Starting phenix.real_space_refine on Tue Apr 16 20:25:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvg_17965/04_2024/8pvg_17965.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvg_17965/04_2024/8pvg_17965.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvg_17965/04_2024/8pvg_17965.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvg_17965/04_2024/8pvg_17965.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvg_17965/04_2024/8pvg_17965.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvg_17965/04_2024/8pvg_17965.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 252 5.16 5 C 25752 2.51 5 N 6960 2.21 5 O 7764 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 63": "OE1" <-> "OE2" Residue "A ASP 71": "OD1" <-> "OD2" Residue "A ASP 78": "OD1" <-> "OD2" Residue "A ARG 111": "NH1" <-> "NH2" Residue "A GLU 113": "OE1" <-> "OE2" Residue "A TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 191": "OD1" <-> "OD2" Residue "A GLU 235": "OE1" <-> "OE2" Residue "A TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 358": "OE1" <-> "OE2" Residue "A TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 399": "OD1" <-> "OD2" Residue "A ASP 425": "OD1" <-> "OD2" Residue "A PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 437": "OD1" <-> "OD2" Residue "A GLU 438": "OE1" <-> "OE2" Residue "A GLU 450": "OE1" <-> "OE2" Residue "B PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 63": "OE1" <-> "OE2" Residue "B ASP 71": "OD1" <-> "OD2" Residue "B ASP 78": "OD1" <-> "OD2" Residue "B ARG 111": "NH1" <-> "NH2" Residue "B GLU 113": "OE1" <-> "OE2" Residue "B TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 191": "OD1" <-> "OD2" Residue "B GLU 235": "OE1" <-> "OE2" Residue "B TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 358": "OE1" <-> "OE2" Residue "B TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 399": "OD1" <-> "OD2" Residue "B ASP 425": "OD1" <-> "OD2" Residue "B PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 437": "OD1" <-> "OD2" Residue "B GLU 438": "OE1" <-> "OE2" Residue "B GLU 450": "OE1" <-> "OE2" Residue "C PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 63": "OE1" <-> "OE2" Residue "C ASP 71": "OD1" <-> "OD2" Residue "C ASP 78": "OD1" <-> "OD2" Residue "C ARG 111": "NH1" <-> "NH2" Residue "C GLU 113": "OE1" <-> "OE2" Residue "C TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 191": "OD1" <-> "OD2" Residue "C GLU 235": "OE1" <-> "OE2" Residue "C TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 358": "OE1" <-> "OE2" Residue "C TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 399": "OD1" <-> "OD2" Residue "C ASP 425": "OD1" <-> "OD2" Residue "C PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 437": "OD1" <-> "OD2" Residue "C GLU 438": "OE1" <-> "OE2" Residue "C GLU 450": "OE1" <-> "OE2" Residue "D PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 63": "OE1" <-> "OE2" Residue "D ASP 71": "OD1" <-> "OD2" Residue "D ASP 78": "OD1" <-> "OD2" Residue "D ARG 111": "NH1" <-> "NH2" Residue "D GLU 113": "OE1" <-> "OE2" Residue "D TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 191": "OD1" <-> "OD2" Residue "D GLU 235": "OE1" <-> "OE2" Residue "D TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 358": "OE1" <-> "OE2" Residue "D TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 399": "OD1" <-> "OD2" Residue "D ASP 425": "OD1" <-> "OD2" Residue "D PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 437": "OD1" <-> "OD2" Residue "D GLU 438": "OE1" <-> "OE2" Residue "D GLU 450": "OE1" <-> "OE2" Residue "E PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 63": "OE1" <-> "OE2" Residue "E ASP 71": "OD1" <-> "OD2" Residue "E ASP 78": "OD1" <-> "OD2" Residue "E ARG 111": "NH1" <-> "NH2" Residue "E GLU 113": "OE1" <-> "OE2" Residue "E TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 191": "OD1" <-> "OD2" Residue "E GLU 235": "OE1" <-> "OE2" Residue "E TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 358": "OE1" <-> "OE2" Residue "E TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 399": "OD1" <-> "OD2" Residue "E ASP 425": "OD1" <-> "OD2" Residue "E PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 437": "OD1" <-> "OD2" Residue "E GLU 438": "OE1" <-> "OE2" Residue "E GLU 450": "OE1" <-> "OE2" Residue "F PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 63": "OE1" <-> "OE2" Residue "F ASP 71": "OD1" <-> "OD2" Residue "F ASP 78": "OD1" <-> "OD2" Residue "F ARG 111": "NH1" <-> "NH2" Residue "F GLU 113": "OE1" <-> "OE2" Residue "F TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 191": "OD1" <-> "OD2" Residue "F GLU 235": "OE1" <-> "OE2" Residue "F TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 358": "OE1" <-> "OE2" Residue "F TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 399": "OD1" <-> "OD2" Residue "F ASP 425": "OD1" <-> "OD2" Residue "F PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 437": "OD1" <-> "OD2" Residue "F GLU 438": "OE1" <-> "OE2" Residue "F GLU 450": "OE1" <-> "OE2" Residue "G PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 63": "OE1" <-> "OE2" Residue "G ASP 71": "OD1" <-> "OD2" Residue "G ASP 78": "OD1" <-> "OD2" Residue "G ARG 111": "NH1" <-> "NH2" Residue "G GLU 113": "OE1" <-> "OE2" Residue "G TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 191": "OD1" <-> "OD2" Residue "G GLU 235": "OE1" <-> "OE2" Residue "G TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 358": "OE1" <-> "OE2" Residue "G TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 399": "OD1" <-> "OD2" Residue "G ASP 425": "OD1" <-> "OD2" Residue "G PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 437": "OD1" <-> "OD2" Residue "G GLU 438": "OE1" <-> "OE2" Residue "G GLU 450": "OE1" <-> "OE2" Residue "H PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 63": "OE1" <-> "OE2" Residue "H ASP 71": "OD1" <-> "OD2" Residue "H ASP 78": "OD1" <-> "OD2" Residue "H ARG 111": "NH1" <-> "NH2" Residue "H GLU 113": "OE1" <-> "OE2" Residue "H TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 191": "OD1" <-> "OD2" Residue "H GLU 235": "OE1" <-> "OE2" Residue "H TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 358": "OE1" <-> "OE2" Residue "H TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 399": "OD1" <-> "OD2" Residue "H ASP 425": "OD1" <-> "OD2" Residue "H PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 437": "OD1" <-> "OD2" Residue "H GLU 438": "OE1" <-> "OE2" Residue "H GLU 450": "OE1" <-> "OE2" Residue "I PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 63": "OE1" <-> "OE2" Residue "I ASP 71": "OD1" <-> "OD2" Residue "I ASP 78": "OD1" <-> "OD2" Residue "I ARG 111": "NH1" <-> "NH2" Residue "I GLU 113": "OE1" <-> "OE2" Residue "I TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 191": "OD1" <-> "OD2" Residue "I GLU 235": "OE1" <-> "OE2" Residue "I TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 358": "OE1" <-> "OE2" Residue "I TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 399": "OD1" <-> "OD2" Residue "I ASP 425": "OD1" <-> "OD2" Residue "I PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 437": "OD1" <-> "OD2" Residue "I GLU 438": "OE1" <-> "OE2" Residue "I GLU 450": "OE1" <-> "OE2" Residue "J PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 63": "OE1" <-> "OE2" Residue "J ASP 71": "OD1" <-> "OD2" Residue "J ASP 78": "OD1" <-> "OD2" Residue "J ARG 111": "NH1" <-> "NH2" Residue "J GLU 113": "OE1" <-> "OE2" Residue "J TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 191": "OD1" <-> "OD2" Residue "J GLU 235": "OE1" <-> "OE2" Residue "J TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 358": "OE1" <-> "OE2" Residue "J TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 399": "OD1" <-> "OD2" Residue "J ASP 425": "OD1" <-> "OD2" Residue "J PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 437": "OD1" <-> "OD2" Residue "J GLU 438": "OE1" <-> "OE2" Residue "J GLU 450": "OE1" <-> "OE2" Residue "K PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 63": "OE1" <-> "OE2" Residue "K ASP 71": "OD1" <-> "OD2" Residue "K ASP 78": "OD1" <-> "OD2" Residue "K ARG 111": "NH1" <-> "NH2" Residue "K GLU 113": "OE1" <-> "OE2" Residue "K TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 191": "OD1" <-> "OD2" Residue "K GLU 235": "OE1" <-> "OE2" Residue "K TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 358": "OE1" <-> "OE2" Residue "K TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 399": "OD1" <-> "OD2" Residue "K ASP 425": "OD1" <-> "OD2" Residue "K PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 437": "OD1" <-> "OD2" Residue "K GLU 438": "OE1" <-> "OE2" Residue "K GLU 450": "OE1" <-> "OE2" Residue "L PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 63": "OE1" <-> "OE2" Residue "L ASP 71": "OD1" <-> "OD2" Residue "L ASP 78": "OD1" <-> "OD2" Residue "L ARG 111": "NH1" <-> "NH2" Residue "L GLU 113": "OE1" <-> "OE2" Residue "L TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 191": "OD1" <-> "OD2" Residue "L GLU 235": "OE1" <-> "OE2" Residue "L TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 358": "OE1" <-> "OE2" Residue "L TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 399": "OD1" <-> "OD2" Residue "L ASP 425": "OD1" <-> "OD2" Residue "L PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 437": "OD1" <-> "OD2" Residue "L GLU 438": "OE1" <-> "OE2" Residue "L GLU 450": "OE1" <-> "OE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 40728 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3394 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 23, 'TRANS': 411} Chain breaks: 1 Chain: "B" Number of atoms: 3394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3394 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 23, 'TRANS': 411} Chain breaks: 1 Chain: "C" Number of atoms: 3394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3394 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 23, 'TRANS': 411} Chain breaks: 1 Chain: "D" Number of atoms: 3394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3394 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 23, 'TRANS': 411} Chain breaks: 1 Chain: "E" Number of atoms: 3394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3394 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 23, 'TRANS': 411} Chain breaks: 1 Chain: "F" Number of atoms: 3394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3394 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 23, 'TRANS': 411} Chain breaks: 1 Chain: "G" Number of atoms: 3394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3394 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 23, 'TRANS': 411} Chain breaks: 1 Chain: "H" Number of atoms: 3394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3394 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 23, 'TRANS': 411} Chain breaks: 1 Chain: "I" Number of atoms: 3394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3394 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 23, 'TRANS': 411} Chain breaks: 1 Chain: "J" Number of atoms: 3394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3394 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 23, 'TRANS': 411} Chain breaks: 1 Chain: "K" Number of atoms: 3394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3394 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 23, 'TRANS': 411} Chain breaks: 1 Chain: "L" Number of atoms: 3394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3394 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 23, 'TRANS': 411} Chain breaks: 1 Time building chain proxies: 21.00, per 1000 atoms: 0.52 Number of scatterers: 40728 At special positions: 0 Unit cell: (151.434, 159.894, 115.902, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 252 16.00 O 7764 8.00 N 6960 7.00 C 25752 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: 14.98 Conformation dependent library (CDL) restraints added in 6.9 seconds 10344 Ramachandran restraints generated. 5172 Oldfield, 0 Emsley, 5172 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9720 Finding SS restraints... Secondary structure from input PDB file: 204 helices and 36 sheets defined 42.1% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.62 Creating SS restraints... Processing helix chain 'A' and resid 2 through 14 removed outlier: 3.714A pdb=" N VAL A 6 " --> pdb=" O SER A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 42 through 47 Processing helix chain 'A' and resid 72 through 75 removed outlier: 3.589A pdb=" N ALA A 75 " --> pdb=" O ALA A 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 72 through 75' Processing helix chain 'A' and resid 104 through 120 removed outlier: 3.514A pdb=" N GLY A 120 " --> pdb=" O LEU A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 203 Processing helix chain 'A' and resid 229 through 250 Processing helix chain 'A' and resid 287 through 291 Processing helix chain 'A' and resid 292 through 305 Processing helix chain 'A' and resid 305 through 314 removed outlier: 3.904A pdb=" N LEU A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 321 Processing helix chain 'A' and resid 367 through 385 Processing helix chain 'A' and resid 414 through 425 Processing helix chain 'A' and resid 426 through 431 Processing helix chain 'A' and resid 432 through 434 No H-bonds generated for 'chain 'A' and resid 432 through 434' Processing helix chain 'A' and resid 436 through 456 removed outlier: 3.968A pdb=" N GLU A 450 " --> pdb=" O LEU A 446 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG A 453 " --> pdb=" O GLU A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 467 Processing helix chain 'B' and resid 2 through 14 removed outlier: 3.714A pdb=" N VAL B 6 " --> pdb=" O SER B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 39 No H-bonds generated for 'chain 'B' and resid 37 through 39' Processing helix chain 'B' and resid 42 through 47 Processing helix chain 'B' and resid 72 through 75 removed outlier: 3.588A pdb=" N ALA B 75 " --> pdb=" O ALA B 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 72 through 75' Processing helix chain 'B' and resid 104 through 120 removed outlier: 3.515A pdb=" N GLY B 120 " --> pdb=" O LEU B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 203 Processing helix chain 'B' and resid 229 through 250 Processing helix chain 'B' and resid 287 through 291 Processing helix chain 'B' and resid 292 through 305 Processing helix chain 'B' and resid 305 through 314 removed outlier: 3.903A pdb=" N LEU B 312 " --> pdb=" O ALA B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 321 Processing helix chain 'B' and resid 367 through 385 Processing helix chain 'B' and resid 414 through 425 Processing helix chain 'B' and resid 426 through 431 Processing helix chain 'B' and resid 432 through 434 No H-bonds generated for 'chain 'B' and resid 432 through 434' Processing helix chain 'B' and resid 436 through 456 removed outlier: 3.968A pdb=" N GLU B 450 " --> pdb=" O LEU B 446 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG B 453 " --> pdb=" O GLU B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 467 Processing helix chain 'C' and resid 2 through 14 removed outlier: 3.714A pdb=" N VAL C 6 " --> pdb=" O SER C 2 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 42 through 47 Processing helix chain 'C' and resid 72 through 75 removed outlier: 3.588A pdb=" N ALA C 75 " --> pdb=" O ALA C 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 72 through 75' Processing helix chain 'C' and resid 104 through 120 removed outlier: 3.515A pdb=" N GLY C 120 " --> pdb=" O LEU C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 203 Processing helix chain 'C' and resid 229 through 250 Processing helix chain 'C' and resid 287 through 291 Processing helix chain 'C' and resid 292 through 305 Processing helix chain 'C' and resid 305 through 314 removed outlier: 3.903A pdb=" N LEU C 312 " --> pdb=" O ALA C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 321 Processing helix chain 'C' and resid 367 through 385 Processing helix chain 'C' and resid 414 through 425 Processing helix chain 'C' and resid 426 through 431 Processing helix chain 'C' and resid 432 through 434 No H-bonds generated for 'chain 'C' and resid 432 through 434' Processing helix chain 'C' and resid 436 through 456 removed outlier: 3.968A pdb=" N GLU C 450 " --> pdb=" O LEU C 446 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG C 453 " --> pdb=" O GLU C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 467 Processing helix chain 'D' and resid 2 through 14 removed outlier: 3.714A pdb=" N VAL D 6 " --> pdb=" O SER D 2 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 42 through 47 Processing helix chain 'D' and resid 72 through 75 removed outlier: 3.589A pdb=" N ALA D 75 " --> pdb=" O ALA D 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 72 through 75' Processing helix chain 'D' and resid 104 through 120 removed outlier: 3.514A pdb=" N GLY D 120 " --> pdb=" O LEU D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 203 Processing helix chain 'D' and resid 229 through 250 Processing helix chain 'D' and resid 287 through 291 Processing helix chain 'D' and resid 292 through 305 Processing helix chain 'D' and resid 305 through 314 removed outlier: 3.904A pdb=" N LEU D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 321 Processing helix chain 'D' and resid 367 through 385 Processing helix chain 'D' and resid 414 through 425 Processing helix chain 'D' and resid 426 through 431 Processing helix chain 'D' and resid 432 through 434 No H-bonds generated for 'chain 'D' and resid 432 through 434' Processing helix chain 'D' and resid 436 through 456 removed outlier: 3.968A pdb=" N GLU D 450 " --> pdb=" O LEU D 446 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG D 453 " --> pdb=" O GLU D 449 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 467 Processing helix chain 'E' and resid 2 through 14 removed outlier: 3.714A pdb=" N VAL E 6 " --> pdb=" O SER E 2 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 39 No H-bonds generated for 'chain 'E' and resid 37 through 39' Processing helix chain 'E' and resid 42 through 47 Processing helix chain 'E' and resid 72 through 75 removed outlier: 3.588A pdb=" N ALA E 75 " --> pdb=" O ALA E 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 72 through 75' Processing helix chain 'E' and resid 104 through 120 removed outlier: 3.515A pdb=" N GLY E 120 " --> pdb=" O LEU E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 203 Processing helix chain 'E' and resid 229 through 250 Processing helix chain 'E' and resid 287 through 291 Processing helix chain 'E' and resid 292 through 305 Processing helix chain 'E' and resid 305 through 314 removed outlier: 3.903A pdb=" N LEU E 312 " --> pdb=" O ALA E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 321 Processing helix chain 'E' and resid 367 through 385 Processing helix chain 'E' and resid 414 through 425 Processing helix chain 'E' and resid 426 through 431 Processing helix chain 'E' and resid 432 through 434 No H-bonds generated for 'chain 'E' and resid 432 through 434' Processing helix chain 'E' and resid 436 through 456 removed outlier: 3.968A pdb=" N GLU E 450 " --> pdb=" O LEU E 446 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG E 453 " --> pdb=" O GLU E 449 " (cutoff:3.500A) Processing helix chain 'E' and resid 459 through 467 Processing helix chain 'F' and resid 2 through 14 removed outlier: 3.714A pdb=" N VAL F 6 " --> pdb=" O SER F 2 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 39 No H-bonds generated for 'chain 'F' and resid 37 through 39' Processing helix chain 'F' and resid 42 through 47 Processing helix chain 'F' and resid 72 through 75 removed outlier: 3.588A pdb=" N ALA F 75 " --> pdb=" O ALA F 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 72 through 75' Processing helix chain 'F' and resid 104 through 120 removed outlier: 3.515A pdb=" N GLY F 120 " --> pdb=" O LEU F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 203 Processing helix chain 'F' and resid 229 through 250 Processing helix chain 'F' and resid 287 through 291 Processing helix chain 'F' and resid 292 through 305 Processing helix chain 'F' and resid 305 through 314 removed outlier: 3.903A pdb=" N LEU F 312 " --> pdb=" O ALA F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 321 Processing helix chain 'F' and resid 367 through 385 Processing helix chain 'F' and resid 414 through 425 Processing helix chain 'F' and resid 426 through 431 Processing helix chain 'F' and resid 432 through 434 No H-bonds generated for 'chain 'F' and resid 432 through 434' Processing helix chain 'F' and resid 436 through 456 removed outlier: 3.968A pdb=" N GLU F 450 " --> pdb=" O LEU F 446 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG F 453 " --> pdb=" O GLU F 449 " (cutoff:3.500A) Processing helix chain 'F' and resid 459 through 467 Processing helix chain 'G' and resid 2 through 14 removed outlier: 3.714A pdb=" N VAL G 6 " --> pdb=" O SER G 2 " (cutoff:3.500A) Processing helix chain 'G' and resid 37 through 39 No H-bonds generated for 'chain 'G' and resid 37 through 39' Processing helix chain 'G' and resid 42 through 47 Processing helix chain 'G' and resid 72 through 75 removed outlier: 3.589A pdb=" N ALA G 75 " --> pdb=" O ALA G 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 72 through 75' Processing helix chain 'G' and resid 104 through 120 removed outlier: 3.514A pdb=" N GLY G 120 " --> pdb=" O LEU G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 203 Processing helix chain 'G' and resid 229 through 250 Processing helix chain 'G' and resid 287 through 291 Processing helix chain 'G' and resid 292 through 305 Processing helix chain 'G' and resid 305 through 314 removed outlier: 3.904A pdb=" N LEU G 312 " --> pdb=" O ALA G 308 " (cutoff:3.500A) Processing helix chain 'G' and resid 317 through 321 Processing helix chain 'G' and resid 367 through 385 Processing helix chain 'G' and resid 414 through 425 Processing helix chain 'G' and resid 426 through 431 Processing helix chain 'G' and resid 432 through 434 No H-bonds generated for 'chain 'G' and resid 432 through 434' Processing helix chain 'G' and resid 436 through 456 removed outlier: 3.968A pdb=" N GLU G 450 " --> pdb=" O LEU G 446 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG G 453 " --> pdb=" O GLU G 449 " (cutoff:3.500A) Processing helix chain 'G' and resid 459 through 467 Processing helix chain 'H' and resid 2 through 14 removed outlier: 3.714A pdb=" N VAL H 6 " --> pdb=" O SER H 2 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 39 No H-bonds generated for 'chain 'H' and resid 37 through 39' Processing helix chain 'H' and resid 42 through 47 Processing helix chain 'H' and resid 72 through 75 removed outlier: 3.588A pdb=" N ALA H 75 " --> pdb=" O ALA H 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 72 through 75' Processing helix chain 'H' and resid 104 through 120 removed outlier: 3.515A pdb=" N GLY H 120 " --> pdb=" O LEU H 116 " (cutoff:3.500A) Processing helix chain 'H' and resid 190 through 203 Processing helix chain 'H' and resid 229 through 250 Processing helix chain 'H' and resid 287 through 291 Processing helix chain 'H' and resid 292 through 305 Processing helix chain 'H' and resid 305 through 314 removed outlier: 3.903A pdb=" N LEU H 312 " --> pdb=" O ALA H 308 " (cutoff:3.500A) Processing helix chain 'H' and resid 317 through 321 Processing helix chain 'H' and resid 367 through 385 Processing helix chain 'H' and resid 414 through 425 Processing helix chain 'H' and resid 426 through 431 Processing helix chain 'H' and resid 432 through 434 No H-bonds generated for 'chain 'H' and resid 432 through 434' Processing helix chain 'H' and resid 436 through 456 removed outlier: 3.968A pdb=" N GLU H 450 " --> pdb=" O LEU H 446 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG H 453 " --> pdb=" O GLU H 449 " (cutoff:3.500A) Processing helix chain 'H' and resid 459 through 467 Processing helix chain 'I' and resid 2 through 14 removed outlier: 3.714A pdb=" N VAL I 6 " --> pdb=" O SER I 2 " (cutoff:3.500A) Processing helix chain 'I' and resid 37 through 39 No H-bonds generated for 'chain 'I' and resid 37 through 39' Processing helix chain 'I' and resid 42 through 47 Processing helix chain 'I' and resid 72 through 75 removed outlier: 3.588A pdb=" N ALA I 75 " --> pdb=" O ALA I 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 72 through 75' Processing helix chain 'I' and resid 104 through 120 removed outlier: 3.515A pdb=" N GLY I 120 " --> pdb=" O LEU I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 190 through 203 Processing helix chain 'I' and resid 229 through 250 Processing helix chain 'I' and resid 287 through 291 Processing helix chain 'I' and resid 292 through 305 Processing helix chain 'I' and resid 305 through 314 removed outlier: 3.903A pdb=" N LEU I 312 " --> pdb=" O ALA I 308 " (cutoff:3.500A) Processing helix chain 'I' and resid 317 through 321 Processing helix chain 'I' and resid 367 through 385 Processing helix chain 'I' and resid 414 through 425 Processing helix chain 'I' and resid 426 through 431 Processing helix chain 'I' and resid 432 through 434 No H-bonds generated for 'chain 'I' and resid 432 through 434' Processing helix chain 'I' and resid 436 through 456 removed outlier: 3.968A pdb=" N GLU I 450 " --> pdb=" O LEU I 446 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG I 453 " --> pdb=" O GLU I 449 " (cutoff:3.500A) Processing helix chain 'I' and resid 459 through 467 Processing helix chain 'J' and resid 2 through 14 removed outlier: 3.714A pdb=" N VAL J 6 " --> pdb=" O SER J 2 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 39 No H-bonds generated for 'chain 'J' and resid 37 through 39' Processing helix chain 'J' and resid 42 through 47 Processing helix chain 'J' and resid 72 through 75 removed outlier: 3.589A pdb=" N ALA J 75 " --> pdb=" O ALA J 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 72 through 75' Processing helix chain 'J' and resid 104 through 120 removed outlier: 3.514A pdb=" N GLY J 120 " --> pdb=" O LEU J 116 " (cutoff:3.500A) Processing helix chain 'J' and resid 190 through 203 Processing helix chain 'J' and resid 229 through 250 Processing helix chain 'J' and resid 287 through 291 Processing helix chain 'J' and resid 292 through 305 Processing helix chain 'J' and resid 305 through 314 removed outlier: 3.904A pdb=" N LEU J 312 " --> pdb=" O ALA J 308 " (cutoff:3.500A) Processing helix chain 'J' and resid 317 through 321 Processing helix chain 'J' and resid 367 through 385 Processing helix chain 'J' and resid 414 through 425 Processing helix chain 'J' and resid 426 through 431 Processing helix chain 'J' and resid 432 through 434 No H-bonds generated for 'chain 'J' and resid 432 through 434' Processing helix chain 'J' and resid 436 through 456 removed outlier: 3.968A pdb=" N GLU J 450 " --> pdb=" O LEU J 446 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG J 453 " --> pdb=" O GLU J 449 " (cutoff:3.500A) Processing helix chain 'J' and resid 459 through 467 Processing helix chain 'K' and resid 2 through 14 removed outlier: 3.714A pdb=" N VAL K 6 " --> pdb=" O SER K 2 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 39 No H-bonds generated for 'chain 'K' and resid 37 through 39' Processing helix chain 'K' and resid 42 through 47 Processing helix chain 'K' and resid 72 through 75 removed outlier: 3.588A pdb=" N ALA K 75 " --> pdb=" O ALA K 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 72 through 75' Processing helix chain 'K' and resid 104 through 120 removed outlier: 3.515A pdb=" N GLY K 120 " --> pdb=" O LEU K 116 " (cutoff:3.500A) Processing helix chain 'K' and resid 190 through 203 Processing helix chain 'K' and resid 229 through 250 Processing helix chain 'K' and resid 287 through 291 Processing helix chain 'K' and resid 292 through 305 Processing helix chain 'K' and resid 305 through 314 removed outlier: 3.903A pdb=" N LEU K 312 " --> pdb=" O ALA K 308 " (cutoff:3.500A) Processing helix chain 'K' and resid 317 through 321 Processing helix chain 'K' and resid 367 through 385 Processing helix chain 'K' and resid 414 through 425 Processing helix chain 'K' and resid 426 through 431 Processing helix chain 'K' and resid 432 through 434 No H-bonds generated for 'chain 'K' and resid 432 through 434' Processing helix chain 'K' and resid 436 through 456 removed outlier: 3.968A pdb=" N GLU K 450 " --> pdb=" O LEU K 446 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG K 453 " --> pdb=" O GLU K 449 " (cutoff:3.500A) Processing helix chain 'K' and resid 459 through 467 Processing helix chain 'L' and resid 2 through 14 removed outlier: 3.714A pdb=" N VAL L 6 " --> pdb=" O SER L 2 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 39 No H-bonds generated for 'chain 'L' and resid 37 through 39' Processing helix chain 'L' and resid 42 through 47 Processing helix chain 'L' and resid 72 through 75 removed outlier: 3.588A pdb=" N ALA L 75 " --> pdb=" O ALA L 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 72 through 75' Processing helix chain 'L' and resid 104 through 120 removed outlier: 3.515A pdb=" N GLY L 120 " --> pdb=" O LEU L 116 " (cutoff:3.500A) Processing helix chain 'L' and resid 190 through 203 Processing helix chain 'L' and resid 229 through 250 Processing helix chain 'L' and resid 287 through 291 Processing helix chain 'L' and resid 292 through 305 Processing helix chain 'L' and resid 305 through 314 removed outlier: 3.903A pdb=" N LEU L 312 " --> pdb=" O ALA L 308 " (cutoff:3.500A) Processing helix chain 'L' and resid 317 through 321 Processing helix chain 'L' and resid 367 through 385 Processing helix chain 'L' and resid 414 through 425 Processing helix chain 'L' and resid 426 through 431 Processing helix chain 'L' and resid 432 through 434 No H-bonds generated for 'chain 'L' and resid 432 through 434' Processing helix chain 'L' and resid 436 through 456 removed outlier: 3.968A pdb=" N GLU L 450 " --> pdb=" O LEU L 446 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG L 453 " --> pdb=" O GLU L 449 " (cutoff:3.500A) Processing helix chain 'L' and resid 459 through 467 Processing sheet with id= 1, first strand: chain 'A' and resid 17 through 23 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 29 through 35 current: chain 'A' and resid 66 through 70 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 66 through 70 current: chain 'A' and resid 85 through 93 Processing sheet with id= 2, first strand: chain 'A' and resid 124 through 136 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 124 through 136 current: chain 'A' and resid 219 through 224 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 219 through 224 current: chain 'A' and resid 280 through 281 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 280 through 281 current: chain 'A' and resid 342 through 345 Processing sheet with id= 3, first strand: chain 'A' and resid 138 through 144 removed outlier: 3.766A pdb=" N GLY A 147 " --> pdb=" O SER A 144 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'B' and resid 17 through 23 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 29 through 35 current: chain 'B' and resid 66 through 70 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 66 through 70 current: chain 'B' and resid 85 through 93 Processing sheet with id= 5, first strand: chain 'B' and resid 124 through 136 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 124 through 136 current: chain 'B' and resid 219 through 224 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 219 through 224 current: chain 'B' and resid 280 through 281 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 280 through 281 current: chain 'B' and resid 342 through 345 Processing sheet with id= 6, first strand: chain 'B' and resid 138 through 144 removed outlier: 3.766A pdb=" N GLY B 147 " --> pdb=" O SER B 144 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'C' and resid 17 through 23 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 29 through 35 current: chain 'C' and resid 66 through 70 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 66 through 70 current: chain 'C' and resid 85 through 93 Processing sheet with id= 8, first strand: chain 'C' and resid 124 through 136 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 124 through 136 current: chain 'C' and resid 219 through 224 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 219 through 224 current: chain 'C' and resid 280 through 281 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 280 through 281 current: chain 'C' and resid 342 through 345 Processing sheet with id= 9, first strand: chain 'C' and resid 138 through 144 removed outlier: 3.766A pdb=" N GLY C 147 " --> pdb=" O SER C 144 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'D' and resid 17 through 23 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 29 through 35 current: chain 'D' and resid 66 through 70 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 66 through 70 current: chain 'D' and resid 85 through 93 Processing sheet with id= 11, first strand: chain 'D' and resid 124 through 136 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 124 through 136 current: chain 'D' and resid 219 through 224 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 219 through 224 current: chain 'D' and resid 280 through 281 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 280 through 281 current: chain 'D' and resid 342 through 345 Processing sheet with id= 12, first strand: chain 'D' and resid 138 through 144 removed outlier: 3.766A pdb=" N GLY D 147 " --> pdb=" O SER D 144 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'E' and resid 17 through 23 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 29 through 35 current: chain 'E' and resid 66 through 70 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 66 through 70 current: chain 'E' and resid 85 through 93 Processing sheet with id= 14, first strand: chain 'E' and resid 124 through 136 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 124 through 136 current: chain 'E' and resid 219 through 224 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 219 through 224 current: chain 'E' and resid 280 through 281 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 280 through 281 current: chain 'E' and resid 342 through 345 Processing sheet with id= 15, first strand: chain 'E' and resid 138 through 144 removed outlier: 3.766A pdb=" N GLY E 147 " --> pdb=" O SER E 144 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'F' and resid 17 through 23 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 29 through 35 current: chain 'F' and resid 66 through 70 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 66 through 70 current: chain 'F' and resid 85 through 93 Processing sheet with id= 17, first strand: chain 'F' and resid 124 through 136 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 124 through 136 current: chain 'F' and resid 219 through 224 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 219 through 224 current: chain 'F' and resid 280 through 281 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 280 through 281 current: chain 'F' and resid 342 through 345 Processing sheet with id= 18, first strand: chain 'F' and resid 138 through 144 removed outlier: 3.766A pdb=" N GLY F 147 " --> pdb=" O SER F 144 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'G' and resid 17 through 23 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 29 through 35 current: chain 'G' and resid 66 through 70 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 66 through 70 current: chain 'G' and resid 85 through 93 Processing sheet with id= 20, first strand: chain 'G' and resid 124 through 136 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 124 through 136 current: chain 'G' and resid 219 through 224 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 219 through 224 current: chain 'G' and resid 280 through 281 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 280 through 281 current: chain 'G' and resid 342 through 345 Processing sheet with id= 21, first strand: chain 'G' and resid 138 through 144 removed outlier: 3.766A pdb=" N GLY G 147 " --> pdb=" O SER G 144 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'H' and resid 17 through 23 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 29 through 35 current: chain 'H' and resid 66 through 70 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 66 through 70 current: chain 'H' and resid 85 through 93 Processing sheet with id= 23, first strand: chain 'H' and resid 124 through 136 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 124 through 136 current: chain 'H' and resid 219 through 224 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 219 through 224 current: chain 'H' and resid 280 through 281 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 280 through 281 current: chain 'H' and resid 342 through 345 Processing sheet with id= 24, first strand: chain 'H' and resid 138 through 144 removed outlier: 3.766A pdb=" N GLY H 147 " --> pdb=" O SER H 144 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'I' and resid 17 through 23 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 29 through 35 current: chain 'I' and resid 66 through 70 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 66 through 70 current: chain 'I' and resid 85 through 93 Processing sheet with id= 26, first strand: chain 'I' and resid 124 through 136 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 124 through 136 current: chain 'I' and resid 219 through 224 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 219 through 224 current: chain 'I' and resid 280 through 281 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 280 through 281 current: chain 'I' and resid 342 through 345 Processing sheet with id= 27, first strand: chain 'I' and resid 138 through 144 removed outlier: 3.766A pdb=" N GLY I 147 " --> pdb=" O SER I 144 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'J' and resid 17 through 23 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 29 through 35 current: chain 'J' and resid 66 through 70 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 66 through 70 current: chain 'J' and resid 85 through 93 Processing sheet with id= 29, first strand: chain 'J' and resid 124 through 136 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 124 through 136 current: chain 'J' and resid 219 through 224 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 219 through 224 current: chain 'J' and resid 280 through 281 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 280 through 281 current: chain 'J' and resid 342 through 345 Processing sheet with id= 30, first strand: chain 'J' and resid 138 through 144 removed outlier: 3.766A pdb=" N GLY J 147 " --> pdb=" O SER J 144 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'K' and resid 17 through 23 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 29 through 35 current: chain 'K' and resid 66 through 70 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 66 through 70 current: chain 'K' and resid 85 through 93 Processing sheet with id= 32, first strand: chain 'K' and resid 124 through 136 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 124 through 136 current: chain 'K' and resid 219 through 224 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 219 through 224 current: chain 'K' and resid 280 through 281 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 280 through 281 current: chain 'K' and resid 342 through 345 Processing sheet with id= 33, first strand: chain 'K' and resid 138 through 144 removed outlier: 3.766A pdb=" N GLY K 147 " --> pdb=" O SER K 144 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'L' and resid 17 through 23 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 29 through 35 current: chain 'L' and resid 66 through 70 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 66 through 70 current: chain 'L' and resid 85 through 93 Processing sheet with id= 35, first strand: chain 'L' and resid 124 through 136 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 124 through 136 current: chain 'L' and resid 219 through 224 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 219 through 224 current: chain 'L' and resid 280 through 281 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 280 through 281 current: chain 'L' and resid 342 through 345 Processing sheet with id= 36, first strand: chain 'L' and resid 138 through 144 removed outlier: 3.766A pdb=" N GLY L 147 " --> pdb=" O SER L 144 " (cutoff:3.500A) 1548 hydrogen bonds defined for protein. 4464 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: 13.88 Time building geometry restraints manager: 16.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8988 1.34 - 1.46: 13428 1.46 - 1.58: 18756 1.58 - 1.71: 0 1.71 - 1.83: 456 Bond restraints: 41628 Sorted by residual: bond pdb=" C ILE I 408 " pdb=" N PRO I 409 " ideal model delta sigma weight residual 1.332 1.371 -0.040 1.30e-02 5.92e+03 9.26e+00 bond pdb=" C ILE C 408 " pdb=" N PRO C 409 " ideal model delta sigma weight residual 1.332 1.371 -0.040 1.30e-02 5.92e+03 9.26e+00 bond pdb=" C ILE F 408 " pdb=" N PRO F 409 " ideal model delta sigma weight residual 1.332 1.371 -0.040 1.30e-02 5.92e+03 9.26e+00 bond pdb=" C ILE K 408 " pdb=" N PRO K 409 " ideal model delta sigma weight residual 1.332 1.371 -0.040 1.30e-02 5.92e+03 9.26e+00 bond pdb=" C ILE A 408 " pdb=" N PRO A 409 " ideal model delta sigma weight residual 1.332 1.371 -0.040 1.30e-02 5.92e+03 9.24e+00 ... (remaining 41623 not shown) Histogram of bond angle deviations from ideal: 98.11 - 105.62: 1272 105.62 - 113.12: 19172 113.12 - 120.62: 21808 120.62 - 128.13: 13764 128.13 - 135.63: 288 Bond angle restraints: 56304 Sorted by residual: angle pdb=" CA PHE F 398 " pdb=" CB PHE F 398 " pdb=" CG PHE F 398 " ideal model delta sigma weight residual 113.80 121.44 -7.64 1.00e+00 1.00e+00 5.84e+01 angle pdb=" CA PHE K 398 " pdb=" CB PHE K 398 " pdb=" CG PHE K 398 " ideal model delta sigma weight residual 113.80 121.44 -7.64 1.00e+00 1.00e+00 5.84e+01 angle pdb=" CA PHE I 398 " pdb=" CB PHE I 398 " pdb=" CG PHE I 398 " ideal model delta sigma weight residual 113.80 121.44 -7.64 1.00e+00 1.00e+00 5.84e+01 angle pdb=" CA PHE C 398 " pdb=" CB PHE C 398 " pdb=" CG PHE C 398 " ideal model delta sigma weight residual 113.80 121.44 -7.64 1.00e+00 1.00e+00 5.84e+01 angle pdb=" CA PHE H 398 " pdb=" CB PHE H 398 " pdb=" CG PHE H 398 " ideal model delta sigma weight residual 113.80 121.41 -7.61 1.00e+00 1.00e+00 5.79e+01 ... (remaining 56299 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.66: 22668 16.66 - 33.33: 1920 33.33 - 49.99: 444 49.99 - 66.66: 96 66.66 - 83.32: 36 Dihedral angle restraints: 25164 sinusoidal: 10080 harmonic: 15084 Sorted by residual: dihedral pdb=" CA SER F 64 " pdb=" C SER F 64 " pdb=" N ASP F 65 " pdb=" CA ASP F 65 " ideal model delta harmonic sigma weight residual -180.00 -152.44 -27.56 0 5.00e+00 4.00e-02 3.04e+01 dihedral pdb=" CA SER C 64 " pdb=" C SER C 64 " pdb=" N ASP C 65 " pdb=" CA ASP C 65 " ideal model delta harmonic sigma weight residual 180.00 -152.44 -27.56 0 5.00e+00 4.00e-02 3.04e+01 dihedral pdb=" CA SER I 64 " pdb=" C SER I 64 " pdb=" N ASP I 65 " pdb=" CA ASP I 65 " ideal model delta harmonic sigma weight residual 180.00 -152.44 -27.56 0 5.00e+00 4.00e-02 3.04e+01 ... (remaining 25161 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 3152 0.048 - 0.095: 1612 0.095 - 0.143: 968 0.143 - 0.190: 328 0.190 - 0.238: 72 Chirality restraints: 6132 Sorted by residual: chirality pdb=" CA HIS F 210 " pdb=" N HIS F 210 " pdb=" C HIS F 210 " pdb=" CB HIS F 210 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CA HIS I 210 " pdb=" N HIS I 210 " pdb=" C HIS I 210 " pdb=" CB HIS I 210 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CA HIS C 210 " pdb=" N HIS C 210 " pdb=" C HIS C 210 " pdb=" CB HIS C 210 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.41e+00 ... (remaining 6129 not shown) Planarity restraints: 7452 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE G 398 " 0.038 2.00e-02 2.50e+03 2.48e-02 1.08e+01 pdb=" CG PHE G 398 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE G 398 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 PHE G 398 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE G 398 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 PHE G 398 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE G 398 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE J 398 " 0.038 2.00e-02 2.50e+03 2.48e-02 1.08e+01 pdb=" CG PHE J 398 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE J 398 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 PHE J 398 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE J 398 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 PHE J 398 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE J 398 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 398 " -0.038 2.00e-02 2.50e+03 2.48e-02 1.08e+01 pdb=" CG PHE D 398 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE D 398 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 PHE D 398 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE D 398 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 PHE D 398 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE D 398 " -0.019 2.00e-02 2.50e+03 ... (remaining 7449 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 1140 2.70 - 3.25: 38772 3.25 - 3.80: 63084 3.80 - 4.35: 92504 4.35 - 4.90: 148924 Nonbonded interactions: 344424 Sorted by model distance: nonbonded pdb=" O LEU I 282 " pdb=" OG SER I 292 " model vdw 2.147 2.440 nonbonded pdb=" O LEU C 282 " pdb=" OG SER C 292 " model vdw 2.147 2.440 nonbonded pdb=" O LEU F 282 " pdb=" OG SER F 292 " model vdw 2.147 2.440 nonbonded pdb=" O LEU K 282 " pdb=" OG SER K 292 " model vdw 2.147 2.440 nonbonded pdb=" O LEU J 282 " pdb=" OG SER J 292 " model vdw 2.148 2.440 ... (remaining 344419 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.390 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: 0.050 Extract box with map and model: 14.880 Check model and map are aligned: 0.620 Set scattering table: 0.390 Process input model: 98.900 Find NCS groups from input model: 2.940 Set up NCS constraints: 0.310 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 124.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.043 41628 Z= 0.607 Angle : 1.543 8.585 56304 Z= 1.023 Chirality : 0.076 0.238 6132 Planarity : 0.007 0.047 7452 Dihedral : 14.003 83.320 15444 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.10 % Allowed : 4.14 % Favored : 94.75 % Cbeta Deviations : 0.25 % 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: -0.95 (0.11), residues: 5172 helix: 0.02 (0.11), residues: 1944 sheet: -0.47 (0.15), residues: 1140 loop : -1.22 (0.13), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.006 TRP I 58 HIS 0.028 0.005 HIS J 210 PHE 0.038 0.006 PHE B 398 TYR 0.022 0.006 TYR C 101 ARG 0.031 0.006 ARG J 193 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10344 Ramachandran restraints generated. 5172 Oldfield, 0 Emsley, 5172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10344 Ramachandran restraints generated. 5172 Oldfield, 0 Emsley, 5172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1100 residues out of total 4344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 1052 time to evaluate : 4.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.9255 (ttm) cc_final: 0.9005 (ttm) REVERT: A 14 GLU cc_start: 0.8512 (tp30) cc_final: 0.7734 (tm-30) REVERT: A 19 ASP cc_start: 0.8368 (t70) cc_final: 0.7832 (t0) REVERT: A 28 LYS cc_start: 0.8073 (tptm) cc_final: 0.7859 (ttpp) REVERT: A 30 GLN cc_start: 0.8025 (mm-40) cc_final: 0.7340 (mp10) REVERT: A 38 GLN cc_start: 0.8659 (mm110) cc_final: 0.8374 (mm110) REVERT: A 69 MET cc_start: 0.8601 (tpp) cc_final: 0.8100 (mmm) REVERT: A 94 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8204 (mp0) REVERT: A 208 GLU cc_start: 0.7981 (pt0) cc_final: 0.7702 (mt-10) REVERT: A 216 THR cc_start: 0.8643 (m) cc_final: 0.8325 (p) REVERT: A 229 MET cc_start: 0.8964 (ttm) cc_final: 0.8636 (ttm) REVERT: A 353 LYS cc_start: 0.9514 (mttt) cc_final: 0.9288 (tppt) REVERT: A 393 MET cc_start: 0.8904 (mmt) cc_final: 0.8678 (mmm) REVERT: A 437 ASP cc_start: 0.8320 (m-30) cc_final: 0.8097 (m-30) REVERT: B 14 GLU cc_start: 0.8495 (tp30) cc_final: 0.7838 (tm-30) REVERT: B 19 ASP cc_start: 0.8202 (t70) cc_final: 0.7878 (t0) REVERT: B 30 GLN cc_start: 0.7955 (mm-40) cc_final: 0.7335 (mp10) REVERT: B 38 GLN cc_start: 0.8578 (mm110) cc_final: 0.8277 (mm110) REVERT: B 69 MET cc_start: 0.8562 (tpp) cc_final: 0.8056 (tpt) REVERT: B 94 GLU cc_start: 0.8425 (mt-10) cc_final: 0.8051 (mp0) REVERT: B 99 GLN cc_start: 0.8477 (mm-40) cc_final: 0.8145 (tt0) REVERT: B 137 ASP cc_start: 0.8665 (t0) cc_final: 0.8458 (m-30) REVERT: B 208 GLU cc_start: 0.7953 (pt0) cc_final: 0.7388 (mt-10) REVERT: B 216 THR cc_start: 0.8605 (m) cc_final: 0.8165 (p) REVERT: B 353 LYS cc_start: 0.9517 (mttt) cc_final: 0.9307 (tppt) REVERT: B 437 ASP cc_start: 0.8385 (m-30) cc_final: 0.8174 (m-30) REVERT: C 14 GLU cc_start: 0.8480 (tp30) cc_final: 0.7775 (tm-30) REVERT: C 28 LYS cc_start: 0.8139 (tptm) cc_final: 0.7936 (ttpp) REVERT: C 30 GLN cc_start: 0.7988 (mm-40) cc_final: 0.7252 (mp10) REVERT: C 38 GLN cc_start: 0.8533 (mm110) cc_final: 0.8275 (mm110) REVERT: C 69 MET cc_start: 0.8644 (tpp) cc_final: 0.8157 (tpt) REVERT: C 94 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8152 (mp0) REVERT: C 137 ASP cc_start: 0.8669 (t0) cc_final: 0.8425 (m-30) REVERT: C 208 GLU cc_start: 0.7995 (pt0) cc_final: 0.7567 (mt-10) REVERT: C 216 THR cc_start: 0.8605 (m) cc_final: 0.8240 (p) REVERT: C 353 LYS cc_start: 0.9533 (mttt) cc_final: 0.9285 (tppt) REVERT: C 393 MET cc_start: 0.8922 (mmt) cc_final: 0.8704 (mmm) REVERT: D 9 MET cc_start: 0.9255 (ttm) cc_final: 0.9006 (ttm) REVERT: D 14 GLU cc_start: 0.8510 (tp30) cc_final: 0.7733 (tm-30) REVERT: D 19 ASP cc_start: 0.8367 (t70) cc_final: 0.7830 (t0) REVERT: D 28 LYS cc_start: 0.8070 (tptm) cc_final: 0.7860 (ttpp) REVERT: D 30 GLN cc_start: 0.8023 (mm-40) cc_final: 0.7340 (mp10) REVERT: D 38 GLN cc_start: 0.8659 (mm110) cc_final: 0.8373 (mm110) REVERT: D 69 MET cc_start: 0.8598 (tpp) cc_final: 0.8097 (mmm) REVERT: D 94 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8203 (mp0) REVERT: D 208 GLU cc_start: 0.7982 (pt0) cc_final: 0.7701 (mt-10) REVERT: D 216 THR cc_start: 0.8646 (m) cc_final: 0.8329 (p) REVERT: D 229 MET cc_start: 0.8967 (ttm) cc_final: 0.8639 (ttm) REVERT: D 353 LYS cc_start: 0.9515 (mttt) cc_final: 0.9290 (tppt) REVERT: D 393 MET cc_start: 0.8901 (mmt) cc_final: 0.8676 (mmm) REVERT: D 437 ASP cc_start: 0.8326 (m-30) cc_final: 0.8102 (m-30) REVERT: E 14 GLU cc_start: 0.8496 (tp30) cc_final: 0.7839 (tm-30) REVERT: E 19 ASP cc_start: 0.8204 (t70) cc_final: 0.7876 (t0) REVERT: E 30 GLN cc_start: 0.7953 (mm-40) cc_final: 0.7330 (mp10) REVERT: E 38 GLN cc_start: 0.8575 (mm110) cc_final: 0.8273 (mm110) REVERT: E 69 MET cc_start: 0.8561 (tpp) cc_final: 0.8052 (tpt) REVERT: E 94 GLU cc_start: 0.8421 (mt-10) cc_final: 0.8049 (mp0) REVERT: E 99 GLN cc_start: 0.8477 (mm-40) cc_final: 0.8147 (tt0) REVERT: E 137 ASP cc_start: 0.8662 (t0) cc_final: 0.8458 (m-30) REVERT: E 208 GLU cc_start: 0.7950 (pt0) cc_final: 0.7386 (mt-10) REVERT: E 216 THR cc_start: 0.8607 (m) cc_final: 0.8165 (p) REVERT: E 353 LYS cc_start: 0.9516 (mttt) cc_final: 0.9306 (tppt) REVERT: E 437 ASP cc_start: 0.8383 (m-30) cc_final: 0.8172 (m-30) REVERT: F 14 GLU cc_start: 0.8481 (tp30) cc_final: 0.7775 (tm-30) REVERT: F 28 LYS cc_start: 0.8141 (tptm) cc_final: 0.7939 (ttpp) REVERT: F 30 GLN cc_start: 0.7989 (mm-40) cc_final: 0.7254 (mp10) REVERT: F 38 GLN cc_start: 0.8534 (mm110) cc_final: 0.8276 (mm110) REVERT: F 69 MET cc_start: 0.8642 (tpp) cc_final: 0.8154 (tpt) REVERT: F 94 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8153 (mp0) REVERT: F 137 ASP cc_start: 0.8671 (t0) cc_final: 0.8427 (m-30) REVERT: F 208 GLU cc_start: 0.7998 (pt0) cc_final: 0.7569 (mt-10) REVERT: F 216 THR cc_start: 0.8600 (m) cc_final: 0.8236 (p) REVERT: F 353 LYS cc_start: 0.9533 (mttt) cc_final: 0.9286 (tppt) REVERT: F 393 MET cc_start: 0.8923 (mmt) cc_final: 0.8706 (mmm) REVERT: G 9 MET cc_start: 0.9254 (ttm) cc_final: 0.9005 (ttm) REVERT: G 14 GLU cc_start: 0.8510 (tp30) cc_final: 0.7733 (tm-30) REVERT: G 19 ASP cc_start: 0.8371 (t70) cc_final: 0.7830 (t0) REVERT: G 28 LYS cc_start: 0.8071 (tptm) cc_final: 0.7859 (ttpp) REVERT: G 30 GLN cc_start: 0.8025 (mm-40) cc_final: 0.7337 (mp10) REVERT: G 38 GLN cc_start: 0.8656 (mm110) cc_final: 0.8371 (mm110) REVERT: G 69 MET cc_start: 0.8595 (tpp) cc_final: 0.8096 (mmm) REVERT: G 94 GLU cc_start: 0.8430 (mt-10) cc_final: 0.8203 (mp0) REVERT: G 208 GLU cc_start: 0.7983 (pt0) cc_final: 0.7701 (mt-10) REVERT: G 216 THR cc_start: 0.8646 (m) cc_final: 0.8326 (p) REVERT: G 229 MET cc_start: 0.8962 (ttm) cc_final: 0.8633 (ttm) REVERT: G 353 LYS cc_start: 0.9515 (mttt) cc_final: 0.9290 (tppt) REVERT: G 393 MET cc_start: 0.8902 (mmt) cc_final: 0.8678 (mmm) REVERT: G 437 ASP cc_start: 0.8321 (m-30) cc_final: 0.8099 (m-30) REVERT: H 14 GLU cc_start: 0.8496 (tp30) cc_final: 0.7839 (tm-30) REVERT: H 19 ASP cc_start: 0.8203 (t70) cc_final: 0.7881 (t0) REVERT: H 30 GLN cc_start: 0.7953 (mm-40) cc_final: 0.7333 (mp10) REVERT: H 38 GLN cc_start: 0.8575 (mm110) cc_final: 0.8275 (mm110) REVERT: H 69 MET cc_start: 0.8565 (tpp) cc_final: 0.8056 (tpt) REVERT: H 94 GLU cc_start: 0.8423 (mt-10) cc_final: 0.8050 (mp0) REVERT: H 99 GLN cc_start: 0.8475 (mm-40) cc_final: 0.8146 (tt0) REVERT: H 137 ASP cc_start: 0.8666 (t0) cc_final: 0.8456 (m-30) REVERT: H 208 GLU cc_start: 0.7947 (pt0) cc_final: 0.7383 (mt-10) REVERT: H 216 THR cc_start: 0.8608 (m) cc_final: 0.8167 (p) REVERT: H 353 LYS cc_start: 0.9516 (mttt) cc_final: 0.9308 (tppt) REVERT: H 437 ASP cc_start: 0.8382 (m-30) cc_final: 0.8173 (m-30) REVERT: I 14 GLU cc_start: 0.8481 (tp30) cc_final: 0.7776 (tm-30) REVERT: I 28 LYS cc_start: 0.8143 (tptm) cc_final: 0.7942 (ttpp) REVERT: I 30 GLN cc_start: 0.7991 (mm-40) cc_final: 0.7254 (mp10) REVERT: I 38 GLN cc_start: 0.8532 (mm110) cc_final: 0.8274 (mm110) REVERT: I 69 MET cc_start: 0.8642 (tpp) cc_final: 0.8155 (tpt) REVERT: I 94 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8154 (mp0) REVERT: I 137 ASP cc_start: 0.8670 (t0) cc_final: 0.8426 (m-30) REVERT: I 208 GLU cc_start: 0.7997 (pt0) cc_final: 0.7566 (mt-10) REVERT: I 216 THR cc_start: 0.8604 (m) cc_final: 0.8240 (p) REVERT: I 353 LYS cc_start: 0.9532 (mttt) cc_final: 0.9287 (tppt) REVERT: I 393 MET cc_start: 0.8923 (mmt) cc_final: 0.8705 (mmm) REVERT: J 9 MET cc_start: 0.9255 (ttm) cc_final: 0.9005 (ttm) REVERT: J 14 GLU cc_start: 0.8511 (tp30) cc_final: 0.7733 (tm-30) REVERT: J 19 ASP cc_start: 0.8368 (t70) cc_final: 0.7831 (t0) REVERT: J 28 LYS cc_start: 0.8072 (tptm) cc_final: 0.7861 (ttpp) REVERT: J 30 GLN cc_start: 0.8022 (mm-40) cc_final: 0.7340 (mp10) REVERT: J 38 GLN cc_start: 0.8661 (mm110) cc_final: 0.8376 (mm110) REVERT: J 69 MET cc_start: 0.8595 (tpp) cc_final: 0.8095 (mmm) REVERT: J 94 GLU cc_start: 0.8433 (mt-10) cc_final: 0.8204 (mp0) REVERT: J 208 GLU cc_start: 0.7984 (pt0) cc_final: 0.7707 (mt-10) REVERT: J 216 THR cc_start: 0.8648 (m) cc_final: 0.8331 (p) REVERT: J 229 MET cc_start: 0.8963 (ttm) cc_final: 0.8636 (ttm) REVERT: J 353 LYS cc_start: 0.9515 (mttt) cc_final: 0.9290 (tppt) REVERT: J 393 MET cc_start: 0.8903 (mmt) cc_final: 0.8679 (mmm) REVERT: J 437 ASP cc_start: 0.8321 (m-30) cc_final: 0.8099 (m-30) REVERT: K 14 GLU cc_start: 0.8480 (tp30) cc_final: 0.7774 (tm-30) REVERT: K 30 GLN cc_start: 0.7985 (mm-40) cc_final: 0.7252 (mp10) REVERT: K 38 GLN cc_start: 0.8533 (mm110) cc_final: 0.8275 (mm110) REVERT: K 69 MET cc_start: 0.8642 (tpp) cc_final: 0.8154 (tpt) REVERT: K 94 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8152 (mp0) REVERT: K 137 ASP cc_start: 0.8669 (t0) cc_final: 0.8426 (m-30) REVERT: K 208 GLU cc_start: 0.7997 (pt0) cc_final: 0.7568 (mt-10) REVERT: K 216 THR cc_start: 0.8601 (m) cc_final: 0.8238 (p) REVERT: K 353 LYS cc_start: 0.9534 (mttt) cc_final: 0.9288 (tppt) REVERT: K 393 MET cc_start: 0.8923 (mmt) cc_final: 0.8704 (mmm) REVERT: L 14 GLU cc_start: 0.8495 (tp30) cc_final: 0.7838 (tm-30) REVERT: L 19 ASP cc_start: 0.8197 (t70) cc_final: 0.7875 (t0) REVERT: L 30 GLN cc_start: 0.7946 (mm-40) cc_final: 0.7328 (mp10) REVERT: L 38 GLN cc_start: 0.8576 (mm110) cc_final: 0.8275 (mm110) REVERT: L 69 MET cc_start: 0.8562 (tpp) cc_final: 0.8051 (tpt) REVERT: L 94 GLU cc_start: 0.8422 (mt-10) cc_final: 0.8049 (mp0) REVERT: L 99 GLN cc_start: 0.8474 (mm-40) cc_final: 0.8146 (tt0) REVERT: L 137 ASP cc_start: 0.8662 (t0) cc_final: 0.8457 (m-30) REVERT: L 208 GLU cc_start: 0.7948 (pt0) cc_final: 0.7384 (mt-10) REVERT: L 216 THR cc_start: 0.8603 (m) cc_final: 0.8163 (p) REVERT: L 353 LYS cc_start: 0.9517 (mttt) cc_final: 0.9307 (tppt) REVERT: L 437 ASP cc_start: 0.8382 (m-30) cc_final: 0.8173 (m-30) outliers start: 48 outliers final: 16 residues processed: 1088 average time/residue: 0.5592 time to fit residues: 973.6156 Evaluate side-chains 697 residues out of total 4344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 681 time to evaluate : 4.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 HIS Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 210 HIS Chi-restraints excluded: chain D residue 210 HIS Chi-restraints excluded: chain E residue 210 HIS Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 210 HIS Chi-restraints excluded: chain G residue 210 HIS Chi-restraints excluded: chain H residue 210 HIS Chi-restraints excluded: chain I residue 55 ILE Chi-restraints excluded: chain I residue 210 HIS Chi-restraints excluded: chain J residue 210 HIS Chi-restraints excluded: chain K residue 55 ILE Chi-restraints excluded: chain K residue 210 HIS Chi-restraints excluded: chain L residue 210 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 435 optimal weight: 2.9990 chunk 391 optimal weight: 0.9990 chunk 217 optimal weight: 0.8980 chunk 133 optimal weight: 1.9990 chunk 263 optimal weight: 0.9980 chunk 208 optimal weight: 5.9990 chunk 404 optimal weight: 2.9990 chunk 156 optimal weight: 0.8980 chunk 245 optimal weight: 2.9990 chunk 301 optimal weight: 10.0000 chunk 468 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN B 30 GLN B 278 ASN D 278 ASN E 30 GLN E 278 ASN G 278 ASN H 30 GLN H 278 ASN J 278 ASN K 30 GLN L 30 GLN L 278 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 41628 Z= 0.183 Angle : 0.593 9.126 56304 Z= 0.303 Chirality : 0.044 0.134 6132 Planarity : 0.004 0.048 7452 Dihedral : 5.067 24.891 5660 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.04 % Allowed : 9.09 % Favored : 89.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.12), residues: 5172 helix: 2.06 (0.12), residues: 1788 sheet: 0.08 (0.16), residues: 1140 loop : -0.82 (0.14), residues: 2244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP L 58 HIS 0.002 0.001 HIS D 212 PHE 0.044 0.002 PHE C 398 TYR 0.016 0.002 TYR I 239 ARG 0.004 0.001 ARG J 249 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10344 Ramachandran restraints generated. 5172 Oldfield, 0 Emsley, 5172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10344 Ramachandran restraints generated. 5172 Oldfield, 0 Emsley, 5172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 752 residues out of total 4344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 707 time to evaluate : 4.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.8266 (tptm) cc_final: 0.8019 (mmmt) REVERT: A 30 GLN cc_start: 0.7926 (mm-40) cc_final: 0.7325 (mp10) REVERT: A 94 GLU cc_start: 0.8437 (mt-10) cc_final: 0.8235 (mp0) REVERT: A 208 GLU cc_start: 0.8138 (pt0) cc_final: 0.7857 (tm-30) REVERT: A 216 THR cc_start: 0.8952 (m) cc_final: 0.8535 (p) REVERT: B 14 GLU cc_start: 0.8521 (tp30) cc_final: 0.7841 (tm-30) REVERT: B 30 GLN cc_start: 0.7741 (mm110) cc_final: 0.7263 (mp10) REVERT: B 94 GLU cc_start: 0.8448 (mt-10) cc_final: 0.8117 (mp0) REVERT: B 99 GLN cc_start: 0.8529 (mm-40) cc_final: 0.8149 (tt0) REVERT: B 137 ASP cc_start: 0.8722 (t0) cc_final: 0.8453 (m-30) REVERT: B 208 GLU cc_start: 0.8135 (pt0) cc_final: 0.7636 (tm-30) REVERT: B 216 THR cc_start: 0.8854 (m) cc_final: 0.8405 (p) REVERT: B 353 LYS cc_start: 0.9516 (mttt) cc_final: 0.9292 (tppt) REVERT: B 438 GLU cc_start: 0.8042 (pt0) cc_final: 0.7738 (pp20) REVERT: C 14 GLU cc_start: 0.8571 (tp30) cc_final: 0.8076 (tm-30) REVERT: C 30 GLN cc_start: 0.7952 (mm-40) cc_final: 0.7317 (mp10) REVERT: C 69 MET cc_start: 0.8782 (tpp) cc_final: 0.8575 (tpt) REVERT: C 94 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8164 (mp0) REVERT: C 208 GLU cc_start: 0.8159 (pt0) cc_final: 0.7818 (tm-30) REVERT: C 216 THR cc_start: 0.8821 (m) cc_final: 0.8367 (p) REVERT: C 353 LYS cc_start: 0.9517 (mttt) cc_final: 0.9305 (tppt) REVERT: C 462 GLU cc_start: 0.8574 (mt-10) cc_final: 0.8337 (mt-10) REVERT: D 28 LYS cc_start: 0.8264 (tptm) cc_final: 0.8018 (mmmt) REVERT: D 30 GLN cc_start: 0.7923 (mm-40) cc_final: 0.7325 (mp10) REVERT: D 94 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8232 (mp0) REVERT: D 208 GLU cc_start: 0.8138 (pt0) cc_final: 0.7856 (tm-30) REVERT: D 216 THR cc_start: 0.8955 (m) cc_final: 0.8535 (p) REVERT: E 14 GLU cc_start: 0.8520 (tp30) cc_final: 0.7840 (tm-30) REVERT: E 30 GLN cc_start: 0.7739 (mm110) cc_final: 0.7260 (mp10) REVERT: E 94 GLU cc_start: 0.8448 (mt-10) cc_final: 0.8117 (mp0) REVERT: E 99 GLN cc_start: 0.8528 (mm-40) cc_final: 0.8150 (tt0) REVERT: E 137 ASP cc_start: 0.8719 (t0) cc_final: 0.8453 (m-30) REVERT: E 208 GLU cc_start: 0.8136 (pt0) cc_final: 0.7621 (tm-30) REVERT: E 216 THR cc_start: 0.8852 (m) cc_final: 0.8398 (p) REVERT: E 353 LYS cc_start: 0.9515 (mttt) cc_final: 0.9291 (tppt) REVERT: E 438 GLU cc_start: 0.8042 (pt0) cc_final: 0.7740 (pp20) REVERT: F 14 GLU cc_start: 0.8571 (tp30) cc_final: 0.8077 (tm-30) REVERT: F 30 GLN cc_start: 0.7950 (mm-40) cc_final: 0.7317 (mp10) REVERT: F 69 MET cc_start: 0.8781 (tpp) cc_final: 0.8572 (tpt) REVERT: F 94 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8165 (mp0) REVERT: F 208 GLU cc_start: 0.8156 (pt0) cc_final: 0.7816 (tm-30) REVERT: F 216 THR cc_start: 0.8820 (m) cc_final: 0.8367 (p) REVERT: F 353 LYS cc_start: 0.9517 (mttt) cc_final: 0.9305 (tppt) REVERT: F 462 GLU cc_start: 0.8579 (mt-10) cc_final: 0.8341 (mt-10) REVERT: G 28 LYS cc_start: 0.8266 (tptm) cc_final: 0.8019 (mmmt) REVERT: G 30 GLN cc_start: 0.7921 (mm-40) cc_final: 0.7322 (mp10) REVERT: G 94 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8234 (mp0) REVERT: G 208 GLU cc_start: 0.8138 (pt0) cc_final: 0.7856 (tm-30) REVERT: G 216 THR cc_start: 0.8953 (m) cc_final: 0.8532 (p) REVERT: H 14 GLU cc_start: 0.8521 (tp30) cc_final: 0.7842 (tm-30) REVERT: H 30 GLN cc_start: 0.7740 (mm110) cc_final: 0.7264 (mp10) REVERT: H 94 GLU cc_start: 0.8448 (mt-10) cc_final: 0.8117 (mp0) REVERT: H 99 GLN cc_start: 0.8525 (mm-40) cc_final: 0.8149 (tt0) REVERT: H 137 ASP cc_start: 0.8723 (t0) cc_final: 0.8451 (m-30) REVERT: H 208 GLU cc_start: 0.8133 (pt0) cc_final: 0.7620 (tm-30) REVERT: H 216 THR cc_start: 0.8851 (m) cc_final: 0.8401 (p) REVERT: H 353 LYS cc_start: 0.9515 (mttt) cc_final: 0.9293 (tppt) REVERT: H 438 GLU cc_start: 0.8042 (pt0) cc_final: 0.7736 (pp20) REVERT: I 14 GLU cc_start: 0.8571 (tp30) cc_final: 0.8077 (tm-30) REVERT: I 30 GLN cc_start: 0.7943 (mm-40) cc_final: 0.7312 (mp10) REVERT: I 69 MET cc_start: 0.8782 (tpp) cc_final: 0.8574 (tpt) REVERT: I 94 GLU cc_start: 0.8470 (mt-10) cc_final: 0.8165 (mp0) REVERT: I 208 GLU cc_start: 0.8161 (pt0) cc_final: 0.7816 (tm-30) REVERT: I 216 THR cc_start: 0.8819 (m) cc_final: 0.8363 (p) REVERT: I 353 LYS cc_start: 0.9517 (mttt) cc_final: 0.9305 (tppt) REVERT: I 462 GLU cc_start: 0.8639 (mt-10) cc_final: 0.8357 (mt-10) REVERT: J 28 LYS cc_start: 0.8265 (tptm) cc_final: 0.8020 (mmmt) REVERT: J 30 GLN cc_start: 0.7921 (mm-40) cc_final: 0.7323 (mp10) REVERT: J 94 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8234 (mp0) REVERT: J 208 GLU cc_start: 0.8138 (pt0) cc_final: 0.7860 (tm-30) REVERT: J 216 THR cc_start: 0.8954 (m) cc_final: 0.8534 (p) REVERT: K 14 GLU cc_start: 0.8570 (tp30) cc_final: 0.8077 (tm-30) REVERT: K 28 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.8016 (mtpp) REVERT: K 30 GLN cc_start: 0.7864 (mm110) cc_final: 0.7278 (mp10) REVERT: K 69 MET cc_start: 0.8783 (tpp) cc_final: 0.8572 (tpt) REVERT: K 94 GLU cc_start: 0.8472 (mt-10) cc_final: 0.8165 (mp0) REVERT: K 208 GLU cc_start: 0.8159 (pt0) cc_final: 0.7819 (tm-30) REVERT: K 216 THR cc_start: 0.8816 (m) cc_final: 0.8363 (p) REVERT: K 353 LYS cc_start: 0.9517 (mttt) cc_final: 0.9305 (tppt) REVERT: K 462 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8352 (mt-10) REVERT: L 14 GLU cc_start: 0.8520 (tp30) cc_final: 0.7842 (tm-30) REVERT: L 30 GLN cc_start: 0.7740 (mm110) cc_final: 0.7261 (mp10) REVERT: L 94 GLU cc_start: 0.8450 (mt-10) cc_final: 0.8116 (mp0) REVERT: L 99 GLN cc_start: 0.8524 (mm-40) cc_final: 0.8149 (tt0) REVERT: L 137 ASP cc_start: 0.8721 (t0) cc_final: 0.8452 (m-30) REVERT: L 208 GLU cc_start: 0.8134 (pt0) cc_final: 0.7621 (tm-30) REVERT: L 216 THR cc_start: 0.8852 (m) cc_final: 0.8397 (p) REVERT: L 353 LYS cc_start: 0.9516 (mttt) cc_final: 0.9293 (tppt) REVERT: L 438 GLU cc_start: 0.8043 (pt0) cc_final: 0.7739 (pp20) outliers start: 45 outliers final: 20 residues processed: 748 average time/residue: 0.4438 time to fit residues: 548.5602 Evaluate side-chains 613 residues out of total 4344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 592 time to evaluate : 3.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 140 ARG Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 140 ARG Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 140 ARG Chi-restraints excluded: chain H residue 205 LEU Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain K residue 28 LYS Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 140 ARG Chi-restraints excluded: chain L residue 205 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 260 optimal weight: 2.9990 chunk 145 optimal weight: 0.9990 chunk 389 optimal weight: 3.9990 chunk 319 optimal weight: 7.9990 chunk 129 optimal weight: 10.0000 chunk 469 optimal weight: 2.9990 chunk 507 optimal weight: 7.9990 chunk 418 optimal weight: 1.9990 chunk 465 optimal weight: 6.9990 chunk 160 optimal weight: 5.9990 chunk 376 optimal weight: 0.8980 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN B 219 GLN C 219 GLN ** C 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 GLN E 219 GLN F 219 GLN ** F 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 219 GLN H 219 GLN I 219 GLN J 219 GLN K 219 GLN L 219 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 41628 Z= 0.263 Angle : 0.599 10.009 56304 Z= 0.301 Chirality : 0.044 0.154 6132 Planarity : 0.005 0.055 7452 Dihedral : 4.575 24.249 5628 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.27 % Allowed : 11.90 % Favored : 86.83 % 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: 1.01 (0.12), residues: 5172 helix: 2.44 (0.12), residues: 1800 sheet: 0.18 (0.15), residues: 1236 loop : -0.54 (0.14), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP I 58 HIS 0.003 0.001 HIS J 210 PHE 0.029 0.002 PHE K 398 TYR 0.019 0.002 TYR B 239 ARG 0.003 0.000 ARG I 140 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10344 Ramachandran restraints generated. 5172 Oldfield, 0 Emsley, 5172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10344 Ramachandran restraints generated. 5172 Oldfield, 0 Emsley, 5172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 662 residues out of total 4344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 607 time to evaluate : 6.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.8262 (tptm) cc_final: 0.7907 (mmmt) REVERT: A 30 GLN cc_start: 0.8057 (mm-40) cc_final: 0.7404 (mp10) REVERT: A 49 MET cc_start: 0.8669 (mmm) cc_final: 0.8397 (mmm) REVERT: A 94 GLU cc_start: 0.8668 (mt-10) cc_final: 0.8344 (mp0) REVERT: A 208 GLU cc_start: 0.8301 (pt0) cc_final: 0.7721 (tm-30) REVERT: A 216 THR cc_start: 0.8949 (m) cc_final: 0.8527 (p) REVERT: A 235 GLU cc_start: 0.8428 (mt-10) cc_final: 0.8202 (tt0) REVERT: B 5 HIS cc_start: 0.8740 (m-70) cc_final: 0.8249 (t-90) REVERT: B 30 GLN cc_start: 0.7792 (mm110) cc_final: 0.7276 (mp10) REVERT: B 94 GLU cc_start: 0.8682 (mt-10) cc_final: 0.8312 (mp0) REVERT: B 99 GLN cc_start: 0.8640 (mm-40) cc_final: 0.8210 (tt0) REVERT: B 137 ASP cc_start: 0.8794 (t0) cc_final: 0.8520 (m-30) REVERT: B 208 GLU cc_start: 0.8252 (pt0) cc_final: 0.7877 (pt0) REVERT: B 216 THR cc_start: 0.8874 (m) cc_final: 0.8423 (p) REVERT: B 353 LYS cc_start: 0.9516 (mttt) cc_final: 0.9266 (tppt) REVERT: C 4 GLU cc_start: 0.7997 (mp0) cc_final: 0.7775 (mp0) REVERT: C 5 HIS cc_start: 0.8714 (m-70) cc_final: 0.8293 (t-90) REVERT: C 30 GLN cc_start: 0.7944 (mm-40) cc_final: 0.7265 (mp10) REVERT: C 69 MET cc_start: 0.8881 (tpp) cc_final: 0.8673 (tpt) REVERT: C 94 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8296 (mp0) REVERT: C 208 GLU cc_start: 0.8268 (pt0) cc_final: 0.7689 (tm-30) REVERT: C 216 THR cc_start: 0.8848 (m) cc_final: 0.8425 (p) REVERT: C 353 LYS cc_start: 0.9529 (mttt) cc_final: 0.9328 (tppt) REVERT: C 421 GLU cc_start: 0.8771 (mm-30) cc_final: 0.8535 (mm-30) REVERT: C 462 GLU cc_start: 0.8487 (mt-10) cc_final: 0.8265 (mt-10) REVERT: D 28 LYS cc_start: 0.8250 (tptm) cc_final: 0.7901 (mmmt) REVERT: D 30 GLN cc_start: 0.8055 (mm-40) cc_final: 0.7404 (mp10) REVERT: D 49 MET cc_start: 0.8670 (mmm) cc_final: 0.8396 (mmm) REVERT: D 94 GLU cc_start: 0.8667 (mt-10) cc_final: 0.8343 (mp0) REVERT: D 208 GLU cc_start: 0.8301 (pt0) cc_final: 0.7719 (tm-30) REVERT: D 216 THR cc_start: 0.8950 (m) cc_final: 0.8525 (p) REVERT: D 235 GLU cc_start: 0.8433 (mt-10) cc_final: 0.8206 (tt0) REVERT: E 5 HIS cc_start: 0.8743 (m-70) cc_final: 0.8250 (t-90) REVERT: E 30 GLN cc_start: 0.7791 (mm110) cc_final: 0.7274 (mp10) REVERT: E 94 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8310 (mp0) REVERT: E 99 GLN cc_start: 0.8642 (mm-40) cc_final: 0.8213 (tt0) REVERT: E 137 ASP cc_start: 0.8793 (t0) cc_final: 0.8524 (m-30) REVERT: E 208 GLU cc_start: 0.8264 (pt0) cc_final: 0.7352 (tm-30) REVERT: E 216 THR cc_start: 0.8872 (m) cc_final: 0.8418 (p) REVERT: E 353 LYS cc_start: 0.9517 (mttt) cc_final: 0.9263 (tppt) REVERT: F 4 GLU cc_start: 0.7997 (mp0) cc_final: 0.7773 (mp0) REVERT: F 5 HIS cc_start: 0.8715 (m-70) cc_final: 0.8291 (t-90) REVERT: F 30 GLN cc_start: 0.7946 (mm-40) cc_final: 0.7266 (mp10) REVERT: F 69 MET cc_start: 0.8881 (tpp) cc_final: 0.8669 (tpt) REVERT: F 94 GLU cc_start: 0.8680 (mt-10) cc_final: 0.8297 (mp0) REVERT: F 208 GLU cc_start: 0.8270 (pt0) cc_final: 0.7689 (tm-30) REVERT: F 216 THR cc_start: 0.8847 (m) cc_final: 0.8424 (p) REVERT: F 353 LYS cc_start: 0.9529 (mttt) cc_final: 0.9329 (tppt) REVERT: F 421 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8537 (mm-30) REVERT: F 462 GLU cc_start: 0.8494 (mt-10) cc_final: 0.8271 (mt-10) REVERT: G 28 LYS cc_start: 0.8261 (tptm) cc_final: 0.7906 (mmmt) REVERT: G 30 GLN cc_start: 0.8054 (mm-40) cc_final: 0.7403 (mp10) REVERT: G 49 MET cc_start: 0.8672 (mmm) cc_final: 0.8398 (mmm) REVERT: G 94 GLU cc_start: 0.8667 (mt-10) cc_final: 0.8342 (mp0) REVERT: G 208 GLU cc_start: 0.8301 (pt0) cc_final: 0.7718 (tm-30) REVERT: G 216 THR cc_start: 0.8949 (m) cc_final: 0.8521 (p) REVERT: G 235 GLU cc_start: 0.8431 (mt-10) cc_final: 0.8205 (tt0) REVERT: H 5 HIS cc_start: 0.8739 (m-70) cc_final: 0.8248 (t-90) REVERT: H 30 GLN cc_start: 0.7795 (mm110) cc_final: 0.7280 (mp10) REVERT: H 94 GLU cc_start: 0.8682 (mt-10) cc_final: 0.8311 (mp0) REVERT: H 99 GLN cc_start: 0.8637 (mm-40) cc_final: 0.8210 (tt0) REVERT: H 137 ASP cc_start: 0.8793 (t0) cc_final: 0.8520 (m-30) REVERT: H 208 GLU cc_start: 0.8263 (pt0) cc_final: 0.7352 (tm-30) REVERT: H 216 THR cc_start: 0.8870 (m) cc_final: 0.8418 (p) REVERT: H 353 LYS cc_start: 0.9517 (mttt) cc_final: 0.9265 (tppt) REVERT: I 4 GLU cc_start: 0.7998 (mp0) cc_final: 0.7773 (mp0) REVERT: I 5 HIS cc_start: 0.8714 (m-70) cc_final: 0.8290 (t-90) REVERT: I 30 GLN cc_start: 0.7940 (mm-40) cc_final: 0.7266 (mp10) REVERT: I 69 MET cc_start: 0.8882 (tpp) cc_final: 0.8672 (tpt) REVERT: I 94 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8294 (mp0) REVERT: I 208 GLU cc_start: 0.8270 (pt0) cc_final: 0.7689 (tm-30) REVERT: I 216 THR cc_start: 0.8847 (m) cc_final: 0.8421 (p) REVERT: I 353 LYS cc_start: 0.9530 (mttt) cc_final: 0.9328 (tppt) REVERT: I 421 GLU cc_start: 0.8774 (mm-30) cc_final: 0.8535 (mm-30) REVERT: I 462 GLU cc_start: 0.8535 (mt-10) cc_final: 0.8308 (mt-10) REVERT: J 28 LYS cc_start: 0.8251 (tptm) cc_final: 0.7900 (mmmt) REVERT: J 30 GLN cc_start: 0.8053 (mm-40) cc_final: 0.7402 (mp10) REVERT: J 49 MET cc_start: 0.8669 (mmm) cc_final: 0.8395 (mmm) REVERT: J 94 GLU cc_start: 0.8668 (mt-10) cc_final: 0.8345 (mp0) REVERT: J 208 GLU cc_start: 0.8301 (pt0) cc_final: 0.7721 (tm-30) REVERT: J 216 THR cc_start: 0.8995 (m) cc_final: 0.8561 (p) REVERT: J 235 GLU cc_start: 0.8430 (mt-10) cc_final: 0.8204 (tt0) REVERT: K 4 GLU cc_start: 0.7998 (mp0) cc_final: 0.7775 (mp0) REVERT: K 5 HIS cc_start: 0.8715 (m-70) cc_final: 0.8293 (t-90) REVERT: K 30 GLN cc_start: 0.7782 (mm110) cc_final: 0.7145 (mp10) REVERT: K 69 MET cc_start: 0.8882 (tpp) cc_final: 0.8672 (tpt) REVERT: K 94 GLU cc_start: 0.8684 (mt-10) cc_final: 0.8297 (mp0) REVERT: K 208 GLU cc_start: 0.8269 (pt0) cc_final: 0.7691 (tm-30) REVERT: K 216 THR cc_start: 0.8844 (m) cc_final: 0.8422 (p) REVERT: K 421 GLU cc_start: 0.8774 (mm-30) cc_final: 0.8534 (mm-30) REVERT: K 462 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8304 (mt-10) REVERT: L 5 HIS cc_start: 0.8741 (m-70) cc_final: 0.8249 (t-90) REVERT: L 30 GLN cc_start: 0.7790 (mm110) cc_final: 0.7274 (mp10) REVERT: L 94 GLU cc_start: 0.8682 (mt-10) cc_final: 0.8312 (mp0) REVERT: L 99 GLN cc_start: 0.8638 (mm-40) cc_final: 0.8211 (tt0) REVERT: L 137 ASP cc_start: 0.8793 (t0) cc_final: 0.8522 (m-30) REVERT: L 208 GLU cc_start: 0.8263 (pt0) cc_final: 0.7352 (tm-30) REVERT: L 216 THR cc_start: 0.8873 (m) cc_final: 0.8420 (p) REVERT: L 353 LYS cc_start: 0.9518 (mttt) cc_final: 0.9266 (tppt) outliers start: 55 outliers final: 27 residues processed: 651 average time/residue: 0.5154 time to fit residues: 557.1615 Evaluate side-chains 583 residues out of total 4344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 556 time to evaluate : 4.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 327 TYR Chi-restraints excluded: chain B residue 140 ARG Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 48 LYS Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain E residue 140 ARG Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain G residue 48 LYS Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 238 ILE Chi-restraints excluded: chain G residue 327 TYR Chi-restraints excluded: chain H residue 140 ARG Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 205 LEU Chi-restraints excluded: chain J residue 48 LYS Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 238 ILE Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 205 LEU Chi-restraints excluded: chain L residue 140 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 463 optimal weight: 5.9990 chunk 352 optimal weight: 6.9990 chunk 243 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 224 optimal weight: 0.8980 chunk 315 optimal weight: 7.9990 chunk 471 optimal weight: 4.9990 chunk 498 optimal weight: 2.9990 chunk 246 optimal weight: 0.3980 chunk 446 optimal weight: 0.9990 chunk 134 optimal weight: 5.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 ASN ** B 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 310 ASN ** E 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 310 ASN ** H 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 310 ASN ** K 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 41628 Z= 0.266 Angle : 0.578 10.224 56304 Z= 0.286 Chirality : 0.043 0.160 6132 Planarity : 0.004 0.051 7452 Dihedral : 4.405 19.967 5628 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.20 % Allowed : 12.91 % Favored : 85.89 % 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: 1.17 (0.12), residues: 5172 helix: 2.62 (0.12), residues: 1800 sheet: 0.31 (0.15), residues: 1236 loop : -0.53 (0.14), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 58 HIS 0.002 0.001 HIS J 210 PHE 0.020 0.001 PHE C 398 TYR 0.022 0.001 TYR J 239 ARG 0.002 0.000 ARG J 140 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10344 Ramachandran restraints generated. 5172 Oldfield, 0 Emsley, 5172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10344 Ramachandran restraints generated. 5172 Oldfield, 0 Emsley, 5172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 4344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 585 time to evaluate : 5.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.8250 (tptm) cc_final: 0.7946 (mmmt) REVERT: A 30 GLN cc_start: 0.8069 (mm-40) cc_final: 0.7386 (mp10) REVERT: A 208 GLU cc_start: 0.8346 (pt0) cc_final: 0.7958 (pt0) REVERT: A 216 THR cc_start: 0.8937 (m) cc_final: 0.8504 (p) REVERT: A 421 GLU cc_start: 0.8946 (mm-30) cc_final: 0.8513 (mm-30) REVERT: B 5 HIS cc_start: 0.8749 (m-70) cc_final: 0.8236 (t-90) REVERT: B 30 GLN cc_start: 0.7777 (mm110) cc_final: 0.7274 (mp10) REVERT: B 69 MET cc_start: 0.8354 (tpt) cc_final: 0.7810 (tpt) REVERT: B 137 ASP cc_start: 0.8870 (t0) cc_final: 0.8620 (m-30) REVERT: B 208 GLU cc_start: 0.8276 (pt0) cc_final: 0.7888 (pt0) REVERT: B 216 THR cc_start: 0.8875 (m) cc_final: 0.8446 (p) REVERT: B 332 MET cc_start: 0.8401 (mmt) cc_final: 0.8064 (mmt) REVERT: B 353 LYS cc_start: 0.9521 (mttt) cc_final: 0.9318 (tppt) REVERT: B 410 GLN cc_start: 0.7642 (mm-40) cc_final: 0.6932 (mm-40) REVERT: B 438 GLU cc_start: 0.7958 (pt0) cc_final: 0.7630 (pp20) REVERT: C 4 GLU cc_start: 0.7999 (mp0) cc_final: 0.7792 (mp0) REVERT: C 30 GLN cc_start: 0.7972 (mm-40) cc_final: 0.7243 (mp10) REVERT: C 208 GLU cc_start: 0.8236 (pt0) cc_final: 0.7867 (pt0) REVERT: C 216 THR cc_start: 0.8840 (m) cc_final: 0.8417 (p) REVERT: C 421 GLU cc_start: 0.8744 (mm-30) cc_final: 0.8469 (mm-30) REVERT: C 438 GLU cc_start: 0.8543 (mp0) cc_final: 0.8200 (pt0) REVERT: D 28 LYS cc_start: 0.8263 (tptm) cc_final: 0.7949 (mmmt) REVERT: D 30 GLN cc_start: 0.8075 (mm-40) cc_final: 0.7397 (mp10) REVERT: D 208 GLU cc_start: 0.8346 (pt0) cc_final: 0.7959 (pt0) REVERT: D 216 THR cc_start: 0.8937 (m) cc_final: 0.8503 (p) REVERT: D 421 GLU cc_start: 0.8947 (mm-30) cc_final: 0.8517 (mm-30) REVERT: E 5 HIS cc_start: 0.8753 (m-70) cc_final: 0.8239 (t-90) REVERT: E 30 GLN cc_start: 0.7773 (mm110) cc_final: 0.7270 (mp10) REVERT: E 69 MET cc_start: 0.8355 (tpt) cc_final: 0.7811 (tpt) REVERT: E 137 ASP cc_start: 0.8869 (t0) cc_final: 0.8621 (m-30) REVERT: E 208 GLU cc_start: 0.8257 (pt0) cc_final: 0.7528 (tm-30) REVERT: E 216 THR cc_start: 0.8874 (m) cc_final: 0.8443 (p) REVERT: E 332 MET cc_start: 0.8406 (mmt) cc_final: 0.8069 (mmt) REVERT: E 353 LYS cc_start: 0.9523 (mttt) cc_final: 0.9318 (tppt) REVERT: E 410 GLN cc_start: 0.7639 (mm-40) cc_final: 0.6931 (mm-40) REVERT: E 438 GLU cc_start: 0.7960 (pt0) cc_final: 0.7630 (pp20) REVERT: F 4 GLU cc_start: 0.8000 (mp0) cc_final: 0.7792 (mp0) REVERT: F 30 GLN cc_start: 0.7973 (mm-40) cc_final: 0.7242 (mp10) REVERT: F 69 MET cc_start: 0.8868 (tpp) cc_final: 0.8666 (tpt) REVERT: F 208 GLU cc_start: 0.8235 (pt0) cc_final: 0.7867 (pt0) REVERT: F 216 THR cc_start: 0.8840 (m) cc_final: 0.8418 (p) REVERT: F 421 GLU cc_start: 0.8746 (mm-30) cc_final: 0.8471 (mm-30) REVERT: F 438 GLU cc_start: 0.8538 (mp0) cc_final: 0.8196 (pt0) REVERT: G 28 LYS cc_start: 0.8251 (tptm) cc_final: 0.7948 (mmmt) REVERT: G 30 GLN cc_start: 0.8069 (mm-40) cc_final: 0.7387 (mp10) REVERT: G 208 GLU cc_start: 0.8347 (pt0) cc_final: 0.7959 (pt0) REVERT: G 216 THR cc_start: 0.8937 (m) cc_final: 0.8500 (p) REVERT: G 421 GLU cc_start: 0.8946 (mm-30) cc_final: 0.8513 (mm-30) REVERT: H 5 HIS cc_start: 0.8748 (m-70) cc_final: 0.8234 (t-90) REVERT: H 30 GLN cc_start: 0.7777 (mm110) cc_final: 0.7275 (mp10) REVERT: H 69 MET cc_start: 0.8357 (tpt) cc_final: 0.7812 (tpt) REVERT: H 137 ASP cc_start: 0.8871 (t0) cc_final: 0.8619 (m-30) REVERT: H 208 GLU cc_start: 0.8256 (pt0) cc_final: 0.7539 (tm-30) REVERT: H 216 THR cc_start: 0.8872 (m) cc_final: 0.8442 (p) REVERT: H 332 MET cc_start: 0.8405 (mmt) cc_final: 0.8065 (mmt) REVERT: H 353 LYS cc_start: 0.9522 (mttt) cc_final: 0.9318 (tppt) REVERT: H 410 GLN cc_start: 0.7645 (mm-40) cc_final: 0.6933 (mm-40) REVERT: H 438 GLU cc_start: 0.7960 (pt0) cc_final: 0.7632 (pp20) REVERT: I 4 GLU cc_start: 0.8000 (mp0) cc_final: 0.7792 (mp0) REVERT: I 30 GLN cc_start: 0.7967 (mm-40) cc_final: 0.7240 (mp10) REVERT: I 69 MET cc_start: 0.8870 (tpp) cc_final: 0.8670 (tpt) REVERT: I 208 GLU cc_start: 0.8236 (pt0) cc_final: 0.7866 (pt0) REVERT: I 216 THR cc_start: 0.8839 (m) cc_final: 0.8416 (p) REVERT: I 421 GLU cc_start: 0.8746 (mm-30) cc_final: 0.8469 (mm-30) REVERT: I 438 GLU cc_start: 0.8543 (mp0) cc_final: 0.8200 (pt0) REVERT: J 28 LYS cc_start: 0.8261 (tptm) cc_final: 0.7948 (mmmt) REVERT: J 30 GLN cc_start: 0.8074 (mm-40) cc_final: 0.7395 (mp10) REVERT: J 208 GLU cc_start: 0.8342 (pt0) cc_final: 0.7956 (pt0) REVERT: J 216 THR cc_start: 0.8935 (m) cc_final: 0.8507 (p) REVERT: J 421 GLU cc_start: 0.8944 (mm-30) cc_final: 0.8510 (mm-30) REVERT: K 4 GLU cc_start: 0.8000 (mp0) cc_final: 0.7793 (mp0) REVERT: K 30 GLN cc_start: 0.7792 (mm110) cc_final: 0.7131 (mp10) REVERT: K 208 GLU cc_start: 0.8239 (pt0) cc_final: 0.7869 (pt0) REVERT: K 216 THR cc_start: 0.8833 (m) cc_final: 0.8412 (p) REVERT: K 421 GLU cc_start: 0.8744 (mm-30) cc_final: 0.8470 (mm-30) REVERT: K 438 GLU cc_start: 0.8541 (mp0) cc_final: 0.8199 (pt0) REVERT: L 5 HIS cc_start: 0.8751 (m-70) cc_final: 0.8237 (t-90) REVERT: L 30 GLN cc_start: 0.7776 (mm110) cc_final: 0.7272 (mp10) REVERT: L 69 MET cc_start: 0.8353 (tpt) cc_final: 0.7811 (tpt) REVERT: L 137 ASP cc_start: 0.8870 (t0) cc_final: 0.8620 (m-30) REVERT: L 208 GLU cc_start: 0.8254 (pt0) cc_final: 0.7531 (tm-30) REVERT: L 216 THR cc_start: 0.8873 (m) cc_final: 0.8443 (p) REVERT: L 332 MET cc_start: 0.8408 (mmt) cc_final: 0.8072 (mmt) REVERT: L 353 LYS cc_start: 0.9523 (mttt) cc_final: 0.9318 (tppt) REVERT: L 410 GLN cc_start: 0.7644 (mm-40) cc_final: 0.6931 (mm-40) REVERT: L 438 GLU cc_start: 0.7959 (pt0) cc_final: 0.7630 (pp20) outliers start: 52 outliers final: 20 residues processed: 621 average time/residue: 0.4761 time to fit residues: 499.5443 Evaluate side-chains 578 residues out of total 4344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 558 time to evaluate : 3.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain B residue 140 ARG Chi-restraints excluded: chain C residue 436 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 48 LYS Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain E residue 140 ARG Chi-restraints excluded: chain F residue 436 THR Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 48 LYS Chi-restraints excluded: chain G residue 238 ILE Chi-restraints excluded: chain H residue 140 ARG Chi-restraints excluded: chain I residue 436 THR Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 48 LYS Chi-restraints excluded: chain J residue 238 ILE Chi-restraints excluded: chain K residue 436 THR Chi-restraints excluded: chain L residue 140 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 415 optimal weight: 0.6980 chunk 283 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 371 optimal weight: 1.9990 chunk 205 optimal weight: 5.9990 chunk 425 optimal weight: 6.9990 chunk 344 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 254 optimal weight: 0.9980 chunk 447 optimal weight: 4.9990 chunk 125 optimal weight: 6.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.4065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 41628 Z= 0.294 Angle : 0.592 10.475 56304 Z= 0.289 Chirality : 0.043 0.160 6132 Planarity : 0.004 0.051 7452 Dihedral : 4.349 19.527 5628 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.04 % Allowed : 13.54 % Favored : 85.43 % 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: 1.24 (0.12), residues: 5172 helix: 2.56 (0.12), residues: 1812 sheet: 0.39 (0.15), residues: 1236 loop : -0.43 (0.14), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 58 HIS 0.002 0.001 HIS A 210 PHE 0.017 0.001 PHE C 398 TYR 0.020 0.001 TYR I 239 ARG 0.002 0.000 ARG J 21 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10344 Ramachandran restraints generated. 5172 Oldfield, 0 Emsley, 5172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10344 Ramachandran restraints generated. 5172 Oldfield, 0 Emsley, 5172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 4344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 550 time to evaluate : 4.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.8225 (tptm) cc_final: 0.7952 (mmmt) REVERT: A 30 GLN cc_start: 0.8126 (mm-40) cc_final: 0.7464 (mp10) REVERT: A 208 GLU cc_start: 0.8309 (pt0) cc_final: 0.7541 (tm-30) REVERT: A 216 THR cc_start: 0.8990 (m) cc_final: 0.8555 (p) REVERT: B 30 GLN cc_start: 0.7839 (mm110) cc_final: 0.7327 (mp10) REVERT: B 69 MET cc_start: 0.8388 (tpt) cc_final: 0.7874 (tpt) REVERT: B 137 ASP cc_start: 0.8861 (t0) cc_final: 0.8605 (m-30) REVERT: B 208 GLU cc_start: 0.8258 (pt0) cc_final: 0.7571 (tm-30) REVERT: B 216 THR cc_start: 0.8916 (m) cc_final: 0.8476 (p) REVERT: B 332 MET cc_start: 0.8436 (mmt) cc_final: 0.8094 (mmt) REVERT: B 410 GLN cc_start: 0.7666 (mm-40) cc_final: 0.6997 (mm-40) REVERT: B 438 GLU cc_start: 0.7977 (pt0) cc_final: 0.7653 (pp20) REVERT: C 69 MET cc_start: 0.8620 (tpt) cc_final: 0.8178 (tpt) REVERT: C 99 GLN cc_start: 0.9132 (tt0) cc_final: 0.8503 (mt0) REVERT: C 208 GLU cc_start: 0.8218 (pt0) cc_final: 0.7532 (tm-30) REVERT: C 216 THR cc_start: 0.8854 (m) cc_final: 0.8443 (p) REVERT: C 421 GLU cc_start: 0.8742 (mm-30) cc_final: 0.8458 (mm-30) REVERT: C 438 GLU cc_start: 0.8546 (mp0) cc_final: 0.8233 (pt0) REVERT: D 28 LYS cc_start: 0.8237 (tptm) cc_final: 0.7954 (mmmt) REVERT: D 30 GLN cc_start: 0.8121 (mm-40) cc_final: 0.7462 (mp10) REVERT: D 208 GLU cc_start: 0.8307 (pt0) cc_final: 0.7538 (tm-30) REVERT: D 216 THR cc_start: 0.8990 (m) cc_final: 0.8554 (p) REVERT: E 30 GLN cc_start: 0.7842 (mm110) cc_final: 0.7330 (mp10) REVERT: E 69 MET cc_start: 0.8389 (tpt) cc_final: 0.7872 (tpt) REVERT: E 137 ASP cc_start: 0.8859 (t0) cc_final: 0.8604 (m-30) REVERT: E 208 GLU cc_start: 0.8255 (pt0) cc_final: 0.7575 (tm-30) REVERT: E 216 THR cc_start: 0.8917 (m) cc_final: 0.8477 (p) REVERT: E 332 MET cc_start: 0.8433 (mmt) cc_final: 0.8093 (mmt) REVERT: E 410 GLN cc_start: 0.7665 (mm-40) cc_final: 0.6999 (mm-40) REVERT: E 438 GLU cc_start: 0.7977 (pt0) cc_final: 0.7653 (pp20) REVERT: F 69 MET cc_start: 0.8844 (tpp) cc_final: 0.8163 (tpt) REVERT: F 99 GLN cc_start: 0.9136 (tt0) cc_final: 0.8504 (mt0) REVERT: F 208 GLU cc_start: 0.8220 (pt0) cc_final: 0.7533 (tm-30) REVERT: F 216 THR cc_start: 0.8854 (m) cc_final: 0.8445 (p) REVERT: F 421 GLU cc_start: 0.8744 (mm-30) cc_final: 0.8460 (mm-30) REVERT: F 438 GLU cc_start: 0.8543 (mp0) cc_final: 0.8231 (pt0) REVERT: G 28 LYS cc_start: 0.8226 (tptm) cc_final: 0.7952 (mmmt) REVERT: G 30 GLN cc_start: 0.8126 (mm-40) cc_final: 0.7464 (mp10) REVERT: G 208 GLU cc_start: 0.8309 (pt0) cc_final: 0.7537 (tm-30) REVERT: G 216 THR cc_start: 0.8990 (m) cc_final: 0.8552 (p) REVERT: H 30 GLN cc_start: 0.7838 (mm110) cc_final: 0.7325 (mp10) REVERT: H 69 MET cc_start: 0.8390 (tpt) cc_final: 0.7873 (tpt) REVERT: H 137 ASP cc_start: 0.8859 (t0) cc_final: 0.8603 (m-30) REVERT: H 208 GLU cc_start: 0.8256 (pt0) cc_final: 0.7578 (tm-30) REVERT: H 216 THR cc_start: 0.8913 (m) cc_final: 0.8475 (p) REVERT: H 332 MET cc_start: 0.8438 (mmt) cc_final: 0.8094 (mmt) REVERT: H 410 GLN cc_start: 0.7670 (mm-40) cc_final: 0.7002 (mm-40) REVERT: H 438 GLU cc_start: 0.7979 (pt0) cc_final: 0.7655 (pp20) REVERT: I 69 MET cc_start: 0.8845 (tpp) cc_final: 0.8162 (tpt) REVERT: I 99 GLN cc_start: 0.9136 (tt0) cc_final: 0.8505 (mt0) REVERT: I 208 GLU cc_start: 0.8219 (pt0) cc_final: 0.7532 (tm-30) REVERT: I 216 THR cc_start: 0.8853 (m) cc_final: 0.8442 (p) REVERT: I 421 GLU cc_start: 0.8743 (mm-30) cc_final: 0.8450 (mm-30) REVERT: I 438 GLU cc_start: 0.8541 (mp0) cc_final: 0.8208 (pt0) REVERT: J 28 LYS cc_start: 0.8237 (tptm) cc_final: 0.7953 (mmmt) REVERT: J 30 GLN cc_start: 0.8122 (mm-40) cc_final: 0.7463 (mp10) REVERT: J 208 GLU cc_start: 0.8297 (pt0) cc_final: 0.7547 (tm-30) REVERT: J 216 THR cc_start: 0.8998 (m) cc_final: 0.8568 (p) REVERT: K 69 MET cc_start: 0.8622 (tpt) cc_final: 0.8177 (tpt) REVERT: K 99 GLN cc_start: 0.9129 (tt0) cc_final: 0.8502 (mt0) REVERT: K 208 GLU cc_start: 0.8222 (pt0) cc_final: 0.7535 (tm-30) REVERT: K 216 THR cc_start: 0.8850 (m) cc_final: 0.8439 (p) REVERT: K 421 GLU cc_start: 0.8740 (mm-30) cc_final: 0.8451 (mm-30) REVERT: K 438 GLU cc_start: 0.8539 (mp0) cc_final: 0.8209 (pt0) REVERT: L 30 GLN cc_start: 0.7846 (mm110) cc_final: 0.7333 (mp10) REVERT: L 69 MET cc_start: 0.8386 (tpt) cc_final: 0.7872 (tpt) REVERT: L 137 ASP cc_start: 0.8859 (t0) cc_final: 0.8604 (m-30) REVERT: L 208 GLU cc_start: 0.8258 (pt0) cc_final: 0.7589 (tm-30) REVERT: L 216 THR cc_start: 0.8916 (m) cc_final: 0.8475 (p) REVERT: L 332 MET cc_start: 0.8437 (mmt) cc_final: 0.8096 (mmt) REVERT: L 410 GLN cc_start: 0.7669 (mm-40) cc_final: 0.6999 (mm-40) REVERT: L 438 GLU cc_start: 0.7977 (pt0) cc_final: 0.7654 (pp20) outliers start: 45 outliers final: 37 residues processed: 583 average time/residue: 0.5548 time to fit residues: 543.8282 Evaluate side-chains 566 residues out of total 4344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 529 time to evaluate : 4.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain B residue 140 ARG Chi-restraints excluded: chain B residue 261 MET Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 436 THR Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 48 LYS Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain E residue 140 ARG Chi-restraints excluded: chain E residue 261 MET Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 436 THR Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 48 LYS Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 238 ILE Chi-restraints excluded: chain H residue 140 ARG Chi-restraints excluded: chain H residue 261 MET Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 436 THR Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 48 LYS Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 238 ILE Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 281 ASN Chi-restraints excluded: chain K residue 436 THR Chi-restraints excluded: chain L residue 140 ARG Chi-restraints excluded: chain L residue 261 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 167 optimal weight: 2.9990 chunk 449 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 292 optimal weight: 4.9990 chunk 123 optimal weight: 7.9990 chunk 499 optimal weight: 0.8980 chunk 414 optimal weight: 2.9990 chunk 231 optimal weight: 0.9980 chunk 41 optimal weight: 7.9990 chunk 165 optimal weight: 6.9990 chunk 262 optimal weight: 5.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.4265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 41628 Z= 0.275 Angle : 0.578 10.220 56304 Z= 0.282 Chirality : 0.043 0.155 6132 Planarity : 0.004 0.053 7452 Dihedral : 4.261 18.813 5628 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.31 % Allowed : 14.64 % Favored : 84.05 % 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: 1.27 (0.12), residues: 5172 helix: 2.58 (0.12), residues: 1800 sheet: 0.39 (0.15), residues: 1236 loop : -0.38 (0.14), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 58 HIS 0.002 0.001 HIS B 210 PHE 0.015 0.001 PHE L 398 TYR 0.018 0.001 TYR K 239 ARG 0.002 0.000 ARG J 21 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10344 Ramachandran restraints generated. 5172 Oldfield, 0 Emsley, 5172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10344 Ramachandran restraints generated. 5172 Oldfield, 0 Emsley, 5172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 4344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 543 time to evaluate : 4.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.8212 (tptm) cc_final: 0.7942 (mmmt) REVERT: A 30 GLN cc_start: 0.8064 (mm-40) cc_final: 0.7423 (mp10) REVERT: A 99 GLN cc_start: 0.9073 (tt0) cc_final: 0.8462 (mt0) REVERT: A 208 GLU cc_start: 0.8290 (pt0) cc_final: 0.7506 (tm-30) REVERT: A 216 THR cc_start: 0.9045 (m) cc_final: 0.8586 (p) REVERT: A 235 GLU cc_start: 0.8658 (mt-10) cc_final: 0.8447 (tt0) REVERT: B 30 GLN cc_start: 0.7781 (mm110) cc_final: 0.7275 (mp10) REVERT: B 69 MET cc_start: 0.8388 (tpt) cc_final: 0.7872 (tpt) REVERT: B 137 ASP cc_start: 0.8866 (t0) cc_final: 0.8599 (m-30) REVERT: B 208 GLU cc_start: 0.8239 (pt0) cc_final: 0.7546 (tm-30) REVERT: B 216 THR cc_start: 0.8889 (m) cc_final: 0.8471 (p) REVERT: B 332 MET cc_start: 0.8440 (mmt) cc_final: 0.8171 (mmt) REVERT: B 410 GLN cc_start: 0.7624 (mm-40) cc_final: 0.7134 (mm-40) REVERT: B 438 GLU cc_start: 0.7968 (pt0) cc_final: 0.7644 (pp20) REVERT: C 30 GLN cc_start: 0.7747 (mp10) cc_final: 0.7250 (mp10) REVERT: C 69 MET cc_start: 0.8625 (tpt) cc_final: 0.8171 (tpt) REVERT: C 99 GLN cc_start: 0.9111 (tt0) cc_final: 0.8536 (mt0) REVERT: C 208 GLU cc_start: 0.8198 (pt0) cc_final: 0.7464 (tm-30) REVERT: C 216 THR cc_start: 0.8873 (m) cc_final: 0.8475 (p) REVERT: C 421 GLU cc_start: 0.8741 (mm-30) cc_final: 0.8443 (mm-30) REVERT: C 438 GLU cc_start: 0.8524 (mp0) cc_final: 0.8216 (pt0) REVERT: D 28 LYS cc_start: 0.8214 (tptm) cc_final: 0.7943 (mmmt) REVERT: D 30 GLN cc_start: 0.8063 (mm-40) cc_final: 0.7423 (mp10) REVERT: D 99 GLN cc_start: 0.9072 (tt0) cc_final: 0.8462 (mt0) REVERT: D 208 GLU cc_start: 0.8288 (pt0) cc_final: 0.7502 (tm-30) REVERT: D 216 THR cc_start: 0.9044 (m) cc_final: 0.8584 (p) REVERT: D 235 GLU cc_start: 0.8661 (mt-10) cc_final: 0.8449 (tt0) REVERT: E 30 GLN cc_start: 0.7774 (mm110) cc_final: 0.7267 (mp10) REVERT: E 69 MET cc_start: 0.8388 (tpt) cc_final: 0.7872 (tpt) REVERT: E 137 ASP cc_start: 0.8864 (t0) cc_final: 0.8598 (m-30) REVERT: E 208 GLU cc_start: 0.8217 (pt0) cc_final: 0.7537 (tm-30) REVERT: E 216 THR cc_start: 0.8888 (m) cc_final: 0.8470 (p) REVERT: E 332 MET cc_start: 0.8424 (mmt) cc_final: 0.8154 (mmt) REVERT: E 410 GLN cc_start: 0.7601 (mm-40) cc_final: 0.7094 (mm-40) REVERT: E 438 GLU cc_start: 0.7970 (pt0) cc_final: 0.7646 (pp20) REVERT: F 30 GLN cc_start: 0.7747 (mp10) cc_final: 0.7249 (mp10) REVERT: F 69 MET cc_start: 0.8842 (tpp) cc_final: 0.8134 (tpt) REVERT: F 99 GLN cc_start: 0.9113 (tt0) cc_final: 0.8537 (mt0) REVERT: F 208 GLU cc_start: 0.8196 (pt0) cc_final: 0.7464 (tm-30) REVERT: F 216 THR cc_start: 0.8875 (m) cc_final: 0.8475 (p) REVERT: F 421 GLU cc_start: 0.8744 (mm-30) cc_final: 0.8445 (mm-30) REVERT: F 438 GLU cc_start: 0.8519 (mp0) cc_final: 0.8211 (pt0) REVERT: G 28 LYS cc_start: 0.8214 (tptm) cc_final: 0.7943 (mmmt) REVERT: G 30 GLN cc_start: 0.8064 (mm-40) cc_final: 0.7423 (mp10) REVERT: G 99 GLN cc_start: 0.9072 (tt0) cc_final: 0.8463 (mt0) REVERT: G 208 GLU cc_start: 0.8291 (pt0) cc_final: 0.7502 (tm-30) REVERT: G 216 THR cc_start: 0.9045 (m) cc_final: 0.8582 (p) REVERT: G 235 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8452 (tt0) REVERT: H 30 GLN cc_start: 0.7781 (mm110) cc_final: 0.7274 (mp10) REVERT: H 69 MET cc_start: 0.8390 (tpt) cc_final: 0.7871 (tpt) REVERT: H 137 ASP cc_start: 0.8865 (t0) cc_final: 0.8598 (m-30) REVERT: H 208 GLU cc_start: 0.8230 (pt0) cc_final: 0.7535 (tm-30) REVERT: H 216 THR cc_start: 0.8886 (m) cc_final: 0.8468 (p) REVERT: H 332 MET cc_start: 0.8440 (mmt) cc_final: 0.8169 (mmt) REVERT: H 410 GLN cc_start: 0.7629 (mm-40) cc_final: 0.7136 (mm-40) REVERT: H 438 GLU cc_start: 0.7969 (pt0) cc_final: 0.7646 (pp20) REVERT: I 30 GLN cc_start: 0.7740 (mp10) cc_final: 0.7242 (mp10) REVERT: I 69 MET cc_start: 0.8843 (tpp) cc_final: 0.8136 (tpt) REVERT: I 99 GLN cc_start: 0.9113 (tt0) cc_final: 0.8537 (mt0) REVERT: I 208 GLU cc_start: 0.8196 (pt0) cc_final: 0.7462 (tm-30) REVERT: I 216 THR cc_start: 0.8871 (m) cc_final: 0.8472 (p) REVERT: I 421 GLU cc_start: 0.8743 (mm-30) cc_final: 0.8443 (mm-30) REVERT: I 438 GLU cc_start: 0.8536 (mp0) cc_final: 0.8207 (pt0) REVERT: J 28 LYS cc_start: 0.8215 (tptm) cc_final: 0.7943 (mmmt) REVERT: J 30 GLN cc_start: 0.8063 (mm-40) cc_final: 0.7423 (mp10) REVERT: J 99 GLN cc_start: 0.9071 (tt0) cc_final: 0.8463 (mt0) REVERT: J 208 GLU cc_start: 0.8286 (pt0) cc_final: 0.7502 (tm-30) REVERT: J 216 THR cc_start: 0.9044 (m) cc_final: 0.8585 (p) REVERT: J 235 GLU cc_start: 0.8660 (mt-10) cc_final: 0.8450 (tt0) REVERT: K 30 GLN cc_start: 0.7775 (mp10) cc_final: 0.6836 (mp10) REVERT: K 69 MET cc_start: 0.8626 (tpt) cc_final: 0.8171 (tpt) REVERT: K 99 GLN cc_start: 0.9108 (tt0) cc_final: 0.8535 (mt0) REVERT: K 208 GLU cc_start: 0.8201 (pt0) cc_final: 0.7466 (tm-30) REVERT: K 216 THR cc_start: 0.8870 (m) cc_final: 0.8472 (p) REVERT: K 421 GLU cc_start: 0.8742 (mm-30) cc_final: 0.8443 (mm-30) REVERT: K 438 GLU cc_start: 0.8535 (mp0) cc_final: 0.8208 (pt0) REVERT: L 30 GLN cc_start: 0.7779 (mm110) cc_final: 0.7270 (mp10) REVERT: L 69 MET cc_start: 0.8385 (tpt) cc_final: 0.7870 (tpt) REVERT: L 137 ASP cc_start: 0.8866 (t0) cc_final: 0.8598 (m-30) REVERT: L 208 GLU cc_start: 0.8217 (pt0) cc_final: 0.7544 (tm-30) REVERT: L 216 THR cc_start: 0.8887 (m) cc_final: 0.8468 (p) REVERT: L 332 MET cc_start: 0.8429 (mmt) cc_final: 0.8159 (mmt) REVERT: L 410 GLN cc_start: 0.7604 (mm-40) cc_final: 0.7094 (mm-40) REVERT: L 438 GLU cc_start: 0.7972 (pt0) cc_final: 0.7648 (pp20) outliers start: 57 outliers final: 45 residues processed: 580 average time/residue: 0.5320 time to fit residues: 515.5274 Evaluate side-chains 569 residues out of total 4344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 524 time to evaluate : 4.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain B residue 140 ARG Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 261 MET Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 436 THR Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 48 LYS Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain E residue 140 ARG Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 261 MET Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 255 THR Chi-restraints excluded: chain F residue 436 THR Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 48 LYS Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 255 THR Chi-restraints excluded: chain H residue 140 ARG Chi-restraints excluded: chain H residue 205 LEU Chi-restraints excluded: chain H residue 261 MET Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 255 THR Chi-restraints excluded: chain I residue 436 THR Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 48 LYS Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 255 THR Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 255 THR Chi-restraints excluded: chain K residue 281 ASN Chi-restraints excluded: chain K residue 436 THR Chi-restraints excluded: chain L residue 140 ARG Chi-restraints excluded: chain L residue 205 LEU Chi-restraints excluded: chain L residue 261 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 481 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 284 optimal weight: 5.9990 chunk 364 optimal weight: 3.9990 chunk 282 optimal weight: 2.9990 chunk 420 optimal weight: 0.7980 chunk 278 optimal weight: 0.7980 chunk 497 optimal weight: 0.7980 chunk 311 optimal weight: 1.9990 chunk 303 optimal weight: 1.9990 chunk 229 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN ** B 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 GLN ** C 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 GLN ** E 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 219 GLN ** F 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 30 GLN ** H 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 219 GLN ** I 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 30 GLN K 219 GLN ** K 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.4461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 41628 Z= 0.156 Angle : 0.535 9.739 56304 Z= 0.258 Chirality : 0.042 0.141 6132 Planarity : 0.004 0.053 7452 Dihedral : 3.946 16.059 5628 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.15 % Allowed : 15.63 % Favored : 83.22 % 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: 1.34 (0.12), residues: 5172 helix: 2.65 (0.12), residues: 1800 sheet: 0.42 (0.15), residues: 1236 loop : -0.34 (0.14), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP G 58 HIS 0.002 0.000 HIS C 37 PHE 0.014 0.001 PHE C 398 TYR 0.017 0.001 TYR I 239 ARG 0.002 0.000 ARG G 338 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10344 Ramachandran restraints generated. 5172 Oldfield, 0 Emsley, 5172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10344 Ramachandran restraints generated. 5172 Oldfield, 0 Emsley, 5172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 4344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 562 time to evaluate : 4.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8203 (mp0) cc_final: 0.7971 (mp0) REVERT: A 30 GLN cc_start: 0.7999 (mm110) cc_final: 0.7384 (mp10) REVERT: A 99 GLN cc_start: 0.9037 (tt0) cc_final: 0.8442 (mt0) REVERT: A 208 GLU cc_start: 0.8233 (pt0) cc_final: 0.7882 (pt0) REVERT: A 216 THR cc_start: 0.8914 (m) cc_final: 0.8424 (p) REVERT: A 229 MET cc_start: 0.9044 (tpt) cc_final: 0.8812 (tpt) REVERT: A 235 GLU cc_start: 0.8606 (mt-10) cc_final: 0.8397 (tt0) REVERT: B 30 GLN cc_start: 0.7637 (mm110) cc_final: 0.7305 (mp10) REVERT: B 69 MET cc_start: 0.8368 (tpt) cc_final: 0.7796 (tpt) REVERT: B 137 ASP cc_start: 0.8841 (t0) cc_final: 0.8557 (m-30) REVERT: B 208 GLU cc_start: 0.8199 (pt0) cc_final: 0.7474 (tm-30) REVERT: B 216 THR cc_start: 0.8810 (m) cc_final: 0.8281 (p) REVERT: B 332 MET cc_start: 0.8446 (mmt) cc_final: 0.8179 (mmt) REVERT: B 410 GLN cc_start: 0.7452 (mm-40) cc_final: 0.6952 (mm-40) REVERT: C 30 GLN cc_start: 0.7619 (mp10) cc_final: 0.6762 (mp10) REVERT: C 69 MET cc_start: 0.8658 (tpt) cc_final: 0.8196 (tpt) REVERT: C 99 GLN cc_start: 0.9139 (tt0) cc_final: 0.8581 (mt0) REVERT: C 208 GLU cc_start: 0.8111 (pt0) cc_final: 0.7383 (tm-30) REVERT: C 216 THR cc_start: 0.8816 (m) cc_final: 0.8321 (p) REVERT: C 421 GLU cc_start: 0.8727 (mm-30) cc_final: 0.8425 (mm-30) REVERT: D 30 GLN cc_start: 0.8005 (mm110) cc_final: 0.7388 (mp10) REVERT: D 99 GLN cc_start: 0.9035 (tt0) cc_final: 0.8441 (mt0) REVERT: D 208 GLU cc_start: 0.8233 (pt0) cc_final: 0.7893 (pt0) REVERT: D 216 THR cc_start: 0.8894 (m) cc_final: 0.8409 (p) REVERT: D 229 MET cc_start: 0.9045 (tpt) cc_final: 0.8810 (tpt) REVERT: D 235 GLU cc_start: 0.8608 (mt-10) cc_final: 0.8400 (tt0) REVERT: E 30 GLN cc_start: 0.7632 (mm110) cc_final: 0.7301 (mp10) REVERT: E 69 MET cc_start: 0.8372 (tpt) cc_final: 0.7799 (tpt) REVERT: E 137 ASP cc_start: 0.8837 (t0) cc_final: 0.8557 (m-30) REVERT: E 208 GLU cc_start: 0.8211 (pt0) cc_final: 0.7554 (tm-30) REVERT: E 216 THR cc_start: 0.8805 (m) cc_final: 0.8275 (p) REVERT: E 332 MET cc_start: 0.8404 (mmt) cc_final: 0.8109 (mmt) REVERT: E 410 GLN cc_start: 0.7448 (mm-40) cc_final: 0.6950 (mm-40) REVERT: F 30 GLN cc_start: 0.7618 (mp10) cc_final: 0.6761 (mp10) REVERT: F 45 GLU cc_start: 0.9137 (tp30) cc_final: 0.8645 (tp30) REVERT: F 69 MET cc_start: 0.8854 (tpp) cc_final: 0.8112 (tpt) REVERT: F 99 GLN cc_start: 0.9118 (tt0) cc_final: 0.8551 (mt0) REVERT: F 208 GLU cc_start: 0.8112 (pt0) cc_final: 0.7384 (tm-30) REVERT: F 216 THR cc_start: 0.8819 (m) cc_final: 0.8324 (p) REVERT: F 421 GLU cc_start: 0.8730 (mm-30) cc_final: 0.8426 (mm-30) REVERT: G 4 GLU cc_start: 0.8204 (mp0) cc_final: 0.7972 (mp0) REVERT: G 30 GLN cc_start: 0.8006 (mm110) cc_final: 0.7388 (mp10) REVERT: G 99 GLN cc_start: 0.9035 (tt0) cc_final: 0.8441 (mt0) REVERT: G 208 GLU cc_start: 0.8234 (pt0) cc_final: 0.7881 (pt0) REVERT: G 216 THR cc_start: 0.8893 (m) cc_final: 0.8406 (p) REVERT: G 229 MET cc_start: 0.9044 (tpt) cc_final: 0.8811 (tpt) REVERT: G 235 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8401 (tt0) REVERT: H 30 GLN cc_start: 0.7636 (mm110) cc_final: 0.7304 (mp10) REVERT: H 69 MET cc_start: 0.8367 (tpt) cc_final: 0.7792 (tpt) REVERT: H 137 ASP cc_start: 0.8838 (t0) cc_final: 0.8556 (m-30) REVERT: H 208 GLU cc_start: 0.8237 (pt0) cc_final: 0.7532 (tm-30) REVERT: H 216 THR cc_start: 0.8802 (m) cc_final: 0.8275 (p) REVERT: H 332 MET cc_start: 0.8446 (mmt) cc_final: 0.8180 (mmt) REVERT: H 410 GLN cc_start: 0.7456 (mm-40) cc_final: 0.6955 (mm-40) REVERT: I 30 GLN cc_start: 0.7617 (mp10) cc_final: 0.6758 (mp10) REVERT: I 45 GLU cc_start: 0.9137 (tp30) cc_final: 0.8646 (tp30) REVERT: I 69 MET cc_start: 0.8855 (tpp) cc_final: 0.8113 (tpt) REVERT: I 99 GLN cc_start: 0.9118 (tt0) cc_final: 0.8551 (mt0) REVERT: I 208 GLU cc_start: 0.8110 (pt0) cc_final: 0.7381 (tm-30) REVERT: I 216 THR cc_start: 0.8816 (m) cc_final: 0.8321 (p) REVERT: I 421 GLU cc_start: 0.8730 (mm-30) cc_final: 0.8426 (mm-30) REVERT: J 30 GLN cc_start: 0.8002 (mm110) cc_final: 0.7384 (mp10) REVERT: J 99 GLN cc_start: 0.9034 (tt0) cc_final: 0.8441 (mt0) REVERT: J 208 GLU cc_start: 0.8237 (pt0) cc_final: 0.7896 (pt0) REVERT: J 216 THR cc_start: 0.8848 (m) cc_final: 0.8377 (p) REVERT: J 229 MET cc_start: 0.9045 (tpt) cc_final: 0.8809 (tpt) REVERT: J 235 GLU cc_start: 0.8606 (mt-10) cc_final: 0.8399 (tt0) REVERT: K 28 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.7896 (mtpp) REVERT: K 30 GLN cc_start: 0.7680 (mp10) cc_final: 0.6733 (mp10) REVERT: K 69 MET cc_start: 0.8662 (tpt) cc_final: 0.8199 (tpt) REVERT: K 99 GLN cc_start: 0.9137 (tt0) cc_final: 0.8581 (mt0) REVERT: K 208 GLU cc_start: 0.8113 (pt0) cc_final: 0.7384 (tm-30) REVERT: K 216 THR cc_start: 0.8816 (m) cc_final: 0.8321 (p) REVERT: K 421 GLU cc_start: 0.8729 (mm-30) cc_final: 0.8425 (mm-30) REVERT: L 30 GLN cc_start: 0.7636 (mm110) cc_final: 0.7302 (mp10) REVERT: L 69 MET cc_start: 0.8367 (tpt) cc_final: 0.7795 (tpt) REVERT: L 137 ASP cc_start: 0.8840 (t0) cc_final: 0.8563 (m-30) REVERT: L 208 GLU cc_start: 0.8225 (pt0) cc_final: 0.7544 (tm-30) REVERT: L 216 THR cc_start: 0.8804 (m) cc_final: 0.8275 (p) REVERT: L 332 MET cc_start: 0.8409 (mmt) cc_final: 0.8114 (mmt) REVERT: L 410 GLN cc_start: 0.7452 (mm-40) cc_final: 0.6955 (mm-40) outliers start: 50 outliers final: 40 residues processed: 604 average time/residue: 0.5032 time to fit residues: 509.1394 Evaluate side-chains 555 residues out of total 4344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 514 time to evaluate : 4.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain B residue 140 ARG Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 261 MET Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 48 LYS Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain E residue 140 ARG Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 261 MET Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 48 LYS Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 255 THR Chi-restraints excluded: chain H residue 140 ARG Chi-restraints excluded: chain H residue 205 LEU Chi-restraints excluded: chain H residue 255 THR Chi-restraints excluded: chain H residue 261 MET Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 48 LYS Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 255 THR Chi-restraints excluded: chain K residue 28 LYS Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain L residue 140 ARG Chi-restraints excluded: chain L residue 205 LEU Chi-restraints excluded: chain L residue 255 THR Chi-restraints excluded: chain L residue 261 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 307 optimal weight: 7.9990 chunk 198 optimal weight: 0.8980 chunk 297 optimal weight: 0.0980 chunk 149 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 316 optimal weight: 3.9990 chunk 338 optimal weight: 0.0020 chunk 245 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 chunk 390 optimal weight: 5.9990 overall best weight: 1.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 202 GLN ** E 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 202 GLN ** H 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 202 GLN ** L 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.4577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 41628 Z= 0.188 Angle : 0.554 10.814 56304 Z= 0.266 Chirality : 0.042 0.142 6132 Planarity : 0.004 0.051 7452 Dihedral : 3.916 17.092 5628 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.22 % Allowed : 16.11 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.12), residues: 5172 helix: 2.64 (0.12), residues: 1800 sheet: 0.49 (0.15), residues: 1236 loop : -0.29 (0.14), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP K 58 HIS 0.002 0.000 HIS J 210 PHE 0.013 0.001 PHE B 398 TYR 0.019 0.001 TYR K 239 ARG 0.002 0.000 ARG D 21 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10344 Ramachandran restraints generated. 5172 Oldfield, 0 Emsley, 5172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10344 Ramachandran restraints generated. 5172 Oldfield, 0 Emsley, 5172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 4344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 516 time to evaluate : 4.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8210 (mp0) cc_final: 0.7964 (mp0) REVERT: A 30 GLN cc_start: 0.7915 (mm110) cc_final: 0.7254 (mp10) REVERT: A 99 GLN cc_start: 0.9082 (tt0) cc_final: 0.8511 (mt0) REVERT: A 208 GLU cc_start: 0.8234 (pt0) cc_final: 0.7468 (tm-30) REVERT: A 216 THR cc_start: 0.8913 (m) cc_final: 0.8446 (p) REVERT: A 229 MET cc_start: 0.9063 (tpt) cc_final: 0.8806 (tpt) REVERT: A 235 GLU cc_start: 0.8615 (mt-10) cc_final: 0.8403 (tt0) REVERT: B 30 GLN cc_start: 0.7627 (mm110) cc_final: 0.7297 (mp10) REVERT: B 69 MET cc_start: 0.8392 (tpt) cc_final: 0.7876 (tpt) REVERT: B 137 ASP cc_start: 0.8850 (t0) cc_final: 0.8575 (m-30) REVERT: B 208 GLU cc_start: 0.8188 (pt0) cc_final: 0.7479 (tm-30) REVERT: B 216 THR cc_start: 0.8851 (m) cc_final: 0.8362 (p) REVERT: B 332 MET cc_start: 0.8404 (mmt) cc_final: 0.8109 (mmt) REVERT: B 410 GLN cc_start: 0.7391 (mm-40) cc_final: 0.6717 (mm-40) REVERT: C 30 GLN cc_start: 0.7618 (mp10) cc_final: 0.6725 (mp10) REVERT: C 69 MET cc_start: 0.8674 (tpt) cc_final: 0.8198 (tpt) REVERT: C 99 GLN cc_start: 0.9152 (tt0) cc_final: 0.8573 (mt0) REVERT: C 208 GLU cc_start: 0.8098 (pt0) cc_final: 0.7358 (tm-30) REVERT: C 216 THR cc_start: 0.8846 (m) cc_final: 0.8370 (p) REVERT: C 421 GLU cc_start: 0.8732 (mm-30) cc_final: 0.8430 (mm-30) REVERT: D 4 GLU cc_start: 0.8205 (mp0) cc_final: 0.7961 (mp0) REVERT: D 30 GLN cc_start: 0.7924 (mm110) cc_final: 0.7327 (mp10) REVERT: D 99 GLN cc_start: 0.9079 (tt0) cc_final: 0.8511 (mt0) REVERT: D 208 GLU cc_start: 0.8231 (pt0) cc_final: 0.7885 (pt0) REVERT: D 216 THR cc_start: 0.8915 (m) cc_final: 0.8448 (p) REVERT: D 229 MET cc_start: 0.9063 (tpt) cc_final: 0.8804 (tpt) REVERT: D 235 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8403 (tt0) REVERT: E 30 GLN cc_start: 0.7626 (mm110) cc_final: 0.7296 (mp10) REVERT: E 69 MET cc_start: 0.8394 (tpt) cc_final: 0.7877 (tpt) REVERT: E 137 ASP cc_start: 0.8848 (t0) cc_final: 0.8576 (m-30) REVERT: E 208 GLU cc_start: 0.8204 (pt0) cc_final: 0.7525 (tm-30) REVERT: E 216 THR cc_start: 0.8846 (m) cc_final: 0.8358 (p) REVERT: E 235 GLU cc_start: 0.8414 (mt-10) cc_final: 0.8212 (tt0) REVERT: E 332 MET cc_start: 0.8429 (mmt) cc_final: 0.8128 (mmt) REVERT: E 410 GLN cc_start: 0.7387 (mm-40) cc_final: 0.6713 (mm-40) REVERT: F 30 GLN cc_start: 0.7616 (mp10) cc_final: 0.6724 (mp10) REVERT: F 45 GLU cc_start: 0.9136 (tp30) cc_final: 0.8661 (tp30) REVERT: F 69 MET cc_start: 0.8855 (tpp) cc_final: 0.8098 (tpt) REVERT: F 99 GLN cc_start: 0.9126 (tt0) cc_final: 0.8534 (mt0) REVERT: F 208 GLU cc_start: 0.8099 (pt0) cc_final: 0.7360 (tm-30) REVERT: F 216 THR cc_start: 0.8847 (m) cc_final: 0.8372 (p) REVERT: F 421 GLU cc_start: 0.8736 (mm-30) cc_final: 0.8432 (mm-30) REVERT: G 4 GLU cc_start: 0.8210 (mp0) cc_final: 0.7964 (mp0) REVERT: G 30 GLN cc_start: 0.7918 (mm110) cc_final: 0.7256 (mp10) REVERT: G 99 GLN cc_start: 0.9080 (tt0) cc_final: 0.8512 (mt0) REVERT: G 208 GLU cc_start: 0.8231 (pt0) cc_final: 0.7463 (tm-30) REVERT: G 216 THR cc_start: 0.8915 (m) cc_final: 0.8442 (p) REVERT: G 229 MET cc_start: 0.9063 (tpt) cc_final: 0.8805 (tpt) REVERT: G 235 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8406 (tt0) REVERT: H 30 GLN cc_start: 0.7627 (mm110) cc_final: 0.7297 (mp10) REVERT: H 69 MET cc_start: 0.8392 (tpt) cc_final: 0.7874 (tpt) REVERT: H 137 ASP cc_start: 0.8850 (t0) cc_final: 0.8574 (m-30) REVERT: H 208 GLU cc_start: 0.8222 (pt0) cc_final: 0.7515 (tm-30) REVERT: H 216 THR cc_start: 0.8846 (m) cc_final: 0.8358 (p) REVERT: H 332 MET cc_start: 0.8404 (mmt) cc_final: 0.8108 (mmt) REVERT: H 410 GLN cc_start: 0.7396 (mm-40) cc_final: 0.6721 (mm-40) REVERT: I 30 GLN cc_start: 0.7615 (mp10) cc_final: 0.6719 (mp10) REVERT: I 45 GLU cc_start: 0.9135 (tp30) cc_final: 0.8659 (tp30) REVERT: I 69 MET cc_start: 0.8859 (tpp) cc_final: 0.8104 (tpt) REVERT: I 99 GLN cc_start: 0.9126 (tt0) cc_final: 0.8535 (mt0) REVERT: I 208 GLU cc_start: 0.8101 (pt0) cc_final: 0.7360 (tm-30) REVERT: I 216 THR cc_start: 0.8844 (m) cc_final: 0.8369 (p) REVERT: I 421 GLU cc_start: 0.8735 (mm-30) cc_final: 0.8432 (mm-30) REVERT: J 4 GLU cc_start: 0.8205 (mp0) cc_final: 0.7939 (mp0) REVERT: J 30 GLN cc_start: 0.7917 (mm110) cc_final: 0.7257 (mp10) REVERT: J 99 GLN cc_start: 0.9078 (tt0) cc_final: 0.8511 (mt0) REVERT: J 208 GLU cc_start: 0.8238 (pt0) cc_final: 0.7891 (pt0) REVERT: J 216 THR cc_start: 0.8913 (m) cc_final: 0.8443 (p) REVERT: J 229 MET cc_start: 0.9063 (tpt) cc_final: 0.8769 (tpt) REVERT: J 235 GLU cc_start: 0.8615 (mt-10) cc_final: 0.8404 (tt0) REVERT: K 28 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.7900 (mtpp) REVERT: K 30 GLN cc_start: 0.7695 (mp10) cc_final: 0.6742 (mp10) REVERT: K 69 MET cc_start: 0.8676 (tpt) cc_final: 0.8200 (tpt) REVERT: K 99 GLN cc_start: 0.9145 (tt0) cc_final: 0.8564 (mt0) REVERT: K 208 GLU cc_start: 0.8097 (pt0) cc_final: 0.7358 (tm-30) REVERT: K 216 THR cc_start: 0.8842 (m) cc_final: 0.8368 (p) REVERT: K 421 GLU cc_start: 0.8733 (mm-30) cc_final: 0.8430 (mm-30) REVERT: L 30 GLN cc_start: 0.7628 (mm110) cc_final: 0.7295 (mp10) REVERT: L 69 MET cc_start: 0.8391 (tpt) cc_final: 0.7874 (tpt) REVERT: L 137 ASP cc_start: 0.8850 (t0) cc_final: 0.8576 (m-30) REVERT: L 208 GLU cc_start: 0.8198 (pt0) cc_final: 0.7519 (tm-30) REVERT: L 216 THR cc_start: 0.8846 (m) cc_final: 0.8357 (p) REVERT: L 235 GLU cc_start: 0.8414 (mt-10) cc_final: 0.8211 (tt0) REVERT: L 332 MET cc_start: 0.8434 (mmt) cc_final: 0.8132 (mmt) REVERT: L 410 GLN cc_start: 0.7391 (mm-40) cc_final: 0.6715 (mm-40) outliers start: 53 outliers final: 46 residues processed: 557 average time/residue: 0.4997 time to fit residues: 467.5270 Evaluate side-chains 549 residues out of total 4344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 502 time to evaluate : 4.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain B residue 140 ARG Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 261 MET Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 48 LYS Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain E residue 140 ARG Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 261 MET Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 255 THR Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 48 LYS Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 255 THR Chi-restraints excluded: chain G residue 257 MET Chi-restraints excluded: chain H residue 140 ARG Chi-restraints excluded: chain H residue 205 LEU Chi-restraints excluded: chain H residue 255 THR Chi-restraints excluded: chain H residue 261 MET Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 255 THR Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 48 LYS Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 255 THR Chi-restraints excluded: chain K residue 28 LYS Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 255 THR Chi-restraints excluded: chain L residue 140 ARG Chi-restraints excluded: chain L residue 205 LEU Chi-restraints excluded: chain L residue 255 THR Chi-restraints excluded: chain L residue 261 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 452 optimal weight: 0.5980 chunk 476 optimal weight: 5.9990 chunk 434 optimal weight: 10.0000 chunk 463 optimal weight: 0.5980 chunk 278 optimal weight: 3.9990 chunk 201 optimal weight: 0.9980 chunk 363 optimal weight: 9.9990 chunk 142 optimal weight: 0.8980 chunk 418 optimal weight: 0.9980 chunk 438 optimal weight: 1.9990 chunk 461 optimal weight: 0.2980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN ** B 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 GLN ** E 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 219 GLN ** H 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 219 GLN ** K 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.4704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 41628 Z= 0.149 Angle : 0.539 10.849 56304 Z= 0.258 Chirality : 0.042 0.143 6132 Planarity : 0.004 0.052 7452 Dihedral : 3.785 16.351 5628 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.31 % Allowed : 16.00 % Favored : 82.69 % 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: 1.45 (0.12), residues: 5172 helix: 2.90 (0.12), residues: 1728 sheet: 0.48 (0.15), residues: 1260 loop : -0.32 (0.14), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP G 58 HIS 0.002 0.000 HIS K 459 PHE 0.012 0.001 PHE E 398 TYR 0.018 0.001 TYR I 239 ARG 0.001 0.000 ARG L 447 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10344 Ramachandran restraints generated. 5172 Oldfield, 0 Emsley, 5172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10344 Ramachandran restraints generated. 5172 Oldfield, 0 Emsley, 5172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 4344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 543 time to evaluate : 4.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8207 (mp0) cc_final: 0.7930 (mp0) REVERT: A 30 GLN cc_start: 0.7823 (mm110) cc_final: 0.7141 (mp10) REVERT: A 99 GLN cc_start: 0.9087 (tt0) cc_final: 0.8469 (mt0) REVERT: A 216 THR cc_start: 0.8903 (m) cc_final: 0.8428 (p) REVERT: A 226 PHE cc_start: 0.8474 (m-80) cc_final: 0.8173 (m-80) REVERT: A 229 MET cc_start: 0.9059 (tpt) cc_final: 0.8807 (tpt) REVERT: A 235 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8412 (tt0) REVERT: B 30 GLN cc_start: 0.7599 (mm110) cc_final: 0.7299 (mp10) REVERT: B 69 MET cc_start: 0.8388 (tpt) cc_final: 0.7868 (tpt) REVERT: B 137 ASP cc_start: 0.8818 (t0) cc_final: 0.8561 (m-30) REVERT: B 208 GLU cc_start: 0.8167 (pt0) cc_final: 0.7488 (tm-30) REVERT: B 216 THR cc_start: 0.8830 (m) cc_final: 0.8273 (p) REVERT: B 332 MET cc_start: 0.8387 (mmt) cc_final: 0.8059 (mmt) REVERT: B 410 GLN cc_start: 0.7303 (mm-40) cc_final: 0.6619 (mm-40) REVERT: C 30 GLN cc_start: 0.7559 (mp10) cc_final: 0.6645 (mp10) REVERT: C 99 GLN cc_start: 0.9105 (tt0) cc_final: 0.8541 (mt0) REVERT: C 208 GLU cc_start: 0.8062 (pt0) cc_final: 0.7725 (pt0) REVERT: C 216 THR cc_start: 0.8850 (m) cc_final: 0.8351 (p) REVERT: C 421 GLU cc_start: 0.8720 (mm-30) cc_final: 0.8442 (mm-30) REVERT: D 4 GLU cc_start: 0.8198 (mp0) cc_final: 0.7928 (mp0) REVERT: D 30 GLN cc_start: 0.7823 (mm110) cc_final: 0.7141 (mp10) REVERT: D 99 GLN cc_start: 0.9077 (tt0) cc_final: 0.8462 (mt0) REVERT: D 208 GLU cc_start: 0.8200 (pt0) cc_final: 0.7859 (pt0) REVERT: D 216 THR cc_start: 0.8911 (m) cc_final: 0.8422 (p) REVERT: D 226 PHE cc_start: 0.8480 (m-80) cc_final: 0.8193 (m-80) REVERT: D 229 MET cc_start: 0.9060 (tpt) cc_final: 0.8809 (tpt) REVERT: D 235 GLU cc_start: 0.8639 (mt-10) cc_final: 0.8418 (tt0) REVERT: E 30 GLN cc_start: 0.7573 (mm110) cc_final: 0.7271 (mp10) REVERT: E 69 MET cc_start: 0.8388 (tpt) cc_final: 0.7868 (tpt) REVERT: E 137 ASP cc_start: 0.8817 (t0) cc_final: 0.8562 (m-30) REVERT: E 208 GLU cc_start: 0.8133 (pt0) cc_final: 0.7505 (tm-30) REVERT: E 216 THR cc_start: 0.8828 (m) cc_final: 0.8272 (p) REVERT: E 235 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8214 (tt0) REVERT: F 30 GLN cc_start: 0.7550 (mp10) cc_final: 0.6638 (mp10) REVERT: F 45 GLU cc_start: 0.9135 (tp30) cc_final: 0.8659 (tp30) REVERT: F 69 MET cc_start: 0.8880 (tpp) cc_final: 0.8160 (tpt) REVERT: F 99 GLN cc_start: 0.9125 (tt0) cc_final: 0.8551 (mt0) REVERT: F 208 GLU cc_start: 0.8063 (pt0) cc_final: 0.7726 (pt0) REVERT: F 216 THR cc_start: 0.8850 (m) cc_final: 0.8350 (p) REVERT: F 421 GLU cc_start: 0.8722 (mm-30) cc_final: 0.8440 (mm-30) REVERT: G 4 GLU cc_start: 0.8209 (mp0) cc_final: 0.7932 (mp0) REVERT: G 30 GLN cc_start: 0.7825 (mm110) cc_final: 0.7143 (mp10) REVERT: G 99 GLN cc_start: 0.9086 (tt0) cc_final: 0.8469 (mt0) REVERT: G 216 THR cc_start: 0.8902 (m) cc_final: 0.8423 (p) REVERT: G 226 PHE cc_start: 0.8474 (m-80) cc_final: 0.8171 (m-80) REVERT: G 229 MET cc_start: 0.9060 (tpt) cc_final: 0.8809 (tpt) REVERT: G 235 GLU cc_start: 0.8638 (mt-10) cc_final: 0.8416 (tt0) REVERT: H 30 GLN cc_start: 0.7573 (mm110) cc_final: 0.7270 (mp10) REVERT: H 69 MET cc_start: 0.8387 (tpt) cc_final: 0.7865 (tpt) REVERT: H 137 ASP cc_start: 0.8819 (t0) cc_final: 0.8561 (m-30) REVERT: H 208 GLU cc_start: 0.8155 (pt0) cc_final: 0.7500 (tm-30) REVERT: H 216 THR cc_start: 0.8826 (m) cc_final: 0.8271 (p) REVERT: H 235 GLU cc_start: 0.8415 (mt-10) cc_final: 0.8211 (tt0) REVERT: H 332 MET cc_start: 0.8387 (mmt) cc_final: 0.8059 (mmt) REVERT: H 410 GLN cc_start: 0.7309 (mm-40) cc_final: 0.6626 (mm-40) REVERT: I 30 GLN cc_start: 0.7543 (mp10) cc_final: 0.6634 (mp10) REVERT: I 45 GLU cc_start: 0.9134 (tp30) cc_final: 0.8657 (tp30) REVERT: I 69 MET cc_start: 0.8884 (tpp) cc_final: 0.8164 (tpt) REVERT: I 99 GLN cc_start: 0.9125 (tt0) cc_final: 0.8553 (mt0) REVERT: I 208 GLU cc_start: 0.8064 (pt0) cc_final: 0.7729 (pt0) REVERT: I 216 THR cc_start: 0.8847 (m) cc_final: 0.8347 (p) REVERT: I 421 GLU cc_start: 0.8725 (mm-30) cc_final: 0.8444 (mm-30) REVERT: J 4 GLU cc_start: 0.8201 (mp0) cc_final: 0.7931 (mp0) REVERT: J 30 GLN cc_start: 0.7824 (mm110) cc_final: 0.7140 (mp10) REVERT: J 99 GLN cc_start: 0.9074 (tt0) cc_final: 0.8460 (mt0) REVERT: J 208 GLU cc_start: 0.8219 (pt0) cc_final: 0.7871 (pt0) REVERT: J 216 THR cc_start: 0.8913 (m) cc_final: 0.8425 (p) REVERT: J 226 PHE cc_start: 0.8483 (m-80) cc_final: 0.8198 (m-80) REVERT: J 229 MET cc_start: 0.9045 (tpt) cc_final: 0.8796 (tpt) REVERT: J 235 GLU cc_start: 0.8642 (mt-10) cc_final: 0.8418 (tt0) REVERT: K 26 LYS cc_start: 0.9297 (mmtp) cc_final: 0.9090 (mmmm) REVERT: K 28 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.7962 (mtpp) REVERT: K 30 GLN cc_start: 0.7631 (mp10) cc_final: 0.6720 (mp10) REVERT: K 99 GLN cc_start: 0.9103 (tt0) cc_final: 0.8540 (mt0) REVERT: K 208 GLU cc_start: 0.8059 (pt0) cc_final: 0.7724 (pt0) REVERT: K 216 THR cc_start: 0.8845 (m) cc_final: 0.8347 (p) REVERT: K 421 GLU cc_start: 0.8722 (mm-30) cc_final: 0.8442 (mm-30) REVERT: L 30 GLN cc_start: 0.7576 (mm110) cc_final: 0.7269 (mp10) REVERT: L 69 MET cc_start: 0.8386 (tpt) cc_final: 0.7866 (tpt) REVERT: L 137 ASP cc_start: 0.8819 (t0) cc_final: 0.8562 (m-30) REVERT: L 208 GLU cc_start: 0.8154 (pt0) cc_final: 0.7502 (tm-30) REVERT: L 216 THR cc_start: 0.8827 (m) cc_final: 0.8272 (p) REVERT: L 235 GLU cc_start: 0.8417 (mt-10) cc_final: 0.8213 (tt0) outliers start: 57 outliers final: 52 residues processed: 590 average time/residue: 0.5038 time to fit residues: 503.5022 Evaluate side-chains 569 residues out of total 4344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 516 time to evaluate : 5.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain B residue 140 ARG Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 261 MET Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 48 LYS Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain E residue 140 ARG Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 261 MET Chi-restraints excluded: chain E residue 436 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 255 THR Chi-restraints excluded: chain F residue 436 THR Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 48 LYS Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 255 THR Chi-restraints excluded: chain G residue 257 MET Chi-restraints excluded: chain H residue 140 ARG Chi-restraints excluded: chain H residue 205 LEU Chi-restraints excluded: chain H residue 255 THR Chi-restraints excluded: chain H residue 261 MET Chi-restraints excluded: chain H residue 436 THR Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 255 THR Chi-restraints excluded: chain I residue 436 THR Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 48 LYS Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 255 THR Chi-restraints excluded: chain K residue 28 LYS Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 255 THR Chi-restraints excluded: chain L residue 140 ARG Chi-restraints excluded: chain L residue 205 LEU Chi-restraints excluded: chain L residue 255 THR Chi-restraints excluded: chain L residue 261 MET Chi-restraints excluded: chain L residue 436 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 304 optimal weight: 6.9990 chunk 490 optimal weight: 8.9990 chunk 299 optimal weight: 7.9990 chunk 232 optimal weight: 7.9990 chunk 340 optimal weight: 6.9990 chunk 514 optimal weight: 6.9990 chunk 473 optimal weight: 10.0000 chunk 409 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 316 optimal weight: 4.9990 chunk 251 optimal weight: 3.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN ** A 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 318 ASN C 219 GLN ** C 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 GLN ** D 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 318 ASN F 219 GLN ** F 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 219 GLN ** G 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 219 GLN ** I 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 318 ASN J 219 GLN ** J 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 219 GLN ** K 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 318 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.4654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.057 41628 Z= 0.594 Angle : 0.763 14.221 56304 Z= 0.373 Chirality : 0.049 0.189 6132 Planarity : 0.005 0.056 7452 Dihedral : 4.661 22.667 5628 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 1.34 % Allowed : 16.78 % Favored : 81.88 % 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: 1.18 (0.12), residues: 5172 helix: 2.26 (0.12), residues: 1800 sheet: 0.59 (0.15), residues: 1200 loop : -0.34 (0.14), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 58 HIS 0.004 0.001 HIS C 459 PHE 0.018 0.002 PHE L 361 TYR 0.031 0.002 TYR D 239 ARG 0.005 0.001 ARG L 21 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10344 Ramachandran restraints generated. 5172 Oldfield, 0 Emsley, 5172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10344 Ramachandran restraints generated. 5172 Oldfield, 0 Emsley, 5172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 4344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 510 time to evaluate : 4.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8207 (mp0) cc_final: 0.7968 (mp0) REVERT: A 30 GLN cc_start: 0.8071 (mm110) cc_final: 0.7409 (mp10) REVERT: A 208 GLU cc_start: 0.8249 (pt0) cc_final: 0.7531 (tm-30) REVERT: A 216 THR cc_start: 0.9038 (m) cc_final: 0.8689 (p) REVERT: A 235 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8366 (tt0) REVERT: B 137 ASP cc_start: 0.8883 (t0) cc_final: 0.8604 (m-30) REVERT: B 208 GLU cc_start: 0.8260 (pt0) cc_final: 0.7507 (tm-30) REVERT: B 216 THR cc_start: 0.8930 (m) cc_final: 0.8559 (p) REVERT: B 332 MET cc_start: 0.8338 (mmt) cc_final: 0.8017 (mmt) REVERT: C 208 GLU cc_start: 0.8233 (pt0) cc_final: 0.7534 (tm-30) REVERT: C 216 THR cc_start: 0.8921 (m) cc_final: 0.8555 (p) REVERT: C 421 GLU cc_start: 0.8786 (mm-30) cc_final: 0.8478 (mm-30) REVERT: C 438 GLU cc_start: 0.8571 (mp0) cc_final: 0.8167 (pp20) REVERT: D 30 GLN cc_start: 0.8074 (mm110) cc_final: 0.7411 (mp10) REVERT: D 208 GLU cc_start: 0.8243 (pt0) cc_final: 0.7528 (tm-30) REVERT: D 216 THR cc_start: 0.9035 (m) cc_final: 0.8684 (p) REVERT: D 235 GLU cc_start: 0.8572 (mt-10) cc_final: 0.8368 (tt0) REVERT: E 137 ASP cc_start: 0.8880 (t0) cc_final: 0.8605 (m-30) REVERT: E 208 GLU cc_start: 0.8259 (pt0) cc_final: 0.7517 (tm-30) REVERT: E 216 THR cc_start: 0.8933 (m) cc_final: 0.8559 (p) REVERT: E 332 MET cc_start: 0.8349 (mmt) cc_final: 0.8031 (mmt) REVERT: F 69 MET cc_start: 0.8773 (tpp) cc_final: 0.8177 (tpt) REVERT: F 208 GLU cc_start: 0.8235 (pt0) cc_final: 0.7535 (tm-30) REVERT: F 216 THR cc_start: 0.8922 (m) cc_final: 0.8556 (p) REVERT: F 421 GLU cc_start: 0.8786 (mm-30) cc_final: 0.8476 (mm-30) REVERT: F 438 GLU cc_start: 0.8568 (mp0) cc_final: 0.8165 (pp20) REVERT: G 4 GLU cc_start: 0.8208 (mp0) cc_final: 0.7970 (mp0) REVERT: G 30 GLN cc_start: 0.8069 (mm110) cc_final: 0.7406 (mp10) REVERT: G 208 GLU cc_start: 0.8249 (pt0) cc_final: 0.7529 (tm-30) REVERT: G 216 THR cc_start: 0.9043 (m) cc_final: 0.8691 (p) REVERT: G 235 GLU cc_start: 0.8569 (mt-10) cc_final: 0.8368 (tt0) REVERT: H 137 ASP cc_start: 0.8881 (t0) cc_final: 0.8603 (m-30) REVERT: H 208 GLU cc_start: 0.8254 (pt0) cc_final: 0.7514 (tm-30) REVERT: H 216 THR cc_start: 0.8928 (m) cc_final: 0.8556 (p) REVERT: H 332 MET cc_start: 0.8337 (mmt) cc_final: 0.8016 (mmt) REVERT: I 69 MET cc_start: 0.8769 (tpp) cc_final: 0.8171 (tpt) REVERT: I 208 GLU cc_start: 0.8241 (pt0) cc_final: 0.7535 (tm-30) REVERT: I 216 THR cc_start: 0.8918 (m) cc_final: 0.8553 (p) REVERT: I 421 GLU cc_start: 0.8784 (mm-30) cc_final: 0.8476 (mm-30) REVERT: I 438 GLU cc_start: 0.8572 (mp0) cc_final: 0.8163 (pp20) REVERT: J 30 GLN cc_start: 0.8072 (mm110) cc_final: 0.7411 (mp10) REVERT: J 208 GLU cc_start: 0.8268 (pt0) cc_final: 0.7540 (tm-30) REVERT: J 216 THR cc_start: 0.9032 (m) cc_final: 0.8679 (p) REVERT: J 235 GLU cc_start: 0.8569 (mt-10) cc_final: 0.8364 (tt0) REVERT: K 208 GLU cc_start: 0.8238 (pt0) cc_final: 0.7534 (tm-30) REVERT: K 216 THR cc_start: 0.8917 (m) cc_final: 0.8553 (p) REVERT: K 421 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8477 (mm-30) REVERT: K 438 GLU cc_start: 0.8571 (mp0) cc_final: 0.8164 (pp20) REVERT: L 137 ASP cc_start: 0.8881 (t0) cc_final: 0.8604 (m-30) REVERT: L 208 GLU cc_start: 0.8257 (pt0) cc_final: 0.7514 (tm-30) REVERT: L 216 THR cc_start: 0.8929 (m) cc_final: 0.8557 (p) REVERT: L 332 MET cc_start: 0.8355 (mmt) cc_final: 0.8037 (mmt) outliers start: 58 outliers final: 44 residues processed: 558 average time/residue: 0.5106 time to fit residues: 476.0551 Evaluate side-chains 545 residues out of total 4344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 501 time to evaluate : 4.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain B residue 140 ARG Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 436 THR Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 48 LYS Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain E residue 140 ARG Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 436 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 255 THR Chi-restraints excluded: chain F residue 436 THR Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 48 LYS Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 255 THR Chi-restraints excluded: chain H residue 140 ARG Chi-restraints excluded: chain H residue 205 LEU Chi-restraints excluded: chain H residue 436 THR Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 255 THR Chi-restraints excluded: chain I residue 436 THR Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 48 LYS Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 255 THR Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 255 THR Chi-restraints excluded: chain K residue 436 THR Chi-restraints excluded: chain L residue 140 ARG Chi-restraints excluded: chain L residue 205 LEU Chi-restraints excluded: chain L residue 436 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 325 optimal weight: 8.9990 chunk 436 optimal weight: 8.9990 chunk 125 optimal weight: 0.5980 chunk 377 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 410 optimal weight: 5.9990 chunk 171 optimal weight: 3.9990 chunk 421 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 75 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN ** A 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 202 GLN ** G 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 318 ASN J 202 GLN ** J 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.092968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.071697 restraints weight = 89020.407| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 3.32 r_work: 0.2942 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.4726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 41628 Z= 0.165 Angle : 0.572 13.242 56304 Z= 0.272 Chirality : 0.042 0.142 6132 Planarity : 0.004 0.049 7452 Dihedral : 4.070 17.001 5628 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.01 % Allowed : 17.15 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.12), residues: 5172 helix: 2.41 (0.12), residues: 1800 sheet: 0.45 (0.15), residues: 1260 loop : -0.22 (0.14), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 58 HIS 0.002 0.001 HIS I 5 PHE 0.014 0.001 PHE K 398 TYR 0.022 0.002 TYR J 239 ARG 0.001 0.000 ARG E 447 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9863.78 seconds wall clock time: 228 minutes 48.00 seconds (13728.00 seconds total)