "OE2" Residue "I ARG 222": "NH1" <-> "NH2" Residue "I ARG 238": "NH1" <-> "NH2" Residue "I GLU 250": "OE1" <-> "OE2" Residue "I ARG 275": "NH1" <-> "NH2" Residue "I ASP 277": "OD1" <-> "OD2" Residue "I TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 289": "NH1" <-> "NH2" Residue "I ASP 310": "OD1" <-> "OD2" Residue "I PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 399": "NH1" <-> "NH2" Residue "I ASP 448": "OD1" <-> "OD2" Residue "J TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 7": "OD1" <-> "OD2" Residue "J TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 54": "OE1" <-> "OE2" Residue "J ASP 58": "OD1" <-> "OD2" Residue "J ARG 76": "NH1" <-> "NH2" Residue "J ARG 85": "NH1" <-> "NH2" Residue "J GLU 129": "OE1" <-> "OE2" Residue "J TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 202": "OE1" <-> "OE2" Residue "J ARG 222": "NH1" <-> "NH2" Residue "J ARG 238": "NH1" <-> "NH2" Residue "J GLU 250": "OE1" <-> "OE2" Residue "J ARG 275": "NH1" <-> "NH2" Residue "J ASP 277": "OD1" <-> "OD2" Residue "J TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 289": "NH1" <-> "NH2" Residue "J ASP 310": "OD1" <-> "OD2" Residue "J PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 399": "NH1" <-> "NH2" Residue "J ASP 448": "OD1" <-> "OD2" Residue "K TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 7": "OD1" <-> "OD2" Residue "K TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 54": "OE1" <-> "OE2" Residue "K ASP 58": "OD1" <-> "OD2" Residue "K ARG 76": "NH1" <-> "NH2" Residue "K ARG 85": "NH1" <-> "NH2" Residue "K GLU 129": "OE1" <-> "OE2" Residue "K TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 202": "OE1" <-> "OE2" Residue "K ARG 222": "NH1" <-> "NH2" Residue "K ARG 238": "NH1" <-> "NH2" Residue "K GLU 250": "OE1" <-> "OE2" Residue "K ARG 275": "NH1" <-> "NH2" Residue "K ASP 277": "OD1" <-> "OD2" Residue "K TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 289": "NH1" <-> "NH2" Residue "K ASP 310": "OD1" <-> "OD2" Residue "K PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 399": "NH1" <-> "NH2" Residue "K ASP 448": "OD1" <-> "OD2" Residue "L TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 7": "OD1" <-> "OD2" Residue "L TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 54": "OE1" <-> "OE2" Residue "L ASP 58": "OD1" <-> "OD2" Residue "L ARG 76": "NH1" <-> "NH2" Residue "L ARG 85": "NH1" <-> "NH2" Residue "L GLU 129": "OE1" <-> "OE2" Residue "L TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 202": "OE1" <-> "OE2" Residue "L ARG 222": "NH1" <-> "NH2" Residue "L ARG 238": "NH1" <-> "NH2" Residue "L GLU 250": "OE1" <-> "OE2" Residue "L ARG 275": "NH1" <-> "NH2" Residue "L ASP 277": "OD1" <-> "OD2" Residue "L TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 289": "NH1" <-> "NH2" Residue "L ASP 310": "OD1" <-> "OD2" Residue "L PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 399": "NH1" <-> "NH2" Residue "L ASP 448": "OD1" <-> "OD2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 41700 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3474 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 446, 3468 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 21, 'TRANS': 424} Chain breaks: 4 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 28 Conformer: "B" Number of residues, atoms: 446, 3468 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 21, 'TRANS': 424} Chain breaks: 4 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 28 bond proxies already assigned to first conformer: 3533 Chain: "B" Number of atoms: 3474 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 446, 3468 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 21, 'TRANS': 424} Chain breaks: 4 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 28 Conformer: "B" Number of residues, atoms: 446, 3468 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 21, 'TRANS': 424} Chain breaks: 4 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 28 bond proxies already assigned to first conformer: 3533 Chain: "C" Number of atoms: 3474 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 446, 3468 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 21, 'TRANS': 424} Chain breaks: 4 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 28 Conformer: "B" Number of residues, atoms: 446, 3468 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 21, 'TRANS': 424} Chain breaks: 4 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 28 bond proxies already assigned to first conformer: 3533 Chain: "D" Number of atoms: 3474 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 446, 3468 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 21, 'TRANS': 424} Chain breaks: 4 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 28 Conformer: "B" Number of residues, atoms: 446, 3468 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 21, 'TRANS': 424} Chain breaks: 4 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 28 bond proxies already assigned to first conformer: 3533 Chain: "E" Number of atoms: 3474 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 446, 3468 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 21, 'TRANS': 424} Chain breaks: 4 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 28 Conformer: "B" Number of residues, atoms: 446, 3468 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 21, 'TRANS': 424} Chain breaks: 4 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 28 bond proxies already assigned to first conformer: 3533 Chain: "F" Number of atoms: 3474 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 446, 3468 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 21, 'TRANS': 424} Chain breaks: 4 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 28 Conformer: "B" Number of residues, atoms: 446, 3468 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 21, 'TRANS': 424} Chain breaks: 4 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 28 bond proxies already assigned to first conformer: 3533 Chain: "G" Number of atoms: 3474 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 446, 3468 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 21, 'TRANS': 424} Chain breaks: 4 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 28 Conformer: "B" Number of residues, atoms: 446, 3468 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 21, 'TRANS': 424} Chain breaks: 4 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 28 bond proxies already assigned to first conformer: 3533 Chain: "H" Number of atoms: 3474 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 446, 3468 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 21, 'TRANS': 424} Chain breaks: 4 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 28 Conformer: "B" Number of residues, atoms: 446, 3468 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 21, 'TRANS': 424} Chain breaks: 4 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 28 bond proxies already assigned to first conformer: 3533 Chain: "I" Number of atoms: 3474 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 446, 3468 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 21, 'TRANS': 424} Chain breaks: 4 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 28 Conformer: "B" Number of residues, atoms: 446, 3468 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 21, 'TRANS': 424} Chain breaks: 4 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 28 bond proxies already assigned to first conformer: 3533 Chain: "J" Number of atoms: 3474 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 446, 3468 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 21, 'TRANS': 424} Chain breaks: 4 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 28 Conformer: "B" Number of residues, atoms: 446, 3468 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 21, 'TRANS': 424} Chain breaks: 4 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 28 bond proxies already assigned to first conformer: 3533 Chain: "K" Number of atoms: 3474 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 446, 3468 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 21, 'TRANS': 424} Chain breaks: 4 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 28 Conformer: "B" Number of residues, atoms: 446, 3468 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 21, 'TRANS': 424} Chain breaks: 4 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 28 bond proxies already assigned to first conformer: 3533 Chain: "L" Number of atoms: 3474 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 446, 3468 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 21, 'TRANS': 424} Chain breaks: 4 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 28 Conformer: "B" Number of residues, atoms: 446, 3468 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 21, 'TRANS': 424} Chain breaks: 4 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 28 bond proxies already assigned to first conformer: 3533 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 973 SG CYS A 134 118.569 187.968 30.521 1.00 95.42 S ATOM 1025 SG CYS A 141 115.102 189.644 31.353 1.00 89.69 S ATOM 4447 SG CYS B 134 73.438 184.699 30.506 1.00 94.23 S ATOM 4499 SG CYS B 141 69.597 184.417 31.337 1.00 85.59 S ATOM 7921 SG CYS C 134 36.004 159.361 30.443 1.00 95.93 S ATOM 7973 SG CYS C 141 32.810 157.210 31.280 1.00 91.08 S ATOM 11395 SG CYS D 134 16.245 118.679 30.435 1.00 96.70 S ATOM 11447 SG CYS D 141 14.539 115.232 31.290 1.00 88.37 S ATOM 14869 SG CYS E 134 19.502 73.499 30.559 1.00 93.99 S ATOM 14921 SG CYS E 141 19.745 69.663 31.423 1.00 85.31 S ATOM 18343 SG CYS F 134 44.881 35.953 30.562 1.00 96.74 S ATOM 18395 SG CYS F 141 47.016 32.756 31.427 1.00 91.60 S ATOM 21817 SG CYS G 134 85.503 16.139 30.550 1.00 97.60 S ATOM 21869 SG CYS G 141 88.949 14.433 31.407 1.00 92.30 S ATOM 25291 SG CYS H 134 130.786 19.437 30.591 1.00 96.37 S ATOM 25343 SG CYS H 141 134.624 19.698 31.444 1.00 86.38 S ATOM 28765 SG CYS I 134 168.269 44.890 30.531 1.00 95.85 S ATOM 28817 SG CYS I 141 171.457 47.051 31.362 1.00 91.18 S ATOM 32239 SG CYS J 134 159.317 168.214 30.534 1.00 95.50 S ATOM 32291 SG CYS J 141 157.145 171.396 31.356 1.00 91.00 S ATOM 35713 SG CYS K 134 188.066 85.639 30.568 1.00 97.71 S ATOM 35765 SG CYS K 141 189.733 89.113 31.391 1.00 92.36 S ATOM 39187 SG CYS L 134 184.729 130.736 30.509 1.00 96.40 S ATOM 39239 SG CYS L 141 184.443 134.578 31.332 1.00 87.66 S Residues with excluded nonbonded symmetry interactions: 12 residue: pdb=" N ACYS A 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS A 236 " occ=0.50 residue: pdb=" N ACYS B 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS B 236 " occ=0.50 residue: pdb=" N ACYS C 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS C 236 " occ=0.50 residue: pdb=" N ACYS D 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS D 236 " occ=0.50 residue: pdb=" N ACYS E 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS E 236 " occ=0.50 residue: pdb=" N ACYS F 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS F 236 " occ=0.50 residue: pdb=" N ACYS G 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS G 236 " occ=0.50 residue: pdb=" N ACYS H 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS H 236 " occ=0.50 residue: pdb=" N ACYS I 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS I 236 " occ=0.50 residue: pdb=" N ACYS J 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS J 236 " occ=0.50 residue: pdb=" N ACYS K 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS K 236 " occ=0.50 residue: pdb=" N ACYS L 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS L 236 " occ=0.50 Time building chain proxies: 39.15, per 1000 atoms: 0.94 Number of scatterers: 41700 At special positions: 0 Unit cell: (205.062, 205.062, 95.238, 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 12 29.99 S 348 16.00 O 7740 8.00 N 7200 7.00 C 26400 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: 14.62 Conformation dependent library (CDL) restraints added in 14.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" NE2 HIS A 79 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 141 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 134 " pdb=" ZN B1001 " pdb="ZN ZN B1001 " - pdb=" NE2 HIS B 79 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 141 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 134 " pdb=" ZN C1001 " pdb="ZN ZN C1001 " - pdb=" NE2 HIS C 79 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 141 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 134 " pdb=" ZN D1001 " pdb="ZN ZN D1001 " - pdb=" NE2 HIS D 79 " pdb="ZN ZN D1001 " - pdb=" SG CYS D 141 " pdb="ZN ZN D1001 " - pdb=" SG CYS D 134 " pdb=" ZN E1001 " pdb="ZN ZN E1001 " - pdb=" NE2 HIS E 79 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 141 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 134 " pdb=" ZN F1001 " pdb="ZN ZN F1001 " - pdb=" NE2 HIS F 79 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 141 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 134 " pdb=" ZN G1001 " pdb="ZN ZN G1001 " - pdb=" NE2 HIS G 79 " pdb="ZN ZN G1001 " - pdb=" SG CYS G 141 " pdb="ZN ZN G1001 " - pdb=" SG CYS G 134 " pdb=" ZN H1001 " pdb="ZN ZN H1001 " - pdb=" NE2 HIS H 79 " pdb="ZN ZN H1001 " - pdb=" SG CYS H 141 " pdb="ZN ZN H1001 " - pdb=" SG CYS H 134 " pdb=" ZN I1001 " pdb="ZN ZN I1001 " - pdb=" NE2 HIS I 79 " pdb="ZN ZN I1001 " - pdb=" SG CYS I 141 " pdb="ZN ZN I1001 " - pdb=" SG CYS I 134 " pdb=" ZN J1001 " pdb="ZN ZN J1001 " - pdb=" NE2 HIS J 79 " pdb="ZN ZN J1001 " - pdb=" SG CYS J 141 " pdb="ZN ZN J1001 " - pdb=" SG CYS J 134 " pdb=" ZN K1001 " pdb="ZN ZN K1001 " - pdb=" NE2 HIS K 79 " pdb="ZN ZN K1001 " - pdb=" SG CYS K 141 " pdb="ZN ZN K1001 " - pdb=" SG CYS K 134 " pdb=" ZN L1001 " pdb="ZN ZN L1001 " - pdb=" NE2 HIS L 79 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 141 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 134 " 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10176 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 72 sheets defined 35.7% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.48 Creating SS restraints... Processing helix chain 'A' and resid 13 through 22 removed outlier: 3.724A pdb=" N ALA A 17 " --> pdb=" O ALA A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 54 Processing helix chain 'A' and resid 67 through 72 removed outlier: 4.260A pdb=" N ARG A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 103 removed outlier: 3.586A pdb=" N ALA A 101 " --> pdb=" O ALA A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 125 Processing helix chain 'A' and resid 157 through 167 Processing helix chain 'A' and resid 180 through 185 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 203 through 205 No H-bonds generated for 'chain 'A' and resid 203 through 205' Processing helix chain 'A' and resid 252 through 257 Processing helix chain 'A' and resid 335 through 342 Processing helix chain 'A' and resid 343 through 348 removed outlier: 3.658A pdb=" N LEU A 346 " --> pdb=" O THR A 343 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR A 348 " --> pdb=" O ILE A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 364 removed outlier: 3.528A pdb=" N GLN A 364 " --> pdb=" O VAL A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 382 No H-bonds generated for 'chain 'A' and resid 380 through 382' Processing helix chain 'A' and resid 383 through 404 Processing helix chain 'A' and resid 461 through 473 removed outlier: 3.640A pdb=" N LEU A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU A 472 " --> pdb=" O ILE A 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 22 removed outlier: 3.724A pdb=" N ALA B 17 " --> pdb=" O ALA B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 54 Processing helix chain 'B' and resid 67 through 72 removed outlier: 4.259A pdb=" N ARG B 71 " --> pdb=" O ALA B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 103 removed outlier: 3.586A pdb=" N ALA B 101 " --> pdb=" O ALA B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 125 Processing helix chain 'B' and resid 157 through 167 Processing helix chain 'B' and resid 180 through 185 Processing helix chain 'B' and resid 193 through 195 No H-bonds generated for 'chain 'B' and resid 193 through 195' Processing helix chain 'B' and resid 203 through 205 No H-bonds generated for 'chain 'B' and resid 203 through 205' Processing helix chain 'B' and resid 252 through 257 Processing helix chain 'B' and resid 335 through 342 Processing helix chain 'B' and resid 343 through 348 removed outlier: 3.658A pdb=" N LEU B 346 " --> pdb=" O THR B 343 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR B 348 " --> pdb=" O ILE B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 364 removed outlier: 3.527A pdb=" N GLN B 364 " --> pdb=" O VAL B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 382 No H-bonds generated for 'chain 'B' and resid 380 through 382' Processing helix chain 'B' and resid 383 through 404 Processing helix chain 'B' and resid 461 through 473 removed outlier: 3.640A pdb=" N LEU B 471 " --> pdb=" O ARG B 467 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU B 472 " --> pdb=" O ILE B 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 22 removed outlier: 3.725A pdb=" N ALA C 17 " --> pdb=" O ALA C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 54 Processing helix chain 'C' and resid 67 through 72 removed outlier: 4.259A pdb=" N ARG C 71 " --> pdb=" O ALA C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 103 removed outlier: 3.586A pdb=" N ALA C 101 " --> pdb=" O ALA C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 125 Processing helix chain 'C' and resid 157 through 167 Processing helix chain 'C' and resid 180 through 185 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 203 through 205 No H-bonds generated for 'chain 'C' and resid 203 through 205' Processing helix chain 'C' and resid 252 through 257 Processing helix chain 'C' and resid 335 through 342 Processing helix chain 'C' and resid 343 through 348 removed outlier: 3.658A pdb=" N LEU C 346 " --> pdb=" O THR C 343 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR C 348 " --> pdb=" O ILE C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 364 removed outlier: 3.529A pdb=" N GLN C 364 " --> pdb=" O VAL C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 382 No H-bonds generated for 'chain 'C' and resid 380 through 382' Processing helix chain 'C' and resid 383 through 404 Processing helix chain 'C' and resid 461 through 473 removed outlier: 3.640A pdb=" N LEU C 471 " --> pdb=" O ARG C 467 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU C 472 " --> pdb=" O ILE C 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 22 removed outlier: 3.724A pdb=" N ALA D 17 " --> pdb=" O ALA D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 54 Processing helix chain 'D' and resid 67 through 72 removed outlier: 4.260A pdb=" N ARG D 71 " --> pdb=" O ALA D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 103 removed outlier: 3.586A pdb=" N ALA D 101 " --> pdb=" O ALA D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 125 Processing helix chain 'D' and resid 157 through 167 Processing helix chain 'D' and resid 180 through 185 Processing helix chain 'D' and resid 193 through 195 No H-bonds generated for 'chain 'D' and resid 193 through 195' Processing helix chain 'D' and resid 203 through 205 No H-bonds generated for 'chain 'D' and resid 203 through 205' Processing helix chain 'D' and resid 252 through 257 Processing helix chain 'D' and resid 335 through 342 Processing helix chain 'D' and resid 343 through 348 removed outlier: 3.659A pdb=" N LEU D 346 " --> pdb=" O THR D 343 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR D 348 " --> pdb=" O ILE D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 364 removed outlier: 3.527A pdb=" N GLN D 364 " --> pdb=" O VAL D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 382 No H-bonds generated for 'chain 'D' and resid 380 through 382' Processing helix chain 'D' and resid 383 through 404 Processing helix chain 'D' and resid 461 through 473 removed outlier: 3.640A pdb=" N LEU D 471 " --> pdb=" O ARG D 467 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU D 472 " --> pdb=" O ILE D 468 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 22 removed outlier: 3.725A pdb=" N ALA E 17 " --> pdb=" O ALA E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 54 Processing helix chain 'E' and resid 67 through 72 removed outlier: 4.259A pdb=" N ARG E 71 " --> pdb=" O ALA E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 103 removed outlier: 3.587A pdb=" N ALA E 101 " --> pdb=" O ALA E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 125 Processing helix chain 'E' and resid 157 through 167 Processing helix chain 'E' and resid 180 through 185 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 203 through 205 No H-bonds generated for 'chain 'E' and resid 203 through 205' Processing helix chain 'E' and resid 252 through 257 Processing helix chain 'E' and resid 335 through 342 Processing helix chain 'E' and resid 343 through 348 removed outlier: 3.658A pdb=" N LEU E 346 " --> pdb=" O THR E 343 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR E 348 " --> pdb=" O ILE E 345 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 364 removed outlier: 3.528A pdb=" N GLN E 364 " --> pdb=" O VAL E 360 " (cutoff:3.500A) Processing helix chain 'E' and resid 380 through 382 No H-bonds generated for 'chain 'E' and resid 380 through 382' Processing helix chain 'E' and resid 383 through 404 Processing helix chain 'E' and resid 461 through 473 removed outlier: 3.640A pdb=" N LEU E 471 " --> pdb=" O ARG E 467 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU E 472 " --> pdb=" O ILE E 468 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 22 removed outlier: 3.725A pdb=" N ALA F 17 " --> pdb=" O ALA F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 54 Processing helix chain 'F' and resid 67 through 72 removed outlier: 4.260A pdb=" N ARG F 71 " --> pdb=" O ALA F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 103 removed outlier: 3.587A pdb=" N ALA F 101 " --> pdb=" O ALA F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 125 Processing helix chain 'F' and resid 157 through 167 Processing helix chain 'F' and resid 180 through 185 Processing helix chain 'F' and resid 193 through 195 No H-bonds generated for 'chain 'F' and resid 193 through 195' Processing helix chain 'F' and resid 203 through 205 No H-bonds generated for 'chain 'F' and resid 203 through 205' Processing helix chain 'F' and resid 252 through 257 Processing helix chain 'F' and resid 335 through 342 Processing helix chain 'F' and resid 343 through 348 removed outlier: 3.658A pdb=" N LEU F 346 " --> pdb=" O THR F 343 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR F 348 " --> pdb=" O ILE F 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 351 through 364 removed outlier: 3.527A pdb=" N GLN F 364 " --> pdb=" O VAL F 360 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 382 No H-bonds generated for 'chain 'F' and resid 380 through 382' Processing helix chain 'F' and resid 383 through 404 Processing helix chain 'F' and resid 461 through 473 removed outlier: 3.640A pdb=" N LEU F 471 " --> pdb=" O ARG F 467 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU F 472 " --> pdb=" O ILE F 468 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 22 removed outlier: 3.724A pdb=" N ALA G 17 " --> pdb=" O ALA G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 37 through 54 Processing helix chain 'G' and resid 67 through 72 removed outlier: 4.261A pdb=" N ARG G 71 " --> pdb=" O ALA G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 103 removed outlier: 3.587A pdb=" N ALA G 101 " --> pdb=" O ALA G 97 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 125 Processing helix chain 'G' and resid 157 through 167 Processing helix chain 'G' and resid 180 through 185 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 203 through 205 No H-bonds generated for 'chain 'G' and resid 203 through 205' Processing helix chain 'G' and resid 252 through 257 Processing helix chain 'G' and resid 335 through 342 Processing helix chain 'G' and resid 343 through 348 removed outlier: 3.658A pdb=" N LEU G 346 " --> pdb=" O THR G 343 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR G 348 " --> pdb=" O ILE G 345 " (cutoff:3.500A) Processing helix chain 'G' and resid 351 through 364 removed outlier: 3.528A pdb=" N GLN G 364 " --> pdb=" O VAL G 360 " (cutoff:3.500A) Processing helix chain 'G' and resid 380 through 382 No H-bonds generated for 'chain 'G' and resid 380 through 382' Processing helix chain 'G' and resid 383 through 404 Processing helix chain 'G' and resid 461 through 473 removed outlier: 3.640A pdb=" N LEU G 471 " --> pdb=" O ARG G 467 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU G 472 " --> pdb=" O ILE G 468 " (cutoff:3.500A) Processing helix chain 'H' and resid 13 through 22 removed outlier: 3.725A pdb=" N ALA H 17 " --> pdb=" O ALA H 13 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 54 Processing helix chain 'H' and resid 67 through 72 removed outlier: 4.260A pdb=" N ARG H 71 " --> pdb=" O ALA H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 103 removed outlier: 3.586A pdb=" N ALA H 101 " --> pdb=" O ALA H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 112 through 125 Processing helix chain 'H' and resid 157 through 167 Processing helix chain 'H' and resid 180 through 185 Processing helix chain 'H' and resid 193 through 195 No H-bonds generated for 'chain 'H' and resid 193 through 195' Processing helix chain 'H' and resid 203 through 205 No H-bonds generated for 'chain 'H' and resid 203 through 205' Processing helix chain 'H' and resid 252 through 257 Processing helix chain 'H' and resid 335 through 342 Processing helix chain 'H' and resid 343 through 348 removed outlier: 3.659A pdb=" N LEU H 346 " --> pdb=" O THR H 343 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR H 348 " --> pdb=" O ILE H 345 " (cutoff:3.500A) Processing helix chain 'H' and resid 351 through 364 removed outlier: 3.528A pdb=" N GLN H 364 " --> pdb=" O VAL H 360 " (cutoff:3.500A) Processing helix chain 'H' and resid 380 through 382 No H-bonds generated for 'chain 'H' and resid 380 through 382' Processing helix chain 'H' and resid 383 through 404 Processing helix chain 'H' and resid 461 through 473 removed outlier: 3.641A pdb=" N LEU H 471 " --> pdb=" O ARG H 467 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU H 472 " --> pdb=" O ILE H 468 " (cutoff:3.500A) Processing helix chain 'I' and resid 13 through 22 removed outlier: 3.725A pdb=" N ALA I 17 " --> pdb=" O ALA I 13 " (cutoff:3.500A) Processing helix chain 'I' and resid 37 through 54 Processing helix chain 'I' and resid 67 through 72 removed outlier: 4.260A pdb=" N ARG I 71 " --> pdb=" O ALA I 67 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 103 removed outlier: 3.586A pdb=" N ALA I 101 " --> pdb=" O ALA I 97 " (cutoff:3.500A) Processing helix chain 'I' and resid 112 through 125 Processing helix chain 'I' and resid 157 through 167 Processing helix chain 'I' and resid 180 through 185 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 203 through 205 No H-bonds generated for 'chain 'I' and resid 203 through 205' Processing helix chain 'I' and resid 252 through 257 Processing helix chain 'I' and resid 335 through 342 Processing helix chain 'I' and resid 343 through 348 removed outlier: 3.658A pdb=" N LEU I 346 " --> pdb=" O THR I 343 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR I 348 " --> pdb=" O ILE I 345 " (cutoff:3.500A) Processing helix chain 'I' and resid 351 through 364 removed outlier: 3.528A pdb=" N GLN I 364 " --> pdb=" O VAL I 360 " (cutoff:3.500A) Processing helix chain 'I' and resid 380 through 382 No H-bonds generated for 'chain 'I' and resid 380 through 382' Processing helix chain 'I' and resid 383 through 404 Processing helix chain 'I' and resid 461 through 473 removed outlier: 3.640A pdb=" N LEU I 471 " --> pdb=" O ARG I 467 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU I 472 " --> pdb=" O ILE I 468 " (cutoff:3.500A) Processing helix chain 'J' and resid 13 through 22 removed outlier: 3.725A pdb=" N ALA J 17 " --> pdb=" O ALA J 13 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 54 Processing helix chain 'J' and resid 67 through 72 removed outlier: 4.260A pdb=" N ARG J 71 " --> pdb=" O ALA J 67 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 103 removed outlier: 3.586A pdb=" N ALA J 101 " --> pdb=" O ALA J 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 125 Processing helix chain 'J' and resid 157 through 167 Processing helix chain 'J' and resid 180 through 185 Processing helix chain 'J' and resid 193 through 195 No H-bonds generated for 'chain 'J' and resid 193 through 195' Processing helix chain 'J' and resid 203 through 205 No H-bonds generated for 'chain 'J' and resid 203 through 205' Processing helix chain 'J' and resid 252 through 257 Processing helix chain 'J' and resid 335 through 342 Processing helix chain 'J' and resid 343 through 348 removed outlier: 3.659A pdb=" N LEU J 346 " --> pdb=" O THR J 343 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR J 348 " --> pdb=" O ILE J 345 " (cutoff:3.500A) Processing helix chain 'J' and resid 351 through 364 removed outlier: 3.528A pdb=" N GLN J 364 " --> pdb=" O VAL J 360 " (cutoff:3.500A) Processing helix chain 'J' and resid 380 through 382 No H-bonds generated for 'chain 'J' and resid 380 through 382' Processing helix chain 'J' and resid 383 through 404 Processing helix chain 'J' and resid 461 through 473 removed outlier: 3.640A pdb=" N LEU J 471 " --> pdb=" O ARG J 467 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU J 472 " --> pdb=" O ILE J 468 " (cutoff:3.500A) Processing helix chain 'K' and resid 13 through 22 removed outlier: 3.725A pdb=" N ALA K 17 " --> pdb=" O ALA K 13 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 54 Processing helix chain 'K' and resid 67 through 72 removed outlier: 4.260A pdb=" N ARG K 71 " --> pdb=" O ALA K 67 " (cutoff:3.500A) Processing helix chain 'K' and resid 88 through 103 removed outlier: 3.586A pdb=" N ALA K 101 " --> pdb=" O ALA K 97 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 125 Processing helix chain 'K' and resid 157 through 167 Processing helix chain 'K' and resid 180 through 185 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 203 through 205 No H-bonds generated for 'chain 'K' and resid 203 through 205' Processing helix chain 'K' and resid 252 through 257 Processing helix chain 'K' and resid 335 through 342 Processing helix chain 'K' and resid 343 through 348 removed outlier: 3.659A pdb=" N LEU K 346 " --> pdb=" O THR K 343 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR K 348 " --> pdb=" O ILE K 345 " (cutoff:3.500A) Processing helix chain 'K' and resid 351 through 364 removed outlier: 3.528A pdb=" N GLN K 364 " --> pdb=" O VAL K 360 " (cutoff:3.500A) Processing helix chain 'K' and resid 380 through 382 No H-bonds generated for 'chain 'K' and resid 380 through 382' Processing helix chain 'K' and resid 383 through 404 Processing helix chain 'K' and resid 461 through 473 removed outlier: 3.640A pdb=" N LEU K 471 " --> pdb=" O ARG K 467 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU K 472 " --> pdb=" O ILE K 468 " (cutoff:3.500A) Processing helix chain 'L' and resid 13 through 22 removed outlier: 3.724A pdb=" N ALA L 17 " --> pdb=" O ALA L 13 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 54 Processing helix chain 'L' and resid 67 through 72 removed outlier: 4.260A pdb=" N ARG L 71 " --> pdb=" O ALA L 67 " (cutoff:3.500A) Processing helix chain 'L' and resid 88 through 103 removed outlier: 3.587A pdb=" N ALA L 101 " --> pdb=" O ALA L 97 " (cutoff:3.500A) Processing helix chain 'L' and resid 112 through 125 Processing helix chain 'L' and resid 157 through 167 Processing helix chain 'L' and resid 180 through 185 Processing helix chain 'L' and resid 193 through 195 No H-bonds generated for 'chain 'L' and resid 193 through 195' Processing helix chain 'L' and resid 203 through 205 No H-bonds generated for 'chain 'L' and resid 203 through 205' Processing helix chain 'L' and resid 252 through 257 Processing helix chain 'L' and resid 335 through 342 Processing helix chain 'L' and resid 343 through 348 removed outlier: 3.658A pdb=" N LEU L 346 " --> pdb=" O THR L 343 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR L 348 " --> pdb=" O ILE L 345 " (cutoff:3.500A) Processing helix chain 'L' and resid 351 through 364 removed outlier: 3.528A pdb=" N GLN L 364 " --> pdb=" O VAL L 360 " (cutoff:3.500A) Processing helix chain 'L' and resid 380 through 382 No H-bonds generated for 'chain 'L' and resid 380 through 382' Processing helix chain 'L' and resid 383 through 404 Processing helix chain 'L' and resid 461 through 473 removed outlier: 3.640A pdb=" N LEU L 471 " --> pdb=" O ARG L 467 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU L 472 " --> pdb=" O ILE L 468 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 6 Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 63 Processing sheet with id=AA3, first strand: chain 'A' and resid 147 through 151 removed outlier: 6.613A pdb=" N TYR A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N SER A 281 " --> pdb=" O TYR A 285 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL A 287 " --> pdb=" O VAL A 279 " (cutoff:3.500A) removed outlier: 8.754A pdb=" N PHE A 447 " --> pdb=" O VAL A 263 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N HIS A 265 " --> pdb=" O PHE A 447 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 246 through 251 removed outlier: 3.648A pdb=" N THR A 197 " --> pdb=" O TYR A 192 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ALA A 189 " --> pdb=" O CYS A 331 " (cutoff:3.500A) removed outlier: 9.303A pdb=" N TYR A 333 " --> pdb=" O ALA A 189 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N ALA A 191 " --> pdb=" O TYR A 333 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 224 through 225 Processing sheet with id=AA6, first strand: chain 'A' and resid 303 through 307 Processing sheet with id=AA7, first strand: chain 'A' and resid 422 through 423 Processing sheet with id=AA8, first strand: chain 'B' and resid 4 through 6 Processing sheet with id=AA9, first strand: chain 'B' and resid 60 through 63 Processing sheet with id=AB1, first strand: chain 'B' and resid 147 through 151 removed outlier: 6.613A pdb=" N TYR B 285 " --> pdb=" O SER B 281 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N SER B 281 " --> pdb=" O TYR B 285 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL B 287 " --> pdb=" O VAL B 279 " (cutoff:3.500A) removed outlier: 8.754A pdb=" N PHE B 447 " --> pdb=" O VAL B 263 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N HIS B 265 " --> pdb=" O PHE B 447 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 246 through 251 removed outlier: 3.647A pdb=" N THR B 197 " --> pdb=" O TYR B 192 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ALA B 189 " --> pdb=" O CYS B 331 " (cutoff:3.500A) removed outlier: 9.304A pdb=" N TYR B 333 " --> pdb=" O ALA B 189 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N ALA B 191 " --> pdb=" O TYR B 333 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 303 through 307 Processing sheet with id=AB4, first strand: chain 'B' and resid 422 through 423 Processing sheet with id=AB5, first strand: chain 'C' and resid 4 through 6 Processing sheet with id=AB6, first strand: chain 'C' and resid 60 through 63 Processing sheet with id=AB7, first strand: chain 'C' and resid 147 through 151 removed outlier: 6.612A pdb=" N TYR C 285 " --> pdb=" O SER C 281 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N SER C 281 " --> pdb=" O TYR C 285 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL C 287 " --> pdb=" O VAL C 279 " (cutoff:3.500A) removed outlier: 8.754A pdb=" N PHE C 447 " --> pdb=" O VAL C 263 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N HIS C 265 " --> pdb=" O PHE C 447 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 246 through 251 removed outlier: 3.648A pdb=" N THR C 197 " --> pdb=" O TYR C 192 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ALA C 189 " --> pdb=" O CYS C 331 " (cutoff:3.500A) removed outlier: 9.304A pdb=" N TYR C 333 " --> pdb=" O ALA C 189 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N ALA C 191 " --> pdb=" O TYR C 333 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 303 through 307 Processing sheet with id=AC1, first strand: chain 'C' and resid 422 through 423 Processing sheet with id=AC2, first strand: chain 'D' and resid 4 through 6 Processing sheet with id=AC3, first strand: chain 'D' and resid 60 through 63 Processing sheet with id=AC4, first strand: chain 'D' and resid 147 through 151 removed outlier: 6.613A pdb=" N TYR D 285 " --> pdb=" O SER D 281 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N SER D 281 " --> pdb=" O TYR D 285 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL D 287 " --> pdb=" O VAL D 279 " (cutoff:3.500A) removed outlier: 8.754A pdb=" N PHE D 447 " --> pdb=" O VAL D 263 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N HIS D 265 " --> pdb=" O PHE D 447 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 246 through 251 removed outlier: 3.647A pdb=" N THR D 197 " --> pdb=" O TYR D 192 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ALA D 189 " --> pdb=" O CYS D 331 " (cutoff:3.500A) removed outlier: 9.303A pdb=" N TYR D 333 " --> pdb=" O ALA D 189 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N ALA D 191 " --> pdb=" O TYR D 333 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 303 through 307 Processing sheet with id=AC7, first strand: chain 'D' and resid 422 through 423 Processing sheet with id=AC8, first strand: chain 'E' and resid 4 through 6 Processing sheet with id=AC9, first strand: chain 'E' and resid 60 through 63 Processing sheet with id=AD1, first strand: chain 'E' and resid 147 through 151 removed outlier: 6.613A pdb=" N TYR E 285 " --> pdb=" O SER E 281 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N SER E 281 " --> pdb=" O TYR E 285 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL E 287 " --> pdb=" O VAL E 279 " (cutoff:3.500A) removed outlier: 8.753A pdb=" N PHE E 447 " --> pdb=" O VAL E 263 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N HIS E 265 " --> pdb=" O PHE E 447 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 246 through 251 removed outlier: 3.647A pdb=" N THR E 197 " --> pdb=" O TYR E 192 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ALA E 189 " --> pdb=" O CYS E 331 " (cutoff:3.500A) removed outlier: 9.304A pdb=" N TYR E 333 " --> pdb=" O ALA E 189 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N ALA E 191 " --> pdb=" O TYR E 333 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 303 through 307 Processing sheet with id=AD4, first strand: chain 'E' and resid 422 through 423 Processing sheet with id=AD5, first strand: chain 'F' and resid 4 through 6 Processing sheet with id=AD6, first strand: chain 'F' and resid 60 through 63 Processing sheet with id=AD7, first strand: chain 'F' and resid 147 through 151 removed outlier: 6.613A pdb=" N TYR F 285 " --> pdb=" O SER F 281 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N SER F 281 " --> pdb=" O TYR F 285 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL F 287 " --> pdb=" O VAL F 279 " (cutoff:3.500A) removed outlier: 8.754A pdb=" N PHE F 447 " --> pdb=" O VAL F 263 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N HIS F 265 " --> pdb=" O PHE F 447 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 246 through 251 removed outlier: 3.647A pdb=" N THR F 197 " --> pdb=" O TYR F 192 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ALA F 189 " --> pdb=" O CYS F 331 " (cutoff:3.500A) removed outlier: 9.304A pdb=" N TYR F 333 " --> pdb=" O ALA F 189 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N ALA F 191 " --> pdb=" O TYR F 333 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 303 through 307 Processing sheet with id=AE1, first strand: chain 'F' and resid 422 through 423 Processing sheet with id=AE2, first strand: chain 'G' and resid 4 through 6 Processing sheet with id=AE3, first strand: chain 'G' and resid 60 through 63 Processing sheet with id=AE4, first strand: chain 'G' and resid 147 through 151 removed outlier: 6.612A pdb=" N TYR G 285 " --> pdb=" O SER G 281 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N SER G 281 " --> pdb=" O TYR G 285 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL G 287 " --> pdb=" O VAL G 279 " (cutoff:3.500A) removed outlier: 8.754A pdb=" N PHE G 447 " --> pdb=" O VAL G 263 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N HIS G 265 " --> pdb=" O PHE G 447 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 246 through 251 removed outlier: 3.647A pdb=" N THR G 197 " --> pdb=" O TYR G 192 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ALA G 189 " --> pdb=" O CYS G 331 " (cutoff:3.500A) removed outlier: 9.304A pdb=" N TYR G 333 " --> pdb=" O ALA G 189 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N ALA G 191 " --> pdb=" O TYR G 333 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 303 through 307 Processing sheet with id=AE7, first strand: chain 'G' and resid 422 through 423 Processing sheet with id=AE8, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AE9, first strand: chain 'H' and resid 60 through 63 Processing sheet with id=AF1, first strand: chain 'H' and resid 147 through 151 removed outlier: 6.613A pdb=" N TYR H 285 " --> pdb=" O SER H 281 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N SER H 281 " --> pdb=" O TYR H 285 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL H 287 " --> pdb=" O VAL H 279 " (cutoff:3.500A) removed outlier: 8.754A pdb=" N PHE H 447 " --> pdb=" O VAL H 263 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N HIS H 265 " --> pdb=" O PHE H 447 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 246 through 251 removed outlier: 3.647A pdb=" N THR H 197 " --> pdb=" O TYR H 192 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ALA H 189 " --> pdb=" O CYS H 331 " (cutoff:3.500A) removed outlier: 9.304A pdb=" N TYR H 333 " --> pdb=" O ALA H 189 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N ALA H 191 " --> pdb=" O TYR H 333 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 303 through 307 Processing sheet with id=AF4, first strand: chain 'H' and resid 421 through 423 removed outlier: 4.003A pdb=" N TRP H 421 " --> pdb=" O SER I 226 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 4 through 6 Processing sheet with id=AF6, first strand: chain 'I' and resid 60 through 63 Processing sheet with id=AF7, first strand: chain 'I' and resid 147 through 151 removed outlier: 6.613A pdb=" N TYR I 285 " --> pdb=" O SER I 281 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N SER I 281 " --> pdb=" O TYR I 285 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL I 287 " --> pdb=" O VAL I 279 " (cutoff:3.500A) removed outlier: 8.754A pdb=" N PHE I 447 " --> pdb=" O VAL I 263 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N HIS I 265 " --> pdb=" O PHE I 447 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 246 through 251 removed outlier: 3.647A pdb=" N THR I 197 " --> pdb=" O TYR I 192 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ALA I 189 " --> pdb=" O CYS I 331 " (cutoff:3.500A) removed outlier: 9.304A pdb=" N TYR I 333 " --> pdb=" O ALA I 189 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N ALA I 191 " --> pdb=" O TYR I 333 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 303 through 307 Processing sheet with id=AG1, first strand: chain 'I' and resid 421 through 423 removed outlier: 3.921A pdb=" N TRP I 421 " --> pdb=" O SER K 226 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'J' and resid 4 through 6 Processing sheet with id=AG3, first strand: chain 'J' and resid 60 through 63 Processing sheet with id=AG4, first strand: chain 'J' and resid 147 through 151 removed outlier: 6.612A pdb=" N TYR J 285 " --> pdb=" O SER J 281 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N SER J 281 " --> pdb=" O TYR J 285 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL J 287 " --> pdb=" O VAL J 279 " (cutoff:3.500A) removed outlier: 8.754A pdb=" N PHE J 447 " --> pdb=" O VAL J 263 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N HIS J 265 " --> pdb=" O PHE J 447 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'J' and resid 246 through 251 removed outlier: 3.647A pdb=" N THR J 197 " --> pdb=" O TYR J 192 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ALA J 189 " --> pdb=" O CYS J 331 " (cutoff:3.500A) removed outlier: 9.304A pdb=" N TYR J 333 " --> pdb=" O ALA J 189 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N ALA J 191 " --> pdb=" O TYR J 333 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'J' and resid 225 through 226 removed outlier: 3.931A pdb=" N TRP L 421 " --> pdb=" O SER J 226 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'J' and resid 303 through 307 Processing sheet with id=AG8, first strand: chain 'K' and resid 4 through 6 Processing sheet with id=AG9, first strand: chain 'K' and resid 60 through 63 Processing sheet with id=AH1, first strand: chain 'K' and resid 147 through 151 removed outlier: 6.613A pdb=" N TYR K 285 " --> pdb=" O SER K 281 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N SER K 281 " --> pdb=" O TYR K 285 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL K 287 " --> pdb=" O VAL K 279 " (cutoff:3.500A) removed outlier: 8.754A pdb=" N PHE K 447 " --> pdb=" O VAL K 263 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N HIS K 265 " --> pdb=" O PHE K 447 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'K' and resid 246 through 251 removed outlier: 3.647A pdb=" N THR K 197 " --> pdb=" O TYR K 192 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ALA K 189 " --> pdb=" O CYS K 331 " (cutoff:3.500A) removed outlier: 9.304A pdb=" N TYR K 333 " --> pdb=" O ALA K 189 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N ALA K 191 " --> pdb=" O TYR K 333 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'K' and resid 303 through 307 Processing sheet with id=AH4, first strand: chain 'K' and resid 422 through 423 Processing sheet with id=AH5, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AH6, first strand: chain 'L' and resid 60 through 63 Processing sheet with id=AH7, first strand: chain 'L' and resid 147 through 151 removed outlier: 6.613A pdb=" N TYR L 285 " --> pdb=" O SER L 281 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N SER L 281 " --> pdb=" O TYR L 285 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL L 287 " --> pdb=" O VAL L 279 " (cutoff:3.500A) removed outlier: 8.754A pdb=" N PHE L 447 " --> pdb=" O VAL L 263 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N HIS L 265 " --> pdb=" O PHE L 447 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'L' and resid 246 through 251 removed outlier: 3.647A pdb=" N THR L 197 " --> pdb=" O TYR L 192 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ALA L 189 " --> pdb=" O CYS L 331 " (cutoff:3.500A) removed outlier: 9.303A pdb=" N TYR L 333 " --> pdb=" O ALA L 189 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N ALA L 191 " --> pdb=" O TYR L 333 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'L' and resid 303 through 307 1825 hydrogen bonds defined for protein. 5262 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: 17.26 Time building geometry restraints manager: 15.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 13419 1.34 - 1.46: 9406 1.46 - 1.58: 19223 1.58 - 1.71: 0 1.71 - 1.83: 516 Bond restraints: 42564 Sorted by residual: bond pdb=" CB GLU F 353 " pdb=" CG GLU F 353 " ideal model delta sigma weight residual 1.520 1.576 -0.056 3.00e-02 1.11e+03 3.46e+00 bond pdb=" CB GLU E 353 " pdb=" CG GLU E 353 " ideal model delta sigma weight residual 1.520 1.576 -0.056 3.00e-02 1.11e+03 3.45e+00 bond pdb=" CB GLU A 353 " pdb=" CG GLU A 353 " ideal model delta sigma weight residual 1.520 1.576 -0.056 3.00e-02 1.11e+03 3.45e+00 bond pdb=" CB GLU C 353 " pdb=" CG GLU C 353 " ideal model delta sigma weight residual 1.520 1.575 -0.055 3.00e-02 1.11e+03 3.42e+00 bond pdb=" CB GLU K 353 " pdb=" CG GLU K 353 " ideal model delta sigma weight residual 1.520 1.575 -0.055 3.00e-02 1.11e+03 3.42e+00 ... (remaining 42559 not shown) Histogram of bond angle deviations from ideal: 99.98 - 106.82: 1356 106.82 - 113.67: 23622 113.67 - 120.51: 16427 120.51 - 127.36: 15763 127.36 - 134.20: 492 Bond angle restraints: 57660 Sorted by residual: angle pdb=" CA GLU L 353 " pdb=" CB GLU L 353 " pdb=" CG GLU L 353 " ideal model delta sigma weight residual 114.10 123.57 -9.47 2.00e+00 2.50e-01 2.24e+01 angle pdb=" CA GLU H 353 " pdb=" CB GLU H 353 " pdb=" CG GLU H 353 " ideal model delta sigma weight residual 114.10 123.54 -9.44 2.00e+00 2.50e-01 2.23e+01 angle pdb=" CA GLU I 353 " pdb=" CB GLU I 353 " pdb=" CG GLU I 353 " ideal model delta sigma weight residual 114.10 123.54 -9.44 2.00e+00 2.50e-01 2.23e+01 angle pdb=" CA GLU G 353 " pdb=" CB GLU G 353 " pdb=" CG GLU G 353 " ideal model delta sigma weight residual 114.10 123.53 -9.43 2.00e+00 2.50e-01 2.22e+01 angle pdb=" CA GLU B 353 " pdb=" CB GLU B 353 " pdb=" CG GLU B 353 " ideal model delta sigma weight residual 114.10 123.52 -9.42 2.00e+00 2.50e-01 2.22e+01 ... (remaining 57655 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 22370 17.58 - 35.16: 2590 35.16 - 52.74: 672 52.74 - 70.32: 144 70.32 - 87.90: 24 Dihedral angle restraints: 25800 sinusoidal: 10092 harmonic: 15708 Sorted by residual: dihedral pdb=" CA TYR K 192 " pdb=" C TYR K 192 " pdb=" N PRO K 193 " pdb=" CA PRO K 193 " ideal model delta harmonic sigma weight residual -180.00 -161.22 -18.78 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA TYR H 192 " pdb=" C TYR H 192 " pdb=" N PRO H 193 " pdb=" CA PRO H 193 " ideal model delta harmonic sigma weight residual 180.00 -161.23 -18.77 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA TYR C 192 " pdb=" C TYR C 192 " pdb=" N PRO C 193 " pdb=" CA PRO C 193 " ideal model delta harmonic sigma weight residual 180.00 -161.23 -18.77 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 25797 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 3254 0.031 - 0.063: 1980 0.063 - 0.094: 816 0.094 - 0.125: 378 0.125 - 0.157: 124 Chirality restraints: 6552 Sorted by residual: chirality pdb=" CA ARG G 411 " pdb=" N ARG G 411 " pdb=" C ARG G 411 " pdb=" CB ARG G 411 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.14e-01 chirality pdb=" CA ARG I 411 " pdb=" N ARG I 411 " pdb=" C ARG I 411 " pdb=" CB ARG I 411 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.04e-01 chirality pdb=" CA ARG F 411 " pdb=" N ARG F 411 " pdb=" C ARG F 411 " pdb=" CB ARG F 411 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.97e-01 ... (remaining 6549 not shown) Planarity restraints: 7308 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP D 89 " -0.031 5.00e-02 4.00e+02 4.65e-02 3.46e+00 pdb=" N PRO D 90 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO D 90 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 90 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 89 " -0.031 5.00e-02 4.00e+02 4.64e-02 3.44e+00 pdb=" N PRO C 90 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO C 90 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 90 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 89 " -0.030 5.00e-02 4.00e+02 4.63e-02 3.43e+00 pdb=" N PRO E 90 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO E 90 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 90 " -0.026 5.00e-02 4.00e+02 ... (remaining 7305 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.50: 135 2.50 - 3.10: 26072 3.10 - 3.70: 58248 3.70 - 4.30: 88425 4.30 - 4.90: 147238 Nonbonded interactions: 320118 Sorted by model distance: nonbonded pdb=" OE2 GLU L 129 " pdb="ZN ZN L1001 " model vdw 1.895 2.230 nonbonded pdb=" OE2 GLU C 129 " pdb="ZN ZN C1001 " model vdw 1.895 2.230 nonbonded pdb=" OE2 GLU E 129 " pdb="ZN ZN E1001 " model vdw 1.895 2.230 nonbonded pdb=" OE2 GLU J 129 " pdb="ZN ZN J1001 " model vdw 1.895 2.230 nonbonded pdb=" OE2 GLU D 129 " pdb="ZN ZN D1001 " model vdw 1.895 2.230 ... (remaining 320113 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' and (resid 2 through 235 or resid 237 through 473 or resid 1001)) selection = (chain 'B' and (resid 2 through 235 or resid 237 through 473 or resid 1001)) selection = (chain 'C' and (resid 2 through 235 or resid 237 through 473 or resid 1001)) selection = (chain 'D' and (resid 2 through 235 or resid 237 through 473 or resid 1001)) selection = (chain 'E' and (resid 2 through 235 or resid 237 through 473 or resid 1001)) selection = (chain 'F' and (resid 2 through 235 or resid 237 through 473 or resid 1001)) selection = (chain 'G' and (resid 2 through 235 or resid 237 through 473 or resid 1001)) selection = (chain 'H' and (resid 2 through 235 or resid 237 through 473 or resid 1001)) selection = (chain 'I' and (resid 2 through 235 or resid 237 through 473 or resid 1001)) selection = (chain 'J' and (resid 2 through 235 or resid 237 through 473 or resid 1001)) selection = (chain 'K' and (resid 2 through 235 or resid 237 through 473 or resid 1001)) selection = (chain 'L' and (resid 2 through 235 or resid 237 through 473 or resid 1001)) } 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=0.50 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: 6.560 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: 0.040 Extract box with map and model: 25.070 Check model and map are aligned: 0.710 Set scattering table: 0.400 Process input model: 136.740 Find NCS groups from input model: 3.360 Set up NCS constraints: 0.280 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:13.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 186.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 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 : 0.005 0.056 42564 Z= 0.339 Angle : 0.781 11.264 57660 Z= 0.427 Chirality : 0.051 0.157 6552 Planarity : 0.005 0.046 7308 Dihedral : 16.240 87.904 15624 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.21 % Allowed : 16.47 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.11), residues: 5268 helix: -0.53 (0.13), residues: 1644 sheet: -0.93 (0.14), residues: 1212 loop : -1.86 (0.10), residues: 2412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 175 HIS 0.006 0.002 HIS K 164 PHE 0.028 0.003 PHE H 183 TYR 0.015 0.002 TYR B 248 ARG 0.010 0.001 ARG E 41 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 370 time to evaluate : 4.443 Fit side-chains REVERT: A 228 MET cc_start: 0.4930 (ttt) cc_final: 0.4315 (tpp) REVERT: A 285 TYR cc_start: 0.8559 (OUTLIER) cc_final: 0.7973 (t80) REVERT: B 285 TYR cc_start: 0.8568 (OUTLIER) cc_final: 0.8149 (t80) REVERT: C 285 TYR cc_start: 0.8491 (OUTLIER) cc_final: 0.8195 (t80) REVERT: D 30 ARG cc_start: 0.4327 (OUTLIER) cc_final: 0.4101 (ptm-80) REVERT: E 285 TYR cc_start: 0.8386 (OUTLIER) cc_final: 0.7905 (t80) REVERT: G 228 MET cc_start: 0.4925 (ttt) cc_final: 0.4441 (tpp) REVERT: H 228 MET cc_start: 0.5014 (ttt) cc_final: 0.4374 (tpt) REVERT: H 285 TYR cc_start: 0.8437 (OUTLIER) cc_final: 0.7838 (t80) REVERT: I 285 TYR cc_start: 0.8452 (OUTLIER) cc_final: 0.7900 (t80) REVERT: J 285 TYR cc_start: 0.8634 (OUTLIER) cc_final: 0.8055 (t80) REVERT: K 41 ARG cc_start: 0.5435 (ttp-110) cc_final: 0.5225 (ttp-110) REVERT: K 110 ARG cc_start: 0.5100 (mtt90) cc_final: 0.4420 (mtt-85) REVERT: K 228 MET cc_start: 0.5206 (ttt) cc_final: 0.4447 (tpp) REVERT: K 285 TYR cc_start: 0.8498 (OUTLIER) cc_final: 0.7867 (t80) outliers start: 99 outliers final: 10 residues processed: 425 average time/residue: 1.6483 time to fit residues: 845.9630 Evaluate side-chains 357 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 338 time to evaluate : 4.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain D residue 30 ARG Chi-restraints excluded: chain E residue 208 LYS Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain E residue 472 LEU Chi-restraints excluded: chain F residue 353 GLU Chi-restraints excluded: chain F residue 472 LEU Chi-restraints excluded: chain G residue 472 LEU Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain I residue 472 LEU Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain K residue 472 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 445 optimal weight: 10.0000 chunk 400 optimal weight: 7.9990 chunk 222 optimal weight: 6.9990 chunk 136 optimal weight: 6.9990 chunk 269 optimal weight: 9.9990 chunk 213 optimal weight: 0.5980 chunk 413 optimal weight: 0.8980 chunk 160 optimal weight: 0.7980 chunk 251 optimal weight: 6.9990 chunk 308 optimal weight: 20.0000 chunk 479 optimal weight: 1.9990 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 209 ASN J 19 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 42564 Z= 0.245 Angle : 0.688 13.235 57660 Z= 0.368 Chirality : 0.048 0.142 6552 Planarity : 0.005 0.046 7308 Dihedral : 5.689 89.951 5864 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.12 % Allowed : 17.05 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.11), residues: 5268 helix: 1.09 (0.13), residues: 1668 sheet: 0.18 (0.15), residues: 1152 loop : -1.67 (0.11), residues: 2448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 175 HIS 0.005 0.001 HIS A 307 PHE 0.019 0.002 PHE L 183 TYR 0.015 0.002 TYR K 248 ARG 0.009 0.001 ARG G 41 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 326 time to evaluate : 5.073 Fit side-chains REVERT: A 228 MET cc_start: 0.5114 (ttt) cc_final: 0.4415 (tpp) REVERT: A 285 TYR cc_start: 0.8695 (OUTLIER) cc_final: 0.8209 (t80) REVERT: B 285 TYR cc_start: 0.8696 (OUTLIER) cc_final: 0.8182 (t80) REVERT: B 292 MET cc_start: 0.6986 (mtm) cc_final: 0.6463 (mtp) REVERT: B 389 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.7443 (tm-30) REVERT: B 402 MET cc_start: 0.7542 (mtm) cc_final: 0.7222 (mtt) REVERT: C 208 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8009 (ttmt) REVERT: C 285 TYR cc_start: 0.8638 (OUTLIER) cc_final: 0.8082 (t80) REVERT: C 342 MET cc_start: 0.8490 (mmm) cc_final: 0.8067 (mmm) REVERT: C 389 GLN cc_start: 0.7856 (OUTLIER) cc_final: 0.7059 (tm-30) REVERT: D 285 TYR cc_start: 0.8646 (OUTLIER) cc_final: 0.8273 (t80) REVERT: E 285 TYR cc_start: 0.8626 (OUTLIER) cc_final: 0.8068 (t80) REVERT: E 389 GLN cc_start: 0.7961 (OUTLIER) cc_final: 0.7430 (tm-30) REVERT: F 41 ARG cc_start: 0.5465 (ttp-110) cc_final: 0.5262 (ttp-110) REVERT: F 285 TYR cc_start: 0.8597 (OUTLIER) cc_final: 0.8193 (t80) REVERT: F 389 GLN cc_start: 0.7880 (OUTLIER) cc_final: 0.7093 (tm-30) REVERT: G 228 MET cc_start: 0.4944 (ttt) cc_final: 0.4543 (tpp) REVERT: G 285 TYR cc_start: 0.8605 (OUTLIER) cc_final: 0.8236 (t80) REVERT: G 292 MET cc_start: 0.6887 (mtp) cc_final: 0.6577 (mtm) REVERT: H 285 TYR cc_start: 0.8630 (OUTLIER) cc_final: 0.8061 (t80) REVERT: H 389 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7457 (tm-30) REVERT: I 285 TYR cc_start: 0.8620 (OUTLIER) cc_final: 0.8077 (t80) REVERT: I 389 GLN cc_start: 0.7849 (OUTLIER) cc_final: 0.7058 (tm-30) REVERT: J 285 TYR cc_start: 0.8671 (OUTLIER) cc_final: 0.8177 (t80) REVERT: J 389 GLN cc_start: 0.7882 (OUTLIER) cc_final: 0.7103 (tm-30) REVERT: K 41 ARG cc_start: 0.5707 (ttp-110) cc_final: 0.5481 (ttp-110) REVERT: K 285 TYR cc_start: 0.8637 (OUTLIER) cc_final: 0.8138 (t80) REVERT: L 285 TYR cc_start: 0.8644 (OUTLIER) cc_final: 0.8230 (t80) REVERT: L 389 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7414 (tm-30) outliers start: 95 outliers final: 28 residues processed: 408 average time/residue: 1.5795 time to fit residues: 788.9025 Evaluate side-chains 365 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 316 time to evaluate : 4.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 389 GLN Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain C residue 208 LYS Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 389 GLN Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain E residue 30 ARG Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 389 GLN Chi-restraints excluded: chain E residue 472 LEU Chi-restraints excluded: chain F residue 30 ARG Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain F residue 389 GLN Chi-restraints excluded: chain F residue 472 LEU Chi-restraints excluded: chain G residue 202 GLU Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 472 LEU Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 320 THR Chi-restraints excluded: chain H residue 389 GLN Chi-restraints excluded: chain H residue 472 LEU Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain I residue 389 GLN Chi-restraints excluded: chain I residue 472 LEU Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain J residue 389 GLN Chi-restraints excluded: chain J residue 472 LEU Chi-restraints excluded: chain K residue 202 GLU Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain K residue 320 THR Chi-restraints excluded: chain L residue 30 ARG Chi-restraints excluded: chain L residue 285 TYR Chi-restraints excluded: chain L residue 320 THR Chi-restraints excluded: chain L residue 389 GLN Chi-restraints excluded: chain L residue 472 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 266 optimal weight: 0.4980 chunk 148 optimal weight: 10.0000 chunk 399 optimal weight: 9.9990 chunk 326 optimal weight: 1.9990 chunk 132 optimal weight: 20.0000 chunk 480 optimal weight: 6.9990 chunk 518 optimal weight: 2.9990 chunk 427 optimal weight: 6.9990 chunk 476 optimal weight: 2.9990 chunk 163 optimal weight: 4.9990 chunk 385 optimal weight: 8.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 42564 Z= 0.264 Angle : 0.695 14.121 57660 Z= 0.371 Chirality : 0.048 0.143 6552 Planarity : 0.005 0.046 7308 Dihedral : 5.411 58.448 5848 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.99 % Allowed : 16.04 % Favored : 80.97 % 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: 5268 helix: 1.47 (0.14), residues: 1656 sheet: 0.36 (0.15), residues: 1152 loop : -1.65 (0.10), residues: 2460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP I 175 HIS 0.004 0.001 HIS G 307 PHE 0.021 0.002 PHE F 183 TYR 0.016 0.002 TYR E 150 ARG 0.007 0.001 ARG K 110 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 319 time to evaluate : 4.776 Fit side-chains REVERT: B 285 TYR cc_start: 0.8714 (OUTLIER) cc_final: 0.8089 (t80) REVERT: B 292 MET cc_start: 0.6900 (mtm) cc_final: 0.6527 (mtp) REVERT: B 389 GLN cc_start: 0.7977 (OUTLIER) cc_final: 0.7475 (tm-30) REVERT: C 99 LYS cc_start: 0.6973 (OUTLIER) cc_final: 0.6476 (mptt) REVERT: C 389 GLN cc_start: 0.7910 (OUTLIER) cc_final: 0.7108 (tm-30) REVERT: D 99 LYS cc_start: 0.6901 (OUTLIER) cc_final: 0.6382 (mptt) REVERT: D 285 TYR cc_start: 0.8633 (OUTLIER) cc_final: 0.8249 (t80) REVERT: E 99 LYS cc_start: 0.7014 (OUTLIER) cc_final: 0.6543 (mptt) REVERT: E 285 TYR cc_start: 0.8702 (OUTLIER) cc_final: 0.8074 (t80) REVERT: E 292 MET cc_start: 0.6803 (mtp) cc_final: 0.6562 (mtm) REVERT: E 389 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.7460 (tm-30) REVERT: F 99 LYS cc_start: 0.6874 (OUTLIER) cc_final: 0.6384 (mptt) REVERT: F 285 TYR cc_start: 0.8598 (OUTLIER) cc_final: 0.8199 (t80) REVERT: F 389 GLN cc_start: 0.7905 (OUTLIER) cc_final: 0.7099 (tm-30) REVERT: G 228 MET cc_start: 0.4849 (ttt) cc_final: 0.4480 (tpp) REVERT: G 285 TYR cc_start: 0.8626 (OUTLIER) cc_final: 0.8243 (t80) REVERT: G 292 MET cc_start: 0.6921 (mtp) cc_final: 0.6677 (mtm) REVERT: H 99 LYS cc_start: 0.6742 (OUTLIER) cc_final: 0.6276 (mptt) REVERT: H 285 TYR cc_start: 0.8703 (OUTLIER) cc_final: 0.8062 (t80) REVERT: H 292 MET cc_start: 0.6827 (mtp) cc_final: 0.6579 (mtm) REVERT: H 389 GLN cc_start: 0.7985 (OUTLIER) cc_final: 0.7473 (tm-30) REVERT: I 389 GLN cc_start: 0.7906 (OUTLIER) cc_final: 0.7112 (tm-30) REVERT: J 285 TYR cc_start: 0.8680 (OUTLIER) cc_final: 0.7999 (t80) REVERT: J 389 GLN cc_start: 0.7913 (OUTLIER) cc_final: 0.7117 (tm-30) REVERT: L 285 TYR cc_start: 0.8631 (OUTLIER) cc_final: 0.8154 (t80) REVERT: L 292 MET cc_start: 0.6933 (mtp) cc_final: 0.6656 (mtm) REVERT: L 389 GLN cc_start: 0.7979 (OUTLIER) cc_final: 0.7484 (tm-30) outliers start: 134 outliers final: 65 residues processed: 431 average time/residue: 1.5543 time to fit residues: 815.7790 Evaluate side-chains 401 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 315 time to evaluate : 4.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 389 GLN Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 389 GLN Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 99 LYS Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain E residue 30 ARG Chi-restraints excluded: chain E residue 99 LYS Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 348 THR Chi-restraints excluded: chain E residue 389 GLN Chi-restraints excluded: chain E residue 472 LEU Chi-restraints excluded: chain F residue 30 ARG Chi-restraints excluded: chain F residue 99 LYS Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain F residue 228 MET Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain F residue 348 THR Chi-restraints excluded: chain F residue 389 GLN Chi-restraints excluded: chain F residue 472 LEU Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 202 GLU Chi-restraints excluded: chain G residue 214 SER Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 99 LYS Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 214 SER Chi-restraints excluded: chain H residue 280 VAL Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 320 THR Chi-restraints excluded: chain H residue 389 GLN Chi-restraints excluded: chain H residue 472 LEU Chi-restraints excluded: chain I residue 24 MET Chi-restraints excluded: chain I residue 214 SER Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain I residue 348 THR Chi-restraints excluded: chain I residue 389 GLN Chi-restraints excluded: chain I residue 472 LEU Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 214 SER Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain J residue 348 THR Chi-restraints excluded: chain J residue 389 GLN Chi-restraints excluded: chain J residue 472 LEU Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 202 GLU Chi-restraints excluded: chain K residue 214 SER Chi-restraints excluded: chain K residue 280 VAL Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain K residue 320 THR Chi-restraints excluded: chain K residue 472 LEU Chi-restraints excluded: chain L residue 30 ARG Chi-restraints excluded: chain L residue 202 GLU Chi-restraints excluded: chain L residue 214 SER Chi-restraints excluded: chain L residue 280 VAL Chi-restraints excluded: chain L residue 285 TYR Chi-restraints excluded: chain L residue 320 THR Chi-restraints excluded: chain L residue 348 THR Chi-restraints excluded: chain L residue 389 GLN Chi-restraints excluded: chain L residue 472 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 474 optimal weight: 4.9990 chunk 361 optimal weight: 10.0000 chunk 249 optimal weight: 0.8980 chunk 53 optimal weight: 10.0000 chunk 229 optimal weight: 10.0000 chunk 322 optimal weight: 2.9990 chunk 482 optimal weight: 0.8980 chunk 510 optimal weight: 3.9990 chunk 251 optimal weight: 0.8980 chunk 456 optimal weight: 10.0000 chunk 137 optimal weight: 9.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 42564 Z= 0.213 Angle : 0.615 11.427 57660 Z= 0.329 Chirality : 0.046 0.139 6552 Planarity : 0.005 0.044 7308 Dihedral : 5.193 59.995 5846 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.85 % Allowed : 16.11 % Favored : 81.04 % 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: -0.04 (0.11), residues: 5268 helix: 1.79 (0.14), residues: 1668 sheet: 0.45 (0.15), residues: 1152 loop : -1.63 (0.10), residues: 2448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP J 175 HIS 0.003 0.001 HIS A 307 PHE 0.019 0.002 PHE I 423 TYR 0.013 0.001 TYR D 248 ARG 0.006 0.000 ARG A 110 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 324 time to evaluate : 4.643 Fit side-chains REVERT: B 389 GLN cc_start: 0.7852 (OUTLIER) cc_final: 0.7361 (tm-30) REVERT: C 389 GLN cc_start: 0.7807 (OUTLIER) cc_final: 0.7010 (tm-30) REVERT: D 285 TYR cc_start: 0.8605 (OUTLIER) cc_final: 0.8272 (t80) REVERT: E 99 LYS cc_start: 0.6911 (OUTLIER) cc_final: 0.6384 (mptt) REVERT: E 389 GLN cc_start: 0.7855 (OUTLIER) cc_final: 0.7351 (tm-30) REVERT: F 99 LYS cc_start: 0.6845 (OUTLIER) cc_final: 0.6363 (mptt) REVERT: F 285 TYR cc_start: 0.8556 (OUTLIER) cc_final: 0.8149 (t80) REVERT: F 389 GLN cc_start: 0.7807 (OUTLIER) cc_final: 0.7002 (tm-30) REVERT: G 228 MET cc_start: 0.4934 (ttt) cc_final: 0.4433 (tpp) REVERT: G 285 TYR cc_start: 0.8609 (OUTLIER) cc_final: 0.8285 (t80) REVERT: G 292 MET cc_start: 0.6892 (mtp) cc_final: 0.6647 (mtm) REVERT: H 389 GLN cc_start: 0.7860 (OUTLIER) cc_final: 0.7359 (tm-30) REVERT: I 389 GLN cc_start: 0.7804 (OUTLIER) cc_final: 0.7013 (tm-30) REVERT: J 389 GLN cc_start: 0.7809 (OUTLIER) cc_final: 0.7015 (tm-30) REVERT: L 222 ARG cc_start: 0.5702 (OUTLIER) cc_final: 0.5277 (ttm-80) REVERT: L 285 TYR cc_start: 0.8605 (OUTLIER) cc_final: 0.8196 (t80) REVERT: L 292 MET cc_start: 0.6868 (mtp) cc_final: 0.6569 (mtm) REVERT: L 389 GLN cc_start: 0.7850 (OUTLIER) cc_final: 0.7367 (tm-30) outliers start: 128 outliers final: 70 residues processed: 430 average time/residue: 1.5472 time to fit residues: 813.9195 Evaluate side-chains 397 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 312 time to evaluate : 4.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 389 GLN Chi-restraints excluded: chain B residue 419 CYS Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 389 GLN Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 348 THR Chi-restraints excluded: chain E residue 30 ARG Chi-restraints excluded: chain E residue 99 LYS Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 348 THR Chi-restraints excluded: chain E residue 389 GLN Chi-restraints excluded: chain E residue 472 LEU Chi-restraints excluded: chain F residue 30 ARG Chi-restraints excluded: chain F residue 99 LYS Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain F residue 389 GLN Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 202 GLU Chi-restraints excluded: chain G residue 214 SER Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 472 LEU Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 214 SER Chi-restraints excluded: chain H residue 280 VAL Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 320 THR Chi-restraints excluded: chain H residue 389 GLN Chi-restraints excluded: chain H residue 472 LEU Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain I residue 214 SER Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain I residue 389 GLN Chi-restraints excluded: chain I residue 472 LEU Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain J residue 214 SER Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain J residue 389 GLN Chi-restraints excluded: chain J residue 419 CYS Chi-restraints excluded: chain J residue 472 LEU Chi-restraints excluded: chain K residue 202 GLU Chi-restraints excluded: chain K residue 214 SER Chi-restraints excluded: chain K residue 280 VAL Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain K residue 320 THR Chi-restraints excluded: chain K residue 378 THR Chi-restraints excluded: chain K residue 419 CYS Chi-restraints excluded: chain K residue 472 LEU Chi-restraints excluded: chain L residue 30 ARG Chi-restraints excluded: chain L residue 202 GLU Chi-restraints excluded: chain L residue 214 SER Chi-restraints excluded: chain L residue 222 ARG Chi-restraints excluded: chain L residue 280 VAL Chi-restraints excluded: chain L residue 285 TYR Chi-restraints excluded: chain L residue 320 THR Chi-restraints excluded: chain L residue 389 GLN Chi-restraints excluded: chain L residue 419 CYS Chi-restraints excluded: chain L residue 472 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 425 optimal weight: 0.9980 chunk 289 optimal weight: 20.0000 chunk 7 optimal weight: 0.9990 chunk 380 optimal weight: 0.9990 chunk 210 optimal weight: 0.9990 chunk 435 optimal weight: 9.9990 chunk 352 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 260 optimal weight: 0.9990 chunk 458 optimal weight: 6.9990 chunk 128 optimal weight: 7.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 209 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 42564 Z= 0.165 Angle : 0.561 12.982 57660 Z= 0.294 Chirality : 0.044 0.142 6552 Planarity : 0.005 0.043 7308 Dihedral : 4.840 59.727 5840 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.34 % Allowed : 16.98 % Favored : 80.68 % 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: 0.16 (0.12), residues: 5268 helix: 2.04 (0.14), residues: 1680 sheet: 0.59 (0.15), residues: 1200 loop : -1.66 (0.11), residues: 2388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 175 HIS 0.002 0.001 HIS K 307 PHE 0.020 0.001 PHE I 423 TYR 0.010 0.001 TYR J 248 ARG 0.007 0.000 ARG A 110 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 328 time to evaluate : 4.997 Fit side-chains REVERT: C 202 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7538 (mm-30) REVERT: C 389 GLN cc_start: 0.7671 (OUTLIER) cc_final: 0.7215 (tt0) REVERT: D 285 TYR cc_start: 0.8559 (OUTLIER) cc_final: 0.8225 (t80) REVERT: F 202 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7553 (mm-30) REVERT: F 285 TYR cc_start: 0.8487 (OUTLIER) cc_final: 0.8138 (t80) REVERT: F 389 GLN cc_start: 0.7668 (OUTLIER) cc_final: 0.7203 (tt0) REVERT: G 285 TYR cc_start: 0.8545 (OUTLIER) cc_final: 0.8237 (t80) REVERT: G 292 MET cc_start: 0.6858 (mtp) cc_final: 0.6615 (mtm) REVERT: I 202 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7543 (mm-30) REVERT: I 389 GLN cc_start: 0.7667 (OUTLIER) cc_final: 0.7214 (tt0) REVERT: J 202 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7529 (mm-30) REVERT: J 389 GLN cc_start: 0.7671 (OUTLIER) cc_final: 0.7214 (tt0) REVERT: L 285 TYR cc_start: 0.8511 (OUTLIER) cc_final: 0.8142 (t80) outliers start: 105 outliers final: 45 residues processed: 420 average time/residue: 1.4940 time to fit residues: 770.7945 Evaluate side-chains 381 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 324 time to evaluate : 4.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 389 GLN Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 348 THR Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 348 THR Chi-restraints excluded: chain F residue 202 GLU Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain F residue 389 GLN Chi-restraints excluded: chain G residue 202 GLU Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 472 LEU Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 280 VAL Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 320 THR Chi-restraints excluded: chain H residue 472 LEU Chi-restraints excluded: chain I residue 202 GLU Chi-restraints excluded: chain I residue 214 SER Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain I residue 389 GLN Chi-restraints excluded: chain J residue 24 MET Chi-restraints excluded: chain J residue 202 GLU Chi-restraints excluded: chain J residue 214 SER Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain J residue 389 GLN Chi-restraints excluded: chain J residue 472 LEU Chi-restraints excluded: chain K residue 202 GLU Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain K residue 320 THR Chi-restraints excluded: chain K residue 472 LEU Chi-restraints excluded: chain L residue 30 ARG Chi-restraints excluded: chain L residue 202 GLU Chi-restraints excluded: chain L residue 280 VAL Chi-restraints excluded: chain L residue 285 TYR Chi-restraints excluded: chain L residue 320 THR Chi-restraints excluded: chain L residue 472 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 171 optimal weight: 10.0000 chunk 459 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 299 optimal weight: 0.9980 chunk 125 optimal weight: 0.5980 chunk 510 optimal weight: 4.9990 chunk 424 optimal weight: 9.9990 chunk 236 optimal weight: 7.9990 chunk 42 optimal weight: 4.9990 chunk 168 optimal weight: 0.9990 chunk 268 optimal weight: 9.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 42564 Z= 0.231 Angle : 0.625 10.143 57660 Z= 0.334 Chirality : 0.047 0.158 6552 Planarity : 0.005 0.044 7308 Dihedral : 5.048 59.830 5836 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.56 % Allowed : 16.69 % Favored : 80.75 % 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: 0.11 (0.11), residues: 5268 helix: 1.98 (0.14), residues: 1668 sheet: 0.55 (0.15), residues: 1152 loop : -1.62 (0.10), residues: 2448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 175 HIS 0.003 0.001 HIS A 307 PHE 0.025 0.002 PHE I 423 TYR 0.014 0.002 TYR A 248 ARG 0.007 0.001 ARG A 110 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 316 time to evaluate : 5.064 Fit side-chains REVERT: B 389 GLN cc_start: 0.7941 (OUTLIER) cc_final: 0.7437 (tm-30) REVERT: C 202 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7560 (mm-30) REVERT: C 389 GLN cc_start: 0.7878 (OUTLIER) cc_final: 0.7089 (tm-30) REVERT: D 285 TYR cc_start: 0.8623 (OUTLIER) cc_final: 0.8263 (t80) REVERT: E 389 GLN cc_start: 0.7945 (OUTLIER) cc_final: 0.7433 (tm-30) REVERT: F 202 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7554 (mm-30) REVERT: F 285 TYR cc_start: 0.8564 (OUTLIER) cc_final: 0.8144 (t80) REVERT: F 389 GLN cc_start: 0.7868 (OUTLIER) cc_final: 0.7071 (tm-30) REVERT: G 285 TYR cc_start: 0.8623 (OUTLIER) cc_final: 0.8279 (t80) REVERT: G 292 MET cc_start: 0.6842 (mtp) cc_final: 0.6549 (mtm) REVERT: H 389 GLN cc_start: 0.7948 (OUTLIER) cc_final: 0.7439 (tm-30) REVERT: I 202 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7586 (mm-30) REVERT: I 389 GLN cc_start: 0.7878 (OUTLIER) cc_final: 0.7096 (tm-30) REVERT: J 202 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7576 (mm-30) REVERT: J 389 GLN cc_start: 0.7881 (OUTLIER) cc_final: 0.7094 (tm-30) REVERT: L 285 TYR cc_start: 0.8606 (OUTLIER) cc_final: 0.8185 (t80) REVERT: L 389 GLN cc_start: 0.7939 (OUTLIER) cc_final: 0.7441 (tm-30) outliers start: 115 outliers final: 73 residues processed: 413 average time/residue: 1.5245 time to fit residues: 773.5885 Evaluate side-chains 403 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 314 time to evaluate : 4.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 389 GLN Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 228 MET Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 389 GLN Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 348 THR Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 348 THR Chi-restraints excluded: chain E residue 389 GLN Chi-restraints excluded: chain E residue 472 LEU Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 202 GLU Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain F residue 389 GLN Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 202 GLU Chi-restraints excluded: chain G residue 214 SER Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 402 MET Chi-restraints excluded: chain G residue 472 LEU Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 214 SER Chi-restraints excluded: chain H residue 280 VAL Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 320 THR Chi-restraints excluded: chain H residue 389 GLN Chi-restraints excluded: chain H residue 472 LEU Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain I residue 202 GLU Chi-restraints excluded: chain I residue 214 SER Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain I residue 389 GLN Chi-restraints excluded: chain I residue 472 LEU Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain J residue 202 GLU Chi-restraints excluded: chain J residue 214 SER Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain J residue 348 THR Chi-restraints excluded: chain J residue 389 GLN Chi-restraints excluded: chain J residue 472 LEU Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 202 GLU Chi-restraints excluded: chain K residue 214 SER Chi-restraints excluded: chain K residue 280 VAL Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain K residue 320 THR Chi-restraints excluded: chain K residue 378 THR Chi-restraints excluded: chain K residue 402 MET Chi-restraints excluded: chain K residue 472 LEU Chi-restraints excluded: chain L residue 30 ARG Chi-restraints excluded: chain L residue 202 GLU Chi-restraints excluded: chain L residue 214 SER Chi-restraints excluded: chain L residue 280 VAL Chi-restraints excluded: chain L residue 285 TYR Chi-restraints excluded: chain L residue 320 THR Chi-restraints excluded: chain L residue 378 THR Chi-restraints excluded: chain L residue 389 GLN Chi-restraints excluded: chain L residue 472 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 492 optimal weight: 9.9990 chunk 57 optimal weight: 10.0000 chunk 291 optimal weight: 3.9990 chunk 373 optimal weight: 4.9990 chunk 289 optimal weight: 7.9990 chunk 430 optimal weight: 6.9990 chunk 285 optimal weight: 1.9990 chunk 508 optimal weight: 0.9980 chunk 318 optimal weight: 0.7980 chunk 310 optimal weight: 8.9990 chunk 234 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 42564 Z= 0.224 Angle : 0.632 14.280 57660 Z= 0.334 Chirality : 0.047 0.164 6552 Planarity : 0.005 0.044 7308 Dihedral : 5.042 59.993 5836 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.65 % Allowed : 16.87 % Favored : 80.48 % 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: 0.11 (0.11), residues: 5268 helix: 1.99 (0.14), residues: 1668 sheet: 0.54 (0.15), residues: 1152 loop : -1.61 (0.10), residues: 2448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 175 HIS 0.003 0.001 HIS G 307 PHE 0.023 0.002 PHE I 423 TYR 0.014 0.002 TYR A 248 ARG 0.006 0.000 ARG A 110 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 321 time to evaluate : 4.642 Fit side-chains REVERT: B 389 GLN cc_start: 0.7914 (OUTLIER) cc_final: 0.7402 (tm-30) REVERT: C 202 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7573 (mm-30) REVERT: C 389 GLN cc_start: 0.7837 (OUTLIER) cc_final: 0.7035 (tm-30) REVERT: D 285 TYR cc_start: 0.8620 (OUTLIER) cc_final: 0.8267 (t80) REVERT: E 228 MET cc_start: 0.5130 (OUTLIER) cc_final: 0.4894 (ttt) REVERT: E 389 GLN cc_start: 0.7917 (OUTLIER) cc_final: 0.7397 (tm-30) REVERT: F 202 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7556 (mm-30) REVERT: F 285 TYR cc_start: 0.8558 (OUTLIER) cc_final: 0.8141 (t80) REVERT: F 389 GLN cc_start: 0.7835 (OUTLIER) cc_final: 0.7028 (tm-30) REVERT: G 285 TYR cc_start: 0.8621 (OUTLIER) cc_final: 0.8285 (t80) REVERT: G 292 MET cc_start: 0.6829 (mtp) cc_final: 0.6558 (mtm) REVERT: H 389 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7404 (tm-30) REVERT: I 202 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7580 (mm-30) REVERT: I 389 GLN cc_start: 0.7837 (OUTLIER) cc_final: 0.7041 (tm-30) REVERT: J 202 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7567 (mm-30) REVERT: J 389 GLN cc_start: 0.7841 (OUTLIER) cc_final: 0.7044 (tm-30) REVERT: L 285 TYR cc_start: 0.8610 (OUTLIER) cc_final: 0.8199 (t80) REVERT: L 389 GLN cc_start: 0.7904 (OUTLIER) cc_final: 0.7399 (tm-30) outliers start: 119 outliers final: 78 residues processed: 413 average time/residue: 1.5109 time to fit residues: 766.3001 Evaluate side-chains 412 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 317 time to evaluate : 4.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 389 GLN Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 228 MET Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 389 GLN Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 348 THR Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 228 MET Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 348 THR Chi-restraints excluded: chain E residue 389 GLN Chi-restraints excluded: chain E residue 472 LEU Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 202 GLU Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain F residue 228 MET Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain F residue 389 GLN Chi-restraints excluded: chain F residue 402 MET Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 72 MET Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 202 GLU Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 472 LEU Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 280 VAL Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 320 THR Chi-restraints excluded: chain H residue 389 GLN Chi-restraints excluded: chain H residue 472 LEU Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain I residue 202 GLU Chi-restraints excluded: chain I residue 214 SER Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain I residue 348 THR Chi-restraints excluded: chain I residue 389 GLN Chi-restraints excluded: chain I residue 402 MET Chi-restraints excluded: chain I residue 472 LEU Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain J residue 202 GLU Chi-restraints excluded: chain J residue 214 SER Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain J residue 348 THR Chi-restraints excluded: chain J residue 389 GLN Chi-restraints excluded: chain J residue 402 MET Chi-restraints excluded: chain J residue 472 LEU Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 139 VAL Chi-restraints excluded: chain K residue 202 GLU Chi-restraints excluded: chain K residue 280 VAL Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain K residue 320 THR Chi-restraints excluded: chain K residue 378 THR Chi-restraints excluded: chain K residue 472 LEU Chi-restraints excluded: chain L residue 30 ARG Chi-restraints excluded: chain L residue 139 VAL Chi-restraints excluded: chain L residue 202 GLU Chi-restraints excluded: chain L residue 228 MET Chi-restraints excluded: chain L residue 280 VAL Chi-restraints excluded: chain L residue 285 TYR Chi-restraints excluded: chain L residue 320 THR Chi-restraints excluded: chain L residue 378 THR Chi-restraints excluded: chain L residue 389 GLN Chi-restraints excluded: chain L residue 472 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 314 optimal weight: 10.0000 chunk 203 optimal weight: 4.9990 chunk 303 optimal weight: 8.9990 chunk 153 optimal weight: 3.9990 chunk 99 optimal weight: 9.9990 chunk 98 optimal weight: 2.9990 chunk 323 optimal weight: 10.0000 chunk 346 optimal weight: 2.9990 chunk 251 optimal weight: 0.9980 chunk 47 optimal weight: 9.9990 chunk 400 optimal weight: 0.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 42564 Z= 0.237 Angle : 0.634 9.770 57660 Z= 0.339 Chirality : 0.047 0.184 6552 Planarity : 0.005 0.045 7308 Dihedral : 5.101 59.989 5836 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.58 % Allowed : 17.02 % Favored : 80.39 % 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: 0.07 (0.11), residues: 5268 helix: 1.97 (0.14), residues: 1668 sheet: 0.50 (0.15), residues: 1152 loop : -1.63 (0.10), residues: 2448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP J 175 HIS 0.004 0.001 HIS D 307 PHE 0.022 0.002 PHE I 423 TYR 0.015 0.002 TYR A 248 ARG 0.006 0.000 ARG A 110 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 316 time to evaluate : 4.948 Fit side-chains REVERT: B 389 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.7434 (tm-30) REVERT: C 202 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7576 (mm-30) REVERT: C 389 GLN cc_start: 0.7883 (OUTLIER) cc_final: 0.7072 (tm-30) REVERT: D 285 TYR cc_start: 0.8635 (OUTLIER) cc_final: 0.8227 (t80) REVERT: E 30 ARG cc_start: 0.4486 (OUTLIER) cc_final: 0.4199 (ptp-110) REVERT: E 228 MET cc_start: 0.5168 (OUTLIER) cc_final: 0.4955 (ttt) REVERT: E 389 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7430 (tm-30) REVERT: F 202 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7576 (mm-30) REVERT: F 285 TYR cc_start: 0.8588 (OUTLIER) cc_final: 0.8166 (t80) REVERT: F 389 GLN cc_start: 0.7882 (OUTLIER) cc_final: 0.7064 (tm-30) REVERT: G 285 TYR cc_start: 0.8635 (OUTLIER) cc_final: 0.8242 (t80) REVERT: G 292 MET cc_start: 0.6874 (mtp) cc_final: 0.6591 (mtm) REVERT: H 389 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7437 (tm-30) REVERT: I 202 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7582 (mm-30) REVERT: I 389 GLN cc_start: 0.7882 (OUTLIER) cc_final: 0.7078 (tm-30) REVERT: J 202 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7570 (mm-30) REVERT: J 389 GLN cc_start: 0.7885 (OUTLIER) cc_final: 0.7079 (tm-30) REVERT: L 285 TYR cc_start: 0.8619 (OUTLIER) cc_final: 0.8131 (t80) REVERT: L 389 GLN cc_start: 0.7958 (OUTLIER) cc_final: 0.7442 (tm-30) outliers start: 116 outliers final: 86 residues processed: 406 average time/residue: 1.4313 time to fit residues: 720.4222 Evaluate side-chains 415 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 311 time to evaluate : 4.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 389 GLN Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 228 MET Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 389 GLN Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 348 THR Chi-restraints excluded: chain E residue 30 ARG Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 228 MET Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 348 THR Chi-restraints excluded: chain E residue 389 GLN Chi-restraints excluded: chain E residue 472 LEU Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 202 GLU Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain F residue 228 MET Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain F residue 389 GLN Chi-restraints excluded: chain F residue 402 MET Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 202 GLU Chi-restraints excluded: chain G residue 214 SER Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 214 SER Chi-restraints excluded: chain H residue 280 VAL Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 320 THR Chi-restraints excluded: chain H residue 389 GLN Chi-restraints excluded: chain H residue 472 LEU Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain I residue 202 GLU Chi-restraints excluded: chain I residue 214 SER Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain I residue 348 THR Chi-restraints excluded: chain I residue 389 GLN Chi-restraints excluded: chain I residue 402 MET Chi-restraints excluded: chain I residue 472 LEU Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain J residue 202 GLU Chi-restraints excluded: chain J residue 214 SER Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain J residue 348 THR Chi-restraints excluded: chain J residue 389 GLN Chi-restraints excluded: chain J residue 402 MET Chi-restraints excluded: chain J residue 472 LEU Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 139 VAL Chi-restraints excluded: chain K residue 202 GLU Chi-restraints excluded: chain K residue 214 SER Chi-restraints excluded: chain K residue 280 VAL Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain K residue 320 THR Chi-restraints excluded: chain K residue 378 THR Chi-restraints excluded: chain K residue 402 MET Chi-restraints excluded: chain K residue 472 LEU Chi-restraints excluded: chain L residue 30 ARG Chi-restraints excluded: chain L residue 139 VAL Chi-restraints excluded: chain L residue 202 GLU Chi-restraints excluded: chain L residue 214 SER Chi-restraints excluded: chain L residue 228 MET Chi-restraints excluded: chain L residue 280 VAL Chi-restraints excluded: chain L residue 285 TYR Chi-restraints excluded: chain L residue 320 THR Chi-restraints excluded: chain L residue 378 THR Chi-restraints excluded: chain L residue 389 GLN Chi-restraints excluded: chain L residue 472 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 462 optimal weight: 3.9990 chunk 487 optimal weight: 9.9990 chunk 444 optimal weight: 5.9990 chunk 474 optimal weight: 4.9990 chunk 285 optimal weight: 4.9990 chunk 206 optimal weight: 7.9990 chunk 372 optimal weight: 0.0570 chunk 145 optimal weight: 3.9990 chunk 428 optimal weight: 0.7980 chunk 448 optimal weight: 6.9990 chunk 472 optimal weight: 0.3980 overall best weight: 1.8502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 42564 Z= 0.206 Angle : 0.611 14.740 57660 Z= 0.322 Chirality : 0.046 0.149 6552 Planarity : 0.005 0.044 7308 Dihedral : 4.976 59.788 5836 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.36 % Allowed : 17.29 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.11), residues: 5268 helix: 2.08 (0.14), residues: 1668 sheet: 0.55 (0.15), residues: 1152 loop : -1.61 (0.10), residues: 2448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP I 175 HIS 0.003 0.001 HIS G 307 PHE 0.021 0.002 PHE I 423 TYR 0.013 0.001 TYR A 248 ARG 0.006 0.000 ARG A 110 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 319 time to evaluate : 4.604 Fit side-chains REVERT: B 389 GLN cc_start: 0.7866 (OUTLIER) cc_final: 0.7363 (tm-30) REVERT: C 202 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7558 (mm-30) REVERT: C 389 GLN cc_start: 0.7808 (OUTLIER) cc_final: 0.7010 (tm-30) REVERT: D 285 TYR cc_start: 0.8604 (OUTLIER) cc_final: 0.8260 (t80) REVERT: E 228 MET cc_start: 0.5093 (OUTLIER) cc_final: 0.4850 (ttt) REVERT: E 389 GLN cc_start: 0.7875 (OUTLIER) cc_final: 0.7367 (tm-30) REVERT: F 202 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7582 (mm-30) REVERT: F 285 TYR cc_start: 0.8545 (OUTLIER) cc_final: 0.8135 (t80) REVERT: F 389 GLN cc_start: 0.7808 (OUTLIER) cc_final: 0.7004 (tm-30) REVERT: G 285 TYR cc_start: 0.8620 (OUTLIER) cc_final: 0.8300 (t80) REVERT: G 292 MET cc_start: 0.6832 (mtp) cc_final: 0.6611 (mtm) REVERT: H 389 GLN cc_start: 0.7872 (OUTLIER) cc_final: 0.7366 (tm-30) REVERT: I 202 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7565 (mm-30) REVERT: I 389 GLN cc_start: 0.7808 (OUTLIER) cc_final: 0.7014 (tm-30) REVERT: J 202 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7554 (mm-30) REVERT: J 389 GLN cc_start: 0.7811 (OUTLIER) cc_final: 0.7016 (tm-30) REVERT: L 285 TYR cc_start: 0.8599 (OUTLIER) cc_final: 0.8187 (t80) REVERT: L 389 GLN cc_start: 0.7865 (OUTLIER) cc_final: 0.7367 (tm-30) outliers start: 106 outliers final: 79 residues processed: 409 average time/residue: 1.4768 time to fit residues: 744.4798 Evaluate side-chains 410 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 314 time to evaluate : 4.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 389 GLN Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 228 MET Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 389 GLN Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 348 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 228 MET Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 348 THR Chi-restraints excluded: chain E residue 389 GLN Chi-restraints excluded: chain E residue 472 LEU Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 202 GLU Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain F residue 348 THR Chi-restraints excluded: chain F residue 389 GLN Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 202 GLU Chi-restraints excluded: chain G residue 214 SER Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 280 VAL Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 320 THR Chi-restraints excluded: chain H residue 389 GLN Chi-restraints excluded: chain H residue 472 LEU Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain I residue 202 GLU Chi-restraints excluded: chain I residue 214 SER Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain I residue 348 THR Chi-restraints excluded: chain I residue 389 GLN Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain J residue 202 GLU Chi-restraints excluded: chain J residue 214 SER Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain J residue 348 THR Chi-restraints excluded: chain J residue 389 GLN Chi-restraints excluded: chain J residue 402 MET Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 139 VAL Chi-restraints excluded: chain K residue 202 GLU Chi-restraints excluded: chain K residue 214 SER Chi-restraints excluded: chain K residue 280 VAL Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain K residue 320 THR Chi-restraints excluded: chain K residue 378 THR Chi-restraints excluded: chain K residue 402 MET Chi-restraints excluded: chain K residue 472 LEU Chi-restraints excluded: chain L residue 30 ARG Chi-restraints excluded: chain L residue 139 VAL Chi-restraints excluded: chain L residue 202 GLU Chi-restraints excluded: chain L residue 214 SER Chi-restraints excluded: chain L residue 228 MET Chi-restraints excluded: chain L residue 280 VAL Chi-restraints excluded: chain L residue 285 TYR Chi-restraints excluded: chain L residue 320 THR Chi-restraints excluded: chain L residue 378 THR Chi-restraints excluded: chain L residue 389 GLN Chi-restraints excluded: chain L residue 472 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 311 optimal weight: 9.9990 chunk 501 optimal weight: 2.9990 chunk 306 optimal weight: 0.9990 chunk 237 optimal weight: 0.8980 chunk 348 optimal weight: 5.9990 chunk 526 optimal weight: 0.9990 chunk 484 optimal weight: 10.0000 chunk 418 optimal weight: 9.9990 chunk 43 optimal weight: 0.8980 chunk 323 optimal weight: 9.9990 chunk 256 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 42564 Z= 0.167 Angle : 0.545 8.159 57660 Z= 0.288 Chirality : 0.044 0.148 6552 Planarity : 0.005 0.043 7308 Dihedral : 4.776 59.786 5836 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.76 % Allowed : 18.00 % Favored : 80.24 % 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: 5268 helix: 2.30 (0.14), residues: 1668 sheet: 0.65 (0.15), residues: 1152 loop : -1.59 (0.10), residues: 2448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 175 HIS 0.002 0.001 HIS G 265 PHE 0.021 0.001 PHE I 423 TYR 0.011 0.001 TYR A 248 ARG 0.005 0.000 ARG A 110 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 327 time to evaluate : 5.070 Fit side-chains REVERT: C 202 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7546 (mm-30) REVERT: C 389 GLN cc_start: 0.7702 (OUTLIER) cc_final: 0.6899 (tm-30) REVERT: D 73 MET cc_start: 0.5326 (tpp) cc_final: 0.5094 (tmm) REVERT: D 285 TYR cc_start: 0.8577 (OUTLIER) cc_final: 0.8236 (t80) REVERT: E 228 MET cc_start: 0.5216 (OUTLIER) cc_final: 0.4964 (ttt) REVERT: F 202 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7558 (mm-30) REVERT: F 285 TYR cc_start: 0.8512 (OUTLIER) cc_final: 0.8150 (t80) REVERT: F 389 GLN cc_start: 0.7702 (OUTLIER) cc_final: 0.7229 (tt0) REVERT: G 285 TYR cc_start: 0.8565 (OUTLIER) cc_final: 0.8247 (t80) REVERT: G 292 MET cc_start: 0.6798 (mtp) cc_final: 0.6568 (mtm) REVERT: H 41 ARG cc_start: 0.5753 (ttp-110) cc_final: 0.5479 (ttp-110) REVERT: I 202 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7553 (mm-30) REVERT: I 389 GLN cc_start: 0.7700 (OUTLIER) cc_final: 0.7239 (tt0) REVERT: J 202 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7541 (mm-30) REVERT: J 389 GLN cc_start: 0.7704 (OUTLIER) cc_final: 0.7241 (tt0) REVERT: L 285 TYR cc_start: 0.8526 (OUTLIER) cc_final: 0.8159 (t80) outliers start: 79 outliers final: 58 residues processed: 397 average time/residue: 1.5236 time to fit residues: 754.4002 Evaluate side-chains 393 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 322 time to evaluate : 4.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 389 GLN Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 348 THR Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 228 MET Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 348 THR Chi-restraints excluded: chain E residue 472 LEU Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 202 GLU Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain F residue 348 THR Chi-restraints excluded: chain F residue 389 GLN Chi-restraints excluded: chain G residue 202 GLU Chi-restraints excluded: chain G residue 214 SER Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 214 SER Chi-restraints excluded: chain H residue 280 VAL Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 320 THR Chi-restraints excluded: chain H residue 472 LEU Chi-restraints excluded: chain I residue 202 GLU Chi-restraints excluded: chain I residue 214 SER Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain I residue 389 GLN Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 202 GLU Chi-restraints excluded: chain J residue 214 SER Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain J residue 389 GLN Chi-restraints excluded: chain K residue 202 GLU Chi-restraints excluded: chain K residue 214 SER Chi-restraints excluded: chain K residue 280 VAL Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain K residue 320 THR Chi-restraints excluded: chain K residue 472 LEU Chi-restraints excluded: chain L residue 30 ARG Chi-restraints excluded: chain L residue 202 GLU Chi-restraints excluded: chain L residue 280 VAL Chi-restraints excluded: chain L residue 285 TYR Chi-restraints excluded: chain L residue 320 THR Chi-restraints excluded: chain L residue 472 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 332 optimal weight: 0.9980 chunk 446 optimal weight: 0.1980 chunk 128 optimal weight: 3.9990 chunk 386 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 116 optimal weight: 4.9990 chunk 419 optimal weight: 4.9990 chunk 175 optimal weight: 8.9990 chunk 430 optimal weight: 8.9990 chunk 53 optimal weight: 9.9990 chunk 77 optimal weight: 0.9980 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.207299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.154283 restraints weight = 104529.600| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 5.92 r_work: 0.3149 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3142 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3142 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 42564 Z= 0.182 Angle : 0.574 14.396 57660 Z= 0.300 Chirality : 0.045 0.143 6552 Planarity : 0.005 0.043 7308 Dihedral : 4.796 59.667 5836 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.85 % Allowed : 18.00 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.11), residues: 5268 helix: 2.32 (0.14), residues: 1668 sheet: 0.67 (0.15), residues: 1152 loop : -1.60 (0.10), residues: 2448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 175 HIS 0.002 0.001 HIS D 307 PHE 0.024 0.002 PHE I 423 TYR 0.012 0.001 TYR A 248 ARG 0.006 0.000 ARG A 110 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14199.75 seconds wall clock time: 256 minutes 3.92 seconds (15363.92 seconds total)