Starting phenix.real_space_refine on Sun Aug 11 11:00:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wqu_37754/08_2024/8wqu_37754.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wqu_37754/08_2024/8wqu_37754.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wqu_37754/08_2024/8wqu_37754.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wqu_37754/08_2024/8wqu_37754.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wqu_37754/08_2024/8wqu_37754.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wqu_37754/08_2024/8wqu_37754.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.151 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 5328 2.21 5 O 6384 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 GLU 59": "OE1" <-> "OE2" Residue "A GLU 67": "OE1" <-> "OE2" Residue "A ARG 105": "NH1" <-> "NH2" Residue "A GLU 164": "OE1" <-> "OE2" Residue "A GLU 178": "OE1" <-> "OE2" Residue "B TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 29": "OE1" <-> "OE2" Residue "B GLU 59": "OE1" <-> "OE2" Residue "B GLU 67": "OE1" <-> "OE2" Residue "B ARG 105": "NH1" <-> "NH2" Residue "B GLU 145": "OE1" <-> "OE2" Residue "B GLU 163": "OE1" <-> "OE2" Residue "B GLU 164": "OE1" <-> "OE2" Residue "B GLU 178": "OE1" <-> "OE2" Residue "C TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 29": "OE1" <-> "OE2" Residue "C GLU 59": "OE1" <-> "OE2" Residue "C GLU 67": "OE1" <-> "OE2" Residue "C ARG 105": "NH1" <-> "NH2" Residue "C GLU 145": "OE1" <-> "OE2" Residue "C GLU 164": "OE1" <-> "OE2" Residue "C GLU 178": "OE1" <-> "OE2" Residue "D GLU 29": "OE1" <-> "OE2" Residue "D GLU 59": "OE1" <-> "OE2" Residue "D GLU 67": "OE1" <-> "OE2" Residue "D ARG 105": "NH1" <-> "NH2" Residue "D GLU 164": "OE1" <-> "OE2" Residue "D GLU 178": "OE1" <-> "OE2" Residue "E GLU 29": "OE1" <-> "OE2" Residue "E GLU 59": "OE1" <-> "OE2" Residue "E GLU 67": "OE1" <-> "OE2" Residue "E ARG 105": "NH1" <-> "NH2" Residue "E GLU 164": "OE1" <-> "OE2" Residue "E GLU 178": "OE1" <-> "OE2" Residue "F TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 29": "OE1" <-> "OE2" Residue "F GLU 59": "OE1" <-> "OE2" Residue "F GLU 67": "OE1" <-> "OE2" Residue "F ARG 105": "NH1" <-> "NH2" Residue "F GLU 164": "OE1" <-> "OE2" Residue "F GLU 178": "OE1" <-> "OE2" Residue "G TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 29": "OE1" <-> "OE2" Residue "G GLU 59": "OE1" <-> "OE2" Residue "G GLU 67": "OE1" <-> "OE2" Residue "G ARG 105": "NH1" <-> "NH2" Residue "G GLU 145": "OE1" <-> "OE2" Residue "G GLU 164": "OE1" <-> "OE2" Residue "G GLU 178": "OE1" <-> "OE2" Residue "H TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 29": "OE1" <-> "OE2" Residue "H GLU 59": "OE1" <-> "OE2" Residue "H GLU 67": "OE1" <-> "OE2" Residue "H ARG 105": "NH1" <-> "NH2" Residue "H GLU 145": "OE1" <-> "OE2" Residue "H GLU 164": "OE1" <-> "OE2" Residue "H GLU 178": "OE1" <-> "OE2" Residue "I TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 29": "OE1" <-> "OE2" Residue "I GLU 59": "OE1" <-> "OE2" Residue "I GLU 67": "OE1" <-> "OE2" Residue "I ARG 105": "NH1" <-> "NH2" Residue "I GLU 164": "OE1" <-> "OE2" Residue "I GLU 178": "OE1" <-> "OE2" Residue "J TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 29": "OE1" <-> "OE2" Residue "J GLU 59": "OE1" <-> "OE2" Residue "J GLU 67": "OE1" <-> "OE2" Residue "J ARG 105": "NH1" <-> "NH2" Residue "J GLU 145": "OE1" <-> "OE2" Residue "J GLU 164": "OE1" <-> "OE2" Residue "J GLU 178": "OE1" <-> "OE2" Residue "K TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 29": "OE1" <-> "OE2" Residue "K GLU 59": "OE1" <-> "OE2" Residue "K GLU 67": "OE1" <-> "OE2" Residue "K ARG 105": "NH1" <-> "NH2" Residue "K GLU 164": "OE1" <-> "OE2" Residue "K GLU 178": "OE1" <-> "OE2" Residue "L GLU 29": "OE1" <-> "OE2" Residue "L GLU 59": "OE1" <-> "OE2" Residue "L GLU 67": "OE1" <-> "OE2" Residue "L ARG 105": "NH1" <-> "NH2" Residue "L GLU 164": "OE1" <-> "OE2" Residue "L GLU 178": "OE1" <-> "OE2" Residue "M GLU 29": "OE1" <-> "OE2" Residue "M GLU 59": "OE1" <-> "OE2" Residue "M GLU 67": "OE1" <-> "OE2" Residue "M ARG 105": "NH1" <-> "NH2" Residue "M GLU 164": "OE1" <-> "OE2" Residue "M GLU 178": "OE1" <-> "OE2" Residue "N GLU 29": "OE1" <-> "OE2" Residue "N GLU 59": "OE1" <-> "OE2" Residue "N GLU 67": "OE1" <-> "OE2" Residue "N ARG 105": "NH1" <-> "NH2" Residue "N GLU 164": "OE1" <-> "OE2" Residue "N GLU 178": "OE1" <-> "OE2" Residue "O TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 29": "OE1" <-> "OE2" Residue "O GLU 59": "OE1" <-> "OE2" Residue "O GLU 67": "OE1" <-> "OE2" Residue "O ARG 105": "NH1" <-> "NH2" Residue "O GLU 145": "OE1" <-> "OE2" Residue "O GLU 164": "OE1" <-> "OE2" Residue "O GLU 178": "OE1" <-> "OE2" Residue "P TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 29": "OE1" <-> "OE2" Residue "P GLU 59": "OE1" <-> "OE2" Residue "P GLU 67": "OE1" <-> "OE2" Residue "P ARG 105": "NH1" <-> "NH2" Residue "P GLU 145": "OE1" <-> "OE2" Residue "P GLU 164": "OE1" <-> "OE2" Residue "P GLU 178": "OE1" <-> "OE2" Residue "Q TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 29": "OE1" <-> "OE2" Residue "Q GLU 59": "OE1" <-> "OE2" Residue "Q GLU 67": "OE1" <-> "OE2" Residue "Q ARG 105": "NH1" <-> "NH2" Residue "Q GLU 164": "OE1" <-> "OE2" Residue "Q GLU 178": "OE1" <-> "OE2" Residue "R TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 29": "OE1" <-> "OE2" Residue "R GLU 59": "OE1" <-> "OE2" Residue "R GLU 67": "OE1" <-> "OE2" Residue "R ARG 105": "NH1" <-> "NH2" Residue "R GLU 164": "OE1" <-> "OE2" Residue "R GLU 178": "OE1" <-> "OE2" Residue "S TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 29": "OE1" <-> "OE2" Residue "S GLU 59": "OE1" <-> "OE2" Residue "S GLU 67": "OE1" <-> "OE2" Residue "S ARG 105": "NH1" <-> "NH2" Residue "S GLU 145": "OE1" <-> "OE2" Residue "S GLU 164": "OE1" <-> "OE2" Residue "S GLU 178": "OE1" <-> "OE2" Residue "T TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 29": "OE1" <-> "OE2" Residue "T GLU 59": "OE1" <-> "OE2" Residue "T GLU 67": "OE1" <-> "OE2" Residue "T ARG 105": "NH1" <-> "NH2" Residue "T GLU 164": "OE1" <-> "OE2" Residue "T GLU 178": "OE1" <-> "OE2" Residue "U TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 29": "OE1" <-> "OE2" Residue "U GLU 59": "OE1" <-> "OE2" Residue "U GLU 67": "OE1" <-> "OE2" Residue "U ARG 105": "NH1" <-> "NH2" Residue "U GLU 164": "OE1" <-> "OE2" Residue "U GLU 178": "OE1" <-> "OE2" Residue "V TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 29": "OE1" <-> "OE2" Residue "V GLU 59": "OE1" <-> "OE2" Residue "V GLU 67": "OE1" <-> "OE2" Residue "V ARG 105": "NH1" <-> "NH2" Residue "V GLU 145": "OE1" <-> "OE2" Residue "V GLU 164": "OE1" <-> "OE2" Residue "V GLU 178": "OE1" <-> "OE2" Residue "W TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 29": "OE1" <-> "OE2" Residue "W GLU 59": "OE1" <-> "OE2" Residue "W GLU 67": "OE1" <-> "OE2" Residue "W ARG 105": "NH1" <-> "NH2" Residue "W GLU 164": "OE1" <-> "OE2" Residue "W GLU 178": "OE1" <-> "OE2" Residue "X TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 29": "OE1" <-> "OE2" Residue "X GLU 59": "OE1" <-> "OE2" Residue "X GLU 67": "OE1" <-> "OE2" Residue "X ARG 105": "NH1" <-> "NH2" Residue "X GLU 145": "OE1" <-> "OE2" Residue "X GLU 164": "OE1" <-> "OE2" Residue "X GLU 178": "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: 32736 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: 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: "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: 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: "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: 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: "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: 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: "P" 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: "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: 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: "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: 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: "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: 30.85, per 1000 atoms: 0.94 Number of scatterers: 32736 At special positions: 0 Unit cell: (132.956, 132.956, 132.956, 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 6384 8.00 N 5328 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: 12.25 Conformation dependent library (CDL) restraints added in 10.8 seconds 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7680 Finding SS restraints... Secondary structure from input PDB file: 177 helices and 12 sheets defined 82.6% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.80 Creating SS restraints... Processing helix chain 'A' and resid 13 through 45 removed outlier: 3.663A pdb=" N ASN A 17 " --> pdb=" O SER A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 63 Processing helix chain 'A' and resid 63 through 77 removed outlier: 4.476A pdb=" N ILE A 69 " --> pdb=" O HIS A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 122 removed outlier: 3.677A pdb=" N ASP A 111 " --> pdb=" O ASN A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 151 removed outlier: 3.530A pdb=" N PHE A 129 " --> pdb=" O ASP A 125 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N TRP A 134 " --> pdb=" O TYR A 130 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N TYR A 135 " --> pdb=" O PHE A 131 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL A 149 " --> pdb=" O GLU A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 155 Processing helix chain 'A' and resid 158 through 171 Processing helix chain 'B' and resid 14 through 45 Processing helix chain 'B' and resid 47 through 63 Processing helix chain 'B' and resid 63 through 77 removed outlier: 4.475A pdb=" N ILE B 69 " --> pdb=" O HIS B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 122 removed outlier: 3.692A pdb=" N ASP B 111 " --> pdb=" O ASN B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 132 Processing helix chain 'B' and resid 132 through 151 removed outlier: 4.019A pdb=" N LEU B 140 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL B 149 " --> pdb=" O GLU B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 155 Processing helix chain 'B' and resid 158 through 171 Processing helix chain 'C' and resid 14 through 45 Processing helix chain 'C' and resid 47 through 63 Processing helix chain 'C' and resid 63 through 77 removed outlier: 4.470A pdb=" N ILE C 69 " --> pdb=" O HIS C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 122 removed outlier: 3.698A pdb=" N ASP C 111 " --> pdb=" O ASN C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 151 removed outlier: 3.525A pdb=" N PHE C 129 " --> pdb=" O ASP C 125 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N TRP C 134 " --> pdb=" O TYR C 130 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N TYR C 135 " --> pdb=" O PHE C 131 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU C 140 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL C 149 " --> pdb=" O GLU C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 155 Processing helix chain 'C' and resid 158 through 171 Processing helix chain 'D' and resid 14 through 45 Processing helix chain 'D' and resid 47 through 63 Processing helix chain 'D' and resid 63 through 77 removed outlier: 4.475A pdb=" N ILE D 69 " --> pdb=" O HIS D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 122 removed outlier: 3.678A pdb=" N ASP D 111 " --> pdb=" O ASN D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 151 removed outlier: 3.527A pdb=" N PHE D 129 " --> pdb=" O ASP D 125 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N TRP D 134 " --> pdb=" O TYR D 130 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N TYR D 135 " --> pdb=" O PHE D 131 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU D 140 " --> pdb=" O VAL D 136 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL D 149 " --> pdb=" O GLU D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 155 Processing helix chain 'D' and resid 158 through 171 Processing helix chain 'E' and resid 14 through 45 Processing helix chain 'E' and resid 47 through 63 Processing helix chain 'E' and resid 63 through 77 removed outlier: 4.473A pdb=" N ILE E 69 " --> pdb=" O HIS E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 122 removed outlier: 3.678A pdb=" N ASP E 111 " --> pdb=" O ASN E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 151 removed outlier: 4.628A pdb=" N TRP E 134 " --> pdb=" O TYR E 130 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N TYR E 135 " --> pdb=" O PHE E 131 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU E 140 " --> pdb=" O VAL E 136 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL E 149 " --> pdb=" O GLU E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 155 Processing helix chain 'E' and resid 158 through 171 Processing helix chain 'F' and resid 14 through 45 Processing helix chain 'F' and resid 47 through 63 Processing helix chain 'F' and resid 63 through 77 removed outlier: 4.468A pdb=" N ILE F 69 " --> pdb=" O HIS F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 122 removed outlier: 3.698A pdb=" N ASP F 111 " --> pdb=" O ASN F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 151 removed outlier: 4.627A pdb=" N TRP F 134 " --> pdb=" O TYR F 130 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N TYR F 135 " --> pdb=" O PHE F 131 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU F 140 " --> pdb=" O VAL F 136 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL F 149 " --> pdb=" O GLU F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 155 Processing helix chain 'F' and resid 158 through 171 Processing helix chain 'G' and resid 14 through 45 Processing helix chain 'G' and resid 47 through 63 Processing helix chain 'G' and resid 63 through 77 removed outlier: 4.470A pdb=" N ILE G 69 " --> pdb=" O HIS G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 122 removed outlier: 3.693A pdb=" N ASP G 111 " --> pdb=" O ASN G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 151 removed outlier: 3.542A pdb=" N PHE G 129 " --> pdb=" O ASP G 125 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR G 130 " --> pdb=" O TYR G 126 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N TRP G 134 " --> pdb=" O TYR G 130 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N TYR G 135 " --> pdb=" O PHE G 131 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU G 140 " --> pdb=" O VAL G 136 " (cutoff:3.500A) removed outlier: 3.958A 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 Processing helix chain 'H' and resid 47 through 63 Processing helix chain 'H' and resid 63 through 77 removed outlier: 4.470A pdb=" N ILE H 69 " --> pdb=" O HIS H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 122 removed outlier: 3.783A pdb=" N LEU H 98 " --> pdb=" O ASP H 94 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP H 111 " --> pdb=" O ASN H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 132 Processing helix chain 'H' and resid 132 through 151 removed outlier: 4.016A pdb=" N LEU H 140 " --> pdb=" O VAL H 136 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL H 149 " --> pdb=" O GLU H 145 " (cutoff:3.500A) Processing helix chain 'H' and resid 152 through 155 Processing helix chain 'H' and resid 158 through 171 Processing helix chain 'I' and resid 14 through 45 Processing helix chain 'I' and resid 47 through 63 Processing helix chain 'I' and resid 63 through 77 removed outlier: 4.469A pdb=" N ILE I 69 " --> pdb=" O HIS I 65 " (cutoff:3.500A) Processing helix chain 'I' and resid 95 through 122 removed outlier: 3.678A pdb=" N ASP I 111 " --> pdb=" O ASN I 107 " (cutoff:3.500A) Processing helix chain 'I' and resid 128 through 151 removed outlier: 4.628A pdb=" N TRP I 134 " --> pdb=" O TYR I 130 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N TYR I 135 " --> pdb=" O PHE I 131 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU I 140 " --> pdb=" O VAL I 136 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL I 149 " --> pdb=" O GLU I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 152 through 155 Processing helix chain 'I' and resid 158 through 171 Processing helix chain 'J' and resid 14 through 45 Processing helix chain 'J' and resid 47 through 63 Processing helix chain 'J' and resid 63 through 77 removed outlier: 4.475A pdb=" N ILE J 69 " --> pdb=" O HIS J 65 " (cutoff:3.500A) Processing helix chain 'J' and resid 95 through 122 removed outlier: 3.692A pdb=" N ASP J 111 " --> pdb=" O ASN J 107 " (cutoff:3.500A) Processing helix chain 'J' and resid 127 through 132 Processing helix chain 'J' and resid 132 through 151 removed outlier: 4.020A pdb=" N LEU J 140 " --> pdb=" O VAL J 136 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL J 149 " --> pdb=" O GLU J 145 " (cutoff:3.500A) Processing helix chain 'J' and resid 152 through 155 Processing helix chain 'J' and resid 158 through 171 Processing helix chain 'K' and resid 14 through 45 Processing helix chain 'K' and resid 47 through 63 Processing helix chain 'K' and resid 63 through 77 removed outlier: 4.473A pdb=" N ILE K 69 " --> pdb=" O HIS K 65 " (cutoff:3.500A) Processing helix chain 'K' and resid 94 through 122 removed outlier: 3.784A pdb=" N LEU K 98 " --> pdb=" O ASP K 94 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASP K 111 " --> pdb=" O ASN K 107 " (cutoff:3.500A) Processing helix chain 'K' and resid 127 through 132 Processing helix chain 'K' and resid 132 through 151 removed outlier: 4.020A pdb=" N LEU K 140 " --> pdb=" O VAL K 136 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL K 149 " --> pdb=" O GLU K 145 " (cutoff:3.500A) Processing helix chain 'K' and resid 152 through 155 Processing helix chain 'K' and resid 158 through 171 Processing helix chain 'L' and resid 14 through 45 Processing helix chain 'L' and resid 47 through 63 Processing helix chain 'L' and resid 63 through 77 removed outlier: 4.472A pdb=" N ILE L 69 " --> pdb=" O HIS L 65 " (cutoff:3.500A) Processing helix chain 'L' and resid 95 through 122 removed outlier: 3.675A pdb=" N ASP L 111 " --> pdb=" O ASN L 107 " (cutoff:3.500A) Processing helix chain 'L' and resid 127 through 132 Processing helix chain 'L' and resid 132 through 151 removed outlier: 4.021A pdb=" N LEU L 140 " --> pdb=" O VAL L 136 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL L 149 " --> pdb=" O GLU L 145 " (cutoff:3.500A) Processing helix chain 'L' and resid 152 through 155 Processing helix chain 'L' and resid 158 through 171 Processing helix chain 'M' and resid 14 through 45 Processing helix chain 'M' and resid 47 through 63 Processing helix chain 'M' and resid 63 through 77 removed outlier: 4.470A pdb=" N ILE M 69 " --> pdb=" O HIS M 65 " (cutoff:3.500A) Processing helix chain 'M' and resid 95 through 122 removed outlier: 3.678A pdb=" N ASP M 111 " --> pdb=" O ASN M 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 131 through 151 removed outlier: 4.263A pdb=" N TYR M 135 " --> pdb=" O PHE M 131 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU M 140 " --> pdb=" O VAL M 136 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL M 149 " --> pdb=" O GLU M 145 " (cutoff:3.500A) Processing helix chain 'M' and resid 152 through 155 Processing helix chain 'M' and resid 158 through 171 Processing helix chain 'N' and resid 14 through 45 Processing helix chain 'N' and resid 47 through 63 Processing helix chain 'N' and resid 63 through 77 removed outlier: 4.475A pdb=" N ILE N 69 " --> pdb=" O HIS N 65 " (cutoff:3.500A) Processing helix chain 'N' and resid 95 through 122 removed outlier: 3.674A pdb=" N ASP N 111 " --> pdb=" O ASN N 107 " (cutoff:3.500A) Processing helix chain 'N' and resid 128 through 151 removed outlier: 4.628A pdb=" N TRP N 134 " --> pdb=" O TYR N 130 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N TYR N 135 " --> pdb=" O PHE N 131 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU N 140 " --> pdb=" O VAL N 136 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL N 149 " --> pdb=" O GLU N 145 " (cutoff:3.500A) Processing helix chain 'N' and resid 152 through 155 Processing helix chain 'N' and resid 158 through 171 Processing helix chain 'O' and resid 14 through 45 Processing helix chain 'O' and resid 47 through 63 Processing helix chain 'O' and resid 63 through 77 removed outlier: 4.468A pdb=" N ILE O 69 " --> pdb=" O HIS O 65 " (cutoff:3.500A) Processing helix chain 'O' and resid 94 through 122 removed outlier: 3.787A pdb=" N LEU O 98 " --> pdb=" O ASP O 94 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP O 111 " --> pdb=" O ASN O 107 " (cutoff:3.500A) Processing helix chain 'O' and resid 128 through 151 removed outlier: 4.624A pdb=" N TRP O 134 " --> pdb=" O TYR O 130 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N TYR O 135 " --> pdb=" O PHE O 131 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU O 140 " --> pdb=" O VAL O 136 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL O 149 " --> pdb=" O GLU O 145 " (cutoff:3.500A) Processing helix chain 'O' and resid 152 through 155 Processing helix chain 'O' and resid 158 through 171 Processing helix chain 'P' and resid 14 through 45 Processing helix chain 'P' and resid 47 through 63 Processing helix chain 'P' and resid 63 through 77 removed outlier: 4.470A pdb=" N ILE P 69 " --> pdb=" O HIS P 65 " (cutoff:3.500A) Processing helix chain 'P' and resid 95 through 122 removed outlier: 3.698A pdb=" N ASP P 111 " --> pdb=" O ASN P 107 " (cutoff:3.500A) Processing helix chain 'P' and resid 127 through 132 Processing helix chain 'P' and resid 132 through 151 removed outlier: 4.020A pdb=" N LEU P 140 " --> pdb=" O VAL P 136 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL P 149 " --> pdb=" O GLU P 145 " (cutoff:3.500A) Processing helix chain 'P' and resid 152 through 155 Processing helix chain 'P' and resid 158 through 171 Processing helix chain 'Q' and resid 14 through 45 Processing helix chain 'Q' and resid 47 through 63 Processing helix chain 'Q' and resid 63 through 77 removed outlier: 4.468A pdb=" N ILE Q 69 " --> pdb=" O HIS Q 65 " (cutoff:3.500A) Processing helix chain 'Q' and resid 95 through 122 removed outlier: 3.678A pdb=" N ASP Q 111 " --> pdb=" O ASN Q 107 " (cutoff:3.500A) Processing helix chain 'Q' and resid 125 through 151 removed outlier: 3.517A pdb=" N PHE Q 129 " --> pdb=" O ASP Q 125 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N TRP Q 134 " --> pdb=" O TYR Q 130 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N TYR Q 135 " --> pdb=" O PHE Q 131 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU Q 140 " --> pdb=" O VAL Q 136 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N VAL Q 149 " --> pdb=" O GLU Q 145 " (cutoff:3.500A) Processing helix chain 'Q' and resid 152 through 155 Processing helix chain 'Q' and resid 158 through 171 Processing helix chain 'R' and resid 14 through 45 Processing helix chain 'R' and resid 47 through 63 Processing helix chain 'R' and resid 63 through 77 removed outlier: 4.469A pdb=" N ILE R 69 " --> pdb=" O HIS R 65 " (cutoff:3.500A) Processing helix chain 'R' and resid 95 through 122 removed outlier: 3.679A pdb=" N ASP R 111 " --> pdb=" O ASN R 107 " (cutoff:3.500A) Processing helix chain 'R' and resid 127 through 132 Processing helix chain 'R' and resid 132 through 151 removed outlier: 4.021A pdb=" N LEU R 140 " --> pdb=" O VAL R 136 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N VAL R 149 " --> pdb=" O GLU R 145 " (cutoff:3.500A) Processing helix chain 'R' and resid 152 through 155 Processing helix chain 'R' and resid 158 through 171 Processing helix chain 'S' and resid 14 through 45 Processing helix chain 'S' and resid 47 through 63 Processing helix chain 'S' and resid 63 through 77 removed outlier: 4.476A pdb=" N ILE S 69 " --> pdb=" O HIS S 65 " (cutoff:3.500A) Processing helix chain 'S' and resid 95 through 122 removed outlier: 3.678A pdb=" N ASP S 111 " --> pdb=" O ASN S 107 " (cutoff:3.500A) Processing helix chain 'S' and resid 125 through 151 removed outlier: 3.551A pdb=" N PHE S 129 " --> pdb=" O ASP S 125 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR S 130 " --> pdb=" O TYR S 126 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N TRP S 134 " --> pdb=" O TYR S 130 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N TYR S 135 " --> pdb=" O PHE S 131 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU S 140 " --> pdb=" O VAL S 136 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL S 149 " --> pdb=" O GLU S 145 " (cutoff:3.500A) Processing helix chain 'S' and resid 152 through 155 Processing helix chain 'S' and resid 158 through 171 Processing helix chain 'T' and resid 14 through 45 Processing helix chain 'T' and resid 47 through 63 Processing helix chain 'T' and resid 63 through 77 removed outlier: 4.472A pdb=" N ILE T 69 " --> pdb=" O HIS T 65 " (cutoff:3.500A) Processing helix chain 'T' and resid 95 through 122 removed outlier: 3.693A pdb=" N ASP T 111 " --> pdb=" O ASN T 107 " (cutoff:3.500A) Processing helix chain 'T' and resid 127 through 132 Processing helix chain 'T' and resid 132 through 151 removed outlier: 4.024A pdb=" N LEU T 140 " --> pdb=" O VAL T 136 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL T 149 " --> pdb=" O GLU T 145 " (cutoff:3.500A) Processing helix chain 'T' and resid 152 through 155 Processing helix chain 'T' and resid 158 through 171 Processing helix chain 'U' and resid 14 through 45 Processing helix chain 'U' and resid 47 through 63 Processing helix chain 'U' and resid 63 through 77 removed outlier: 4.468A pdb=" N ILE U 69 " --> pdb=" O HIS U 65 " (cutoff:3.500A) Processing helix chain 'U' and resid 95 through 122 removed outlier: 3.692A pdb=" N ASP U 111 " --> pdb=" O ASN U 107 " (cutoff:3.500A) Processing helix chain 'U' and resid 128 through 151 removed outlier: 4.627A pdb=" N TRP U 134 " --> pdb=" O TYR U 130 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N TYR U 135 " --> pdb=" O PHE U 131 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU U 140 " --> pdb=" O VAL U 136 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL U 149 " --> pdb=" O GLU U 145 " (cutoff:3.500A) Processing helix chain 'U' and resid 152 through 155 Processing helix chain 'U' and resid 158 through 171 Processing helix chain 'V' and resid 14 through 45 Processing helix chain 'V' and resid 47 through 63 Processing helix chain 'V' and resid 63 through 77 removed outlier: 4.470A pdb=" N ILE V 69 " --> pdb=" O HIS V 65 " (cutoff:3.500A) Processing helix chain 'V' and resid 95 through 122 removed outlier: 3.678A pdb=" N ASP V 111 " --> pdb=" O ASN V 107 " (cutoff:3.500A) Processing helix chain 'V' and resid 131 through 151 removed outlier: 4.369A pdb=" N TYR V 135 " --> pdb=" O PHE V 131 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU V 140 " --> pdb=" O VAL V 136 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL V 149 " --> pdb=" O GLU V 145 " (cutoff:3.500A) Processing helix chain 'V' and resid 152 through 155 Processing helix chain 'V' and resid 158 through 171 Processing helix chain 'W' and resid 14 through 45 Processing helix chain 'W' and resid 47 through 63 Processing helix chain 'W' and resid 63 through 77 removed outlier: 4.476A pdb=" N ILE W 69 " --> pdb=" O HIS W 65 " (cutoff:3.500A) Processing helix chain 'W' and resid 95 through 122 removed outlier: 3.677A pdb=" N ASP W 111 " --> pdb=" O ASN W 107 " (cutoff:3.500A) Processing helix chain 'W' and resid 127 through 132 Processing helix chain 'W' and resid 132 through 151 removed outlier: 4.021A pdb=" N LEU W 140 " --> pdb=" O VAL W 136 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL W 149 " --> pdb=" O GLU W 145 " (cutoff:3.500A) Processing helix chain 'W' and resid 152 through 155 Processing helix chain 'W' and resid 158 through 171 Processing helix chain 'X' and resid 14 through 45 Processing helix chain 'X' and resid 47 through 63 Processing helix chain 'X' and resid 63 through 77 removed outlier: 4.474A pdb=" N ILE X 69 " --> pdb=" O HIS X 65 " (cutoff:3.500A) Processing helix chain 'X' and resid 94 through 122 removed outlier: 3.788A pdb=" N LEU X 98 " --> pdb=" O ASP X 94 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP X 111 " --> pdb=" O ASN X 107 " (cutoff:3.500A) Processing helix chain 'X' and resid 128 through 151 removed outlier: 4.625A pdb=" N TRP X 134 " --> pdb=" O TYR X 130 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N TYR X 135 " --> pdb=" O PHE X 131 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU X 140 " --> pdb=" O VAL X 136 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL X 149 " --> pdb=" O GLU X 145 " (cutoff:3.500A) Processing helix chain 'X' and resid 152 through 155 Processing helix chain 'X' and resid 158 through 171 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 2550 hydrogen bonds defined for protein. 7626 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: 10.66 Time building geometry restraints manager: 13.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 5856 1.28 - 1.41: 8442 1.41 - 1.54: 18870 1.54 - 1.67: 96 1.67 - 1.81: 144 Bond restraints: 33408 Sorted by residual: bond pdb=" C PHE I 129 " pdb=" O PHE I 129 " ideal model delta sigma weight residual 1.237 1.148 0.089 1.31e-02 5.83e+03 4.60e+01 bond pdb=" C PHE E 129 " pdb=" O PHE E 129 " ideal model delta sigma weight residual 1.237 1.148 0.088 1.31e-02 5.83e+03 4.54e+01 bond pdb=" C PHE O 129 " pdb=" O PHE O 129 " ideal model delta sigma weight residual 1.237 1.148 0.088 1.31e-02 5.83e+03 4.54e+01 bond pdb=" C PHE N 129 " pdb=" O PHE N 129 " ideal model delta sigma weight residual 1.237 1.149 0.088 1.31e-02 5.83e+03 4.51e+01 bond pdb=" C PHE F 129 " pdb=" O PHE F 129 " ideal model delta sigma weight residual 1.237 1.149 0.088 1.31e-02 5.83e+03 4.51e+01 ... (remaining 33403 not shown) Histogram of bond angle deviations from ideal: 100.63 - 107.32: 799 107.32 - 114.01: 18926 114.01 - 120.70: 15099 120.70 - 127.39: 10032 127.39 - 134.08: 288 Bond angle restraints: 45144 Sorted by residual: angle pdb=" N TYR A 126 " pdb=" CA TYR A 126 " pdb=" C TYR A 126 " ideal model delta sigma weight residual 113.17 105.18 7.99 1.26e+00 6.30e-01 4.02e+01 angle pdb=" N TYR Q 126 " pdb=" CA TYR Q 126 " pdb=" C TYR Q 126 " ideal model delta sigma weight residual 113.17 105.18 7.99 1.26e+00 6.30e-01 4.02e+01 angle pdb=" N TYR D 126 " pdb=" CA TYR D 126 " pdb=" C TYR D 126 " ideal model delta sigma weight residual 113.17 105.18 7.99 1.26e+00 6.30e-01 4.02e+01 angle pdb=" N TYR C 126 " pdb=" CA TYR C 126 " pdb=" C TYR C 126 " ideal model delta sigma weight residual 113.17 105.21 7.96 1.26e+00 6.30e-01 3.99e+01 angle pdb=" N TYR T 126 " pdb=" CA TYR T 126 " pdb=" C TYR T 126 " ideal model delta sigma weight residual 113.17 105.24 7.93 1.26e+00 6.30e-01 3.96e+01 ... (remaining 45139 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.60: 17913 16.60 - 33.20: 1699 33.20 - 49.80: 247 49.80 - 66.40: 114 66.40 - 83.00: 67 Dihedral angle restraints: 20040 sinusoidal: 8136 harmonic: 11904 Sorted by residual: dihedral pdb=" C ASP A 124 " pdb=" N ASP A 124 " pdb=" CA ASP A 124 " pdb=" CB ASP A 124 " ideal model delta harmonic sigma weight residual -122.60 -139.62 17.02 0 2.50e+00 1.60e-01 4.63e+01 dihedral pdb=" C ASP C 124 " pdb=" N ASP C 124 " pdb=" CA ASP C 124 " pdb=" CB ASP C 124 " ideal model delta harmonic sigma weight residual -122.60 -139.60 17.00 0 2.50e+00 1.60e-01 4.62e+01 dihedral pdb=" C ASP D 124 " pdb=" N ASP D 124 " pdb=" CA ASP D 124 " pdb=" CB ASP D 124 " ideal model delta harmonic sigma weight residual -122.60 -139.59 16.99 0 2.50e+00 1.60e-01 4.62e+01 ... (remaining 20037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.168: 4849 0.168 - 0.336: 23 0.336 - 0.504: 0 0.504 - 0.673: 16 0.673 - 0.841: 8 Chirality restraints: 4896 Sorted by residual: chirality pdb=" CA ASP U 124 " pdb=" N ASP U 124 " pdb=" C ASP U 124 " pdb=" CB ASP U 124 " both_signs ideal model delta sigma weight residual False 2.51 1.67 0.84 2.00e-01 2.50e+01 1.77e+01 chirality pdb=" CA ASP A 124 " pdb=" N ASP A 124 " pdb=" C ASP A 124 " pdb=" CB ASP A 124 " both_signs ideal model delta sigma weight residual False 2.51 1.67 0.84 2.00e-01 2.50e+01 1.77e+01 chirality pdb=" CA ASP C 124 " pdb=" N ASP C 124 " pdb=" C ASP C 124 " pdb=" CB ASP C 124 " both_signs ideal model delta sigma weight residual False 2.51 1.67 0.84 2.00e-01 2.50e+01 1.76e+01 ... (remaining 4893 not shown) Planarity restraints: 5808 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU F 123 " -0.020 2.00e-02 2.50e+03 3.90e-02 1.52e+01 pdb=" C GLU F 123 " 0.068 2.00e-02 2.50e+03 pdb=" O GLU F 123 " -0.025 2.00e-02 2.50e+03 pdb=" N ASP F 124 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU P 123 " -0.019 2.00e-02 2.50e+03 3.87e-02 1.50e+01 pdb=" C GLU P 123 " 0.067 2.00e-02 2.50e+03 pdb=" O GLU P 123 " -0.024 2.00e-02 2.50e+03 pdb=" N ASP P 124 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU G 123 " -0.019 2.00e-02 2.50e+03 3.87e-02 1.50e+01 pdb=" C GLU G 123 " 0.067 2.00e-02 2.50e+03 pdb=" O GLU G 123 " -0.024 2.00e-02 2.50e+03 pdb=" N ASP G 124 " -0.023 2.00e-02 2.50e+03 ... (remaining 5805 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 168 2.64 - 3.20: 27842 3.20 - 3.77: 48410 3.77 - 4.33: 68676 4.33 - 4.90: 114527 Nonbonded interactions: 259623 Sorted by model distance: nonbonded pdb=" NE2 HIS E 65 " pdb="FE FE E 201 " model vdw 2.074 2.340 nonbonded pdb=" NE2 HIS L 65 " pdb="FE FE L 201 " model vdw 2.074 2.340 nonbonded pdb=" NE2 HIS A 65 " pdb="FE FE A 201 " model vdw 2.074 2.340 nonbonded pdb=" NE2 HIS G 65 " pdb="FE FE G 201 " model vdw 2.074 2.340 nonbonded pdb=" NE2 HIS C 65 " pdb="FE FE C 201 " model vdw 2.074 2.340 ... (remaining 259618 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 107 or resid 109 through \ 181 or resid 201)) selection = (chain 'B' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 181 or resid 201)) selection = (chain 'C' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 181 or resid 201)) selection = (chain 'D' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 181 or resid 201)) selection = (chain 'E' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 181 or resid 201)) selection = (chain 'F' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 181 or resid 201)) selection = (chain 'G' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 181 or resid 201)) selection = (chain 'H' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 181 or resid 201)) selection = (chain 'I' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 181 or resid 201)) selection = (chain 'J' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 181 or resid 201)) selection = (chain 'K' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 181 or resid 201)) selection = (chain 'L' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 181 or resid 201)) selection = (chain 'M' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 181 or resid 201)) selection = (chain 'N' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 181 or resid 201)) selection = (chain 'O' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 181 or resid 201)) selection = (chain 'P' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 181 or resid 201)) selection = (chain 'Q' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 181 or resid 201)) selection = (chain 'R' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 181 or resid 201)) selection = (chain 'S' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 181 or resid 201)) selection = (chain 'T' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 181 or resid 201)) selection = (chain 'U' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 181 or resid 201)) selection = (chain 'V' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 181 or resid 201)) selection = (chain 'W' and (resid 13 through 43 or resid 45 through 107 or resid 109 through \ 181 or resid 201)) selection = (chain 'X' and (resid 13 through 43 or resid 45 through 107 or resid 109 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: 0.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.300 Check model and map are aligned: 0.260 Set scattering table: 0.330 Process input model: 101.510 Find NCS groups from input model: 2.060 Set up NCS constraints: 0.180 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:14.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 120.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 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 : 0.010 0.089 33408 Z= 0.612 Angle : 0.750 8.160 45144 Z= 0.453 Chirality : 0.066 0.841 4896 Planarity : 0.005 0.041 5808 Dihedral : 14.543 82.999 12360 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.03 % Allowed : 2.48 % Favored : 97.49 % Cbeta Deviations : 0.62 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.12), residues: 3984 helix: 0.10 (0.08), residues: 3144 sheet: None (None), residues: 0 loop : -2.65 (0.18), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP L 180 HIS 0.005 0.001 HIS G 112 PHE 0.015 0.002 PHE I 129 TYR 0.033 0.004 TYR M 130 ARG 0.009 0.001 ARG J 110 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 521 time to evaluate : 4.149 Fit side-chains REVERT: A 76 ASN cc_start: 0.8166 (p0) cc_final: 0.7507 (p0) REVERT: A 114 LYS cc_start: 0.7856 (ttpt) cc_final: 0.7548 (tttt) REVERT: B 76 ASN cc_start: 0.8075 (p0) cc_final: 0.7406 (p0) REVERT: B 114 LYS cc_start: 0.7854 (ttpt) cc_final: 0.7548 (tttt) REVERT: C 76 ASN cc_start: 0.8077 (p0) cc_final: 0.7413 (p0) REVERT: C 114 LYS cc_start: 0.7874 (ttpt) cc_final: 0.7529 (tttt) REVERT: D 76 ASN cc_start: 0.8169 (p0) cc_final: 0.7533 (p0) REVERT: D 114 LYS cc_start: 0.7869 (ttpt) cc_final: 0.7521 (tttt) REVERT: E 76 ASN cc_start: 0.8057 (p0) cc_final: 0.7386 (p0) REVERT: F 76 ASN cc_start: 0.8032 (p0) cc_final: 0.7357 (p0) REVERT: F 114 LYS cc_start: 0.7840 (ttpt) cc_final: 0.7534 (tttt) REVERT: G 76 ASN cc_start: 0.8075 (p0) cc_final: 0.7401 (p0) REVERT: G 114 LYS cc_start: 0.7859 (ttpt) cc_final: 0.7514 (tttt) REVERT: H 76 ASN cc_start: 0.8073 (p0) cc_final: 0.7404 (p0) REVERT: H 114 LYS cc_start: 0.7874 (ttpt) cc_final: 0.7527 (tttt) REVERT: I 76 ASN cc_start: 0.8075 (p0) cc_final: 0.7401 (p0) REVERT: I 114 LYS cc_start: 0.7860 (ttpt) cc_final: 0.7556 (tttt) REVERT: J 76 ASN cc_start: 0.8087 (p0) cc_final: 0.7423 (p0) REVERT: J 114 LYS cc_start: 0.7870 (ttpt) cc_final: 0.7525 (tttt) REVERT: K 76 ASN cc_start: 0.8090 (p0) cc_final: 0.7417 (p0) REVERT: K 114 LYS cc_start: 0.7861 (ttpt) cc_final: 0.7577 (tttt) REVERT: L 76 ASN cc_start: 0.8059 (p0) cc_final: 0.7397 (p0) REVERT: L 114 LYS cc_start: 0.7846 (ttpt) cc_final: 0.7538 (tttt) REVERT: M 76 ASN cc_start: 0.8046 (p0) cc_final: 0.7368 (p0) REVERT: M 114 LYS cc_start: 0.7879 (ttpt) cc_final: 0.7533 (tttt) REVERT: N 76 ASN cc_start: 0.8157 (p0) cc_final: 0.7495 (p0) REVERT: N 114 LYS cc_start: 0.7858 (ttpt) cc_final: 0.7552 (tttt) REVERT: O 76 ASN cc_start: 0.8053 (p0) cc_final: 0.7384 (p0) REVERT: O 114 LYS cc_start: 0.7849 (ttpt) cc_final: 0.7547 (tttt) REVERT: P 76 ASN cc_start: 0.8052 (p0) cc_final: 0.7374 (p0) REVERT: P 114 LYS cc_start: 0.7863 (ttpt) cc_final: 0.7522 (tttt) REVERT: Q 76 ASN cc_start: 0.8045 (p0) cc_final: 0.7370 (p0) REVERT: Q 114 LYS cc_start: 0.7858 (ttpt) cc_final: 0.7552 (tttt) REVERT: R 76 ASN cc_start: 0.8032 (p0) cc_final: 0.7359 (p0) REVERT: R 114 LYS cc_start: 0.7871 (ttpt) cc_final: 0.7589 (tttt) REVERT: S 76 ASN cc_start: 0.8181 (p0) cc_final: 0.7523 (p0) REVERT: S 114 LYS cc_start: 0.7852 (ttpt) cc_final: 0.7524 (tttt) REVERT: T 76 ASN cc_start: 0.8083 (p0) cc_final: 0.7418 (p0) REVERT: T 114 LYS cc_start: 0.7869 (ttpt) cc_final: 0.7523 (tttt) REVERT: U 76 ASN cc_start: 0.8048 (p0) cc_final: 0.7364 (p0) REVERT: U 114 LYS cc_start: 0.7870 (ttpt) cc_final: 0.7526 (tttt) REVERT: V 76 ASN cc_start: 0.8067 (p0) cc_final: 0.7404 (p0) REVERT: V 114 LYS cc_start: 0.7846 (ttpt) cc_final: 0.7543 (tttt) REVERT: W 76 ASN cc_start: 0.8149 (p0) cc_final: 0.7481 (p0) REVERT: W 114 LYS cc_start: 0.7860 (ttpt) cc_final: 0.7556 (tttt) REVERT: X 76 ASN cc_start: 0.8053 (p0) cc_final: 0.7381 (p0) REVERT: X 114 LYS cc_start: 0.7838 (ttpt) cc_final: 0.7531 (tttt) outliers start: 1 outliers final: 0 residues processed: 522 average time/residue: 1.2438 time to fit residues: 789.3761 Evaluate side-chains 309 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 309 time to evaluate : 3.813 ------------------------------------------------------------------------------- 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: 7.9990 chunk 291 optimal weight: 0.8980 chunk 161 optimal weight: 1.9990 chunk 99 optimal weight: 9.9990 chunk 196 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 300 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 183 optimal weight: 8.9990 chunk 224 optimal weight: 10.0000 chunk 348 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN B 22 GLN C 22 GLN D 22 GLN E 22 GLN F 22 GLN G 22 GLN H 22 GLN I 22 GLN J 22 GLN K 22 GLN M 22 GLN O 22 GLN P 22 GLN Q 22 GLN R 22 GLN S 22 GLN T 22 GLN U 22 GLN V 22 GLN W 22 GLN X 22 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 33408 Z= 0.168 Angle : 0.452 4.404 45144 Z= 0.256 Chirality : 0.036 0.112 4896 Planarity : 0.004 0.039 5808 Dihedral : 3.985 11.940 4320 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.06 % Allowed : 6.33 % Favored : 93.61 % 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: 1.38 (0.13), residues: 3984 helix: 1.63 (0.09), residues: 3120 sheet: None (None), residues: 0 loop : -1.75 (0.18), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP V 134 HIS 0.003 0.001 HIS D 39 PHE 0.013 0.001 PHE E 129 TYR 0.016 0.001 TYR A 24 ARG 0.004 0.000 ARG P 105 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 431 time to evaluate : 3.788 Fit side-chains REVERT: A 114 LYS cc_start: 0.7644 (ttpt) cc_final: 0.7388 (tttt) REVERT: B 114 LYS cc_start: 0.7652 (ttpt) cc_final: 0.7396 (tttt) REVERT: C 114 LYS cc_start: 0.7656 (ttpt) cc_final: 0.7405 (tttt) REVERT: D 114 LYS cc_start: 0.7638 (ttpt) cc_final: 0.7381 (tttt) REVERT: E 114 LYS cc_start: 0.7641 (ttpt) cc_final: 0.7388 (tttt) REVERT: F 114 LYS cc_start: 0.7638 (ttpt) cc_final: 0.7384 (tttt) REVERT: G 114 LYS cc_start: 0.7636 (ttpt) cc_final: 0.7383 (tttt) REVERT: H 114 LYS cc_start: 0.7657 (ttpt) cc_final: 0.7402 (tttt) REVERT: I 114 LYS cc_start: 0.7657 (ttpt) cc_final: 0.7399 (tttt) REVERT: J 114 LYS cc_start: 0.7647 (ttpt) cc_final: 0.7393 (tttt) REVERT: K 114 LYS cc_start: 0.7628 (ttpt) cc_final: 0.7377 (tttt) REVERT: L 114 LYS cc_start: 0.7640 (ttpt) cc_final: 0.7384 (tttt) REVERT: M 114 LYS cc_start: 0.7661 (ttpt) cc_final: 0.7418 (tttt) REVERT: N 114 LYS cc_start: 0.7655 (ttpt) cc_final: 0.7399 (tttt) REVERT: O 114 LYS cc_start: 0.7650 (ttpt) cc_final: 0.7397 (tttt) REVERT: P 114 LYS cc_start: 0.7638 (ttpt) cc_final: 0.7390 (tttt) REVERT: Q 114 LYS cc_start: 0.7647 (ttpt) cc_final: 0.7388 (tttt) REVERT: R 107 ASN cc_start: 0.8803 (OUTLIER) cc_final: 0.8498 (t0) REVERT: R 114 LYS cc_start: 0.7642 (ttpt) cc_final: 0.7389 (tttt) REVERT: S 114 LYS cc_start: 0.7648 (ttpt) cc_final: 0.7389 (tttt) REVERT: T 114 LYS cc_start: 0.7648 (ttpt) cc_final: 0.7396 (tttt) REVERT: U 107 ASN cc_start: 0.8775 (OUTLIER) cc_final: 0.8469 (t0) REVERT: U 114 LYS cc_start: 0.7654 (ttpt) cc_final: 0.7402 (tttt) REVERT: V 114 LYS cc_start: 0.7643 (ttpt) cc_final: 0.7385 (tttt) REVERT: W 114 LYS cc_start: 0.7656 (ttpt) cc_final: 0.7399 (tttt) REVERT: X 114 LYS cc_start: 0.7638 (ttpt) cc_final: 0.7384 (tttt) outliers start: 2 outliers final: 0 residues processed: 433 average time/residue: 1.1944 time to fit residues: 633.1645 Evaluate side-chains 350 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 348 time to evaluate : 3.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 107 ASN Chi-restraints excluded: chain U residue 107 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 193 optimal weight: 8.9990 chunk 108 optimal weight: 3.9990 chunk 290 optimal weight: 0.7980 chunk 237 optimal weight: 0.8980 chunk 96 optimal weight: 10.0000 chunk 349 optimal weight: 6.9990 chunk 377 optimal weight: 6.9990 chunk 311 optimal weight: 4.9990 chunk 346 optimal weight: 8.9990 chunk 119 optimal weight: 9.9990 chunk 280 optimal weight: 2.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 33408 Z= 0.233 Angle : 0.486 5.452 45144 Z= 0.271 Chirality : 0.038 0.115 4896 Planarity : 0.003 0.039 5808 Dihedral : 3.927 11.970 4320 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.10 % Allowed : 8.64 % Favored : 90.26 % 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: 1.73 (0.13), residues: 3984 helix: 1.81 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : -1.45 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP S 180 HIS 0.003 0.001 HIS R 39 PHE 0.012 0.001 PHE F 129 TYR 0.016 0.002 TYR P 24 ARG 0.005 0.001 ARG G 105 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 404 time to evaluate : 3.787 Fit side-chains REVERT: A 114 LYS cc_start: 0.7796 (ttpt) cc_final: 0.7557 (tttt) REVERT: B 105 ARG cc_start: 0.7636 (mmm-85) cc_final: 0.7425 (mmm-85) REVERT: B 114 LYS cc_start: 0.7800 (ttpt) cc_final: 0.7557 (tttt) REVERT: C 105 ARG cc_start: 0.7633 (mmm-85) cc_final: 0.7423 (mmm-85) REVERT: C 107 ASN cc_start: 0.8800 (OUTLIER) cc_final: 0.8543 (t0) REVERT: C 114 LYS cc_start: 0.7807 (ttpt) cc_final: 0.7566 (tttt) REVERT: D 76 ASN cc_start: 0.7298 (p0) cc_final: 0.6810 (p0) REVERT: D 114 LYS cc_start: 0.7792 (ttpt) cc_final: 0.7554 (tttt) REVERT: E 76 ASN cc_start: 0.7318 (p0) cc_final: 0.6931 (p0) REVERT: E 114 LYS cc_start: 0.7797 (ttpt) cc_final: 0.7556 (tttt) REVERT: F 76 ASN cc_start: 0.7290 (p0) cc_final: 0.6904 (p0) REVERT: F 114 LYS cc_start: 0.7796 (ttpt) cc_final: 0.7552 (tttt) REVERT: G 105 ARG cc_start: 0.7633 (mmm-85) cc_final: 0.7421 (mmm-85) REVERT: G 114 LYS cc_start: 0.7793 (ttpt) cc_final: 0.7549 (tttt) REVERT: H 114 LYS cc_start: 0.7808 (ttpt) cc_final: 0.7567 (tttt) REVERT: I 76 ASN cc_start: 0.7304 (p0) cc_final: 0.6811 (p0) REVERT: I 114 LYS cc_start: 0.7803 (ttpt) cc_final: 0.7564 (tttt) REVERT: J 76 ASN cc_start: 0.7322 (p0) cc_final: 0.6940 (p0) REVERT: J 114 LYS cc_start: 0.7799 (ttpt) cc_final: 0.7556 (tttt) REVERT: K 76 ASN cc_start: 0.7342 (p0) cc_final: 0.6961 (p0) REVERT: K 114 LYS cc_start: 0.7789 (ttpt) cc_final: 0.7547 (tttt) REVERT: L 76 ASN cc_start: 0.7301 (p0) cc_final: 0.6816 (p0) REVERT: L 114 LYS cc_start: 0.7798 (ttpt) cc_final: 0.7559 (tttt) REVERT: M 114 LYS cc_start: 0.7809 (ttpt) cc_final: 0.7577 (tttt) REVERT: N 114 LYS cc_start: 0.7803 (ttpt) cc_final: 0.7561 (tttt) REVERT: O 76 ASN cc_start: 0.7302 (p0) cc_final: 0.6805 (p0) REVERT: O 114 LYS cc_start: 0.7805 (ttpt) cc_final: 0.7562 (tttt) REVERT: P 105 ARG cc_start: 0.7634 (mmm-85) cc_final: 0.7422 (mmm-85) REVERT: P 107 ASN cc_start: 0.8789 (OUTLIER) cc_final: 0.8501 (t0) REVERT: P 114 LYS cc_start: 0.7794 (ttpt) cc_final: 0.7553 (tttt) REVERT: Q 76 ASN cc_start: 0.7281 (p0) cc_final: 0.6795 (p0) REVERT: Q 114 LYS cc_start: 0.7797 (ttpt) cc_final: 0.7558 (tttt) REVERT: R 76 ASN cc_start: 0.7294 (p0) cc_final: 0.6915 (p0) REVERT: R 107 ASN cc_start: 0.8736 (OUTLIER) cc_final: 0.8447 (t0) REVERT: R 114 LYS cc_start: 0.7797 (ttpt) cc_final: 0.7555 (tttt) REVERT: S 76 ASN cc_start: 0.7316 (p0) cc_final: 0.6843 (p0) REVERT: S 114 LYS cc_start: 0.7795 (ttpt) cc_final: 0.7552 (tttt) REVERT: T 114 LYS cc_start: 0.7800 (ttpt) cc_final: 0.7557 (tttt) REVERT: U 76 ASN cc_start: 0.7322 (p0) cc_final: 0.6938 (p0) REVERT: U 105 ARG cc_start: 0.7637 (mmm-85) cc_final: 0.7422 (mmm-85) REVERT: U 107 ASN cc_start: 0.8725 (OUTLIER) cc_final: 0.8410 (t0) REVERT: U 114 LYS cc_start: 0.7809 (ttpt) cc_final: 0.7565 (tttt) REVERT: V 114 LYS cc_start: 0.7795 (ttpt) cc_final: 0.7553 (tttt) REVERT: W 76 ASN cc_start: 0.7298 (p0) cc_final: 0.6911 (p0) REVERT: W 114 LYS cc_start: 0.7802 (ttpt) cc_final: 0.7559 (tttt) REVERT: X 114 LYS cc_start: 0.7796 (ttpt) cc_final: 0.7553 (tttt) outliers start: 28 outliers final: 24 residues processed: 408 average time/residue: 1.1490 time to fit residues: 576.4468 Evaluate side-chains 403 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 375 time to evaluate : 3.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain F residue 111 ASP Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain I residue 111 ASP Chi-restraints excluded: chain J residue 111 ASP Chi-restraints excluded: chain K residue 111 ASP Chi-restraints excluded: chain L residue 111 ASP Chi-restraints excluded: chain M residue 111 ASP Chi-restraints excluded: chain N residue 111 ASP Chi-restraints excluded: chain O residue 111 ASP Chi-restraints excluded: chain P residue 107 ASN Chi-restraints excluded: chain P residue 111 ASP Chi-restraints excluded: chain Q residue 111 ASP Chi-restraints excluded: chain R residue 107 ASN Chi-restraints excluded: chain R residue 111 ASP Chi-restraints excluded: chain S residue 111 ASP Chi-restraints excluded: chain T residue 111 ASP Chi-restraints excluded: chain U residue 107 ASN Chi-restraints excluded: chain U residue 111 ASP Chi-restraints excluded: chain V residue 111 ASP Chi-restraints excluded: chain W residue 111 ASP Chi-restraints excluded: chain X residue 111 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 345 optimal weight: 5.9990 chunk 262 optimal weight: 2.9990 chunk 181 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 166 optimal weight: 7.9990 chunk 234 optimal weight: 6.9990 chunk 350 optimal weight: 10.0000 chunk 371 optimal weight: 7.9990 chunk 183 optimal weight: 7.9990 chunk 332 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 33408 Z= 0.288 Angle : 0.521 5.444 45144 Z= 0.288 Chirality : 0.039 0.120 4896 Planarity : 0.004 0.038 5808 Dihedral : 4.003 12.535 4320 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Rotamer: Outliers : 2.03 % Allowed : 9.12 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.13), residues: 3984 helix: 1.83 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : -1.35 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 180 HIS 0.003 0.001 HIS R 36 PHE 0.012 0.002 PHE F 129 TYR 0.016 0.002 TYR X 24 ARG 0.004 0.001 ARG B 105 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 371 time to evaluate : 3.597 Fit side-chains REVERT: A 76 ASN cc_start: 0.7412 (p0) cc_final: 0.7008 (p0) REVERT: B 76 ASN cc_start: 0.7393 (p0) cc_final: 0.6989 (p0) REVERT: B 105 ARG cc_start: 0.7711 (mmm-85) cc_final: 0.7465 (mmm-85) REVERT: B 107 ASN cc_start: 0.8735 (OUTLIER) cc_final: 0.8416 (t0) REVERT: C 76 ASN cc_start: 0.7388 (p0) cc_final: 0.6982 (p0) REVERT: C 105 ARG cc_start: 0.7710 (mmm-85) cc_final: 0.7465 (mmm-85) REVERT: C 107 ASN cc_start: 0.8823 (OUTLIER) cc_final: 0.8568 (t0) REVERT: D 76 ASN cc_start: 0.7406 (p0) cc_final: 0.6906 (p0) REVERT: E 76 ASN cc_start: 0.7397 (p0) cc_final: 0.6898 (p0) REVERT: F 76 ASN cc_start: 0.7332 (p0) cc_final: 0.6826 (p0) REVERT: F 107 ASN cc_start: 0.8814 (OUTLIER) cc_final: 0.8568 (t0) REVERT: G 76 ASN cc_start: 0.7409 (p0) cc_final: 0.7012 (p0) REVERT: G 105 ARG cc_start: 0.7708 (mmm-85) cc_final: 0.7463 (mmm-85) REVERT: H 76 ASN cc_start: 0.7467 (p0) cc_final: 0.7078 (p0) REVERT: H 114 LYS cc_start: 0.7802 (ttpt) cc_final: 0.7549 (tttt) REVERT: I 76 ASN cc_start: 0.7366 (p0) cc_final: 0.6862 (p0) REVERT: J 76 ASN cc_start: 0.7388 (p0) cc_final: 0.6885 (p0) REVERT: K 76 ASN cc_start: 0.7415 (p0) cc_final: 0.6909 (p0) REVERT: L 76 ASN cc_start: 0.7377 (p0) cc_final: 0.6874 (p0) REVERT: M 76 ASN cc_start: 0.7364 (p0) cc_final: 0.6971 (p0) REVERT: N 76 ASN cc_start: 0.7391 (p0) cc_final: 0.6992 (p0) REVERT: O 76 ASN cc_start: 0.7371 (p0) cc_final: 0.6872 (p0) REVERT: O 107 ASN cc_start: 0.8724 (OUTLIER) cc_final: 0.8455 (t0) REVERT: P 76 ASN cc_start: 0.7406 (p0) cc_final: 0.7007 (p0) REVERT: P 105 ARG cc_start: 0.7706 (mmm-85) cc_final: 0.7460 (mmm-85) REVERT: P 107 ASN cc_start: 0.8806 (OUTLIER) cc_final: 0.8553 (t0) REVERT: Q 76 ASN cc_start: 0.7343 (p0) cc_final: 0.6841 (p0) REVERT: R 76 ASN cc_start: 0.7337 (p0) cc_final: 0.6836 (p0) REVERT: R 107 ASN cc_start: 0.8742 (OUTLIER) cc_final: 0.8449 (t0) REVERT: S 76 ASN cc_start: 0.7358 (p0) cc_final: 0.6846 (p0) REVERT: T 76 ASN cc_start: 0.7437 (p0) cc_final: 0.7047 (p0) REVERT: T 107 ASN cc_start: 0.8731 (OUTLIER) cc_final: 0.8465 (t0) REVERT: U 76 ASN cc_start: 0.7412 (p0) cc_final: 0.6910 (p0) REVERT: U 105 ARG cc_start: 0.7706 (mmm-85) cc_final: 0.7459 (mmm-85) REVERT: U 107 ASN cc_start: 0.8738 (OUTLIER) cc_final: 0.8475 (t0) REVERT: V 76 ASN cc_start: 0.7453 (p0) cc_final: 0.7063 (p0) REVERT: V 114 LYS cc_start: 0.7791 (ttpt) cc_final: 0.7537 (tttt) REVERT: W 76 ASN cc_start: 0.7360 (p0) cc_final: 0.6850 (p0) REVERT: X 76 ASN cc_start: 0.7406 (p0) cc_final: 0.7001 (p0) REVERT: X 107 ASN cc_start: 0.8812 (OUTLIER) cc_final: 0.8565 (t0) outliers start: 52 outliers final: 24 residues processed: 381 average time/residue: 1.0523 time to fit residues: 498.7861 Evaluate side-chains 384 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 351 time to evaluate : 3.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain F residue 107 ASN Chi-restraints excluded: chain F residue 111 ASP Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain I residue 111 ASP Chi-restraints excluded: chain J residue 111 ASP Chi-restraints excluded: chain K residue 111 ASP Chi-restraints excluded: chain L residue 111 ASP Chi-restraints excluded: chain M residue 111 ASP Chi-restraints excluded: chain N residue 111 ASP Chi-restraints excluded: chain O residue 107 ASN Chi-restraints excluded: chain O residue 111 ASP Chi-restraints excluded: chain P residue 107 ASN Chi-restraints excluded: chain P residue 111 ASP Chi-restraints excluded: chain Q residue 111 ASP Chi-restraints excluded: chain R residue 107 ASN Chi-restraints excluded: chain R residue 111 ASP Chi-restraints excluded: chain S residue 111 ASP Chi-restraints excluded: chain T residue 107 ASN Chi-restraints excluded: chain T residue 111 ASP Chi-restraints excluded: chain U residue 107 ASN Chi-restraints excluded: chain U residue 111 ASP Chi-restraints excluded: chain V residue 111 ASP Chi-restraints excluded: chain W residue 111 ASP Chi-restraints excluded: chain X residue 107 ASN Chi-restraints excluded: chain X residue 111 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 309 optimal weight: 4.9990 chunk 210 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 276 optimal weight: 0.9990 chunk 153 optimal weight: 2.9990 chunk 316 optimal weight: 5.9990 chunk 256 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 189 optimal weight: 2.9990 chunk 333 optimal weight: 5.9990 chunk 93 optimal weight: 8.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 33408 Z= 0.184 Angle : 0.447 5.462 45144 Z= 0.249 Chirality : 0.037 0.114 4896 Planarity : 0.003 0.037 5808 Dihedral : 3.805 12.727 4320 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.97 % Allowed : 9.29 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.13), residues: 3984 helix: 2.21 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : -1.11 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 180 HIS 0.003 0.001 HIS R 39 PHE 0.010 0.001 PHE O 129 TYR 0.016 0.002 TYR D 24 ARG 0.004 0.001 ARG P 105 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 385 time to evaluate : 3.802 Fit side-chains REVERT: A 107 ASN cc_start: 0.8693 (OUTLIER) cc_final: 0.8399 (t0) REVERT: A 114 LYS cc_start: 0.7615 (ttpt) cc_final: 0.7389 (tttt) REVERT: B 105 ARG cc_start: 0.7628 (mmm-85) cc_final: 0.7395 (mmm-85) REVERT: B 107 ASN cc_start: 0.8699 (OUTLIER) cc_final: 0.8383 (t0) REVERT: B 114 LYS cc_start: 0.7706 (ttpt) cc_final: 0.7490 (tttt) REVERT: C 105 ARG cc_start: 0.7625 (mmm-85) cc_final: 0.7393 (mmm-85) REVERT: C 107 ASN cc_start: 0.8724 (OUTLIER) cc_final: 0.8401 (t0) REVERT: C 114 LYS cc_start: 0.7713 (ttpt) cc_final: 0.7496 (tttt) REVERT: D 76 ASN cc_start: 0.7099 (p0) cc_final: 0.6554 (p0) REVERT: D 107 ASN cc_start: 0.8681 (OUTLIER) cc_final: 0.8387 (t0) REVERT: E 107 ASN cc_start: 0.8687 (OUTLIER) cc_final: 0.8394 (t0) REVERT: F 107 ASN cc_start: 0.8703 (OUTLIER) cc_final: 0.8379 (t0) REVERT: F 114 LYS cc_start: 0.7704 (ttpt) cc_final: 0.7488 (tttt) REVERT: G 105 ARG cc_start: 0.7619 (mmm-85) cc_final: 0.7386 (mmm-85) REVERT: G 107 ASN cc_start: 0.8691 (OUTLIER) cc_final: 0.8376 (t0) REVERT: G 114 LYS cc_start: 0.7699 (ttpt) cc_final: 0.7483 (tttt) REVERT: H 107 ASN cc_start: 0.8690 (OUTLIER) cc_final: 0.8395 (t0) REVERT: H 114 LYS cc_start: 0.7627 (ttpt) cc_final: 0.7405 (tttt) REVERT: I 76 ASN cc_start: 0.7098 (p0) cc_final: 0.6550 (p0) REVERT: I 107 ASN cc_start: 0.8696 (OUTLIER) cc_final: 0.8405 (t0) REVERT: I 114 LYS cc_start: 0.7622 (ttpt) cc_final: 0.7397 (tttt) REVERT: J 76 ASN cc_start: 0.7155 (p0) cc_final: 0.6611 (p0) REVERT: J 105 ARG cc_start: 0.7640 (mmm-85) cc_final: 0.7439 (mmm-85) REVERT: J 107 ASN cc_start: 0.8687 (OUTLIER) cc_final: 0.8372 (t0) REVERT: J 114 LYS cc_start: 0.7704 (ttpt) cc_final: 0.7490 (tttt) REVERT: K 76 ASN cc_start: 0.7175 (p0) cc_final: 0.6629 (p0) REVERT: K 107 ASN cc_start: 0.8686 (OUTLIER) cc_final: 0.8390 (t0) REVERT: K 114 LYS cc_start: 0.7609 (ttpt) cc_final: 0.7386 (tttt) REVERT: L 76 ASN cc_start: 0.7147 (p0) cc_final: 0.6599 (p0) REVERT: L 107 ASN cc_start: 0.8692 (OUTLIER) cc_final: 0.8398 (t0) REVERT: L 114 LYS cc_start: 0.7618 (ttpt) cc_final: 0.7394 (tttt) REVERT: M 107 ASN cc_start: 0.8694 (OUTLIER) cc_final: 0.8400 (t0) REVERT: M 114 LYS cc_start: 0.7625 (ttpt) cc_final: 0.7403 (tttt) REVERT: N 107 ASN cc_start: 0.8685 (OUTLIER) cc_final: 0.8394 (t0) REVERT: N 114 LYS cc_start: 0.7623 (ttpt) cc_final: 0.7397 (tttt) REVERT: O 76 ASN cc_start: 0.7107 (p0) cc_final: 0.6568 (p0) REVERT: O 105 ARG cc_start: 0.7639 (mmm-85) cc_final: 0.7436 (mmm-85) REVERT: O 107 ASN cc_start: 0.8686 (OUTLIER) cc_final: 0.8370 (t0) REVERT: O 114 LYS cc_start: 0.7710 (ttpt) cc_final: 0.7493 (tttt) REVERT: P 105 ARG cc_start: 0.7625 (mmm-85) cc_final: 0.7393 (mmm-85) REVERT: P 107 ASN cc_start: 0.8713 (OUTLIER) cc_final: 0.8391 (t0) REVERT: P 114 LYS cc_start: 0.7700 (ttpt) cc_final: 0.7487 (tttt) REVERT: Q 107 ASN cc_start: 0.8684 (OUTLIER) cc_final: 0.8394 (t0) REVERT: R 107 ASN cc_start: 0.8689 (OUTLIER) cc_final: 0.8394 (t0) REVERT: S 107 ASN cc_start: 0.8688 (OUTLIER) cc_final: 0.8395 (t0) REVERT: S 114 LYS cc_start: 0.7614 (ttpt) cc_final: 0.7391 (tttt) REVERT: T 107 ASN cc_start: 0.8689 (OUTLIER) cc_final: 0.8376 (t0) REVERT: T 114 LYS cc_start: 0.7705 (ttpt) cc_final: 0.7488 (tttt) REVERT: U 105 ARG cc_start: 0.7625 (mmm-85) cc_final: 0.7389 (mmm-85) REVERT: U 107 ASN cc_start: 0.8699 (OUTLIER) cc_final: 0.8379 (t0) REVERT: V 107 ASN cc_start: 0.8690 (OUTLIER) cc_final: 0.8400 (t0) REVERT: V 114 LYS cc_start: 0.7613 (ttpt) cc_final: 0.7390 (tttt) REVERT: W 76 ASN cc_start: 0.7097 (p0) cc_final: 0.6544 (p0) REVERT: W 107 ASN cc_start: 0.8689 (OUTLIER) cc_final: 0.8396 (t0) REVERT: W 114 LYS cc_start: 0.7621 (ttpt) cc_final: 0.7397 (tttt) REVERT: X 107 ASN cc_start: 0.8703 (OUTLIER) cc_final: 0.8378 (t0) REVERT: X 114 LYS cc_start: 0.7700 (ttpt) cc_final: 0.7485 (tttt) outliers start: 48 outliers final: 3 residues processed: 414 average time/residue: 1.0992 time to fit residues: 565.1344 Evaluate side-chains 415 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 388 time to evaluate : 3.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain D residue 107 ASN Chi-restraints excluded: chain E residue 107 ASN Chi-restraints excluded: chain F residue 107 ASN Chi-restraints excluded: chain F residue 111 ASP Chi-restraints excluded: chain G residue 107 ASN Chi-restraints excluded: chain H residue 107 ASN Chi-restraints excluded: chain I residue 107 ASN Chi-restraints excluded: chain J residue 107 ASN Chi-restraints excluded: chain K residue 107 ASN Chi-restraints excluded: chain L residue 107 ASN Chi-restraints excluded: chain M residue 107 ASN Chi-restraints excluded: chain N residue 107 ASN Chi-restraints excluded: chain O residue 107 ASN Chi-restraints excluded: chain P residue 107 ASN Chi-restraints excluded: chain Q residue 107 ASN Chi-restraints excluded: chain R residue 107 ASN Chi-restraints excluded: chain S residue 107 ASN Chi-restraints excluded: chain T residue 107 ASN Chi-restraints excluded: chain U residue 107 ASN Chi-restraints excluded: chain V residue 107 ASN Chi-restraints excluded: chain W residue 107 ASN Chi-restraints excluded: chain X residue 107 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 124 optimal weight: 8.9990 chunk 334 optimal weight: 0.0270 chunk 73 optimal weight: 3.9990 chunk 217 optimal weight: 9.9990 chunk 91 optimal weight: 3.9990 chunk 371 optimal weight: 3.9990 chunk 308 optimal weight: 5.9990 chunk 172 optimal weight: 7.9990 chunk 30 optimal weight: 9.9990 chunk 122 optimal weight: 7.9990 chunk 195 optimal weight: 0.8980 overall best weight: 2.5844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 33408 Z= 0.221 Angle : 0.472 5.564 45144 Z= 0.262 Chirality : 0.038 0.118 4896 Planarity : 0.003 0.036 5808 Dihedral : 3.837 13.201 4320 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 1.97 % Allowed : 10.14 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.35 (0.13), residues: 3984 helix: 2.21 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : -1.03 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 180 HIS 0.002 0.001 HIS U 36 PHE 0.011 0.001 PHE E 129 TYR 0.016 0.002 TYR P 24 ARG 0.003 0.001 ARG O 110 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 379 time to evaluate : 3.869 Fit side-chains REVERT: A 107 ASN cc_start: 0.8699 (OUTLIER) cc_final: 0.8405 (t0) REVERT: B 105 ARG cc_start: 0.7648 (mmm-85) cc_final: 0.7409 (mmm-85) REVERT: B 107 ASN cc_start: 0.8705 (OUTLIER) cc_final: 0.8392 (t0) REVERT: B 114 LYS cc_start: 0.7729 (ttpt) cc_final: 0.7508 (tttt) REVERT: C 105 ARG cc_start: 0.7648 (mmm-85) cc_final: 0.7410 (mmm-85) REVERT: C 107 ASN cc_start: 0.8721 (OUTLIER) cc_final: 0.8402 (t0) REVERT: C 114 LYS cc_start: 0.7738 (ttpt) cc_final: 0.7516 (tttt) REVERT: D 76 ASN cc_start: 0.7235 (p0) cc_final: 0.6689 (p0) REVERT: D 107 ASN cc_start: 0.8686 (OUTLIER) cc_final: 0.8389 (t0) REVERT: E 107 ASN cc_start: 0.8693 (OUTLIER) cc_final: 0.8397 (t0) REVERT: F 107 ASN cc_start: 0.8704 (OUTLIER) cc_final: 0.8388 (t0) REVERT: G 105 ARG cc_start: 0.7642 (mmm-85) cc_final: 0.7402 (mmm-85) REVERT: G 107 ASN cc_start: 0.8702 (OUTLIER) cc_final: 0.8384 (t0) REVERT: H 76 ASN cc_start: 0.7338 (p0) cc_final: 0.6967 (p0) REVERT: I 76 ASN cc_start: 0.7236 (p0) cc_final: 0.6690 (p0) REVERT: I 107 ASN cc_start: 0.8703 (OUTLIER) cc_final: 0.8412 (t0) REVERT: J 76 ASN cc_start: 0.7261 (p0) cc_final: 0.6674 (p0) REVERT: J 105 ARG cc_start: 0.7732 (mmm-85) cc_final: 0.7517 (mmm-85) REVERT: J 107 ASN cc_start: 0.8694 (OUTLIER) cc_final: 0.8377 (t0) REVERT: K 76 ASN cc_start: 0.7286 (p0) cc_final: 0.6695 (p0) REVERT: K 107 ASN cc_start: 0.8688 (OUTLIER) cc_final: 0.8393 (t0) REVERT: L 76 ASN cc_start: 0.7277 (p0) cc_final: 0.6735 (p0) REVERT: L 107 ASN cc_start: 0.8695 (OUTLIER) cc_final: 0.8402 (t0) REVERT: M 76 ASN cc_start: 0.7291 (p0) cc_final: 0.6953 (p0) REVERT: M 107 ASN cc_start: 0.8702 (OUTLIER) cc_final: 0.8406 (t0) REVERT: N 107 ASN cc_start: 0.8693 (OUTLIER) cc_final: 0.8401 (t0) REVERT: O 76 ASN cc_start: 0.7255 (p0) cc_final: 0.6708 (p0) REVERT: O 105 ARG cc_start: 0.7705 (mmm-85) cc_final: 0.7487 (mmm-85) REVERT: O 107 ASN cc_start: 0.8696 (OUTLIER) cc_final: 0.8376 (t0) REVERT: P 105 ARG cc_start: 0.7647 (mmm-85) cc_final: 0.7406 (mmm-85) REVERT: P 107 ASN cc_start: 0.8711 (OUTLIER) cc_final: 0.8392 (t0) REVERT: Q 107 ASN cc_start: 0.8690 (OUTLIER) cc_final: 0.8398 (t0) REVERT: R 107 ASN cc_start: 0.8695 (OUTLIER) cc_final: 0.8395 (t0) REVERT: S 76 ASN cc_start: 0.7381 (p0) cc_final: 0.7042 (p0) REVERT: S 107 ASN cc_start: 0.8694 (OUTLIER) cc_final: 0.8399 (t0) REVERT: T 76 ASN cc_start: 0.7294 (p0) cc_final: 0.6914 (p0) REVERT: T 107 ASN cc_start: 0.8706 (OUTLIER) cc_final: 0.8384 (t0) REVERT: U 105 ARG cc_start: 0.7648 (mmm-85) cc_final: 0.7407 (mmm-85) REVERT: U 107 ASN cc_start: 0.8709 (OUTLIER) cc_final: 0.8383 (t0) REVERT: V 76 ASN cc_start: 0.7312 (p0) cc_final: 0.6932 (p0) REVERT: V 107 ASN cc_start: 0.8700 (OUTLIER) cc_final: 0.8407 (t0) REVERT: W 76 ASN cc_start: 0.7252 (p0) cc_final: 0.6695 (p0) REVERT: W 107 ASN cc_start: 0.8698 (OUTLIER) cc_final: 0.8405 (t0) REVERT: X 76 ASN cc_start: 0.7329 (p0) cc_final: 0.6991 (p0) REVERT: X 107 ASN cc_start: 0.8703 (OUTLIER) cc_final: 0.8376 (t0) outliers start: 47 outliers final: 3 residues processed: 404 average time/residue: 1.0801 time to fit residues: 545.1079 Evaluate side-chains 370 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 344 time to evaluate : 3.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain D residue 107 ASN Chi-restraints excluded: chain E residue 107 ASN Chi-restraints excluded: chain F residue 107 ASN Chi-restraints excluded: chain F residue 111 ASP Chi-restraints excluded: chain G residue 107 ASN Chi-restraints excluded: chain I residue 107 ASN Chi-restraints excluded: chain J residue 107 ASN Chi-restraints excluded: chain K residue 107 ASN Chi-restraints excluded: chain L residue 107 ASN Chi-restraints excluded: chain M residue 107 ASN Chi-restraints excluded: chain N residue 107 ASN Chi-restraints excluded: chain O residue 107 ASN Chi-restraints excluded: chain P residue 107 ASN Chi-restraints excluded: chain Q residue 107 ASN Chi-restraints excluded: chain R residue 107 ASN Chi-restraints excluded: chain S residue 107 ASN Chi-restraints excluded: chain T residue 107 ASN Chi-restraints excluded: chain U residue 107 ASN Chi-restraints excluded: chain V residue 107 ASN Chi-restraints excluded: chain W residue 107 ASN Chi-restraints excluded: chain X residue 107 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 358 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 211 optimal weight: 0.9990 chunk 271 optimal weight: 1.9990 chunk 210 optimal weight: 1.9990 chunk 312 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 370 optimal weight: 0.8980 chunk 231 optimal weight: 20.0000 chunk 225 optimal weight: 0.7980 chunk 170 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 33408 Z= 0.144 Angle : 0.416 5.640 45144 Z= 0.233 Chirality : 0.036 0.114 4896 Planarity : 0.003 0.036 5808 Dihedral : 3.647 12.960 4320 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.46 % Allowed : 11.06 % Favored : 87.47 % 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 (0.13), residues: 3984 helix: 2.51 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : -0.79 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 180 HIS 0.004 0.001 HIS E 39 PHE 0.008 0.001 PHE F 129 TYR 0.015 0.001 TYR D 24 ARG 0.003 0.000 ARG U 110 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 355 time to evaluate : 4.028 Fit side-chains REVERT: A 107 ASN cc_start: 0.8651 (OUTLIER) cc_final: 0.8368 (t0) REVERT: B 107 ASN cc_start: 0.8663 (OUTLIER) cc_final: 0.8364 (t0) REVERT: C 107 ASN cc_start: 0.8671 (OUTLIER) cc_final: 0.8372 (t0) REVERT: C 114 LYS cc_start: 0.7623 (ttpt) cc_final: 0.7422 (tttt) REVERT: D 107 ASN cc_start: 0.8638 (OUTLIER) cc_final: 0.8353 (t0) REVERT: E 107 ASN cc_start: 0.8650 (OUTLIER) cc_final: 0.8367 (t0) REVERT: F 107 ASN cc_start: 0.8652 (OUTLIER) cc_final: 0.8354 (t0) REVERT: F 114 LYS cc_start: 0.7609 (ttpt) cc_final: 0.7408 (tttt) REVERT: G 107 ASN cc_start: 0.8653 (OUTLIER) cc_final: 0.8348 (t0) REVERT: H 107 ASN cc_start: 0.8650 (OUTLIER) cc_final: 0.8367 (t0) REVERT: H 114 LYS cc_start: 0.7652 (ttpt) cc_final: 0.7447 (tttt) REVERT: I 107 ASN cc_start: 0.8654 (OUTLIER) cc_final: 0.8375 (t0) REVERT: J 107 ASN cc_start: 0.8645 (OUTLIER) cc_final: 0.8338 (t0) REVERT: K 107 ASN cc_start: 0.8639 (OUTLIER) cc_final: 0.8354 (t0) REVERT: L 107 ASN cc_start: 0.8648 (OUTLIER) cc_final: 0.8368 (t0) REVERT: M 107 ASN cc_start: 0.8655 (OUTLIER) cc_final: 0.8374 (t0) REVERT: N 107 ASN cc_start: 0.8647 (OUTLIER) cc_final: 0.8367 (t0) REVERT: N 114 LYS cc_start: 0.7651 (ttpt) cc_final: 0.7442 (tttt) REVERT: O 107 ASN cc_start: 0.8647 (OUTLIER) cc_final: 0.8340 (t0) REVERT: P 107 ASN cc_start: 0.8661 (OUTLIER) cc_final: 0.8362 (t0) REVERT: Q 107 ASN cc_start: 0.8642 (OUTLIER) cc_final: 0.8361 (t0) REVERT: R 107 ASN cc_start: 0.8644 (OUTLIER) cc_final: 0.8359 (t0) REVERT: S 107 ASN cc_start: 0.8645 (OUTLIER) cc_final: 0.8361 (t0) REVERT: T 107 ASN cc_start: 0.8655 (OUTLIER) cc_final: 0.8354 (t0) REVERT: U 107 ASN cc_start: 0.8659 (OUTLIER) cc_final: 0.8352 (t0) REVERT: V 107 ASN cc_start: 0.8653 (OUTLIER) cc_final: 0.8376 (t0) REVERT: W 107 ASN cc_start: 0.8652 (OUTLIER) cc_final: 0.8372 (t0) REVERT: X 107 ASN cc_start: 0.8649 (OUTLIER) cc_final: 0.8342 (t0) outliers start: 28 outliers final: 0 residues processed: 379 average time/residue: 1.0464 time to fit residues: 509.5445 Evaluate side-chains 367 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 343 time to evaluate : 3.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain D residue 107 ASN Chi-restraints excluded: chain E residue 107 ASN Chi-restraints excluded: chain F residue 107 ASN Chi-restraints excluded: chain G residue 107 ASN Chi-restraints excluded: chain H residue 107 ASN Chi-restraints excluded: chain I residue 107 ASN Chi-restraints excluded: chain J residue 107 ASN Chi-restraints excluded: chain K residue 107 ASN Chi-restraints excluded: chain L residue 107 ASN Chi-restraints excluded: chain M residue 107 ASN Chi-restraints excluded: chain N residue 107 ASN Chi-restraints excluded: chain O residue 107 ASN Chi-restraints excluded: chain P residue 107 ASN Chi-restraints excluded: chain Q residue 107 ASN Chi-restraints excluded: chain R residue 107 ASN Chi-restraints excluded: chain S residue 107 ASN Chi-restraints excluded: chain T residue 107 ASN Chi-restraints excluded: chain U residue 107 ASN Chi-restraints excluded: chain V residue 107 ASN Chi-restraints excluded: chain W residue 107 ASN Chi-restraints excluded: chain X residue 107 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 228 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 chunk 221 optimal weight: 9.9990 chunk 111 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 71 optimal weight: 8.9990 chunk 235 optimal weight: 0.8980 chunk 252 optimal weight: 0.9980 chunk 182 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 290 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 33408 Z= 0.133 Angle : 0.404 5.963 45144 Z= 0.225 Chirality : 0.036 0.120 4896 Planarity : 0.003 0.036 5808 Dihedral : 3.531 12.859 4320 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.83 % Allowed : 10.92 % Favored : 87.25 % 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: 3.03 (0.13), residues: 3984 helix: 2.65 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : -0.61 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 180 HIS 0.004 0.001 HIS K 39 PHE 0.008 0.001 PHE E 129 TYR 0.014 0.001 TYR N 24 ARG 0.003 0.000 ARG F 110 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 384 time to evaluate : 3.878 Fit side-chains REVERT: A 107 ASN cc_start: 0.8665 (OUTLIER) cc_final: 0.8401 (t0) REVERT: B 107 ASN cc_start: 0.8678 (OUTLIER) cc_final: 0.8394 (t0) REVERT: C 107 ASN cc_start: 0.8686 (OUTLIER) cc_final: 0.8404 (t0) REVERT: D 107 ASN cc_start: 0.8652 (OUTLIER) cc_final: 0.8385 (t0) REVERT: E 107 ASN cc_start: 0.8665 (OUTLIER) cc_final: 0.8399 (t0) REVERT: F 107 ASN cc_start: 0.8665 (OUTLIER) cc_final: 0.8382 (t0) REVERT: G 107 ASN cc_start: 0.8667 (OUTLIER) cc_final: 0.8380 (t0) REVERT: H 107 ASN cc_start: 0.8666 (OUTLIER) cc_final: 0.8400 (t0) REVERT: I 107 ASN cc_start: 0.8667 (OUTLIER) cc_final: 0.8406 (t0) REVERT: J 107 ASN cc_start: 0.8672 (OUTLIER) cc_final: 0.8389 (t0) REVERT: K 107 ASN cc_start: 0.8655 (OUTLIER) cc_final: 0.8386 (t0) REVERT: L 107 ASN cc_start: 0.8661 (OUTLIER) cc_final: 0.8398 (t0) REVERT: M 107 ASN cc_start: 0.8668 (OUTLIER) cc_final: 0.8404 (t0) REVERT: N 107 ASN cc_start: 0.8659 (OUTLIER) cc_final: 0.8397 (t0) REVERT: O 107 ASN cc_start: 0.8676 (OUTLIER) cc_final: 0.8392 (t0) REVERT: P 107 ASN cc_start: 0.8674 (OUTLIER) cc_final: 0.8387 (t0) REVERT: Q 107 ASN cc_start: 0.8656 (OUTLIER) cc_final: 0.8394 (t0) REVERT: R 107 ASN cc_start: 0.8673 (OUTLIER) cc_final: 0.8407 (t0) REVERT: S 107 ASN cc_start: 0.8657 (OUTLIER) cc_final: 0.8391 (t0) REVERT: T 107 ASN cc_start: 0.8670 (OUTLIER) cc_final: 0.8388 (t0) REVERT: U 107 ASN cc_start: 0.8687 (OUTLIER) cc_final: 0.8402 (t0) REVERT: V 107 ASN cc_start: 0.8668 (OUTLIER) cc_final: 0.8409 (t0) REVERT: W 107 ASN cc_start: 0.8662 (OUTLIER) cc_final: 0.8400 (t0) REVERT: X 107 ASN cc_start: 0.8660 (OUTLIER) cc_final: 0.8372 (t0) outliers start: 41 outliers final: 0 residues processed: 408 average time/residue: 1.1247 time to fit residues: 566.8343 Evaluate side-chains 359 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 335 time to evaluate : 3.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain D residue 107 ASN Chi-restraints excluded: chain E residue 107 ASN Chi-restraints excluded: chain F residue 107 ASN Chi-restraints excluded: chain G residue 107 ASN Chi-restraints excluded: chain H residue 107 ASN Chi-restraints excluded: chain I residue 107 ASN Chi-restraints excluded: chain J residue 107 ASN Chi-restraints excluded: chain K residue 107 ASN Chi-restraints excluded: chain L residue 107 ASN Chi-restraints excluded: chain M residue 107 ASN Chi-restraints excluded: chain N residue 107 ASN Chi-restraints excluded: chain O residue 107 ASN Chi-restraints excluded: chain P residue 107 ASN Chi-restraints excluded: chain Q residue 107 ASN Chi-restraints excluded: chain R residue 107 ASN Chi-restraints excluded: chain S residue 107 ASN Chi-restraints excluded: chain T residue 107 ASN Chi-restraints excluded: chain U residue 107 ASN Chi-restraints excluded: chain V residue 107 ASN Chi-restraints excluded: chain W residue 107 ASN Chi-restraints excluded: chain X residue 107 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: 3.9990 chunk 323 optimal weight: 2.9990 chunk 344 optimal weight: 0.2980 chunk 207 optimal weight: 5.9990 chunk 150 optimal weight: 3.9990 chunk 270 optimal weight: 0.9980 chunk 105 optimal weight: 5.9990 chunk 311 optimal weight: 10.0000 chunk 326 optimal weight: 2.9990 chunk 343 optimal weight: 6.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 33408 Z= 0.197 Angle : 0.443 5.598 45144 Z= 0.249 Chirality : 0.038 0.125 4896 Planarity : 0.003 0.036 5808 Dihedral : 3.671 13.250 4320 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.41 % Allowed : 13.77 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.74 (0.13), residues: 3984 helix: 2.43 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : -0.63 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 180 HIS 0.003 0.001 HIS R 39 PHE 0.009 0.001 PHE E 129 TYR 0.016 0.002 TYR D 24 ARG 0.003 0.000 ARG B 110 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 369 time to evaluate : 3.837 Fit side-chains REVERT: A 107 ASN cc_start: 0.8667 (OUTLIER) cc_final: 0.8392 (t0) REVERT: B 107 ASN cc_start: 0.8683 (OUTLIER) cc_final: 0.8383 (t0) REVERT: C 107 ASN cc_start: 0.8695 (OUTLIER) cc_final: 0.8394 (t0) REVERT: D 107 ASN cc_start: 0.8655 (OUTLIER) cc_final: 0.8378 (t0) REVERT: E 107 ASN cc_start: 0.8667 (OUTLIER) cc_final: 0.8392 (t0) REVERT: F 107 ASN cc_start: 0.8682 (OUTLIER) cc_final: 0.8381 (t0) REVERT: G 107 ASN cc_start: 0.8676 (OUTLIER) cc_final: 0.8376 (t0) REVERT: H 107 ASN cc_start: 0.8668 (OUTLIER) cc_final: 0.8395 (t0) REVERT: I 107 ASN cc_start: 0.8673 (OUTLIER) cc_final: 0.8401 (t0) REVERT: J 107 ASN cc_start: 0.8679 (OUTLIER) cc_final: 0.8376 (t0) REVERT: K 107 ASN cc_start: 0.8655 (OUTLIER) cc_final: 0.8377 (t0) REVERT: L 107 ASN cc_start: 0.8664 (OUTLIER) cc_final: 0.8386 (t0) REVERT: M 107 ASN cc_start: 0.8671 (OUTLIER) cc_final: 0.8393 (t0) REVERT: N 107 ASN cc_start: 0.8664 (OUTLIER) cc_final: 0.8392 (t0) REVERT: O 107 ASN cc_start: 0.8683 (OUTLIER) cc_final: 0.8380 (t0) REVERT: P 107 ASN cc_start: 0.8682 (OUTLIER) cc_final: 0.8380 (t0) REVERT: Q 107 ASN cc_start: 0.8657 (OUTLIER) cc_final: 0.8387 (t0) REVERT: R 107 ASN cc_start: 0.8655 (OUTLIER) cc_final: 0.8383 (t0) REVERT: S 107 ASN cc_start: 0.8662 (OUTLIER) cc_final: 0.8385 (t0) REVERT: T 107 ASN cc_start: 0.8686 (OUTLIER) cc_final: 0.8387 (t0) REVERT: U 107 ASN cc_start: 0.8681 (OUTLIER) cc_final: 0.8380 (t0) REVERT: V 107 ASN cc_start: 0.8669 (OUTLIER) cc_final: 0.8399 (t0) REVERT: W 107 ASN cc_start: 0.8668 (OUTLIER) cc_final: 0.8396 (t0) REVERT: X 107 ASN cc_start: 0.8680 (OUTLIER) cc_final: 0.8375 (t0) outliers start: 26 outliers final: 0 residues processed: 393 average time/residue: 1.0286 time to fit residues: 512.8897 Evaluate side-chains 390 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 366 time to evaluate : 3.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain D residue 107 ASN Chi-restraints excluded: chain E residue 107 ASN Chi-restraints excluded: chain F residue 107 ASN Chi-restraints excluded: chain G residue 107 ASN Chi-restraints excluded: chain H residue 107 ASN Chi-restraints excluded: chain I residue 107 ASN Chi-restraints excluded: chain J residue 107 ASN Chi-restraints excluded: chain K residue 107 ASN Chi-restraints excluded: chain L residue 107 ASN Chi-restraints excluded: chain M residue 107 ASN Chi-restraints excluded: chain N residue 107 ASN Chi-restraints excluded: chain O residue 107 ASN Chi-restraints excluded: chain P residue 107 ASN Chi-restraints excluded: chain Q residue 107 ASN Chi-restraints excluded: chain R residue 107 ASN Chi-restraints excluded: chain S residue 107 ASN Chi-restraints excluded: chain T residue 107 ASN Chi-restraints excluded: chain U residue 107 ASN Chi-restraints excluded: chain V residue 107 ASN Chi-restraints excluded: chain W residue 107 ASN Chi-restraints excluded: chain X residue 107 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 226 optimal weight: 0.9990 chunk 364 optimal weight: 4.9990 chunk 222 optimal weight: 0.8980 chunk 173 optimal weight: 0.0010 chunk 253 optimal weight: 5.9990 chunk 382 optimal weight: 9.9990 chunk 352 optimal weight: 10.0000 chunk 304 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 235 optimal weight: 7.9990 chunk 186 optimal weight: 7.9990 overall best weight: 2.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 33408 Z= 0.219 Angle : 0.468 6.053 45144 Z= 0.260 Chirality : 0.038 0.124 4896 Planarity : 0.003 0.035 5808 Dihedral : 3.758 13.578 4320 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.35 % Allowed : 13.51 % Favored : 85.14 % 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: 2.62 (0.13), residues: 3984 helix: 2.34 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : -0.66 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 180 HIS 0.002 0.001 HIS K 39 PHE 0.011 0.001 PHE E 129 TYR 0.016 0.002 TYR I 24 ARG 0.003 0.000 ARG X 110 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7968 Ramachandran restraints generated. 3984 Oldfield, 0 Emsley, 3984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 370 time to evaluate : 3.811 Fit side-chains REVERT: A 107 ASN cc_start: 0.8686 (OUTLIER) cc_final: 0.8400 (t0) REVERT: B 107 ASN cc_start: 0.8700 (OUTLIER) cc_final: 0.8394 (t0) REVERT: C 107 ASN cc_start: 0.8713 (OUTLIER) cc_final: 0.8401 (t0) REVERT: D 107 ASN cc_start: 0.8674 (OUTLIER) cc_final: 0.8388 (t0) REVERT: E 107 ASN cc_start: 0.8686 (OUTLIER) cc_final: 0.8399 (t0) REVERT: F 107 ASN cc_start: 0.8693 (OUTLIER) cc_final: 0.8385 (t0) REVERT: G 107 ASN cc_start: 0.8696 (OUTLIER) cc_final: 0.8384 (t0) REVERT: H 107 ASN cc_start: 0.8687 (OUTLIER) cc_final: 0.8401 (t0) REVERT: I 107 ASN cc_start: 0.8690 (OUTLIER) cc_final: 0.8406 (t0) REVERT: J 107 ASN cc_start: 0.8696 (OUTLIER) cc_final: 0.8386 (t0) REVERT: K 107 ASN cc_start: 0.8675 (OUTLIER) cc_final: 0.8387 (t0) REVERT: L 107 ASN cc_start: 0.8683 (OUTLIER) cc_final: 0.8398 (t0) REVERT: M 107 ASN cc_start: 0.8689 (OUTLIER) cc_final: 0.8404 (t0) REVERT: N 107 ASN cc_start: 0.8682 (OUTLIER) cc_final: 0.8398 (t0) REVERT: O 107 ASN cc_start: 0.8700 (OUTLIER) cc_final: 0.8391 (t0) REVERT: P 107 ASN cc_start: 0.8700 (OUTLIER) cc_final: 0.8389 (t0) REVERT: Q 107 ASN cc_start: 0.8678 (OUTLIER) cc_final: 0.8395 (t0) REVERT: R 107 ASN cc_start: 0.8675 (OUTLIER) cc_final: 0.8393 (t0) REVERT: S 107 ASN cc_start: 0.8681 (OUTLIER) cc_final: 0.8395 (t0) REVERT: T 107 ASN cc_start: 0.8700 (OUTLIER) cc_final: 0.8395 (t0) REVERT: U 107 ASN cc_start: 0.8695 (OUTLIER) cc_final: 0.8388 (t0) REVERT: V 107 ASN cc_start: 0.8689 (OUTLIER) cc_final: 0.8405 (t0) REVERT: W 107 ASN cc_start: 0.8686 (OUTLIER) cc_final: 0.8403 (t0) REVERT: X 107 ASN cc_start: 0.8695 (OUTLIER) cc_final: 0.8386 (t0) outliers start: 24 outliers final: 0 residues processed: 394 average time/residue: 1.0542 time to fit residues: 530.9311 Evaluate side-chains 394 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 370 time to evaluate : 4.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain D residue 107 ASN Chi-restraints excluded: chain E residue 107 ASN Chi-restraints excluded: chain F residue 107 ASN Chi-restraints excluded: chain G residue 107 ASN Chi-restraints excluded: chain H residue 107 ASN Chi-restraints excluded: chain I residue 107 ASN Chi-restraints excluded: chain J residue 107 ASN Chi-restraints excluded: chain K residue 107 ASN Chi-restraints excluded: chain L residue 107 ASN Chi-restraints excluded: chain M residue 107 ASN Chi-restraints excluded: chain N residue 107 ASN Chi-restraints excluded: chain O residue 107 ASN Chi-restraints excluded: chain P residue 107 ASN Chi-restraints excluded: chain Q residue 107 ASN Chi-restraints excluded: chain R residue 107 ASN Chi-restraints excluded: chain S residue 107 ASN Chi-restraints excluded: chain T residue 107 ASN Chi-restraints excluded: chain U residue 107 ASN Chi-restraints excluded: chain V residue 107 ASN Chi-restraints excluded: chain W residue 107 ASN Chi-restraints excluded: chain X residue 107 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 241 optimal weight: 6.9990 chunk 324 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 280 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 305 optimal weight: 5.9990 chunk 127 optimal weight: 2.9990 chunk 313 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.147511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.125262 restraints weight = 210622.995| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 4.46 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3463 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3463 r_free = 0.3463 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3463 r_free = 0.3463 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3463 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 33408 Z= 0.155 Angle : 0.420 5.573 45144 Z= 0.236 Chirality : 0.037 0.115 4896 Planarity : 0.003 0.036 5808 Dihedral : 3.618 13.191 4320 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.35 % Allowed : 13.40 % Favored : 85.25 % 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: 2.89 (0.13), residues: 3984 helix: 2.52 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : -0.53 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP S 180 HIS 0.004 0.001 HIS D 39 PHE 0.008 0.001 PHE F 129 TYR 0.015 0.001 TYR D 24 ARG 0.003 0.000 ARG T 110 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9240.46 seconds wall clock time: 164 minutes 41.12 seconds (9881.12 seconds total)