Starting phenix.real_space_refine on Sun Aug 11 09:43:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wqv_37755/08_2024/8wqv_37755.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wqv_37755/08_2024/8wqv_37755.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wqv_37755/08_2024/8wqv_37755.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wqv_37755/08_2024/8wqv_37755.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wqv_37755/08_2024/8wqv_37755.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wqv_37755/08_2024/8wqv_37755.cif" } resolution = 2.7 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= 0.004 sd= 0.165 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 24 7.16 5 S 72 5.16 5 C 20928 2.51 5 N 5321 2.21 5 O 6392 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 29": "OE1" <-> "OE2" Residue "A ASP 42": "OD1" <-> "OD2" Residue "A ASP 46": "OD1" <-> "OD2" Residue "A GLU 59": "OE1" <-> "OE2" Residue "A ASP 71": "OD1" <-> "OD2" Residue "A ARG 105": "NH1" <-> "NH2" Residue "A ASP 111": "OD1" <-> "OD2" Residue "A GLU 145": "OE1" <-> "OE2" Residue "B GLU 29": "OE1" <-> "OE2" Residue "B ASP 42": "OD1" <-> "OD2" Residue "B ASP 46": "OD1" <-> "OD2" Residue "B GLU 59": "OE1" <-> "OE2" Residue "B ARG 105": "NH1" <-> "NH2" Residue "B ASP 111": "OD1" <-> "OD2" Residue "B GLU 145": "OE1" <-> "OE2" Residue "B GLU 164": "OE1" <-> "OE2" Residue "C GLU 29": "OE1" <-> "OE2" Residue "C ASP 42": "OD1" <-> "OD2" Residue "C ASP 46": "OD1" <-> "OD2" Residue "C GLU 59": "OE1" <-> "OE2" Residue "C ASP 71": "OD1" <-> "OD2" Residue "C ARG 105": "NH1" <-> "NH2" Residue "C ASP 111": "OD1" <-> "OD2" Residue "C GLU 145": "OE1" <-> "OE2" Residue "C GLU 164": "OE1" <-> "OE2" Residue "D GLU 29": "OE1" <-> "OE2" Residue "D ASP 42": "OD1" <-> "OD2" Residue "D ASP 46": "OD1" <-> "OD2" Residue "D GLU 59": "OE1" <-> "OE2" Residue "D ASP 71": "OD1" <-> "OD2" Residue "D ARG 105": "NH1" <-> "NH2" Residue "D ASP 111": "OD1" <-> "OD2" Residue "D GLU 145": "OE1" <-> "OE2" Residue "E GLU 29": "OE1" <-> "OE2" Residue "E ASP 42": "OD1" <-> "OD2" Residue "E ASP 46": "OD1" <-> "OD2" Residue "E GLU 59": "OE1" <-> "OE2" Residue "E ASP 71": "OD1" <-> "OD2" Residue "E ARG 105": "NH1" <-> "NH2" Residue "E ASP 111": "OD1" <-> "OD2" Residue "E GLU 145": "OE1" <-> "OE2" Residue "F GLU 29": "OE1" <-> "OE2" Residue "F ASP 42": "OD1" <-> "OD2" Residue "F ASP 46": "OD1" <-> "OD2" Residue "F GLU 59": "OE1" <-> "OE2" Residue "F ASP 71": "OD1" <-> "OD2" Residue "F ARG 105": "NH1" <-> "NH2" Residue "F ASP 111": "OD1" <-> "OD2" Residue "F GLU 145": "OE1" <-> "OE2" Residue "G GLU 29": "OE1" <-> "OE2" Residue "G ASP 42": "OD1" <-> "OD2" Residue "G ASP 46": "OD1" <-> "OD2" Residue "G GLU 59": "OE1" <-> "OE2" Residue "G ASP 71": "OD1" <-> "OD2" Residue "G ARG 105": "NH1" <-> "NH2" Residue "G ASP 111": "OD1" <-> "OD2" Residue "G GLU 145": "OE1" <-> "OE2" Residue "G GLU 164": "OE1" <-> "OE2" Residue "H GLU 29": "OE1" <-> "OE2" Residue "H ASP 42": "OD1" <-> "OD2" Residue "H ASP 46": "OD1" <-> "OD2" Residue "H GLU 59": "OE1" <-> "OE2" Residue "H ARG 105": "NH1" <-> "NH2" Residue "H ASP 111": "OD1" <-> "OD2" Residue "H GLU 145": "OE1" <-> "OE2" Residue "H GLU 164": "OE1" <-> "OE2" Residue "I GLU 29": "OE1" <-> "OE2" Residue "I ASP 42": "OD1" <-> "OD2" Residue "I ASP 46": "OD1" <-> "OD2" Residue "I GLU 59": "OE1" <-> "OE2" Residue "I ARG 105": "NH1" <-> "NH2" Residue "I ASP 111": "OD1" <-> "OD2" Residue "I GLU 145": "OE1" <-> "OE2" Residue "I GLU 164": "OE1" <-> "OE2" Residue "J GLU 29": "OE1" <-> "OE2" Residue "J ASP 42": "OD1" <-> "OD2" Residue "J ASP 46": "OD1" <-> "OD2" Residue "J GLU 59": "OE1" <-> "OE2" Residue "J ARG 105": "NH1" <-> "NH2" Residue "J ASP 111": "OD1" <-> "OD2" Residue "J GLU 145": "OE1" <-> "OE2" Residue "J GLU 164": "OE1" <-> "OE2" Residue "K GLU 29": "OE1" <-> "OE2" Residue "K ASP 42": "OD1" <-> "OD2" Residue "K ASP 46": "OD1" <-> "OD2" Residue "K GLU 59": "OE1" <-> "OE2" Residue "K ASP 71": "OD1" <-> "OD2" Residue "K ARG 105": "NH1" <-> "NH2" Residue "K ASP 111": "OD1" <-> "OD2" Residue "K GLU 145": "OE1" <-> "OE2" Residue "L GLU 29": "OE1" <-> "OE2" Residue "L ASP 42": "OD1" <-> "OD2" Residue "L ASP 46": "OD1" <-> "OD2" Residue "L GLU 59": "OE1" <-> "OE2" Residue "L ASP 71": "OD1" <-> "OD2" Residue "L ARG 105": "NH1" <-> "NH2" Residue "L ASP 111": "OD1" <-> "OD2" Residue "L GLU 145": "OE1" <-> "OE2" Residue "M GLU 29": "OE1" <-> "OE2" Residue "M ASP 42": "OD1" <-> "OD2" Residue "M ASP 46": "OD1" <-> "OD2" Residue "M GLU 59": "OE1" <-> "OE2" Residue "M ARG 105": "NH1" <-> "NH2" Residue "M ASP 111": "OD1" <-> "OD2" Residue "M GLU 145": "OE1" <-> "OE2" Residue "M GLU 164": "OE1" <-> "OE2" Residue "N GLU 29": "OE1" <-> "OE2" Residue "N ASP 42": "OD1" <-> "OD2" Residue "N ASP 46": "OD1" <-> "OD2" Residue "N GLU 59": "OE1" <-> "OE2" Residue "N ASP 71": "OD1" <-> "OD2" Residue "N ARG 105": "NH1" <-> "NH2" Residue "N ASP 111": "OD1" <-> "OD2" Residue "N GLU 145": "OE1" <-> "OE2" Residue "O GLU 29": "OE1" <-> "OE2" Residue "O ASP 42": "OD1" <-> "OD2" Residue "O GLU 59": "OE1" <-> "OE2" Residue "O GLU 67": "OE1" <-> "OE2" Residue "O ARG 105": "NH1" <-> "NH2" Residue "O ASP 111": "OD1" <-> "OD2" Residue "O GLU 145": "OE1" <-> "OE2" Residue "O GLU 164": "OE1" <-> "OE2" Residue "P GLU 29": "OE1" <-> "OE2" Residue "P ASP 42": "OD1" <-> "OD2" Residue "P ASP 46": "OD1" <-> "OD2" Residue "P GLU 59": "OE1" <-> "OE2" Residue "P ARG 105": "NH1" <-> "NH2" Residue "P ASP 111": "OD1" <-> "OD2" Residue "P GLU 145": "OE1" <-> "OE2" Residue "P GLU 164": "OE1" <-> "OE2" Residue "Q GLU 29": "OE1" <-> "OE2" Residue "Q ASP 42": "OD1" <-> "OD2" Residue "Q ASP 46": "OD1" <-> "OD2" Residue "Q GLU 59": "OE1" <-> "OE2" Residue "Q ASP 71": "OD1" <-> "OD2" Residue "Q ARG 105": "NH1" <-> "NH2" Residue "Q ASP 111": "OD1" <-> "OD2" Residue "Q GLU 145": "OE1" <-> "OE2" Residue "R GLU 29": "OE1" <-> "OE2" Residue "R ASP 42": "OD1" <-> "OD2" Residue "R ASP 46": "OD1" <-> "OD2" Residue "R GLU 59": "OE1" <-> "OE2" Residue "R ASP 71": "OD1" <-> "OD2" Residue "R ARG 105": "NH1" <-> "NH2" Residue "R ASP 111": "OD1" <-> "OD2" Residue "R GLU 145": "OE1" <-> "OE2" Residue "R GLU 164": "OE1" <-> "OE2" Residue "S GLU 29": "OE1" <-> "OE2" Residue "S ASP 42": "OD1" <-> "OD2" Residue "S ASP 46": "OD1" <-> "OD2" Residue "S GLU 59": "OE1" <-> "OE2" Residue "S ASP 71": "OD1" <-> "OD2" Residue "S ARG 105": "NH1" <-> "NH2" Residue "S ASP 111": "OD1" <-> "OD2" Residue "S GLU 145": "OE1" <-> "OE2" Residue "S GLU 164": "OE1" <-> "OE2" Residue "T GLU 29": "OE1" <-> "OE2" Residue "T ASP 42": "OD1" <-> "OD2" Residue "T ASP 46": "OD1" <-> "OD2" Residue "T GLU 59": "OE1" <-> "OE2" Residue "T ARG 105": "NH1" <-> "NH2" Residue "T ASP 111": "OD1" <-> "OD2" Residue "T GLU 145": "OE1" <-> "OE2" Residue "T GLU 164": "OE1" <-> "OE2" Residue "U GLU 29": "OE1" <-> "OE2" Residue "U ASP 42": "OD1" <-> "OD2" Residue "U ASP 46": "OD1" <-> "OD2" Residue "U GLU 59": "OE1" <-> "OE2" Residue "U ASP 71": "OD1" <-> "OD2" Residue "U ARG 105": "NH1" <-> "NH2" Residue "U ASP 111": "OD1" <-> "OD2" Residue "U GLU 145": "OE1" <-> "OE2" Residue "U GLU 164": "OE1" <-> "OE2" Residue "V GLU 29": "OE1" <-> "OE2" Residue "V ASP 42": "OD1" <-> "OD2" Residue "V ASP 46": "OD1" <-> "OD2" Residue "V GLU 59": "OE1" <-> "OE2" Residue "V ARG 105": "NH1" <-> "NH2" Residue "V ASP 111": "OD1" <-> "OD2" Residue "V GLU 145": "OE1" <-> "OE2" Residue "V GLU 164": "OE1" <-> "OE2" Residue "W GLU 29": "OE1" <-> "OE2" Residue "W ASP 42": "OD1" <-> "OD2" Residue "W ASP 46": "OD1" <-> "OD2" Residue "W GLU 59": "OE1" <-> "OE2" Residue "W ASP 71": "OD1" <-> "OD2" Residue "W ARG 105": "NH1" <-> "NH2" Residue "W ASP 111": "OD1" <-> "OD2" Residue "W GLU 145": "OE1" <-> "OE2" Residue "W GLU 164": "OE1" <-> "OE2" Residue "X GLU 29": "OE1" <-> "OE2" Residue "X ASP 42": "OD1" <-> "OD2" Residue "X ASP 46": "OD1" <-> "OD2" Residue "X GLU 59": "OE1" <-> "OE2" Residue "X ASP 71": "OD1" <-> "OD2" Residue "X ARG 105": "NH1" <-> "NH2" Residue "X ASP 111": "OD1" <-> "OD2" Residue "X GLU 145": "OE1" <-> "OE2" Residue "X GLU 168": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 32737 Number of models: 1 Model: "" Number of chains: 48 Chain: "A" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "B" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "C" Number of atoms: 1353 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 163, 1335 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 2, 'TRANS': 160} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 163, 1335 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 2, 'TRANS': 160} Chain breaks: 1 bond proxies already assigned to first conformer: 1341 Chain: "D" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "E" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "F" Number of atoms: 1353 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 163, 1335 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 2, 'TRANS': 160} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 163, 1335 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 2, 'TRANS': 160} Chain breaks: 1 bond proxies already assigned to first conformer: 1341 Chain: "G" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "H" Number of atoms: 1353 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 163, 1335 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 2, 'TRANS': 160} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 163, 1335 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 2, 'TRANS': 160} Chain breaks: 1 bond proxies already assigned to first conformer: 1341 Chain: "I" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "J" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "K" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "L" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "M" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "N" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "O" Number of atoms: 1353 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 163, 1335 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 2, 'TRANS': 160} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 163, 1335 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 2, 'TRANS': 160} Chain breaks: 2 bond proxies already assigned to first conformer: 1340 Chain: "P" Number of atoms: 1353 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 163, 1335 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 2, 'TRANS': 160} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 163, 1335 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 2, 'TRANS': 160} Chain breaks: 1 bond proxies already assigned to first conformer: 1341 Chain: "Q" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "R" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "S" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "T" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "U" Number of atoms: 1372 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 165, 1354 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 2, 'TRANS': 162} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 165, 1354 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 2, 'TRANS': 162} Chain breaks: 1 bond proxies already assigned to first conformer: 1361 Chain: "V" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "W" Number of atoms: 1363 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "X" Number of atoms: 1405 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 169, 1387 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 2, 'TRANS': 166} Conformer: "B" Number of residues, atoms: 169, 1387 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 2, 'TRANS': 166} bond proxies already assigned to first conformer: 1395 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 48 residue: pdb=" N AGLU A 44 " occ=0.48 ... (16 atoms not shown) pdb=" OE2BGLU A 44 " occ=0.52 residue: pdb=" N AGLU A 108 " occ=0.46 ... (16 atoms not shown) pdb=" OE2BGLU A 108 " occ=0.54 residue: pdb=" N AGLU B 44 " occ=0.48 ... (16 atoms not shown) pdb=" OE2BGLU B 44 " occ=0.52 residue: pdb=" N AGLU B 108 " occ=0.46 ... (16 atoms not shown) pdb=" OE2BGLU B 108 " occ=0.54 residue: pdb=" N AGLU C 44 " occ=0.48 ... (16 atoms not shown) pdb=" OE2BGLU C 44 " occ=0.52 residue: pdb=" N AGLU C 108 " occ=0.46 ... (16 atoms not shown) pdb=" OE2BGLU C 108 " occ=0.54 residue: pdb=" N AGLU D 44 " occ=0.48 ... (16 atoms not shown) pdb=" OE2BGLU D 44 " occ=0.52 residue: pdb=" N AGLU D 108 " occ=0.46 ... (16 atoms not shown) pdb=" OE2BGLU D 108 " occ=0.54 residue: pdb=" N AGLU E 44 " occ=0.48 ... (16 atoms not shown) pdb=" OE2BGLU E 44 " occ=0.52 residue: pdb=" N AGLU E 108 " occ=0.46 ... (16 atoms not shown) pdb=" OE2BGLU E 108 " occ=0.54 residue: pdb=" N AGLU F 44 " occ=0.48 ... (16 atoms not shown) pdb=" OE2BGLU F 44 " occ=0.52 residue: pdb=" N AGLU F 108 " occ=0.46 ... (16 atoms not shown) pdb=" OE2BGLU F 108 " occ=0.54 ... (remaining 36 not shown) Time building chain proxies: 31.04, per 1000 atoms: 0.95 Number of scatterers: 32737 At special positions: 0 Unit cell: (130.859, 130.859, 130.859, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 24 26.01 S 72 16.00 O 6392 8.00 N 5321 7.00 C 20928 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.53 Conformation dependent library (CDL) restraints added in 11.0 seconds 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7682 Finding SS restraints... Secondary structure from input PDB file: 169 helices and 12 sheets defined 85.9% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.02 Creating SS restraints... Processing helix chain 'A' and resid 13 through 45 removed outlier: 3.555A pdb=" N PHE A 45 " --> pdb=" O ALA A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 63 Processing helix chain 'A' and resid 63 through 77 removed outlier: 4.596A pdb=" N ILE A 69 " --> pdb=" O HIS A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 123 removed outlier: 3.635A pdb=" N ASP A 111 " --> pdb=" O ASN A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 151 removed outlier: 4.565A pdb=" N TRP A 134 " --> pdb=" O TYR A 130 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N TYR A 135 " --> pdb=" O PHE A 131 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL A 149 " --> pdb=" O GLU A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 156 removed outlier: 3.750A pdb=" N SER A 155 " --> pdb=" O LYS A 151 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER A 156 " --> pdb=" O LEU A 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 151 through 156' Processing helix chain 'A' and resid 158 through 171 Processing helix chain 'B' and resid 14 through 45 removed outlier: 3.553A pdb=" N PHE B 45 " --> pdb=" O ALA B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 63 Processing helix chain 'B' and resid 63 through 77 removed outlier: 4.622A pdb=" N ILE B 69 " --> pdb=" O HIS B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 123 removed outlier: 3.573A pdb=" N LEU B 98 " --> pdb=" O ASP B 94 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP B 111 " --> pdb=" O ASN B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 151 removed outlier: 4.565A pdb=" N TRP B 134 " --> pdb=" O TYR B 130 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N TYR B 135 " --> pdb=" O PHE B 131 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU B 140 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL B 149 " --> pdb=" O GLU B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 156 removed outlier: 3.735A pdb=" N SER B 155 " --> pdb=" O LYS B 151 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 151 through 156' Processing helix chain 'B' and resid 158 through 171 Processing helix chain 'C' and resid 14 through 45 removed outlier: 3.554A pdb=" N PHE C 45 " --> pdb=" O ALA C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 63 Processing helix chain 'C' and resid 63 through 77 removed outlier: 4.597A pdb=" N ILE C 69 " --> pdb=" O HIS C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 123 removed outlier: 3.574A pdb=" N LEU C 98 " --> pdb=" O ASP C 94 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP C 111 " --> pdb=" O ASN C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 151 removed outlier: 4.565A pdb=" N TRP C 134 " --> pdb=" O TYR C 130 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N TYR C 135 " --> pdb=" O PHE C 131 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU C 140 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL C 149 " --> pdb=" O GLU C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 156 removed outlier: 3.735A pdb=" N SER C 155 " --> pdb=" O LYS C 151 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 151 through 156' Processing helix chain 'C' and resid 158 through 171 Processing helix chain 'D' and resid 14 through 45 removed outlier: 3.557A pdb=" N PHE D 45 " --> pdb=" O ALA D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 63 Processing helix chain 'D' and resid 63 through 77 removed outlier: 4.597A pdb=" N ILE D 69 " --> pdb=" O HIS D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 123 removed outlier: 3.588A pdb=" N LEU D 98 " --> pdb=" O ASP D 94 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP D 111 " --> pdb=" O ASN D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 151 removed outlier: 4.564A pdb=" N TRP D 134 " --> pdb=" O TYR D 130 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N TYR D 135 " --> pdb=" O PHE D 131 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU D 140 " --> pdb=" O VAL D 136 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL D 149 " --> pdb=" O GLU D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 156 removed outlier: 3.738A pdb=" N SER D 155 " --> pdb=" O LYS D 151 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER D 156 " --> pdb=" O LEU D 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 151 through 156' Processing helix chain 'D' and resid 158 through 171 Processing helix chain 'E' and resid 14 through 45 removed outlier: 3.554A pdb=" N PHE E 45 " --> pdb=" O ALA E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 63 Processing helix chain 'E' and resid 63 through 77 removed outlier: 4.595A pdb=" N ILE E 69 " --> pdb=" O HIS E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 123 removed outlier: 3.585A pdb=" N LEU E 98 " --> pdb=" O ASP E 94 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP E 111 " --> pdb=" O ASN E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 151 removed outlier: 4.565A pdb=" N TRP E 134 " --> pdb=" O TYR E 130 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N TYR E 135 " --> pdb=" O PHE E 131 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU E 140 " --> pdb=" O VAL E 136 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL E 149 " --> pdb=" O GLU E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 151 through 156 removed outlier: 3.735A pdb=" N SER E 155 " --> pdb=" O LYS E 151 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER E 156 " --> pdb=" O LEU E 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 151 through 156' Processing helix chain 'E' and resid 158 through 171 Processing helix chain 'F' and resid 14 through 45 removed outlier: 3.556A pdb=" N PHE F 45 " --> pdb=" O ALA F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 63 Processing helix chain 'F' and resid 63 through 77 removed outlier: 4.596A pdb=" N ILE F 69 " --> pdb=" O HIS F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 123 removed outlier: 3.586A pdb=" N LEU F 98 " --> pdb=" O ASP F 94 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP F 111 " --> pdb=" O ASN F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 151 removed outlier: 4.565A pdb=" N TRP F 134 " --> pdb=" O TYR F 130 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N TYR F 135 " --> pdb=" O PHE F 131 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU F 140 " --> pdb=" O VAL F 136 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL F 149 " --> pdb=" O GLU F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 151 through 156 removed outlier: 3.741A pdb=" N SER F 155 " --> pdb=" O LYS F 151 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER F 156 " --> pdb=" O LEU F 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 151 through 156' Processing helix chain 'F' and resid 158 through 171 Processing helix chain 'G' and resid 14 through 45 removed outlier: 3.553A pdb=" N PHE G 45 " --> pdb=" O ALA G 41 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 63 Processing helix chain 'G' and resid 63 through 77 removed outlier: 4.596A pdb=" N ILE G 69 " --> pdb=" O HIS G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 94 through 123 removed outlier: 3.579A pdb=" N LEU G 98 " --> pdb=" O ASP G 94 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP G 111 " --> pdb=" O ASN G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 151 removed outlier: 4.565A pdb=" N TRP G 134 " --> pdb=" O TYR G 130 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N TYR G 135 " --> pdb=" O PHE G 131 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU G 140 " --> pdb=" O VAL G 136 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL G 149 " --> pdb=" O GLU G 145 " (cutoff:3.500A) Processing helix chain 'G' and resid 152 through 155 Processing helix chain 'G' and resid 158 through 171 Processing helix chain 'H' and resid 14 through 45 removed outlier: 3.555A pdb=" N PHE H 45 " --> pdb=" O ALA H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 63 Processing helix chain 'H' and resid 63 through 77 removed outlier: 4.622A pdb=" N ILE H 69 " --> pdb=" O HIS H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 123 removed outlier: 3.567A pdb=" N LEU H 98 " --> pdb=" O ASP H 94 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP H 111 " --> pdb=" O ASN H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 151 removed outlier: 4.564A pdb=" N TRP H 134 " --> pdb=" O TYR H 130 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N TYR H 135 " --> pdb=" O PHE H 131 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU H 140 " --> pdb=" O VAL H 136 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL H 149 " --> pdb=" O GLU H 145 " (cutoff:3.500A) Processing helix chain 'H' and resid 151 through 156 removed outlier: 3.734A pdb=" N SER H 155 " --> pdb=" O LYS H 151 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER H 156 " --> pdb=" O LEU H 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 151 through 156' Processing helix chain 'H' and resid 158 through 171 Processing helix chain 'I' and resid 14 through 45 removed outlier: 3.554A pdb=" N PHE I 45 " --> pdb=" O ALA I 41 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 63 Processing helix chain 'I' and resid 63 through 77 removed outlier: 4.614A pdb=" N ILE I 69 " --> pdb=" O HIS I 65 " (cutoff:3.500A) Processing helix chain 'I' and resid 94 through 123 removed outlier: 3.571A pdb=" N LEU I 98 " --> pdb=" O ASP I 94 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP I 111 " --> pdb=" O ASN I 107 " (cutoff:3.500A) Processing helix chain 'I' and resid 125 through 151 removed outlier: 4.564A pdb=" N TRP I 134 " --> pdb=" O TYR I 130 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N TYR I 135 " --> pdb=" O PHE I 131 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU I 140 " --> pdb=" O VAL I 136 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL I 149 " --> pdb=" O GLU I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 151 through 156 removed outlier: 3.732A pdb=" N SER I 155 " --> pdb=" O LYS I 151 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER I 156 " --> pdb=" O LEU I 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 151 through 156' Processing helix chain 'I' and resid 158 through 171 Processing helix chain 'J' and resid 14 through 45 removed outlier: 3.555A pdb=" N PHE J 45 " --> pdb=" O ALA J 41 " (cutoff:3.500A) Processing helix chain 'J' and resid 47 through 63 Processing helix chain 'J' and resid 63 through 77 removed outlier: 4.622A pdb=" N ILE J 69 " --> pdb=" O HIS J 65 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 123 removed outlier: 3.572A pdb=" N LEU J 98 " --> pdb=" O ASP J 94 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP J 111 " --> pdb=" O ASN J 107 " (cutoff:3.500A) Processing helix chain 'J' and resid 125 through 151 removed outlier: 4.565A pdb=" N TRP J 134 " --> pdb=" O TYR J 130 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N TYR J 135 " --> pdb=" O PHE J 131 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU J 140 " --> pdb=" O VAL J 136 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL J 149 " --> pdb=" O GLU J 145 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 156 removed outlier: 3.734A pdb=" N SER J 155 " --> pdb=" O LYS J 151 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER J 156 " --> pdb=" O LEU J 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 151 through 156' Processing helix chain 'J' and resid 158 through 171 Processing helix chain 'K' and resid 14 through 45 removed outlier: 3.555A pdb=" N PHE K 45 " --> pdb=" O ALA K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 47 through 63 Processing helix chain 'K' and resid 63 through 77 removed outlier: 4.600A pdb=" N ILE K 69 " --> pdb=" O HIS K 65 " (cutoff:3.500A) Processing helix chain 'K' and resid 94 through 123 removed outlier: 3.585A pdb=" N LEU K 98 " --> pdb=" O ASP K 94 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP K 111 " --> pdb=" O ASN K 107 " (cutoff:3.500A) Processing helix chain 'K' and resid 125 through 151 removed outlier: 4.565A pdb=" N TRP K 134 " --> pdb=" O TYR K 130 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N TYR K 135 " --> pdb=" O PHE K 131 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU K 140 " --> pdb=" O VAL K 136 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL K 149 " --> pdb=" O GLU K 145 " (cutoff:3.500A) Processing helix chain 'K' and resid 151 through 156 removed outlier: 3.751A pdb=" N SER K 155 " --> pdb=" O LYS K 151 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER K 156 " --> pdb=" O LEU K 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 151 through 156' Processing helix chain 'K' and resid 158 through 171 Processing helix chain 'L' and resid 14 through 45 removed outlier: 3.555A pdb=" N PHE L 45 " --> pdb=" O ALA L 41 " (cutoff:3.500A) Processing helix chain 'L' and resid 47 through 63 Processing helix chain 'L' and resid 63 through 77 removed outlier: 4.596A pdb=" N ILE L 69 " --> pdb=" O HIS L 65 " (cutoff:3.500A) Processing helix chain 'L' and resid 94 through 123 removed outlier: 3.586A pdb=" N LEU L 98 " --> pdb=" O ASP L 94 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP L 111 " --> pdb=" O ASN L 107 " (cutoff:3.500A) Processing helix chain 'L' and resid 125 through 151 removed outlier: 4.565A pdb=" N TRP L 134 " --> pdb=" O TYR L 130 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N TYR L 135 " --> pdb=" O PHE L 131 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU L 140 " --> pdb=" O VAL L 136 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL L 149 " --> pdb=" O GLU L 145 " (cutoff:3.500A) Processing helix chain 'L' and resid 151 through 156 removed outlier: 3.753A pdb=" N SER L 155 " --> pdb=" O LYS L 151 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER L 156 " --> pdb=" O LEU L 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 151 through 156' Processing helix chain 'L' and resid 158 through 171 Processing helix chain 'M' and resid 14 through 45 removed outlier: 3.555A pdb=" N PHE M 45 " --> pdb=" O ALA M 41 " (cutoff:3.500A) Processing helix chain 'M' and resid 47 through 63 Processing helix chain 'M' and resid 63 through 77 removed outlier: 4.622A pdb=" N ILE M 69 " --> pdb=" O HIS M 65 " (cutoff:3.500A) Processing helix chain 'M' and resid 94 through 123 removed outlier: 3.590A pdb=" N LEU M 98 " --> pdb=" O ASP M 94 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP M 111 " --> pdb=" O ASN M 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 125 through 151 removed outlier: 4.565A pdb=" N TRP M 134 " --> pdb=" O TYR M 130 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N TYR M 135 " --> pdb=" O PHE M 131 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU M 140 " --> pdb=" O VAL M 136 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL M 149 " --> pdb=" O GLU M 145 " (cutoff:3.500A) Processing helix chain 'M' and resid 151 through 156 removed outlier: 3.734A pdb=" N SER M 155 " --> pdb=" O LYS M 151 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER M 156 " --> pdb=" O LEU M 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 151 through 156' Processing helix chain 'M' and resid 158 through 171 Processing helix chain 'N' and resid 14 through 45 removed outlier: 3.555A pdb=" N PHE N 45 " --> pdb=" O ALA N 41 " (cutoff:3.500A) Processing helix chain 'N' and resid 47 through 63 Processing helix chain 'N' and resid 63 through 77 removed outlier: 4.596A pdb=" N ILE N 69 " --> pdb=" O HIS N 65 " (cutoff:3.500A) Processing helix chain 'N' and resid 94 through 123 removed outlier: 3.583A pdb=" N LEU N 98 " --> pdb=" O ASP N 94 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP N 111 " --> pdb=" O ASN N 107 " (cutoff:3.500A) Processing helix chain 'N' and resid 125 through 151 removed outlier: 4.564A pdb=" N TRP N 134 " --> pdb=" O TYR N 130 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N TYR N 135 " --> pdb=" O PHE N 131 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU N 140 " --> pdb=" O VAL N 136 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL N 149 " --> pdb=" O GLU N 145 " (cutoff:3.500A) Processing helix chain 'N' and resid 151 through 156 removed outlier: 3.740A pdb=" N SER N 155 " --> pdb=" O LYS N 151 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER N 156 " --> pdb=" O LEU N 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 151 through 156' Processing helix chain 'N' and resid 158 through 171 Processing helix chain 'O' and resid 14 through 45 removed outlier: 3.568A pdb=" N PHE O 45 " --> pdb=" O ALA O 41 " (cutoff:3.500A) Processing helix chain 'O' and resid 47 through 55 Processing helix chain 'O' and resid 58 through 63 Processing helix chain 'O' and resid 63 through 77 removed outlier: 4.625A pdb=" N ILE O 69 " --> pdb=" O HIS O 65 " (cutoff:3.500A) Processing helix chain 'O' and resid 94 through 123 removed outlier: 3.590A pdb=" N LEU O 98 " --> pdb=" O ASP O 94 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP O 111 " --> pdb=" O ASN O 107 " (cutoff:3.500A) Processing helix chain 'O' and resid 125 through 151 removed outlier: 4.565A pdb=" N TRP O 134 " --> pdb=" O TYR O 130 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N TYR O 135 " --> pdb=" O PHE O 131 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU O 140 " --> pdb=" O VAL O 136 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL O 149 " --> pdb=" O GLU O 145 " (cutoff:3.500A) Processing helix chain 'O' and resid 151 through 156 removed outlier: 3.729A pdb=" N SER O 155 " --> pdb=" O LYS O 151 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER O 156 " --> pdb=" O LEU O 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 151 through 156' Processing helix chain 'O' and resid 158 through 171 Processing helix chain 'P' and resid 14 through 45 removed outlier: 3.554A pdb=" N PHE P 45 " --> pdb=" O ALA P 41 " (cutoff:3.500A) Processing helix chain 'P' and resid 47 through 63 Processing helix chain 'P' and resid 63 through 77 removed outlier: 4.601A pdb=" N ILE P 69 " --> pdb=" O HIS P 65 " (cutoff:3.500A) Processing helix chain 'P' and resid 94 through 123 removed outlier: 3.569A pdb=" N LEU P 98 " --> pdb=" O ASP P 94 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP P 111 " --> pdb=" O ASN P 107 " (cutoff:3.500A) Processing helix chain 'P' and resid 125 through 151 removed outlier: 4.565A pdb=" N TRP P 134 " --> pdb=" O TYR P 130 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N TYR P 135 " --> pdb=" O PHE P 131 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU P 140 " --> pdb=" O VAL P 136 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL P 149 " --> pdb=" O GLU P 145 " (cutoff:3.500A) Processing helix chain 'P' and resid 151 through 156 removed outlier: 3.734A pdb=" N SER P 155 " --> pdb=" O LYS P 151 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER P 156 " --> pdb=" O LEU P 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 151 through 156' Processing helix chain 'P' and resid 158 through 171 Processing helix chain 'Q' and resid 14 through 45 removed outlier: 3.556A pdb=" N PHE Q 45 " --> pdb=" O ALA Q 41 " (cutoff:3.500A) Processing helix chain 'Q' and resid 47 through 63 Processing helix chain 'Q' and resid 63 through 77 removed outlier: 4.596A pdb=" N ILE Q 69 " --> pdb=" O HIS Q 65 " (cutoff:3.500A) Processing helix chain 'Q' and resid 94 through 123 removed outlier: 3.586A pdb=" N LEU Q 98 " --> pdb=" O ASP Q 94 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP Q 111 " --> pdb=" O ASN Q 107 " (cutoff:3.500A) Processing helix chain 'Q' and resid 125 through 151 removed outlier: 4.564A pdb=" N TRP Q 134 " --> pdb=" O TYR Q 130 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N TYR Q 135 " --> pdb=" O PHE Q 131 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU Q 140 " --> pdb=" O VAL Q 136 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL Q 149 " --> pdb=" O GLU Q 145 " (cutoff:3.500A) Processing helix chain 'Q' and resid 151 through 156 removed outlier: 3.737A pdb=" N SER Q 155 " --> pdb=" O LYS Q 151 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER Q 156 " --> pdb=" O LEU Q 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 151 through 156' Processing helix chain 'Q' and resid 158 through 171 Processing helix chain 'R' and resid 14 through 45 removed outlier: 3.554A pdb=" N PHE R 45 " --> pdb=" O ALA R 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 47 through 63 Processing helix chain 'R' and resid 63 through 77 removed outlier: 4.596A pdb=" N ILE R 69 " --> pdb=" O HIS R 65 " (cutoff:3.500A) Processing helix chain 'R' and resid 94 through 123 removed outlier: 3.588A pdb=" N LEU R 98 " --> pdb=" O ASP R 94 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP R 111 " --> pdb=" O ASN R 107 " (cutoff:3.500A) Processing helix chain 'R' and resid 125 through 151 removed outlier: 4.564A pdb=" N TRP R 134 " --> pdb=" O TYR R 130 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N TYR R 135 " --> pdb=" O PHE R 131 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU R 140 " --> pdb=" O VAL R 136 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL R 149 " --> pdb=" O GLU R 145 " (cutoff:3.500A) Processing helix chain 'R' and resid 151 through 156 removed outlier: 3.735A pdb=" N SER R 155 " --> pdb=" O LYS R 151 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER R 156 " --> pdb=" O LEU R 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 151 through 156' Processing helix chain 'R' and resid 158 through 171 Processing helix chain 'S' and resid 14 through 45 removed outlier: 3.554A pdb=" N PHE S 45 " --> pdb=" O ALA S 41 " (cutoff:3.500A) Processing helix chain 'S' and resid 47 through 63 Processing helix chain 'S' and resid 63 through 77 removed outlier: 4.596A pdb=" N ILE S 69 " --> pdb=" O HIS S 65 " (cutoff:3.500A) Processing helix chain 'S' and resid 94 through 123 removed outlier: 3.571A pdb=" N LEU S 98 " --> pdb=" O ASP S 94 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP S 111 " --> pdb=" O ASN S 107 " (cutoff:3.500A) Processing helix chain 'S' and resid 125 through 151 removed outlier: 4.564A pdb=" N TRP S 134 " --> pdb=" O TYR S 130 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N TYR S 135 " --> pdb=" O PHE S 131 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU S 140 " --> pdb=" O VAL S 136 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL S 149 " --> pdb=" O GLU S 145 " (cutoff:3.500A) Processing helix chain 'S' and resid 151 through 156 removed outlier: 3.734A pdb=" N SER S 155 " --> pdb=" O LYS S 151 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER S 156 " --> pdb=" O LEU S 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 151 through 156' Processing helix chain 'S' and resid 158 through 171 Processing helix chain 'T' and resid 14 through 45 removed outlier: 3.554A pdb=" N PHE T 45 " --> pdb=" O ALA T 41 " (cutoff:3.500A) Processing helix chain 'T' and resid 47 through 63 Processing helix chain 'T' and resid 63 through 77 removed outlier: 4.622A pdb=" N ILE T 69 " --> pdb=" O HIS T 65 " (cutoff:3.500A) Processing helix chain 'T' and resid 94 through 123 removed outlier: 3.575A pdb=" N LEU T 98 " --> pdb=" O ASP T 94 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP T 111 " --> pdb=" O ASN T 107 " (cutoff:3.500A) Processing helix chain 'T' and resid 125 through 151 removed outlier: 4.564A pdb=" N TRP T 134 " --> pdb=" O TYR T 130 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N TYR T 135 " --> pdb=" O PHE T 131 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU T 140 " --> pdb=" O VAL T 136 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL T 149 " --> pdb=" O GLU T 145 " (cutoff:3.500A) Processing helix chain 'T' and resid 151 through 156 removed outlier: 3.734A pdb=" N SER T 155 " --> pdb=" O LYS T 151 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER T 156 " --> pdb=" O LEU T 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 151 through 156' Processing helix chain 'T' and resid 158 through 171 Processing helix chain 'U' and resid 14 through 45 removed outlier: 3.554A pdb=" N PHE U 45 " --> pdb=" O ALA U 41 " (cutoff:3.500A) Processing helix chain 'U' and resid 47 through 63 Processing helix chain 'U' and resid 63 through 77 removed outlier: 4.601A pdb=" N ILE U 69 " --> pdb=" O HIS U 65 " (cutoff:3.500A) Processing helix chain 'U' and resid 94 through 123 removed outlier: 3.584A pdb=" N LEU U 98 " --> pdb=" O ASP U 94 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP U 111 " --> pdb=" O ASN U 107 " (cutoff:3.500A) Processing helix chain 'U' and resid 125 through 151 removed outlier: 4.565A pdb=" N TRP U 134 " --> pdb=" O TYR U 130 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N TYR U 135 " --> pdb=" O PHE U 131 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU U 140 " --> pdb=" O VAL U 136 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL U 149 " --> pdb=" O GLU U 145 " (cutoff:3.500A) Processing helix chain 'U' and resid 151 through 156 removed outlier: 3.735A pdb=" N SER U 155 " --> pdb=" O LYS U 151 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER U 156 " --> pdb=" O LEU U 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 151 through 156' Processing helix chain 'U' and resid 158 through 171 Processing helix chain 'V' and resid 14 through 45 removed outlier: 3.554A pdb=" N PHE V 45 " --> pdb=" O ALA V 41 " (cutoff:3.500A) Processing helix chain 'V' and resid 47 through 63 Processing helix chain 'V' and resid 63 through 77 removed outlier: 4.621A pdb=" N ILE V 69 " --> pdb=" O HIS V 65 " (cutoff:3.500A) Processing helix chain 'V' and resid 94 through 123 removed outlier: 3.586A pdb=" N LEU V 98 " --> pdb=" O ASP V 94 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP V 111 " --> pdb=" O ASN V 107 " (cutoff:3.500A) Processing helix chain 'V' and resid 125 through 151 removed outlier: 4.565A pdb=" N TRP V 134 " --> pdb=" O TYR V 130 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N TYR V 135 " --> pdb=" O PHE V 131 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU V 140 " --> pdb=" O VAL V 136 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL V 149 " --> pdb=" O GLU V 145 " (cutoff:3.500A) Processing helix chain 'V' and resid 151 through 156 removed outlier: 3.734A pdb=" N SER V 155 " --> pdb=" O LYS V 151 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER V 156 " --> pdb=" O LEU V 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 151 through 156' Processing helix chain 'V' and resid 158 through 171 Processing helix chain 'W' and resid 14 through 45 removed outlier: 3.553A pdb=" N PHE W 45 " --> pdb=" O ALA W 41 " (cutoff:3.500A) Processing helix chain 'W' and resid 47 through 63 Processing helix chain 'W' and resid 63 through 77 removed outlier: 4.596A pdb=" N ILE W 69 " --> pdb=" O HIS W 65 " (cutoff:3.500A) Processing helix chain 'W' and resid 94 through 123 removed outlier: 3.582A pdb=" N LEU W 98 " --> pdb=" O ASP W 94 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP W 111 " --> pdb=" O ASN W 107 " (cutoff:3.500A) Processing helix chain 'W' and resid 125 through 151 removed outlier: 4.564A pdb=" N TRP W 134 " --> pdb=" O TYR W 130 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N TYR W 135 " --> pdb=" O PHE W 131 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU W 140 " --> pdb=" O VAL W 136 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL W 149 " --> pdb=" O GLU W 145 " (cutoff:3.500A) Processing helix chain 'W' and resid 151 through 156 removed outlier: 3.734A pdb=" N SER W 155 " --> pdb=" O LYS W 151 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER W 156 " --> pdb=" O LEU W 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 151 through 156' Processing helix chain 'W' and resid 158 through 171 Processing helix chain 'X' and resid 14 through 45 removed outlier: 3.553A pdb=" N PHE X 45 " --> pdb=" O ALA X 41 " (cutoff:3.500A) Processing helix chain 'X' and resid 47 through 63 Processing helix chain 'X' and resid 63 through 77 removed outlier: 4.596A pdb=" N ILE X 69 " --> pdb=" O HIS X 65 " (cutoff:3.500A) Processing helix chain 'X' and resid 94 through 123 removed outlier: 3.586A pdb=" N LEU X 98 " --> pdb=" O ASP X 94 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP X 111 " --> pdb=" O ASN X 107 " (cutoff:3.500A) Processing helix chain 'X' and resid 125 through 151 removed outlier: 4.566A pdb=" N TRP X 134 " --> pdb=" O TYR X 130 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N TYR X 135 " --> pdb=" O PHE X 131 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU X 140 " --> pdb=" O VAL X 136 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL X 149 " --> pdb=" O GLU X 145 " (cutoff:3.500A) Processing helix chain 'X' and resid 151 through 156 removed outlier: 3.731A pdb=" N SER X 155 " --> pdb=" O LYS X 151 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER X 156 " --> pdb=" O LEU X 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 151 through 156' Processing helix chain 'X' and resid 158 through 172 removed outlier: 3.657A pdb=" N LYS X 172 " --> pdb=" O GLU X 168 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 87 Processing sheet with id=AA2, first strand: chain 'B' and resid 83 through 87 Processing sheet with id=AA3, first strand: chain 'C' and resid 83 through 87 Processing sheet with id=AA4, first strand: chain 'D' and resid 83 through 87 Processing sheet with id=AA5, first strand: chain 'I' and resid 83 through 87 Processing sheet with id=AA6, first strand: chain 'J' and resid 83 through 87 Processing sheet with id=AA7, first strand: chain 'K' and resid 83 through 87 Processing sheet with id=AA8, first strand: chain 'L' and resid 83 through 87 Processing sheet with id=AA9, first strand: chain 'M' and resid 83 through 87 Processing sheet with id=AB1, first strand: chain 'N' and resid 83 through 87 Processing sheet with id=AB2, first strand: chain 'O' and resid 83 through 87 Processing sheet with id=AB3, first strand: chain 'P' and resid 83 through 87 2588 hydrogen bonds defined for protein. 7785 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.80 Time building geometry restraints manager: 13.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10741 1.34 - 1.46: 4465 1.46 - 1.57: 18054 1.57 - 1.69: 0 1.69 - 1.80: 144 Bond restraints: 33404 Sorted by residual: bond pdb=" CB VAL M 86 " pdb=" CG1 VAL M 86 " ideal model delta sigma weight residual 1.521 1.483 0.038 3.30e-02 9.18e+02 1.31e+00 bond pdb=" C LEU M 32 " pdb=" O LEU M 32 " ideal model delta sigma weight residual 1.237 1.248 -0.012 1.17e-02 7.31e+03 9.99e-01 bond pdb=" C ALA M 104 " pdb=" O ALA M 104 " ideal model delta sigma weight residual 1.237 1.248 -0.011 1.17e-02 7.31e+03 9.14e-01 bond pdb=" C ARG R 137 " pdb=" O ARG R 137 " ideal model delta sigma weight residual 1.237 1.248 -0.011 1.19e-02 7.06e+03 8.96e-01 bond pdb=" C ARG K 137 " pdb=" O ARG K 137 " ideal model delta sigma weight residual 1.237 1.248 -0.011 1.19e-02 7.06e+03 8.96e-01 ... (remaining 33399 not shown) Histogram of bond angle deviations from ideal: 100.70 - 107.39: 719 107.39 - 114.08: 19005 114.08 - 120.77: 15226 120.77 - 127.46: 9925 127.46 - 134.15: 260 Bond angle restraints: 45135 Sorted by residual: angle pdb=" C ARG V 75 " pdb=" N ASN V 76 " pdb=" CA ASN V 76 " ideal model delta sigma weight residual 122.54 119.24 3.30 1.65e+00 3.67e-01 4.01e+00 angle pdb=" C ARG A 75 " pdb=" N ASN A 76 " pdb=" CA ASN A 76 " ideal model delta sigma weight residual 122.54 119.25 3.29 1.65e+00 3.67e-01 3.98e+00 angle pdb=" C ARG X 75 " pdb=" N ASN X 76 " pdb=" CA ASN X 76 " ideal model delta sigma weight residual 122.54 119.26 3.28 1.65e+00 3.67e-01 3.96e+00 angle pdb=" CA TYR P 126 " pdb=" CB TYR P 126 " pdb=" CG TYR P 126 " ideal model delta sigma weight residual 113.90 110.32 3.58 1.80e+00 3.09e-01 3.96e+00 angle pdb=" C ARG B 75 " pdb=" N ASN B 76 " pdb=" CA ASN B 76 " ideal model delta sigma weight residual 122.54 119.26 3.28 1.65e+00 3.67e-01 3.95e+00 ... (remaining 45130 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.06: 17684 17.06 - 34.12: 1913 34.12 - 51.19: 326 51.19 - 68.25: 73 68.25 - 85.31: 55 Dihedral angle restraints: 20051 sinusoidal: 8144 harmonic: 11907 Sorted by residual: dihedral pdb=" CA ASP A 94 " pdb=" C ASP A 94 " pdb=" N ALA A 95 " pdb=" CA ALA A 95 " ideal model delta harmonic sigma weight residual 180.00 160.76 19.24 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA ASP M 94 " pdb=" C ASP M 94 " pdb=" N ALA M 95 " pdb=" CA ALA M 95 " ideal model delta harmonic sigma weight residual 180.00 161.26 18.74 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA ASP H 94 " pdb=" C ASP H 94 " pdb=" N ALA H 95 " pdb=" CA ALA H 95 " ideal model delta harmonic sigma weight residual 180.00 161.38 18.62 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 20048 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 2211 0.025 - 0.050: 1506 0.050 - 0.075: 856 0.075 - 0.100: 140 0.100 - 0.125: 184 Chirality restraints: 4897 Sorted by residual: chirality pdb=" CA ILE I 91 " pdb=" N ILE I 91 " pdb=" C ILE I 91 " pdb=" CB ILE I 91 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.92e-01 chirality pdb=" CA ILE S 91 " pdb=" N ILE S 91 " pdb=" C ILE S 91 " pdb=" CB ILE S 91 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.87e-01 chirality pdb=" CA ASN S 76 " pdb=" N ASN S 76 " pdb=" C ASN S 76 " pdb=" CB ASN S 76 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.86e-01 ... (remaining 4894 not shown) Planarity restraints: 5807 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR U 126 " 0.016 2.00e-02 2.50e+03 9.29e-03 1.73e+00 pdb=" CG TYR U 126 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR U 126 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR U 126 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR U 126 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR U 126 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR U 126 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR U 126 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR T 126 " 0.016 2.00e-02 2.50e+03 9.28e-03 1.72e+00 pdb=" CG TYR T 126 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR T 126 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR T 126 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR T 126 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR T 126 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR T 126 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR T 126 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR V 126 " 0.016 2.00e-02 2.50e+03 9.27e-03 1.72e+00 pdb=" CG TYR V 126 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR V 126 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR V 126 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR V 126 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR V 126 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR V 126 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR V 126 " 0.004 2.00e-02 2.50e+03 ... (remaining 5804 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 95 2.55 - 3.13: 23515 3.13 - 3.72: 49299 3.72 - 4.31: 71494 4.31 - 4.90: 118851 Nonbonded interactions: 263254 Sorted by model distance: nonbonded pdb=" OD2 ASP E 138 " pdb="FE FE E 201 " model vdw 1.957 2.260 nonbonded pdb=" OD2 ASP W 138 " pdb="FE FE W 201 " model vdw 1.957 2.260 nonbonded pdb=" OD2 ASP C 138 " pdb="FE FE C 201 " model vdw 1.957 2.260 nonbonded pdb=" OD2 ASP L 138 " pdb="FE FE L 201 " model vdw 1.957 2.260 nonbonded pdb=" OD2 ASP R 138 " pdb="FE FE R 201 " model vdw 1.957 2.260 ... (remaining 263249 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 13 through 43 or resid 45 through 55 or resid 57 through 1 \ 07 or resid 109 through 171 or resid 178 through 181 or resid 201)) selection = (chain 'B' and (resid 13 through 43 or resid 45 through 55 or resid 57 through 1 \ 07 or resid 109 through 171 or resid 178 through 181 or resid 201)) selection = (chain 'C' and (resid 13 through 43 or resid 45 through 55 or resid 57 through 1 \ 07 or resid 109 through 181 or resid 201)) selection = (chain 'D' and (resid 13 through 43 or resid 45 through 55 or resid 57 through 1 \ 07 or resid 109 through 171 or resid 178 through 181 or resid 201)) selection = (chain 'E' and (resid 13 through 43 or resid 45 through 55 or resid 57 through 1 \ 07 or resid 109 through 171 or resid 178 through 181 or resid 201)) selection = (chain 'F' and (resid 13 through 43 or resid 45 through 55 or resid 57 through 1 \ 07 or resid 109 through 181 or resid 201)) selection = (chain 'G' and (resid 13 through 43 or resid 45 through 55 or resid 57 through 1 \ 07 or resid 109 through 171 or resid 178 through 181 or resid 201)) selection = (chain 'H' and (resid 13 through 43 or resid 45 through 55 or resid 57 through 1 \ 07 or resid 109 through 181 or resid 201)) selection = (chain 'I' and (resid 13 through 43 or resid 45 through 55 or resid 57 through 1 \ 07 or resid 109 through 171 or resid 178 through 181 or resid 201)) selection = (chain 'J' and (resid 13 through 43 or resid 45 through 55 or resid 57 through 1 \ 07 or resid 109 through 171 or resid 178 through 181 or resid 201)) selection = (chain 'K' and (resid 13 through 43 or resid 45 through 55 or resid 57 through 1 \ 07 or resid 109 through 171 or resid 178 through 181 or resid 201)) selection = (chain 'L' and (resid 13 through 43 or resid 45 through 55 or resid 57 through 1 \ 07 or resid 109 through 171 or resid 178 through 181 or resid 201)) selection = (chain 'M' and (resid 13 through 43 or resid 45 through 55 or resid 57 through 1 \ 07 or resid 109 through 171 or resid 178 through 181 or resid 201)) selection = (chain 'N' and (resid 13 through 43 or resid 45 through 55 or resid 57 through 1 \ 07 or resid 109 through 171 or resid 178 through 181 or resid 201)) selection = (chain 'O' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 171 or resid 178 through 181 or resid 201)) selection = (chain 'P' and (resid 13 through 43 or resid 45 through 55 or resid 57 through 1 \ 07 or resid 109 through 181 or resid 201)) selection = (chain 'Q' and (resid 13 through 43 or resid 45 through 55 or resid 57 through 1 \ 07 or resid 109 through 171 or resid 178 through 181 or resid 201)) selection = (chain 'R' and (resid 13 through 43 or resid 45 through 55 or resid 57 through 1 \ 07 or resid 109 through 171 or resid 178 through 181 or resid 201)) selection = (chain 'S' and (resid 13 through 43 or resid 45 through 55 or resid 57 through 1 \ 07 or resid 109 through 171 or resid 178 through 181 or resid 201)) selection = (chain 'T' and (resid 13 through 43 or resid 45 through 55 or resid 57 through 1 \ 07 or resid 109 through 171 or resid 178 through 181 or resid 201)) selection = (chain 'U' and (resid 13 through 43 or resid 45 through 55 or resid 57 through 1 \ 07 or resid 109 through 171 or resid 178 through 181 or resid 201)) selection = (chain 'V' and (resid 13 through 43 or resid 45 through 55 or resid 57 through 1 \ 07 or resid 109 through 171 or resid 178 through 181 or resid 201)) selection = (chain 'W' and (resid 13 through 43 or resid 45 through 55 or resid 57 through 1 \ 07 or resid 109 through 171 or resid 178 through 181 or resid 201)) selection = (chain 'X' and (resid 13 through 43 or resid 45 through 55 or resid 57 through 1 \ 07 or resid 109 through 171 or resid 178 through 181 or resid 201)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.46 max=1.00 mean=0.99 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: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.150 Check model and map are aligned: 0.220 Set scattering table: 0.280 Process input model: 105.200 Find NCS groups from input model: 2.480 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 122.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 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 : 0.006 0.038 33404 Z= 0.389 Angle : 0.591 4.044 45135 Z= 0.345 Chirality : 0.043 0.125 4897 Planarity : 0.004 0.032 5807 Dihedral : 14.833 85.311 12369 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.35 % Allowed : 2.67 % Favored : 95.98 % 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: -1.60 (0.11), residues: 3985 helix: -0.50 (0.08), residues: 3141 sheet: None (None), residues: 0 loop : -2.78 (0.12), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP X 180 HIS 0.004 0.001 HIS K 36 PHE 0.009 0.002 PHE N 153 TYR 0.020 0.003 TYR U 126 ARG 0.004 0.001 ARG R 105 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 3457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 521 time to evaluate : 4.036 Fit side-chains REVERT: A 151 LYS cc_start: 0.8370 (pttm) cc_final: 0.7650 (mtmt) REVERT: B 55 GLN cc_start: 0.8354 (tp40) cc_final: 0.8148 (tp-100) REVERT: B 151 LYS cc_start: 0.8376 (pttm) cc_final: 0.7667 (mtmt) REVERT: C 151 LYS cc_start: 0.8364 (pttm) cc_final: 0.7648 (mtmt) REVERT: D 151 LYS cc_start: 0.8376 (pttm) cc_final: 0.7659 (mtmt) REVERT: E 151 LYS cc_start: 0.8366 (pttm) cc_final: 0.7648 (mtmt) REVERT: F 151 LYS cc_start: 0.8369 (pttm) cc_final: 0.7652 (mtmt) REVERT: G 151 LYS cc_start: 0.8361 (pttm) cc_final: 0.7642 (mtmt) REVERT: H 55 GLN cc_start: 0.8360 (tp40) cc_final: 0.8150 (tp-100) REVERT: H 151 LYS cc_start: 0.8375 (pttm) cc_final: 0.7660 (mtmt) REVERT: I 151 LYS cc_start: 0.8385 (pttm) cc_final: 0.7671 (mtmt) REVERT: J 151 LYS cc_start: 0.8372 (pttm) cc_final: 0.7662 (mtmt) REVERT: K 141 LYS cc_start: 0.7885 (tttt) cc_final: 0.7678 (ttpt) REVERT: K 151 LYS cc_start: 0.8366 (pttm) cc_final: 0.7648 (mtmt) REVERT: L 151 LYS cc_start: 0.8370 (pttm) cc_final: 0.7652 (mtmt) REVERT: M 151 LYS cc_start: 0.8370 (pttm) cc_final: 0.7655 (mtmt) REVERT: N 151 LYS cc_start: 0.8382 (pttm) cc_final: 0.7668 (mtmt) REVERT: O 141 LYS cc_start: 0.7885 (tttt) cc_final: 0.7681 (ttpt) REVERT: O 151 LYS cc_start: 0.8363 (pttm) cc_final: 0.7645 (mtmt) REVERT: P 151 LYS cc_start: 0.8377 (pttm) cc_final: 0.7668 (mtmt) REVERT: Q 151 LYS cc_start: 0.8367 (pttm) cc_final: 0.7645 (mtmt) REVERT: R 151 LYS cc_start: 0.8377 (pttm) cc_final: 0.7660 (mtmt) REVERT: S 151 LYS cc_start: 0.8372 (pttm) cc_final: 0.7659 (mtmt) REVERT: T 55 GLN cc_start: 0.8357 (tp40) cc_final: 0.8149 (tp-100) REVERT: T 151 LYS cc_start: 0.8364 (pttm) cc_final: 0.7648 (mtmt) REVERT: U 141 LYS cc_start: 0.7897 (tttt) cc_final: 0.7694 (ttpt) REVERT: U 151 LYS cc_start: 0.8369 (pttm) cc_final: 0.7655 (mtmt) REVERT: V 55 GLN cc_start: 0.8361 (tp40) cc_final: 0.8148 (tp-100) REVERT: V 151 LYS cc_start: 0.8368 (pttm) cc_final: 0.7656 (mtmt) REVERT: W 151 LYS cc_start: 0.8376 (pttm) cc_final: 0.7665 (mtmt) REVERT: X 114 LYS cc_start: 0.8117 (ttpt) cc_final: 0.7910 (tttt) REVERT: X 141 LYS cc_start: 0.7931 (tttt) cc_final: 0.7691 (ttpt) REVERT: X 151 LYS cc_start: 0.8378 (pttm) cc_final: 0.7664 (mtmt) outliers start: 0 outliers final: 0 residues processed: 521 average time/residue: 1.8376 time to fit residues: 1091.5404 Evaluate side-chains 358 residues out of total 3457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 358 time to evaluate : 3.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 324 optimal weight: 1.9990 chunk 291 optimal weight: 3.9990 chunk 161 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 196 optimal weight: 2.9990 chunk 155 optimal weight: 0.9980 chunk 300 optimal weight: 0.9990 chunk 116 optimal weight: 0.9990 chunk 183 optimal weight: 8.9990 chunk 224 optimal weight: 10.0000 chunk 348 optimal weight: 0.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 39 HIS A 55 GLN A 76 ASN B 14 ASN B 39 HIS B 76 ASN C 14 ASN C 39 HIS C 55 GLN C 76 ASN D 14 ASN D 39 HIS D 55 GLN D 76 ASN E 14 ASN E 39 HIS E 55 GLN E 76 ASN F 14 ASN F 39 HIS F 55 GLN F 76 ASN G 14 ASN G 39 HIS G 55 GLN G 76 ASN H 14 ASN H 39 HIS H 76 ASN I 14 ASN I 39 HIS I 55 GLN I 76 ASN J 14 ASN J 39 HIS J 76 ASN K 14 ASN K 39 HIS K 55 GLN K 76 ASN L 14 ASN L 39 HIS L 55 GLN L 76 ASN M 14 ASN M 39 HIS M 55 GLN M 76 ASN N 14 ASN N 39 HIS N 55 GLN N 76 ASN O 14 ASN O 39 HIS O 76 ASN P 14 ASN P 39 HIS P 55 GLN P 76 ASN Q 14 ASN Q 39 HIS Q 55 GLN Q 76 ASN R 14 ASN R 39 HIS R 55 GLN R 76 ASN S 14 ASN S 39 HIS S 55 GLN S 76 ASN T 14 ASN T 39 HIS T 76 ASN U 14 ASN U 39 HIS U 55 GLN U 76 ASN V 14 ASN V 39 HIS V 76 ASN W 14 ASN W 39 HIS W 55 GLN W 76 ASN X 14 ASN X 39 HIS X 55 GLN X 76 ASN Total number of N/Q/H flips: 90 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 33404 Z= 0.141 Angle : 0.419 3.538 45135 Z= 0.244 Chirality : 0.036 0.116 4897 Planarity : 0.003 0.030 5807 Dihedral : 4.007 13.866 4321 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Rotamer: Outliers : 2.28 % Allowed : 8.81 % Favored : 88.91 % 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: 1.16 (0.12), residues: 3985 helix: 1.41 (0.09), residues: 3167 sheet: None (None), residues: 0 loop : -1.73 (0.17), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP J 180 HIS 0.002 0.001 HIS A 36 PHE 0.004 0.001 PHE T 53 TYR 0.008 0.001 TYR X 49 ARG 0.001 0.000 ARG F 110 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 3457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 442 time to evaluate : 4.174 Fit side-chains REVERT: A 76 ASN cc_start: 0.8087 (OUTLIER) cc_final: 0.7872 (p0) REVERT: A 111 ASP cc_start: 0.7471 (t0) cc_final: 0.7170 (t70) REVERT: B 55 GLN cc_start: 0.8391 (tp40) cc_final: 0.8145 (tp-100) REVERT: B 76 ASN cc_start: 0.8074 (OUTLIER) cc_final: 0.7850 (p0) REVERT: B 111 ASP cc_start: 0.7465 (t0) cc_final: 0.7161 (t70) REVERT: C 76 ASN cc_start: 0.8084 (OUTLIER) cc_final: 0.7873 (p0) REVERT: C 111 ASP cc_start: 0.7478 (t0) cc_final: 0.7176 (t70) REVERT: D 76 ASN cc_start: 0.8090 (OUTLIER) cc_final: 0.7874 (p0) REVERT: D 111 ASP cc_start: 0.7481 (t0) cc_final: 0.7182 (t70) REVERT: D 114 LYS cc_start: 0.7886 (ttpt) cc_final: 0.7679 (tttt) REVERT: E 76 ASN cc_start: 0.8089 (OUTLIER) cc_final: 0.7875 (p0) REVERT: E 111 ASP cc_start: 0.7480 (t0) cc_final: 0.7178 (t70) REVERT: F 76 ASN cc_start: 0.8088 (OUTLIER) cc_final: 0.7875 (p0) REVERT: F 111 ASP cc_start: 0.7468 (t0) cc_final: 0.7178 (t70) REVERT: F 114 LYS cc_start: 0.7867 (ttpt) cc_final: 0.7654 (tttt) REVERT: G 76 ASN cc_start: 0.8120 (OUTLIER) cc_final: 0.7889 (p0) REVERT: G 111 ASP cc_start: 0.7471 (t0) cc_final: 0.7165 (t70) REVERT: H 55 GLN cc_start: 0.8379 (tp40) cc_final: 0.8118 (tp-100) REVERT: H 76 ASN cc_start: 0.8081 (OUTLIER) cc_final: 0.7855 (p0) REVERT: H 111 ASP cc_start: 0.7479 (t0) cc_final: 0.7176 (t70) REVERT: I 76 ASN cc_start: 0.8068 (OUTLIER) cc_final: 0.7847 (p0) REVERT: I 111 ASP cc_start: 0.7484 (t0) cc_final: 0.7179 (t70) REVERT: J 76 ASN cc_start: 0.8061 (OUTLIER) cc_final: 0.7832 (p0) REVERT: J 111 ASP cc_start: 0.7474 (t0) cc_final: 0.7169 (t70) REVERT: K 76 ASN cc_start: 0.8097 (OUTLIER) cc_final: 0.7881 (p0) REVERT: K 111 ASP cc_start: 0.7463 (t0) cc_final: 0.7156 (t70) REVERT: K 141 LYS cc_start: 0.7655 (tttt) cc_final: 0.7445 (ttpt) REVERT: L 76 ASN cc_start: 0.8095 (OUTLIER) cc_final: 0.7879 (p0) REVERT: L 111 ASP cc_start: 0.7473 (t0) cc_final: 0.7176 (t70) REVERT: M 76 ASN cc_start: 0.8082 (OUTLIER) cc_final: 0.7854 (p0) REVERT: M 111 ASP cc_start: 0.7474 (t0) cc_final: 0.7176 (t70) REVERT: N 76 ASN cc_start: 0.8104 (OUTLIER) cc_final: 0.7891 (p0) REVERT: N 111 ASP cc_start: 0.7473 (t0) cc_final: 0.7170 (t70) REVERT: O 76 ASN cc_start: 0.8128 (OUTLIER) cc_final: 0.7908 (p0) REVERT: O 111 ASP cc_start: 0.7481 (t0) cc_final: 0.7181 (t70) REVERT: O 141 LYS cc_start: 0.7687 (tttt) cc_final: 0.7432 (ttpt) REVERT: O 151 LYS cc_start: 0.8215 (pttm) cc_final: 0.7564 (mtmt) REVERT: P 76 ASN cc_start: 0.8126 (OUTLIER) cc_final: 0.7908 (p0) REVERT: P 111 ASP cc_start: 0.7468 (t0) cc_final: 0.7167 (t70) REVERT: Q 76 ASN cc_start: 0.8094 (OUTLIER) cc_final: 0.7870 (p0) REVERT: Q 111 ASP cc_start: 0.7482 (t0) cc_final: 0.7179 (t70) REVERT: R 76 ASN cc_start: 0.8085 (OUTLIER) cc_final: 0.7872 (p0) REVERT: R 111 ASP cc_start: 0.7467 (t0) cc_final: 0.7164 (t70) REVERT: S 76 ASN cc_start: 0.8125 (OUTLIER) cc_final: 0.7898 (p0) REVERT: S 111 ASP cc_start: 0.7488 (t0) cc_final: 0.7182 (t70) REVERT: T 55 GLN cc_start: 0.8397 (tp40) cc_final: 0.8148 (tp-100) REVERT: T 76 ASN cc_start: 0.8062 (OUTLIER) cc_final: 0.7850 (p0) REVERT: T 111 ASP cc_start: 0.7469 (t0) cc_final: 0.7163 (t70) REVERT: U 76 ASN cc_start: 0.8110 (OUTLIER) cc_final: 0.7892 (p0) REVERT: U 111 ASP cc_start: 0.7475 (t0) cc_final: 0.7170 (t70) REVERT: U 141 LYS cc_start: 0.7663 (tttt) cc_final: 0.7455 (ttpt) REVERT: V 55 GLN cc_start: 0.8405 (tp40) cc_final: 0.8151 (tp-100) REVERT: V 76 ASN cc_start: 0.8070 (OUTLIER) cc_final: 0.7843 (p0) REVERT: V 111 ASP cc_start: 0.7482 (t0) cc_final: 0.7182 (t70) REVERT: W 76 ASN cc_start: 0.8120 (OUTLIER) cc_final: 0.7897 (p0) REVERT: W 111 ASP cc_start: 0.7474 (t0) cc_final: 0.7169 (t70) REVERT: X 76 ASN cc_start: 0.8108 (OUTLIER) cc_final: 0.7879 (p0) REVERT: X 111 ASP cc_start: 0.7472 (t0) cc_final: 0.7169 (t70) REVERT: X 141 LYS cc_start: 0.7789 (tttt) cc_final: 0.7543 (ttpt) outliers start: 33 outliers final: 7 residues processed: 442 average time/residue: 1.3873 time to fit residues: 728.7740 Evaluate side-chains 380 residues out of total 3457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 349 time to evaluate : 3.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain C residue 76 ASN Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 89 LYS Chi-restraints excluded: chain E residue 76 ASN Chi-restraints excluded: chain F residue 76 ASN Chi-restraints excluded: chain F residue 89 LYS Chi-restraints excluded: chain G residue 76 ASN Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain I residue 76 ASN Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain K residue 76 ASN Chi-restraints excluded: chain K residue 89 LYS Chi-restraints excluded: chain L residue 76 ASN Chi-restraints excluded: chain M residue 76 ASN Chi-restraints excluded: chain N residue 76 ASN Chi-restraints excluded: chain O residue 76 ASN Chi-restraints excluded: chain O residue 89 LYS Chi-restraints excluded: chain P residue 76 ASN Chi-restraints excluded: chain Q residue 76 ASN Chi-restraints excluded: chain R residue 76 ASN Chi-restraints excluded: chain R residue 89 LYS Chi-restraints excluded: chain S residue 76 ASN Chi-restraints excluded: chain T residue 76 ASN Chi-restraints excluded: chain U residue 76 ASN Chi-restraints excluded: chain U residue 89 LYS Chi-restraints excluded: chain V residue 76 ASN Chi-restraints excluded: chain W residue 76 ASN Chi-restraints excluded: chain X residue 76 ASN Chi-restraints excluded: chain X residue 89 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 193 optimal weight: 9.9990 chunk 108 optimal weight: 0.9990 chunk 290 optimal weight: 8.9990 chunk 237 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 chunk 349 optimal weight: 4.9990 chunk 377 optimal weight: 1.9990 chunk 311 optimal weight: 9.9990 chunk 346 optimal weight: 0.9990 chunk 119 optimal weight: 6.9990 chunk 280 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B 76 ASN C 76 ASN D 76 ASN E 76 ASN F 76 ASN G 76 ASN H 76 ASN I 76 ASN J 76 ASN K 76 ASN L 76 ASN M 76 ASN N 76 ASN O 76 ASN P 76 ASN Q 76 ASN R 76 ASN S 76 ASN T 76 ASN U 76 ASN V 76 ASN W 76 ASN X 76 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 33404 Z= 0.173 Angle : 0.425 3.256 45135 Z= 0.246 Chirality : 0.037 0.116 4897 Planarity : 0.003 0.031 5807 Dihedral : 3.853 13.531 4321 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.89 % Allowed : 11.93 % Favored : 86.18 % 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: 1.88 (0.12), residues: 3985 helix: 1.95 (0.09), residues: 3167 sheet: None (None), residues: 0 loop : -1.62 (0.17), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP X 180 HIS 0.002 0.001 HIS R 36 PHE 0.005 0.001 PHE J 53 TYR 0.013 0.001 TYR G 126 ARG 0.002 0.000 ARG S 110 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 3457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 380 time to evaluate : 3.899 Fit side-chains REVERT: A 76 ASN cc_start: 0.8092 (OUTLIER) cc_final: 0.7878 (p0) REVERT: A 111 ASP cc_start: 0.7491 (t0) cc_final: 0.7216 (t70) REVERT: B 55 GLN cc_start: 0.8412 (tp40) cc_final: 0.8162 (tp-100) REVERT: B 111 ASP cc_start: 0.7488 (t0) cc_final: 0.7177 (t70) REVERT: C 76 ASN cc_start: 0.8091 (OUTLIER) cc_final: 0.7876 (p0) REVERT: C 111 ASP cc_start: 0.7498 (t0) cc_final: 0.7219 (t70) REVERT: D 76 ASN cc_start: 0.8095 (OUTLIER) cc_final: 0.7879 (p0) REVERT: D 111 ASP cc_start: 0.7500 (t0) cc_final: 0.7192 (t70) REVERT: E 76 ASN cc_start: 0.8097 (OUTLIER) cc_final: 0.7884 (p0) REVERT: E 111 ASP cc_start: 0.7502 (t0) cc_final: 0.7193 (t70) REVERT: F 76 ASN cc_start: 0.8090 (OUTLIER) cc_final: 0.7876 (p0) REVERT: F 111 ASP cc_start: 0.7487 (t0) cc_final: 0.7213 (t70) REVERT: G 111 ASP cc_start: 0.7490 (t0) cc_final: 0.7180 (t70) REVERT: H 55 GLN cc_start: 0.8402 (tp40) cc_final: 0.8146 (tp-100) REVERT: H 111 ASP cc_start: 0.7502 (t0) cc_final: 0.7194 (t70) REVERT: I 111 ASP cc_start: 0.7504 (t0) cc_final: 0.7193 (t70) REVERT: I 151 LYS cc_start: 0.8245 (pttm) cc_final: 0.7608 (mtmt) REVERT: J 111 ASP cc_start: 0.7493 (t0) cc_final: 0.7210 (t70) REVERT: K 76 ASN cc_start: 0.8105 (OUTLIER) cc_final: 0.7890 (p0) REVERT: K 111 ASP cc_start: 0.7483 (t0) cc_final: 0.7171 (t70) REVERT: K 141 LYS cc_start: 0.7677 (tttt) cc_final: 0.7444 (ttpt) REVERT: K 151 LYS cc_start: 0.8229 (pttm) cc_final: 0.7590 (mtmt) REVERT: L 76 ASN cc_start: 0.8099 (OUTLIER) cc_final: 0.7883 (p0) REVERT: L 111 ASP cc_start: 0.7493 (t0) cc_final: 0.7217 (t70) REVERT: M 76 ASN cc_start: 0.8090 (OUTLIER) cc_final: 0.7882 (p0) REVERT: M 111 ASP cc_start: 0.7494 (t0) cc_final: 0.7211 (t70) REVERT: N 76 ASN cc_start: 0.8115 (OUTLIER) cc_final: 0.7902 (p0) REVERT: N 111 ASP cc_start: 0.7495 (t0) cc_final: 0.7183 (t70) REVERT: N 151 LYS cc_start: 0.8245 (pttm) cc_final: 0.7612 (mtmt) REVERT: O 111 ASP cc_start: 0.7500 (t0) cc_final: 0.7222 (t70) REVERT: O 141 LYS cc_start: 0.7688 (tttt) cc_final: 0.7439 (ttpt) REVERT: O 151 LYS cc_start: 0.8230 (pttm) cc_final: 0.7586 (mtmt) REVERT: P 76 ASN cc_start: 0.8130 (OUTLIER) cc_final: 0.7915 (p0) REVERT: P 111 ASP cc_start: 0.7488 (t0) cc_final: 0.7210 (t70) REVERT: Q 76 ASN cc_start: 0.8092 (OUTLIER) cc_final: 0.7869 (p0) REVERT: Q 111 ASP cc_start: 0.7503 (t0) cc_final: 0.7193 (t70) REVERT: R 76 ASN cc_start: 0.8086 (OUTLIER) cc_final: 0.7873 (p0) REVERT: R 111 ASP cc_start: 0.7488 (t0) cc_final: 0.7187 (t70) REVERT: S 111 ASP cc_start: 0.7508 (t0) cc_final: 0.7195 (t70) REVERT: S 151 LYS cc_start: 0.8225 (pttm) cc_final: 0.7590 (mtmt) REVERT: T 55 GLN cc_start: 0.8417 (tp40) cc_final: 0.8163 (tp-100) REVERT: T 76 ASN cc_start: 0.8059 (OUTLIER) cc_final: 0.7841 (p0) REVERT: T 111 ASP cc_start: 0.7490 (t0) cc_final: 0.7176 (t70) REVERT: U 76 ASN cc_start: 0.8119 (OUTLIER) cc_final: 0.7904 (p0) REVERT: U 111 ASP cc_start: 0.7497 (t0) cc_final: 0.7186 (t70) REVERT: U 141 LYS cc_start: 0.7686 (tttt) cc_final: 0.7462 (ttpt) REVERT: V 55 GLN cc_start: 0.8425 (tp40) cc_final: 0.8168 (tp-100) REVERT: V 76 ASN cc_start: 0.8073 (OUTLIER) cc_final: 0.7870 (p0) REVERT: V 111 ASP cc_start: 0.7501 (t0) cc_final: 0.7225 (t70) REVERT: W 111 ASP cc_start: 0.7495 (t0) cc_final: 0.7183 (t70) REVERT: X 76 ASN cc_start: 0.8100 (OUTLIER) cc_final: 0.7872 (p0) REVERT: X 111 ASP cc_start: 0.7495 (t0) cc_final: 0.7190 (t70) REVERT: X 141 LYS cc_start: 0.7745 (tttt) cc_final: 0.7510 (ttpt) outliers start: 34 outliers final: 9 residues processed: 380 average time/residue: 1.6788 time to fit residues: 746.6028 Evaluate side-chains 348 residues out of total 3457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 323 time to evaluate : 3.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 89 LYS Chi-restraints excluded: chain C residue 76 ASN Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 89 LYS Chi-restraints excluded: chain E residue 76 ASN Chi-restraints excluded: chain F residue 76 ASN Chi-restraints excluded: chain F residue 89 LYS Chi-restraints excluded: chain K residue 76 ASN Chi-restraints excluded: chain K residue 89 LYS Chi-restraints excluded: chain L residue 76 ASN Chi-restraints excluded: chain L residue 89 LYS Chi-restraints excluded: chain M residue 76 ASN Chi-restraints excluded: chain N residue 76 ASN Chi-restraints excluded: chain O residue 89 LYS Chi-restraints excluded: chain P residue 76 ASN Chi-restraints excluded: chain Q residue 76 ASN Chi-restraints excluded: chain R residue 76 ASN Chi-restraints excluded: chain R residue 89 LYS Chi-restraints excluded: chain T residue 76 ASN Chi-restraints excluded: chain U residue 76 ASN Chi-restraints excluded: chain U residue 89 LYS Chi-restraints excluded: chain V residue 76 ASN Chi-restraints excluded: chain X residue 76 ASN Chi-restraints excluded: chain X residue 89 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 345 optimal weight: 10.0000 chunk 262 optimal weight: 3.9990 chunk 181 optimal weight: 10.0000 chunk 38 optimal weight: 0.3980 chunk 166 optimal weight: 4.9990 chunk 234 optimal weight: 4.9990 chunk 350 optimal weight: 8.9990 chunk 371 optimal weight: 10.0000 chunk 183 optimal weight: 9.9990 chunk 332 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B 76 ASN C 76 ASN D 76 ASN E 76 ASN F 76 ASN G 76 ASN H 76 ASN I 76 ASN J 76 ASN K 76 ASN L 76 ASN M 76 ASN N 76 ASN O 76 ASN P 76 ASN Q 76 ASN R 76 ASN S 76 ASN T 76 ASN U 76 ASN V 76 ASN W 76 ASN X 76 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 33404 Z= 0.221 Angle : 0.454 3.250 45135 Z= 0.262 Chirality : 0.038 0.120 4897 Planarity : 0.003 0.032 5807 Dihedral : 3.905 14.238 4321 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.63 % Allowed : 12.33 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.12), residues: 3985 helix: 2.03 (0.08), residues: 3167 sheet: None (None), residues: 0 loop : -1.56 (0.17), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP V 180 HIS 0.003 0.001 HIS D 36 PHE 0.007 0.001 PHE L 153 TYR 0.015 0.002 TYR U 126 ARG 0.001 0.000 ARG O 110 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 3457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 327 time to evaluate : 3.956 Fit side-chains REVERT: A 151 LYS cc_start: 0.8320 (pttm) cc_final: 0.7686 (mtmt) REVERT: B 55 GLN cc_start: 0.8382 (tp40) cc_final: 0.8156 (tp-100) REVERT: B 151 LYS cc_start: 0.8329 (pttm) cc_final: 0.7702 (mtmt) REVERT: C 151 LYS cc_start: 0.8316 (pttm) cc_final: 0.7682 (mtmt) REVERT: D 151 LYS cc_start: 0.8323 (pttm) cc_final: 0.7693 (mtmt) REVERT: E 151 LYS cc_start: 0.8320 (pttm) cc_final: 0.7685 (mtmt) REVERT: F 151 LYS cc_start: 0.8322 (pttm) cc_final: 0.7689 (mtmt) REVERT: H 55 GLN cc_start: 0.8407 (tp40) cc_final: 0.8169 (tp-100) REVERT: H 151 LYS cc_start: 0.8325 (pttm) cc_final: 0.7696 (mtmt) REVERT: I 151 LYS cc_start: 0.8334 (pttm) cc_final: 0.7650 (mtmm) REVERT: J 151 LYS cc_start: 0.8326 (pttm) cc_final: 0.7697 (mtmt) REVERT: K 141 LYS cc_start: 0.7804 (tttt) cc_final: 0.7571 (ttpt) REVERT: K 151 LYS cc_start: 0.8314 (pttm) cc_final: 0.7681 (mtmt) REVERT: L 151 LYS cc_start: 0.8317 (pttm) cc_final: 0.7684 (mtmt) REVERT: M 151 LYS cc_start: 0.8321 (pttm) cc_final: 0.7688 (mtmt) REVERT: N 151 LYS cc_start: 0.8332 (pttm) cc_final: 0.7702 (mtmt) REVERT: O 141 LYS cc_start: 0.7719 (tttt) cc_final: 0.7472 (ttpt) REVERT: O 151 LYS cc_start: 0.8320 (pttm) cc_final: 0.7625 (mtmm) REVERT: P 151 LYS cc_start: 0.8328 (pttm) cc_final: 0.7704 (mtmt) REVERT: Q 151 LYS cc_start: 0.8315 (pttm) cc_final: 0.7680 (mtmt) REVERT: R 151 LYS cc_start: 0.8323 (pttm) cc_final: 0.7696 (mtmt) REVERT: S 151 LYS cc_start: 0.8309 (pttm) cc_final: 0.7680 (mtmt) REVERT: T 55 GLN cc_start: 0.8385 (tp40) cc_final: 0.8156 (tp-100) REVERT: T 151 LYS cc_start: 0.8316 (pttm) cc_final: 0.7684 (mtmt) REVERT: U 141 LYS cc_start: 0.7812 (tttt) cc_final: 0.7582 (ttpt) REVERT: V 55 GLN cc_start: 0.8397 (tp40) cc_final: 0.8161 (tp-100) REVERT: V 151 LYS cc_start: 0.8322 (pttm) cc_final: 0.7695 (mtmt) REVERT: W 151 LYS cc_start: 0.8325 (pttm) cc_final: 0.7701 (mtmt) REVERT: X 141 LYS cc_start: 0.7774 (tttt) cc_final: 0.7502 (ttpt) REVERT: X 151 LYS cc_start: 0.8332 (pttm) cc_final: 0.7644 (mtmm) outliers start: 33 outliers final: 9 residues processed: 335 average time/residue: 1.4425 time to fit residues: 574.0502 Evaluate side-chains 290 residues out of total 3457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 281 time to evaluate : 3.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LYS Chi-restraints excluded: chain D residue 89 LYS Chi-restraints excluded: chain F residue 89 LYS Chi-restraints excluded: chain K residue 89 LYS Chi-restraints excluded: chain L residue 89 LYS Chi-restraints excluded: chain O residue 89 LYS Chi-restraints excluded: chain R residue 89 LYS Chi-restraints excluded: chain U residue 89 LYS Chi-restraints excluded: chain X residue 89 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 309 optimal weight: 9.9990 chunk 210 optimal weight: 8.9990 chunk 5 optimal weight: 7.9990 chunk 276 optimal weight: 5.9990 chunk 153 optimal weight: 0.9990 chunk 316 optimal weight: 0.9990 chunk 256 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 189 optimal weight: 0.9990 chunk 333 optimal weight: 7.9990 chunk 93 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B 76 ASN C 76 ASN D 76 ASN E 76 ASN F 76 ASN G 76 ASN H 76 ASN I 76 ASN J 76 ASN K 76 ASN L 76 ASN M 76 ASN N 76 ASN O 76 ASN P 76 ASN Q 76 ASN R 76 ASN S 76 ASN T 76 ASN U 76 ASN V 76 ASN W 76 ASN X 76 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 33404 Z= 0.253 Angle : 0.480 3.373 45135 Z= 0.275 Chirality : 0.039 0.116 4897 Planarity : 0.003 0.031 5807 Dihedral : 3.977 14.851 4321 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.50 % Allowed : 11.46 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.12), residues: 3985 helix: 2.00 (0.08), residues: 3167 sheet: None (None), residues: 0 loop : -1.50 (0.17), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP X 180 HIS 0.003 0.001 HIS V 36 PHE 0.008 0.001 PHE I 153 TYR 0.016 0.002 TYR S 126 ARG 0.001 0.000 ARG D 110 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 3457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 321 time to evaluate : 3.725 Fit side-chains REVERT: A 151 LYS cc_start: 0.8294 (pttm) cc_final: 0.7612 (mtmt) REVERT: B 55 GLN cc_start: 0.8404 (tp40) cc_final: 0.8003 (tp-100) REVERT: B 151 LYS cc_start: 0.8315 (pttm) cc_final: 0.7649 (mtmt) REVERT: C 151 LYS cc_start: 0.8305 (pttm) cc_final: 0.7630 (mtmt) REVERT: D 151 LYS cc_start: 0.8371 (pttm) cc_final: 0.7707 (mtmt) REVERT: E 151 LYS cc_start: 0.8290 (pttm) cc_final: 0.7636 (mtmt) REVERT: F 151 LYS cc_start: 0.8366 (pttm) cc_final: 0.7699 (mtmt) REVERT: G 151 LYS cc_start: 0.8349 (pttm) cc_final: 0.7597 (mtmm) REVERT: H 55 GLN cc_start: 0.8427 (tp40) cc_final: 0.8190 (tp-100) REVERT: H 151 LYS cc_start: 0.8312 (pttm) cc_final: 0.7643 (mtmt) REVERT: I 151 LYS cc_start: 0.8394 (pttm) cc_final: 0.7707 (mtmm) REVERT: J 151 LYS cc_start: 0.8299 (pttm) cc_final: 0.7651 (mtmt) REVERT: K 151 LYS cc_start: 0.8348 (pttm) cc_final: 0.7699 (mtmt) REVERT: L 114 LYS cc_start: 0.8023 (ttpt) cc_final: 0.7802 (tttt) REVERT: L 151 LYS cc_start: 0.8363 (pttm) cc_final: 0.7658 (mtmm) REVERT: M 151 LYS cc_start: 0.8295 (pttm) cc_final: 0.7641 (mtmt) REVERT: N 151 LYS cc_start: 0.8365 (pttm) cc_final: 0.7721 (mtmt) REVERT: O 141 LYS cc_start: 0.7774 (tttt) cc_final: 0.7541 (ttpt) REVERT: O 151 LYS cc_start: 0.8364 (pttm) cc_final: 0.7666 (mtmm) REVERT: P 151 LYS cc_start: 0.8300 (pttm) cc_final: 0.7657 (mtmt) REVERT: Q 151 LYS cc_start: 0.8363 (pttm) cc_final: 0.7694 (mtmt) REVERT: R 151 LYS cc_start: 0.8299 (pttm) cc_final: 0.7624 (mtmt) REVERT: S 151 LYS cc_start: 0.8369 (pttm) cc_final: 0.7669 (mtmm) REVERT: T 55 GLN cc_start: 0.8405 (tp40) cc_final: 0.8003 (tp-100) REVERT: T 151 LYS cc_start: 0.8361 (pttm) cc_final: 0.7694 (mtmt) REVERT: U 151 LYS cc_start: 0.8278 (pttm) cc_final: 0.7618 (mtmt) REVERT: V 55 GLN cc_start: 0.8416 (tp40) cc_final: 0.8009 (tp-100) REVERT: V 151 LYS cc_start: 0.8294 (pttm) cc_final: 0.7645 (mtmt) REVERT: W 151 LYS cc_start: 0.8314 (pttm) cc_final: 0.7648 (mtmt) REVERT: X 141 LYS cc_start: 0.7827 (tttt) cc_final: 0.7573 (ttpt) REVERT: X 151 LYS cc_start: 0.8392 (pttm) cc_final: 0.7701 (mtmm) outliers start: 63 outliers final: 11 residues processed: 369 average time/residue: 1.5211 time to fit residues: 661.7028 Evaluate side-chains 290 residues out of total 3457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 279 time to evaluate : 4.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LYS Chi-restraints excluded: chain D residue 89 LYS Chi-restraints excluded: chain F residue 89 LYS Chi-restraints excluded: chain I residue 76 ASN Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain K residue 89 LYS Chi-restraints excluded: chain L residue 89 LYS Chi-restraints excluded: chain O residue 89 LYS Chi-restraints excluded: chain R residue 89 LYS Chi-restraints excluded: chain U residue 89 LYS Chi-restraints excluded: chain X residue 89 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 124 optimal weight: 5.9990 chunk 334 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 217 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 371 optimal weight: 3.9990 chunk 308 optimal weight: 0.9990 chunk 172 optimal weight: 2.9990 chunk 30 optimal weight: 0.0060 chunk 122 optimal weight: 2.9990 chunk 195 optimal weight: 10.0000 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN C 76 ASN D 76 ASN E 76 ASN F 76 ASN ** G 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 76 ASN J 76 ASN K 76 ASN L 76 ASN M 76 ASN N 76 ASN O 76 ASN P 76 ASN Q 76 ASN R 76 ASN S 76 ASN T 76 ASN U 76 ASN V 76 ASN ** W 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 76 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 33404 Z= 0.115 Angle : 0.381 3.326 45135 Z= 0.223 Chirality : 0.035 0.115 4897 Planarity : 0.003 0.034 5807 Dihedral : 3.586 13.092 4321 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 1.49 % Allowed : 12.52 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.82 (0.12), residues: 3985 helix: 2.65 (0.09), residues: 3167 sheet: None (None), residues: 0 loop : -1.46 (0.16), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP X 180 HIS 0.002 0.000 HIS O 39 PHE 0.007 0.001 PHE J 73 TYR 0.009 0.001 TYR B 126 ARG 0.010 0.000 ARG I 75 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 3457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 367 time to evaluate : 4.118 Fit side-chains REVERT: A 111 ASP cc_start: 0.7484 (t0) cc_final: 0.7168 (t70) REVERT: B 111 ASP cc_start: 0.7448 (t0) cc_final: 0.7117 (t70) REVERT: C 111 ASP cc_start: 0.7464 (t0) cc_final: 0.7126 (t70) REVERT: D 111 ASP cc_start: 0.7485 (t0) cc_final: 0.7167 (t70) REVERT: E 111 ASP cc_start: 0.7458 (t0) cc_final: 0.7134 (t70) REVERT: F 111 ASP cc_start: 0.7485 (t0) cc_final: 0.7168 (t70) REVERT: G 76 ASN cc_start: 0.7765 (p0) cc_final: 0.7505 (p0) REVERT: G 111 ASP cc_start: 0.7451 (t0) cc_final: 0.7123 (t70) REVERT: H 111 ASP cc_start: 0.7459 (t0) cc_final: 0.7131 (t70) REVERT: I 111 ASP cc_start: 0.7471 (t0) cc_final: 0.7142 (t70) REVERT: J 111 ASP cc_start: 0.7452 (t0) cc_final: 0.7111 (t70) REVERT: K 111 ASP cc_start: 0.7441 (t0) cc_final: 0.7114 (t70) REVERT: L 111 ASP cc_start: 0.7456 (t0) cc_final: 0.7132 (t70) REVERT: M 111 ASP cc_start: 0.7462 (t0) cc_final: 0.7132 (t70) REVERT: N 111 ASP cc_start: 0.7452 (t0) cc_final: 0.7124 (t70) REVERT: O 76 ASN cc_start: 0.7849 (OUTLIER) cc_final: 0.7552 (p0) REVERT: O 111 ASP cc_start: 0.7461 (t0) cc_final: 0.7135 (t70) REVERT: O 141 LYS cc_start: 0.7573 (tttt) cc_final: 0.7366 (ttpt) REVERT: P 111 ASP cc_start: 0.7450 (t0) cc_final: 0.7112 (t70) REVERT: Q 111 ASP cc_start: 0.7471 (t0) cc_final: 0.7142 (t70) REVERT: R 111 ASP cc_start: 0.7475 (t0) cc_final: 0.7159 (t70) REVERT: S 76 ASN cc_start: 0.7765 (OUTLIER) cc_final: 0.7471 (p0) REVERT: S 111 ASP cc_start: 0.7474 (t0) cc_final: 0.7143 (t70) REVERT: T 111 ASP cc_start: 0.7449 (t0) cc_final: 0.7119 (t70) REVERT: U 111 ASP cc_start: 0.7452 (t0) cc_final: 0.7124 (t70) REVERT: V 111 ASP cc_start: 0.7465 (t0) cc_final: 0.7140 (t70) REVERT: W 76 ASN cc_start: 0.7780 (p0) cc_final: 0.7526 (p0) REVERT: W 111 ASP cc_start: 0.7459 (t0) cc_final: 0.7130 (t70) REVERT: X 111 ASP cc_start: 0.7488 (t0) cc_final: 0.7171 (t70) REVERT: X 141 LYS cc_start: 0.7688 (tttt) cc_final: 0.7443 (ttpt) outliers start: 29 outliers final: 2 residues processed: 367 average time/residue: 1.5126 time to fit residues: 655.8768 Evaluate side-chains 320 residues out of total 3457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 316 time to evaluate : 3.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 76 ASN Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain O residue 76 ASN Chi-restraints excluded: chain S residue 76 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 358 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 211 optimal weight: 6.9990 chunk 271 optimal weight: 1.9990 chunk 210 optimal weight: 0.9990 chunk 312 optimal weight: 4.9990 chunk 207 optimal weight: 0.9990 chunk 370 optimal weight: 0.9990 chunk 231 optimal weight: 8.9990 chunk 225 optimal weight: 0.9980 chunk 170 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 76 ASN G 76 ASN G 154 ASN H 76 ASN I 76 ASN J 76 ASN O 76 ASN S 76 ASN S 154 ASN W 76 ASN X 154 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 33404 Z= 0.124 Angle : 0.379 3.042 45135 Z= 0.225 Chirality : 0.036 0.144 4897 Planarity : 0.003 0.034 5807 Dihedral : 3.510 12.361 4321 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.90 % Allowed : 13.45 % Favored : 85.65 % 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: 3.08 (0.12), residues: 3985 helix: 2.80 (0.09), residues: 3167 sheet: None (None), residues: 0 loop : -1.24 (0.16), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP N 180 HIS 0.002 0.001 HIS M 39 PHE 0.004 0.001 PHE J 53 TYR 0.010 0.001 TYR K 126 ARG 0.003 0.000 ARG I 75 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 3457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 344 time to evaluate : 4.121 Fit side-chains REVERT: A 111 ASP cc_start: 0.7472 (t0) cc_final: 0.7143 (t70) REVERT: B 111 ASP cc_start: 0.7465 (t0) cc_final: 0.7124 (t70) REVERT: C 111 ASP cc_start: 0.7508 (t0) cc_final: 0.7167 (t70) REVERT: D 111 ASP cc_start: 0.7473 (t0) cc_final: 0.7141 (t70) REVERT: E 111 ASP cc_start: 0.7500 (t0) cc_final: 0.7166 (t70) REVERT: F 111 ASP cc_start: 0.7473 (t0) cc_final: 0.7142 (t70) REVERT: G 76 ASN cc_start: 0.7890 (OUTLIER) cc_final: 0.7606 (p0) REVERT: G 111 ASP cc_start: 0.7472 (t0) cc_final: 0.7125 (t70) REVERT: H 111 ASP cc_start: 0.7504 (t0) cc_final: 0.7168 (t70) REVERT: I 111 ASP cc_start: 0.7509 (t0) cc_final: 0.7173 (t70) REVERT: J 111 ASP cc_start: 0.7496 (t0) cc_final: 0.7156 (t70) REVERT: K 111 ASP cc_start: 0.7490 (t0) cc_final: 0.7148 (t70) REVERT: L 111 ASP cc_start: 0.7502 (t0) cc_final: 0.7167 (t70) REVERT: M 111 ASP cc_start: 0.7499 (t0) cc_final: 0.7159 (t70) REVERT: N 111 ASP cc_start: 0.7498 (t0) cc_final: 0.7160 (t70) REVERT: O 76 ASN cc_start: 0.7877 (OUTLIER) cc_final: 0.7566 (p0) REVERT: O 111 ASP cc_start: 0.7478 (t0) cc_final: 0.7138 (t70) REVERT: P 111 ASP cc_start: 0.7495 (t0) cc_final: 0.7158 (t70) REVERT: Q 111 ASP cc_start: 0.7483 (t0) cc_final: 0.7147 (t70) REVERT: R 111 ASP cc_start: 0.7469 (t0) cc_final: 0.7137 (t70) REVERT: S 76 ASN cc_start: 0.7737 (OUTLIER) cc_final: 0.7453 (p0) REVERT: S 111 ASP cc_start: 0.7509 (t0) cc_final: 0.7168 (t70) REVERT: T 111 ASP cc_start: 0.7464 (t0) cc_final: 0.7120 (t70) REVERT: U 111 ASP cc_start: 0.7499 (t0) cc_final: 0.7159 (t70) REVERT: V 111 ASP cc_start: 0.7483 (t0) cc_final: 0.7143 (t70) REVERT: W 76 ASN cc_start: 0.7907 (OUTLIER) cc_final: 0.7626 (p0) REVERT: W 111 ASP cc_start: 0.7496 (t0) cc_final: 0.7159 (t70) REVERT: X 111 ASP cc_start: 0.7473 (t0) cc_final: 0.7143 (t70) REVERT: X 141 LYS cc_start: 0.7674 (tttt) cc_final: 0.7466 (ttpt) outliers start: 8 outliers final: 0 residues processed: 347 average time/residue: 1.4351 time to fit residues: 590.3273 Evaluate side-chains 320 residues out of total 3457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 316 time to evaluate : 3.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 76 ASN Chi-restraints excluded: chain O residue 76 ASN Chi-restraints excluded: chain S residue 76 ASN Chi-restraints excluded: chain W residue 76 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 228 optimal weight: 8.9990 chunk 147 optimal weight: 6.9990 chunk 221 optimal weight: 5.9990 chunk 111 optimal weight: 0.9980 chunk 72 optimal weight: 0.1980 chunk 71 optimal weight: 7.9990 chunk 235 optimal weight: 1.9990 chunk 252 optimal weight: 4.9990 chunk 182 optimal weight: 6.9990 chunk 34 optimal weight: 8.9990 chunk 290 optimal weight: 0.9980 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN C 76 ASN D 76 ASN E 76 ASN F 76 ASN G 76 ASN I 76 ASN J 76 ASN K 76 ASN L 76 ASN M 76 ASN N 76 ASN O 76 ASN P 76 ASN Q 76 ASN R 76 ASN S 76 ASN T 76 ASN U 76 ASN V 76 ASN W 76 ASN X 76 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 33404 Z= 0.169 Angle : 0.416 3.788 45135 Z= 0.242 Chirality : 0.037 0.153 4897 Planarity : 0.003 0.035 5807 Dihedral : 3.622 12.425 4321 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.29 % Allowed : 13.31 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.91 (0.12), residues: 3985 helix: 2.64 (0.09), residues: 3167 sheet: None (None), residues: 0 loop : -1.09 (0.17), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP N 180 HIS 0.002 0.001 HIS A 36 PHE 0.005 0.001 PHE M 53 TYR 0.012 0.001 TYR K 126 ARG 0.002 0.000 ARG W 75 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 3457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 333 time to evaluate : 3.698 Fit side-chains REVERT: A 111 ASP cc_start: 0.7491 (t0) cc_final: 0.7176 (t70) REVERT: A 124 ASP cc_start: 0.7581 (m-30) cc_final: 0.7378 (m-30) REVERT: A 151 LYS cc_start: 0.7959 (pttm) cc_final: 0.7346 (mtmm) REVERT: B 55 GLN cc_start: 0.8402 (tp40) cc_final: 0.8152 (tp-100) REVERT: B 111 ASP cc_start: 0.7509 (t0) cc_final: 0.7179 (t70) REVERT: B 124 ASP cc_start: 0.7578 (m-30) cc_final: 0.7377 (m-30) REVERT: C 111 ASP cc_start: 0.7521 (t0) cc_final: 0.7195 (t70) REVERT: D 111 ASP cc_start: 0.7498 (t0) cc_final: 0.7179 (t70) REVERT: D 151 LYS cc_start: 0.7964 (pttm) cc_final: 0.7354 (mtmm) REVERT: E 111 ASP cc_start: 0.7516 (t0) cc_final: 0.7198 (t70) REVERT: F 111 ASP cc_start: 0.7520 (t0) cc_final: 0.7210 (t70) REVERT: F 151 LYS cc_start: 0.7962 (pttm) cc_final: 0.7349 (mtmm) REVERT: G 76 ASN cc_start: 0.8213 (OUTLIER) cc_final: 0.7949 (p0) REVERT: G 111 ASP cc_start: 0.7513 (t0) cc_final: 0.7188 (t70) REVERT: H 55 GLN cc_start: 0.8408 (tp40) cc_final: 0.8159 (tp-100) REVERT: H 111 ASP cc_start: 0.7520 (t0) cc_final: 0.7196 (t70) REVERT: I 76 ASN cc_start: 0.8103 (OUTLIER) cc_final: 0.7886 (p0) REVERT: I 111 ASP cc_start: 0.7523 (t0) cc_final: 0.7201 (t70) REVERT: I 151 LYS cc_start: 0.7999 (pttm) cc_final: 0.7398 (mtmm) REVERT: J 76 ASN cc_start: 0.8089 (OUTLIER) cc_final: 0.7885 (p0) REVERT: J 111 ASP cc_start: 0.7518 (t0) cc_final: 0.7189 (t70) REVERT: K 111 ASP cc_start: 0.7503 (t0) cc_final: 0.7180 (t70) REVERT: L 111 ASP cc_start: 0.7515 (t0) cc_final: 0.7198 (t70) REVERT: M 111 ASP cc_start: 0.7515 (t0) cc_final: 0.7193 (t70) REVERT: N 111 ASP cc_start: 0.7513 (t0) cc_final: 0.7191 (t70) REVERT: O 111 ASP cc_start: 0.7520 (t0) cc_final: 0.7197 (t70) REVERT: P 111 ASP cc_start: 0.7511 (t0) cc_final: 0.7184 (t70) REVERT: Q 111 ASP cc_start: 0.7523 (t0) cc_final: 0.7199 (t70) REVERT: R 111 ASP cc_start: 0.7486 (t0) cc_final: 0.7171 (t70) REVERT: R 151 LYS cc_start: 0.7961 (pttm) cc_final: 0.7356 (mtmm) REVERT: S 111 ASP cc_start: 0.7529 (t0) cc_final: 0.7205 (t70) REVERT: T 55 GLN cc_start: 0.8407 (tp40) cc_final: 0.8155 (tp-100) REVERT: T 111 ASP cc_start: 0.7508 (t0) cc_final: 0.7177 (t70) REVERT: U 111 ASP cc_start: 0.7512 (t0) cc_final: 0.7190 (t70) REVERT: V 55 GLN cc_start: 0.8414 (tp40) cc_final: 0.8159 (tp-100) REVERT: V 111 ASP cc_start: 0.7521 (t0) cc_final: 0.7198 (t70) REVERT: W 76 ASN cc_start: 0.8229 (OUTLIER) cc_final: 0.7966 (p0) REVERT: W 111 ASP cc_start: 0.7512 (t0) cc_final: 0.7190 (t70) REVERT: X 111 ASP cc_start: 0.7492 (t0) cc_final: 0.7173 (t70) REVERT: X 141 LYS cc_start: 0.7731 (tttt) cc_final: 0.7500 (ttpt) REVERT: X 151 LYS cc_start: 0.7996 (pttm) cc_final: 0.7393 (mtmm) outliers start: 22 outliers final: 0 residues processed: 349 average time/residue: 1.4979 time to fit residues: 615.7480 Evaluate side-chains 321 residues out of total 3457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 317 time to evaluate : 3.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 76 ASN Chi-restraints excluded: chain I residue 76 ASN Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain W residue 76 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 336 optimal weight: 10.0000 chunk 354 optimal weight: 8.9990 chunk 323 optimal weight: 0.5980 chunk 344 optimal weight: 4.9990 chunk 207 optimal weight: 0.9980 chunk 150 optimal weight: 0.3980 chunk 270 optimal weight: 8.9990 chunk 105 optimal weight: 5.9990 chunk 311 optimal weight: 9.9990 chunk 326 optimal weight: 3.9990 chunk 343 optimal weight: 20.0000 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B 76 ASN C 76 ASN D 76 ASN E 76 ASN F 76 ASN G 76 ASN H 76 ASN I 76 ASN J 76 ASN K 76 ASN L 76 ASN M 76 ASN N 76 ASN O 76 ASN P 76 ASN Q 76 ASN R 76 ASN S 76 ASN T 76 ASN U 76 ASN V 76 ASN W 76 ASN X 76 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 33404 Z= 0.190 Angle : 0.430 3.658 45135 Z= 0.251 Chirality : 0.038 0.114 4897 Planarity : 0.003 0.035 5807 Dihedral : 3.712 12.722 4321 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.35 % Allowed : 13.99 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.80 (0.12), residues: 3985 helix: 2.54 (0.09), residues: 3167 sheet: None (None), residues: 0 loop : -1.05 (0.17), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 180 HIS 0.003 0.001 HIS X 36 PHE 0.006 0.001 PHE G 153 TYR 0.013 0.002 TYR B 126 ARG 0.002 0.000 ARG I 75 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 3457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 320 time to evaluate : 3.825 Fit side-chains REVERT: A 111 ASP cc_start: 0.7505 (t0) cc_final: 0.7194 (t70) REVERT: A 151 LYS cc_start: 0.7958 (pttm) cc_final: 0.7326 (mtmm) REVERT: B 55 GLN cc_start: 0.8412 (tp40) cc_final: 0.8167 (tp-100) REVERT: B 111 ASP cc_start: 0.7483 (t0) cc_final: 0.7163 (t70) REVERT: B 151 LYS cc_start: 0.7994 (pttm) cc_final: 0.7375 (mtmm) REVERT: C 111 ASP cc_start: 0.7522 (t0) cc_final: 0.7209 (t70) REVERT: C 151 LYS cc_start: 0.7983 (pttm) cc_final: 0.7353 (mtmm) REVERT: D 111 ASP cc_start: 0.7506 (t0) cc_final: 0.7193 (t70) REVERT: D 151 LYS cc_start: 0.7993 (pttm) cc_final: 0.7367 (mtmm) REVERT: E 111 ASP cc_start: 0.7503 (t0) cc_final: 0.7181 (t70) REVERT: E 151 LYS cc_start: 0.7985 (pttm) cc_final: 0.7356 (mtmm) REVERT: F 111 ASP cc_start: 0.7504 (t0) cc_final: 0.7193 (t70) REVERT: F 151 LYS cc_start: 0.7961 (pttm) cc_final: 0.7331 (mtmm) REVERT: G 111 ASP cc_start: 0.7516 (t0) cc_final: 0.7201 (t70) REVERT: G 151 LYS cc_start: 0.7987 (pttm) cc_final: 0.7347 (mtmm) REVERT: H 55 GLN cc_start: 0.8419 (tp40) cc_final: 0.8173 (tp-100) REVERT: H 111 ASP cc_start: 0.7502 (t0) cc_final: 0.7180 (t70) REVERT: H 151 LYS cc_start: 0.7989 (pttm) cc_final: 0.7366 (mtmm) REVERT: I 111 ASP cc_start: 0.7507 (t0) cc_final: 0.7187 (t70) REVERT: I 151 LYS cc_start: 0.8004 (pttm) cc_final: 0.7383 (mtmm) REVERT: J 76 ASN cc_start: 0.8227 (OUTLIER) cc_final: 0.8019 (p0) REVERT: J 111 ASP cc_start: 0.7521 (t0) cc_final: 0.7207 (t70) REVERT: J 151 LYS cc_start: 0.7991 (pttm) cc_final: 0.7370 (mtmm) REVERT: K 111 ASP cc_start: 0.7507 (t0) cc_final: 0.7190 (t70) REVERT: K 151 LYS cc_start: 0.7950 (pttm) cc_final: 0.7316 (mtmm) REVERT: L 111 ASP cc_start: 0.7521 (t0) cc_final: 0.7209 (t70) REVERT: L 151 LYS cc_start: 0.7981 (pttm) cc_final: 0.7352 (mtmm) REVERT: M 111 ASP cc_start: 0.7500 (t0) cc_final: 0.7177 (t70) REVERT: M 151 LYS cc_start: 0.7987 (pttm) cc_final: 0.7359 (mtmm) REVERT: N 111 ASP cc_start: 0.7498 (t0) cc_final: 0.7176 (t70) REVERT: N 151 LYS cc_start: 0.7972 (pttm) cc_final: 0.7345 (mtmm) REVERT: O 111 ASP cc_start: 0.7502 (t0) cc_final: 0.7182 (t70) REVERT: O 151 LYS cc_start: 0.7987 (pttm) cc_final: 0.7374 (mtmm) REVERT: P 111 ASP cc_start: 0.7509 (t0) cc_final: 0.7196 (t70) REVERT: P 151 LYS cc_start: 0.7994 (pttm) cc_final: 0.7378 (mtmm) REVERT: Q 111 ASP cc_start: 0.7507 (t0) cc_final: 0.7187 (t70) REVERT: Q 151 LYS cc_start: 0.7983 (pttm) cc_final: 0.7352 (mtmm) REVERT: R 111 ASP cc_start: 0.7519 (t0) cc_final: 0.7211 (t70) REVERT: R 151 LYS cc_start: 0.7987 (pttm) cc_final: 0.7367 (mtmm) REVERT: S 111 ASP cc_start: 0.7513 (t0) cc_final: 0.7190 (t70) REVERT: S 151 LYS cc_start: 0.7987 (pttm) cc_final: 0.7365 (mtmm) REVERT: T 55 GLN cc_start: 0.8394 (tp40) cc_final: 0.8144 (tp-100) REVERT: T 111 ASP cc_start: 0.7506 (t0) cc_final: 0.7191 (t70) REVERT: T 151 LYS cc_start: 0.7980 (pttm) cc_final: 0.7353 (mtmm) REVERT: U 111 ASP cc_start: 0.7517 (t0) cc_final: 0.7203 (t70) REVERT: V 55 GLN cc_start: 0.8426 (tp40) cc_final: 0.8174 (tp-100) REVERT: V 111 ASP cc_start: 0.7501 (t0) cc_final: 0.7183 (t70) REVERT: V 151 LYS cc_start: 0.7990 (pttm) cc_final: 0.7367 (mtmm) REVERT: W 111 ASP cc_start: 0.7495 (t0) cc_final: 0.7173 (t70) REVERT: W 151 LYS cc_start: 0.7992 (pttm) cc_final: 0.7374 (mtmm) REVERT: X 111 ASP cc_start: 0.7522 (t0) cc_final: 0.7220 (t70) REVERT: X 141 LYS cc_start: 0.7747 (tttt) cc_final: 0.7512 (ttpt) REVERT: X 151 LYS cc_start: 0.8003 (pttm) cc_final: 0.7378 (mtmm) outliers start: 24 outliers final: 2 residues processed: 333 average time/residue: 1.6180 time to fit residues: 627.4619 Evaluate side-chains 313 residues out of total 3457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 310 time to evaluate : 3.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain M residue 76 ASN Chi-restraints excluded: chain V residue 76 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 226 optimal weight: 8.9990 chunk 364 optimal weight: 8.9990 chunk 222 optimal weight: 0.7980 chunk 173 optimal weight: 8.9990 chunk 253 optimal weight: 6.9990 chunk 382 optimal weight: 8.9990 chunk 352 optimal weight: 10.0000 chunk 304 optimal weight: 10.0000 chunk 31 optimal weight: 0.9980 chunk 235 optimal weight: 7.9990 chunk 186 optimal weight: 0.8980 overall best weight: 3.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B 76 ASN C 76 ASN D 76 ASN E 76 ASN F 76 ASN G 76 ASN H 76 ASN I 76 ASN J 76 ASN K 76 ASN L 76 ASN M 76 ASN N 76 ASN O 76 ASN P 76 ASN Q 76 ASN R 76 ASN S 76 ASN T 76 ASN U 76 ASN V 76 ASN W 76 ASN X 76 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 33404 Z= 0.272 Angle : 0.495 3.674 45135 Z= 0.283 Chirality : 0.040 0.126 4897 Planarity : 0.003 0.035 5807 Dihedral : 3.888 13.470 4321 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.35 % Allowed : 13.99 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.12), residues: 3985 helix: 2.26 (0.08), residues: 3167 sheet: None (None), residues: 0 loop : -1.13 (0.17), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP T 180 HIS 0.003 0.001 HIS W 56 PHE 0.009 0.002 PHE K 153 TYR 0.018 0.002 TYR T 126 ARG 0.004 0.000 ARG J 75 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 3457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 315 time to evaluate : 4.222 Fit side-chains REVERT: A 111 ASP cc_start: 0.7545 (t0) cc_final: 0.7234 (t70) REVERT: A 151 LYS cc_start: 0.8210 (pttm) cc_final: 0.7569 (mtmm) REVERT: B 55 GLN cc_start: 0.8391 (tp40) cc_final: 0.8164 (tp-100) REVERT: B 151 LYS cc_start: 0.8219 (pttm) cc_final: 0.7611 (mtmm) REVERT: C 151 LYS cc_start: 0.8190 (pttm) cc_final: 0.7570 (mtmm) REVERT: D 151 LYS cc_start: 0.8217 (pttm) cc_final: 0.7603 (mtmm) REVERT: E 151 LYS cc_start: 0.8191 (pttm) cc_final: 0.7573 (mtmm) REVERT: F 151 LYS cc_start: 0.8212 (pttm) cc_final: 0.7571 (mtmm) REVERT: G 151 LYS cc_start: 0.8095 (pttm) cc_final: 0.7394 (mtmm) REVERT: H 55 GLN cc_start: 0.8397 (tp40) cc_final: 0.8169 (tp-100) REVERT: H 151 LYS cc_start: 0.8198 (pttm) cc_final: 0.7585 (mtmm) REVERT: I 151 LYS cc_start: 0.8148 (pttm) cc_final: 0.7496 (mtmm) REVERT: J 151 LYS cc_start: 0.8200 (pttm) cc_final: 0.7588 (mtmm) REVERT: K 151 LYS cc_start: 0.8153 (pttm) cc_final: 0.7491 (mtmm) REVERT: L 151 LYS cc_start: 0.8193 (pttm) cc_final: 0.7574 (mtmm) REVERT: M 151 LYS cc_start: 0.8214 (pttm) cc_final: 0.7599 (mtmm) REVERT: N 151 LYS cc_start: 0.8224 (pttm) cc_final: 0.7586 (mtmm) REVERT: O 151 LYS cc_start: 0.8120 (pttm) cc_final: 0.7478 (mtmm) REVERT: P 151 LYS cc_start: 0.8201 (pttm) cc_final: 0.7593 (mtmm) REVERT: Q 151 LYS cc_start: 0.8208 (pttm) cc_final: 0.7591 (mtmm) REVERT: R 151 LYS cc_start: 0.8198 (pttm) cc_final: 0.7584 (mtmm) REVERT: S 151 LYS cc_start: 0.8198 (pttm) cc_final: 0.7585 (mtmm) REVERT: T 55 GLN cc_start: 0.8392 (tp40) cc_final: 0.8162 (tp-100) REVERT: T 151 LYS cc_start: 0.8190 (pttm) cc_final: 0.7571 (mtmm) REVERT: V 55 GLN cc_start: 0.8403 (tp40) cc_final: 0.8169 (tp-100) REVERT: V 151 LYS cc_start: 0.8214 (pttm) cc_final: 0.7605 (mtmm) REVERT: W 151 LYS cc_start: 0.8217 (pttm) cc_final: 0.7610 (mtmm) REVERT: X 111 ASP cc_start: 0.7540 (t0) cc_final: 0.7232 (t70) REVERT: X 141 LYS cc_start: 0.7846 (tttt) cc_final: 0.7621 (ttpt) REVERT: X 151 LYS cc_start: 0.8146 (pttm) cc_final: 0.7490 (mtmm) outliers start: 24 outliers final: 0 residues processed: 332 average time/residue: 1.6351 time to fit residues: 633.9469 Evaluate side-chains 285 residues out of total 3457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 285 time to evaluate : 3.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 241 optimal weight: 2.9990 chunk 324 optimal weight: 0.8980 chunk 93 optimal weight: 4.9990 chunk 280 optimal weight: 0.6980 chunk 44 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 305 optimal weight: 2.9990 chunk 127 optimal weight: 5.9990 chunk 313 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B 76 ASN C 76 ASN D 76 ASN E 76 ASN F 76 ASN ** G 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN I 76 ASN J 76 ASN K 76 ASN L 76 ASN M 76 ASN N 76 ASN O 76 ASN P 76 ASN Q 76 ASN R 76 ASN S 76 ASN T 76 ASN U 76 ASN V 76 ASN X 76 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.145235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.122463 restraints weight = 231997.243| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 4.26 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3394 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3394 r_free = 0.3394 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3393 r_free = 0.3393 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3393 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 33404 Z= 0.167 Angle : 0.419 3.730 45135 Z= 0.245 Chirality : 0.037 0.117 4897 Planarity : 0.003 0.034 5807 Dihedral : 3.736 12.774 4321 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.29 % Allowed : 13.43 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.81 (0.12), residues: 3985 helix: 2.53 (0.09), residues: 3167 sheet: None (None), residues: 0 loop : -0.98 (0.17), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP X 180 HIS 0.002 0.001 HIS K 36 PHE 0.005 0.001 PHE J 53 TYR 0.012 0.001 TYR N 126 ARG 0.001 0.000 ARG B 110 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10390.42 seconds wall clock time: 253 minutes 21.87 seconds (15201.87 seconds total)