Starting phenix.real_space_refine on Sat Mar 16 05:34:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8emq_28259/03_2024/8emq_28259.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8emq_28259/03_2024/8emq_28259.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8emq_28259/03_2024/8emq_28259.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8emq_28259/03_2024/8emq_28259.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8emq_28259/03_2024/8emq_28259.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8emq_28259/03_2024/8emq_28259.pdb" } resolution = 1.66 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 34800 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians Fe 6 7.16 5 Zn 24 6.06 5 S 192 5.16 5 C 21816 2.51 5 N 6072 2.21 5 O 9695 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 27": "OE1" <-> "OE2" Residue "A ASP 44": "OD1" <-> "OD2" Residue "A ARG 63": "NH1" <-> "NH2" Residue "A ARG 90": "NH1" <-> "NH2" Residue "A GLU 140": "OE1" <-> "OE2" Residue "A GLU 140": "OE1" <-> "OE2" Residue "A GLU 147": "OE1" <-> "OE2" Residue "B GLU 27": "OE1" <-> "OE2" Residue "B ASP 44": "OD1" <-> "OD2" Residue "B ARG 63": "NH1" <-> "NH2" Residue "B ARG 90": "NH1" <-> "NH2" Residue "B GLU 140": "OE1" <-> "OE2" Residue "B GLU 140": "OE1" <-> "OE2" Residue "B GLU 147": "OE1" <-> "OE2" Residue "C GLU 27": "OE1" <-> "OE2" Residue "C ASP 44": "OD1" <-> "OD2" Residue "C ARG 63": "NH1" <-> "NH2" Residue "C ARG 90": "NH1" <-> "NH2" Residue "C GLU 140": "OE1" <-> "OE2" Residue "C GLU 140": "OE1" <-> "OE2" Residue "C GLU 147": "OE1" <-> "OE2" Residue "D GLU 27": "OE1" <-> "OE2" Residue "D ASP 44": "OD1" <-> "OD2" Residue "D ARG 63": "NH1" <-> "NH2" Residue "D ARG 90": "NH1" <-> "NH2" Residue "D GLU 140": "OE1" <-> "OE2" Residue "D GLU 140": "OE1" <-> "OE2" Residue "D GLU 147": "OE1" <-> "OE2" Residue "E GLU 27": "OE1" <-> "OE2" Residue "E ASP 44": "OD1" <-> "OD2" Residue "E ARG 63": "NH1" <-> "NH2" Residue "E ARG 90": "NH1" <-> "NH2" Residue "E GLU 140": "OE1" <-> "OE2" Residue "E GLU 140": "OE1" <-> "OE2" Residue "E GLU 147": "OE1" <-> "OE2" Residue "F GLU 27": "OE1" <-> "OE2" Residue "F ASP 44": "OD1" <-> "OD2" Residue "F ARG 63": "NH1" <-> "NH2" Residue "F ARG 90": "NH1" <-> "NH2" Residue "F GLU 140": "OE1" <-> "OE2" Residue "F GLU 140": "OE1" <-> "OE2" Residue "F GLU 147": "OE1" <-> "OE2" Residue "G GLU 27": "OE1" <-> "OE2" Residue "G ASP 44": "OD1" <-> "OD2" Residue "G ARG 63": "NH1" <-> "NH2" Residue "G ARG 90": "NH1" <-> "NH2" Residue "G GLU 140": "OE1" <-> "OE2" Residue "G GLU 140": "OE1" <-> "OE2" Residue "G GLU 147": "OE1" <-> "OE2" Residue "H GLU 27": "OE1" <-> "OE2" Residue "H ASP 44": "OD1" <-> "OD2" Residue "H ARG 63": "NH1" <-> "NH2" Residue "H ARG 90": "NH1" <-> "NH2" Residue "H GLU 140": "OE1" <-> "OE2" Residue "H GLU 140": "OE1" <-> "OE2" Residue "H GLU 147": "OE1" <-> "OE2" Residue "I GLU 27": "OE1" <-> "OE2" Residue "I ASP 44": "OD1" <-> "OD2" Residue "I ARG 63": "NH1" <-> "NH2" Residue "I ARG 90": "NH1" <-> "NH2" Residue "I GLU 140": "OE1" <-> "OE2" Residue "I GLU 140": "OE1" <-> "OE2" Residue "I GLU 147": "OE1" <-> "OE2" Residue "J GLU 27": "OE1" <-> "OE2" Residue "J ASP 44": "OD1" <-> "OD2" Residue "J ARG 63": "NH1" <-> "NH2" Residue "J ARG 90": "NH1" <-> "NH2" Residue "J GLU 140": "OE1" <-> "OE2" Residue "J GLU 140": "OE1" <-> "OE2" Residue "J GLU 147": "OE1" <-> "OE2" Residue "K GLU 27": "OE1" <-> "OE2" Residue "K ASP 44": "OD1" <-> "OD2" Residue "K ARG 63": "NH1" <-> "NH2" Residue "K ARG 90": "NH1" <-> "NH2" Residue "K GLU 140": "OE1" <-> "OE2" Residue "K GLU 140": "OE1" <-> "OE2" Residue "K GLU 147": "OE1" <-> "OE2" Residue "L GLU 27": "OE1" <-> "OE2" Residue "L ASP 44": "OD1" <-> "OD2" Residue "L ARG 63": "NH1" <-> "NH2" Residue "L ARG 90": "NH1" <-> "NH2" Residue "L GLU 140": "OE1" <-> "OE2" Residue "L GLU 140": "OE1" <-> "OE2" Residue "L GLU 147": "OE1" <-> "OE2" Residue "M GLU 27": "OE1" <-> "OE2" Residue "M ASP 44": "OD1" <-> "OD2" Residue "M ARG 63": "NH1" <-> "NH2" Residue "M ARG 90": "NH1" <-> "NH2" Residue "M GLU 140": "OE1" <-> "OE2" Residue "M GLU 140": "OE1" <-> "OE2" Residue "M GLU 147": "OE1" <-> "OE2" Residue "N GLU 27": "OE1" <-> "OE2" Residue "N ASP 44": "OD1" <-> "OD2" Residue "N ARG 63": "NH1" <-> "NH2" Residue "N ARG 90": "NH1" <-> "NH2" Residue "N GLU 140": "OE1" <-> "OE2" Residue "N GLU 140": "OE1" <-> "OE2" Residue "N GLU 147": "OE1" <-> "OE2" Residue "O GLU 27": "OE1" <-> "OE2" Residue "O ASP 44": "OD1" <-> "OD2" Residue "O ARG 63": "NH1" <-> "NH2" Residue "O ARG 90": "NH1" <-> "NH2" Residue "O GLU 140": "OE1" <-> "OE2" Residue "O GLU 140": "OE1" <-> "OE2" Residue "O GLU 147": "OE1" <-> "OE2" Residue "P GLU 27": "OE1" <-> "OE2" Residue "P ASP 44": "OD1" <-> "OD2" Residue "P ARG 63": "NH1" <-> "NH2" Residue "P ARG 90": "NH1" <-> "NH2" Residue "P GLU 140": "OE1" <-> "OE2" Residue "P GLU 140": "OE1" <-> "OE2" Residue "P GLU 147": "OE1" <-> "OE2" Residue "Q GLU 27": "OE1" <-> "OE2" Residue "Q ASP 44": "OD1" <-> "OD2" Residue "Q ARG 63": "NH1" <-> "NH2" Residue "Q ARG 90": "NH1" <-> "NH2" Residue "Q GLU 140": "OE1" <-> "OE2" Residue "Q GLU 140": "OE1" <-> "OE2" Residue "Q GLU 147": "OE1" <-> "OE2" Residue "R GLU 27": "OE1" <-> "OE2" Residue "R ASP 44": "OD1" <-> "OD2" Residue "R ARG 63": "NH1" <-> "NH2" Residue "R ARG 90": "NH1" <-> "NH2" Residue "R GLU 140": "OE1" <-> "OE2" Residue "R GLU 140": "OE1" <-> "OE2" Residue "R GLU 147": "OE1" <-> "OE2" Residue "S GLU 27": "OE1" <-> "OE2" Residue "S ASP 44": "OD1" <-> "OD2" Residue "S ARG 63": "NH1" <-> "NH2" Residue "S ARG 90": "NH1" <-> "NH2" Residue "S GLU 140": "OE1" <-> "OE2" Residue "S GLU 140": "OE1" <-> "OE2" Residue "S GLU 147": "OE1" <-> "OE2" Residue "T GLU 27": "OE1" <-> "OE2" Residue "T ASP 44": "OD1" <-> "OD2" Residue "T ARG 63": "NH1" <-> "NH2" Residue "T ARG 90": "NH1" <-> "NH2" Residue "T GLU 140": "OE1" <-> "OE2" Residue "T GLU 140": "OE1" <-> "OE2" Residue "T GLU 147": "OE1" <-> "OE2" Residue "U GLU 27": "OE1" <-> "OE2" Residue "U ASP 44": "OD1" <-> "OD2" Residue "U ARG 63": "NH1" <-> "NH2" Residue "U ARG 90": "NH1" <-> "NH2" Residue "U GLU 140": "OE1" <-> "OE2" Residue "U GLU 140": "OE1" <-> "OE2" Residue "U GLU 147": "OE1" <-> "OE2" Residue "V GLU 27": "OE1" <-> "OE2" Residue "V ASP 44": "OD1" <-> "OD2" Residue "V ARG 63": "NH1" <-> "NH2" Residue "V ARG 90": "NH1" <-> "NH2" Residue "V GLU 140": "OE1" <-> "OE2" Residue "V GLU 140": "OE1" <-> "OE2" Residue "V GLU 147": "OE1" <-> "OE2" Residue "W GLU 27": "OE1" <-> "OE2" Residue "W ASP 44": "OD1" <-> "OD2" Residue "W ARG 63": "NH1" <-> "NH2" Residue "W ARG 90": "NH1" <-> "NH2" Residue "W GLU 140": "OE1" <-> "OE2" Residue "W GLU 140": "OE1" <-> "OE2" Residue "W GLU 147": "OE1" <-> "OE2" Residue "X GLU 27": "OE1" <-> "OE2" Residue "X ASP 44": "OD1" <-> "OD2" Residue "X ARG 63": "NH1" <-> "NH2" Residue "X ARG 90": "NH1" <-> "NH2" Residue "X GLU 140": "OE1" <-> "OE2" Residue "X GLU 140": "OE1" <-> "OE2" Residue "X GLU 147": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 37805 Number of models: 1 Model: "" Number of chains: 72 Chain: "A" Number of atoms: 1450 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1392 Chain: "B" Number of atoms: 1450 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1392 Chain: "C" Number of atoms: 1450 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1392 Chain: "D" Number of atoms: 1450 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1392 Chain: "E" Number of atoms: 1450 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1392 Chain: "F" Number of atoms: 1450 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1392 Chain: "G" Number of atoms: 1450 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1392 Chain: "H" Number of atoms: 1450 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1392 Chain: "I" Number of atoms: 1450 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1392 Chain: "J" Number of atoms: 1450 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1392 Chain: "K" Number of atoms: 1450 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1392 Chain: "L" Number of atoms: 1450 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1392 Chain: "M" Number of atoms: 1450 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1392 Chain: "N" Number of atoms: 1450 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1392 Chain: "O" Number of atoms: 1450 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1392 Chain: "P" Number of atoms: 1450 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1392 Chain: "Q" Number of atoms: 1450 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1392 Chain: "R" Number of atoms: 1450 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1392 Chain: "S" Number of atoms: 1450 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1392 Chain: "T" Number of atoms: 1450 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1392 Chain: "U" Number of atoms: 1450 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1392 Chain: "V" Number of atoms: 1450 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1392 Chain: "W" Number of atoms: 1450 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1392 Chain: "X" Number of atoms: 1450 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1392 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 124 Classifications: {'water': 124} Link IDs: {None: 123} Chain: "B" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 124 Classifications: {'water': 124} Link IDs: {None: 123} Chain: "C" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 124 Classifications: {'water': 124} Link IDs: {None: 123} Chain: "D" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 124 Classifications: {'water': 124} Link IDs: {None: 123} Chain: "E" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 124 Classifications: {'water': 124} Link IDs: {None: 123} Chain: "F" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 124 Classifications: {'water': 124} Link IDs: {None: 123} Chain: "G" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 124 Classifications: {'water': 124} Link IDs: {None: 123} Chain: "H" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 124 Classifications: {'water': 124} Link IDs: {None: 123} Chain: "I" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 124 Classifications: {'water': 124} Link IDs: {None: 123} Chain: "J" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 124 Classifications: {'water': 124} Link IDs: {None: 123} Chain: "K" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 123 Classifications: {'water': 123} Link IDs: {None: 122} Chain: "L" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 124 Classifications: {'water': 124} Link IDs: {None: 123} Chain: "M" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 124 Classifications: {'water': 124} Link IDs: {None: 123} Chain: "N" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 124 Classifications: {'water': 124} Link IDs: {None: 123} Chain: "O" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 124 Classifications: {'water': 124} Link IDs: {None: 123} Chain: "P" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 124 Classifications: {'water': 124} Link IDs: {None: 123} Chain: "Q" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 124 Classifications: {'water': 124} Link IDs: {None: 123} Chain: "R" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 124 Classifications: {'water': 124} Link IDs: {None: 123} Chain: "S" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 124 Classifications: {'water': 124} Link IDs: {None: 123} Chain: "T" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 124 Classifications: {'water': 124} Link IDs: {None: 123} Chain: "U" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 124 Classifications: {'water': 124} Link IDs: {None: 123} Chain: "V" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 124 Classifications: {'water': 124} Link IDs: {None: 123} Chain: "W" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 124 Classifications: {'water': 124} Link IDs: {None: 123} Chain: "X" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 124 Classifications: {'water': 124} Link IDs: {None: 123} Residues with excluded nonbonded symmetry interactions: 126 residue: pdb=" N AGLU A 94 " occ=0.49 ... (16 atoms not shown) pdb=" OE2BGLU A 94 " occ=0.51 residue: pdb=" N AILE A 133 " occ=0.65 ... (14 atoms not shown) pdb=" CD1BILE A 133 " occ=0.35 residue: pdb=" N AGLU A 140 " occ=0.46 ... (16 atoms not shown) pdb=" OE2BGLU A 140 " occ=0.54 residue: pdb=" N ASER A 144 " occ=0.55 ... (10 atoms not shown) pdb=" OG BSER A 144 " occ=0.45 residue: pdb=" N ALYS A 172 " occ=0.65 ... (16 atoms not shown) pdb=" NZ BLYS A 172 " occ=0.35 residue: pdb=" N AGLU B 94 " occ=0.48 ... (16 atoms not shown) pdb=" OE2BGLU B 94 " occ=0.52 residue: pdb=" N AILE B 133 " occ=0.64 ... (14 atoms not shown) pdb=" CD1BILE B 133 " occ=0.36 residue: pdb=" N AGLU B 140 " occ=0.48 ... (16 atoms not shown) pdb=" OE2BGLU B 140 " occ=0.52 residue: pdb=" N ASER B 144 " occ=0.55 ... (10 atoms not shown) pdb=" OG BSER B 144 " occ=0.45 residue: pdb=" N ALYS B 172 " occ=0.65 ... (16 atoms not shown) pdb=" NZ BLYS B 172 " occ=0.35 residue: pdb=" N AGLU C 94 " occ=0.49 ... (16 atoms not shown) pdb=" OE2BGLU C 94 " occ=0.51 residue: pdb=" N AILE C 133 " occ=0.66 ... (14 atoms not shown) pdb=" CD1BILE C 133 " occ=0.34 ... (remaining 114 not shown) Time building chain proxies: 25.98, per 1000 atoms: 0.69 Number of scatterers: 37805 At special positions: 0 Unit cell: (132.379, 132.379, 132.379, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 24 29.99 Fe 6 26.01 S 192 16.00 O 9695 8.00 N 6072 7.00 C 21816 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: 13.55 Conformation dependent library (CDL) restraints added in 8.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 201 " pdb="ZN ZN A 201 " - pdb=" ND1 HIS A 65 " pdb=" ZN B 202 " pdb="ZN ZN B 202 " - pdb=" ND1 HIS B 65 " pdb=" ZN C 201 " pdb="ZN ZN C 201 " - pdb=" ND1 HIS C 65 " pdb=" ZN D 201 " pdb="ZN ZN D 201 " - pdb=" ND1 HIS D 65 " pdb=" ZN E 202 " pdb="ZN ZN E 202 " - pdb=" ND1 HIS E 65 " pdb=" ZN F 201 " pdb="ZN ZN F 201 " - pdb=" ND1 HIS F 65 " pdb=" ZN G 201 " pdb="ZN ZN G 201 " - pdb=" ND1 HIS G 65 " pdb=" ZN H 201 " pdb="ZN ZN H 201 " - pdb=" ND1 HIS H 65 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" ND1 HIS I 65 " pdb=" ZN J 202 " pdb="ZN ZN J 202 " - pdb=" ND1 HIS J 65 " pdb=" ZN K 201 " pdb="ZN ZN K 201 " - pdb=" ND1 HIS K 65 " pdb=" ZN L 201 " pdb="ZN ZN L 201 " - pdb=" ND1 HIS L 65 " pdb=" ZN M 201 " pdb="ZN ZN M 201 " - pdb=" ND1 HIS M 65 " pdb=" ZN N 201 " pdb="ZN ZN N 201 " - pdb=" ND1 HIS N 65 " pdb=" ZN O 201 " pdb="ZN ZN O 201 " - pdb=" ND1 HIS O 65 " pdb=" ZN P 201 " pdb="ZN ZN P 201 " - pdb=" ND1 HIS P 65 " pdb=" ZN Q 201 " pdb="ZN ZN Q 201 " - pdb=" ND1 HIS Q 65 " pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" ND1 HIS R 65 " pdb=" ZN S 201 " pdb="ZN ZN S 201 " - pdb=" ND1 HIS S 65 " pdb=" ZN T 201 " pdb="ZN ZN T 201 " - pdb=" ND1 HIS T 65 " pdb=" ZN U 201 " pdb="ZN ZN U 201 " - pdb=" ND1 HIS U 65 " pdb=" ZN V 201 " pdb="ZN ZN V 201 " - pdb=" ND1 HIS V 65 " pdb=" ZN W 201 " pdb="ZN ZN W 201 " - pdb=" ND1 HIS W 65 " pdb=" ZN X 201 " pdb="ZN ZN X 201 " - pdb=" ND1 HIS X 65 " 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8160 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 0 sheets defined 77.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.04 Creating SS restraints... Processing helix chain 'A' and resid 13 through 41 Processing helix chain 'A' and resid 48 through 76 Processing helix chain 'A' and resid 95 through 124 Processing helix chain 'A' and resid 126 through 137 Processing helix chain 'A' and resid 137 through 159 Processing helix chain 'A' and resid 164 through 174 removed outlier: 4.226A pdb=" N TYR A 168 " --> pdb=" O GLY A 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 41 Processing helix chain 'B' and resid 48 through 76 Processing helix chain 'B' and resid 95 through 124 Processing helix chain 'B' and resid 126 through 137 Processing helix chain 'B' and resid 137 through 159 Processing helix chain 'B' and resid 164 through 174 removed outlier: 4.226A pdb=" N TYR B 168 " --> pdb=" O GLY B 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 41 Processing helix chain 'C' and resid 48 through 76 Processing helix chain 'C' and resid 95 through 124 Processing helix chain 'C' and resid 126 through 137 Processing helix chain 'C' and resid 137 through 159 Processing helix chain 'C' and resid 164 through 174 removed outlier: 4.226A pdb=" N TYR C 168 " --> pdb=" O GLY C 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 41 Processing helix chain 'D' and resid 48 through 76 Processing helix chain 'D' and resid 95 through 124 Processing helix chain 'D' and resid 126 through 137 Processing helix chain 'D' and resid 137 through 159 Processing helix chain 'D' and resid 164 through 174 removed outlier: 4.226A pdb=" N TYR D 168 " --> pdb=" O GLY D 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 41 Processing helix chain 'E' and resid 48 through 76 Processing helix chain 'E' and resid 95 through 124 Processing helix chain 'E' and resid 126 through 137 Processing helix chain 'E' and resid 137 through 159 Processing helix chain 'E' and resid 164 through 174 removed outlier: 4.226A pdb=" N TYR E 168 " --> pdb=" O GLY E 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 41 Processing helix chain 'F' and resid 48 through 76 Processing helix chain 'F' and resid 95 through 124 Processing helix chain 'F' and resid 126 through 137 Processing helix chain 'F' and resid 137 through 159 Processing helix chain 'F' and resid 164 through 174 removed outlier: 4.226A pdb=" N TYR F 168 " --> pdb=" O GLY F 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 41 Processing helix chain 'G' and resid 48 through 76 Processing helix chain 'G' and resid 95 through 124 Processing helix chain 'G' and resid 126 through 137 Processing helix chain 'G' and resid 137 through 159 Processing helix chain 'G' and resid 164 through 174 removed outlier: 4.226A pdb=" N TYR G 168 " --> pdb=" O GLY G 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 13 through 41 Processing helix chain 'H' and resid 48 through 76 Processing helix chain 'H' and resid 95 through 124 Processing helix chain 'H' and resid 126 through 137 Processing helix chain 'H' and resid 137 through 159 Processing helix chain 'H' and resid 164 through 174 removed outlier: 4.226A pdb=" N TYR H 168 " --> pdb=" O GLY H 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 13 through 41 Processing helix chain 'I' and resid 48 through 76 Processing helix chain 'I' and resid 95 through 124 Processing helix chain 'I' and resid 126 through 137 Processing helix chain 'I' and resid 137 through 159 Processing helix chain 'I' and resid 164 through 174 removed outlier: 4.226A pdb=" N TYR I 168 " --> pdb=" O GLY I 164 " (cutoff:3.500A) Processing helix chain 'J' and resid 13 through 41 Processing helix chain 'J' and resid 48 through 76 Processing helix chain 'J' and resid 95 through 124 Processing helix chain 'J' and resid 126 through 137 Processing helix chain 'J' and resid 137 through 159 Processing helix chain 'J' and resid 164 through 174 removed outlier: 4.226A pdb=" N TYR J 168 " --> pdb=" O GLY J 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 13 through 41 Processing helix chain 'K' and resid 48 through 76 Processing helix chain 'K' and resid 95 through 124 Processing helix chain 'K' and resid 126 through 137 Processing helix chain 'K' and resid 137 through 159 Processing helix chain 'K' and resid 164 through 174 removed outlier: 4.226A pdb=" N TYR K 168 " --> pdb=" O GLY K 164 " (cutoff:3.500A) Processing helix chain 'L' and resid 13 through 41 Processing helix chain 'L' and resid 48 through 76 Processing helix chain 'L' and resid 95 through 124 Processing helix chain 'L' and resid 126 through 137 Processing helix chain 'L' and resid 137 through 159 Processing helix chain 'L' and resid 164 through 174 removed outlier: 4.226A pdb=" N TYR L 168 " --> pdb=" O GLY L 164 " (cutoff:3.500A) Processing helix chain 'M' and resid 13 through 41 Processing helix chain 'M' and resid 48 through 76 Processing helix chain 'M' and resid 95 through 124 Processing helix chain 'M' and resid 126 through 137 Processing helix chain 'M' and resid 137 through 159 Processing helix chain 'M' and resid 164 through 174 removed outlier: 4.226A pdb=" N TYR M 168 " --> pdb=" O GLY M 164 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 41 Processing helix chain 'N' and resid 48 through 76 Processing helix chain 'N' and resid 95 through 124 Processing helix chain 'N' and resid 126 through 137 Processing helix chain 'N' and resid 137 through 159 Processing helix chain 'N' and resid 164 through 174 removed outlier: 4.226A pdb=" N TYR N 168 " --> pdb=" O GLY N 164 " (cutoff:3.500A) Processing helix chain 'O' and resid 13 through 41 Processing helix chain 'O' and resid 48 through 76 Processing helix chain 'O' and resid 95 through 124 Processing helix chain 'O' and resid 126 through 137 Processing helix chain 'O' and resid 137 through 159 Processing helix chain 'O' and resid 164 through 174 removed outlier: 4.226A pdb=" N TYR O 168 " --> pdb=" O GLY O 164 " (cutoff:3.500A) Processing helix chain 'P' and resid 13 through 41 Processing helix chain 'P' and resid 48 through 76 Processing helix chain 'P' and resid 95 through 124 Processing helix chain 'P' and resid 126 through 137 Processing helix chain 'P' and resid 137 through 159 Processing helix chain 'P' and resid 164 through 174 removed outlier: 4.226A pdb=" N TYR P 168 " --> pdb=" O GLY P 164 " (cutoff:3.500A) Processing helix chain 'Q' and resid 13 through 41 Processing helix chain 'Q' and resid 48 through 76 Processing helix chain 'Q' and resid 95 through 124 Processing helix chain 'Q' and resid 126 through 137 Processing helix chain 'Q' and resid 137 through 159 Processing helix chain 'Q' and resid 164 through 174 removed outlier: 4.226A pdb=" N TYR Q 168 " --> pdb=" O GLY Q 164 " (cutoff:3.500A) Processing helix chain 'R' and resid 13 through 41 Processing helix chain 'R' and resid 48 through 76 Processing helix chain 'R' and resid 95 through 124 Processing helix chain 'R' and resid 126 through 137 Processing helix chain 'R' and resid 137 through 159 Processing helix chain 'R' and resid 164 through 174 removed outlier: 4.226A pdb=" N TYR R 168 " --> pdb=" O GLY R 164 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 41 Processing helix chain 'S' and resid 48 through 76 Processing helix chain 'S' and resid 95 through 124 Processing helix chain 'S' and resid 126 through 137 Processing helix chain 'S' and resid 137 through 159 Processing helix chain 'S' and resid 164 through 174 removed outlier: 4.226A pdb=" N TYR S 168 " --> pdb=" O GLY S 164 " (cutoff:3.500A) Processing helix chain 'T' and resid 13 through 41 Processing helix chain 'T' and resid 48 through 76 Processing helix chain 'T' and resid 95 through 124 Processing helix chain 'T' and resid 126 through 137 Processing helix chain 'T' and resid 137 through 159 Processing helix chain 'T' and resid 164 through 174 removed outlier: 4.226A pdb=" N TYR T 168 " --> pdb=" O GLY T 164 " (cutoff:3.500A) Processing helix chain 'U' and resid 13 through 41 Processing helix chain 'U' and resid 48 through 76 Processing helix chain 'U' and resid 95 through 124 Processing helix chain 'U' and resid 126 through 137 Processing helix chain 'U' and resid 137 through 159 Processing helix chain 'U' and resid 164 through 174 removed outlier: 4.226A pdb=" N TYR U 168 " --> pdb=" O GLY U 164 " (cutoff:3.500A) Processing helix chain 'V' and resid 13 through 41 Processing helix chain 'V' and resid 48 through 76 Processing helix chain 'V' and resid 95 through 124 Processing helix chain 'V' and resid 126 through 137 Processing helix chain 'V' and resid 137 through 159 Processing helix chain 'V' and resid 164 through 174 removed outlier: 4.226A pdb=" N TYR V 168 " --> pdb=" O GLY V 164 " (cutoff:3.500A) Processing helix chain 'W' and resid 13 through 41 Processing helix chain 'W' and resid 48 through 76 Processing helix chain 'W' and resid 95 through 124 Processing helix chain 'W' and resid 126 through 137 Processing helix chain 'W' and resid 137 through 159 Processing helix chain 'W' and resid 164 through 174 removed outlier: 4.226A pdb=" N TYR W 168 " --> pdb=" O GLY W 164 " (cutoff:3.500A) Processing helix chain 'X' and resid 13 through 41 Processing helix chain 'X' and resid 48 through 76 Processing helix chain 'X' and resid 95 through 124 Processing helix chain 'X' and resid 126 through 137 Processing helix chain 'X' and resid 137 through 159 Processing helix chain 'X' and resid 164 through 174 removed outlier: 4.226A pdb=" N TYR X 168 " --> pdb=" O GLY X 164 " (cutoff:3.500A) 2736 hydrogen bonds defined for protein. 8304 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: 10.29 Time building geometry restraints manager: 14.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 8785 1.33 - 1.45: 8782 1.45 - 1.58: 17737 1.58 - 1.71: 0 1.71 - 1.83: 312 Bond restraints: 35616 Sorted by residual: bond pdb=" C ARG J 63 " pdb=" N GLU J 64 " ideal model delta sigma weight residual 1.335 1.225 0.110 1.31e-02 5.83e+03 7.08e+01 bond pdb=" C ARG R 63 " pdb=" N GLU R 64 " ideal model delta sigma weight residual 1.335 1.225 0.110 1.31e-02 5.83e+03 7.08e+01 bond pdb=" C ARG D 63 " pdb=" N GLU D 64 " ideal model delta sigma weight residual 1.335 1.225 0.110 1.31e-02 5.83e+03 7.08e+01 bond pdb=" C ARG I 63 " pdb=" N GLU I 64 " ideal model delta sigma weight residual 1.335 1.225 0.110 1.31e-02 5.83e+03 7.08e+01 bond pdb=" C ARG K 63 " pdb=" N GLU K 64 " ideal model delta sigma weight residual 1.335 1.225 0.110 1.31e-02 5.83e+03 7.08e+01 ... (remaining 35611 not shown) Histogram of bond angle deviations from ideal: 98.89 - 105.92: 528 105.92 - 112.96: 17856 112.96 - 119.99: 14664 119.99 - 127.03: 14688 127.03 - 134.06: 336 Bond angle restraints: 48072 Sorted by residual: angle pdb=" C BILE D 133 " pdb=" N GLU D 134 " pdb=" CA GLU D 134 " ideal model delta sigma weight residual 120.44 131.08 -10.64 1.30e+00 5.92e-01 6.70e+01 angle pdb=" C BILE S 133 " pdb=" N GLU S 134 " pdb=" CA GLU S 134 " ideal model delta sigma weight residual 120.44 131.08 -10.64 1.30e+00 5.92e-01 6.70e+01 angle pdb=" C BILE K 133 " pdb=" N GLU K 134 " pdb=" CA GLU K 134 " ideal model delta sigma weight residual 120.44 131.08 -10.64 1.30e+00 5.92e-01 6.70e+01 angle pdb=" C BILE L 133 " pdb=" N GLU L 134 " pdb=" CA GLU L 134 " ideal model delta sigma weight residual 120.44 131.08 -10.64 1.30e+00 5.92e-01 6.70e+01 angle pdb=" C BILE H 133 " pdb=" N GLU H 134 " pdb=" CA GLU H 134 " ideal model delta sigma weight residual 120.44 131.08 -10.64 1.30e+00 5.92e-01 6.70e+01 ... (remaining 48067 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.04: 20976 28.04 - 56.08: 648 56.08 - 84.12: 144 84.12 - 112.16: 0 112.16 - 140.20: 24 Dihedral angle restraints: 21792 sinusoidal: 9072 harmonic: 12720 Sorted by residual: dihedral pdb=" CB BGLU H 140 " pdb=" CG BGLU H 140 " pdb=" CD BGLU H 140 " pdb=" OE1BGLU H 140 " ideal model delta sinusoidal sigma weight residual 0.00 140.20 -140.20 1 3.00e+01 1.11e-03 1.89e+01 dihedral pdb=" CB BGLU C 140 " pdb=" CG BGLU C 140 " pdb=" CD BGLU C 140 " pdb=" OE1BGLU C 140 " ideal model delta sinusoidal sigma weight residual 0.00 140.20 -140.20 1 3.00e+01 1.11e-03 1.89e+01 dihedral pdb=" CB BGLU A 140 " pdb=" CG BGLU A 140 " pdb=" CD BGLU A 140 " pdb=" OE1BGLU A 140 " ideal model delta sinusoidal sigma weight residual 0.00 140.20 -140.20 1 3.00e+01 1.11e-03 1.89e+01 ... (remaining 21789 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 3336 0.068 - 0.135: 1416 0.135 - 0.202: 144 0.202 - 0.270: 72 0.270 - 0.337: 24 Chirality restraints: 4992 Sorted by residual: chirality pdb=" CB VAL O 8 " pdb=" CA VAL O 8 " pdb=" CG1 VAL O 8 " pdb=" CG2 VAL O 8 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" CB VAL D 8 " pdb=" CA VAL D 8 " pdb=" CG1 VAL D 8 " pdb=" CG2 VAL D 8 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" CB VAL H 8 " pdb=" CA VAL H 8 " pdb=" CG1 VAL H 8 " pdb=" CG2 VAL H 8 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.84e+00 ... (remaining 4989 not shown) Planarity restraints: 6384 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 137 " -0.092 2.00e-02 2.50e+03 4.93e-02 4.86e+01 pdb=" CG TYR D 137 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR D 137 " 0.058 2.00e-02 2.50e+03 pdb=" CD2 TYR D 137 " 0.030 2.00e-02 2.50e+03 pdb=" CE1 TYR D 137 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR D 137 " 0.034 2.00e-02 2.50e+03 pdb=" CZ TYR D 137 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR D 137 " -0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR S 137 " -0.092 2.00e-02 2.50e+03 4.93e-02 4.86e+01 pdb=" CG TYR S 137 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR S 137 " 0.058 2.00e-02 2.50e+03 pdb=" CD2 TYR S 137 " 0.030 2.00e-02 2.50e+03 pdb=" CE1 TYR S 137 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR S 137 " 0.034 2.00e-02 2.50e+03 pdb=" CZ TYR S 137 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR S 137 " -0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR O 137 " -0.092 2.00e-02 2.50e+03 4.93e-02 4.86e+01 pdb=" CG TYR O 137 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR O 137 " 0.058 2.00e-02 2.50e+03 pdb=" CD2 TYR O 137 " 0.030 2.00e-02 2.50e+03 pdb=" CE1 TYR O 137 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR O 137 " 0.034 2.00e-02 2.50e+03 pdb=" CZ TYR O 137 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR O 137 " -0.065 2.00e-02 2.50e+03 ... (remaining 6381 not shown) Histogram of nonbonded interaction distances: 0.73 - 1.57: 96 1.57 - 2.40: 324 2.40 - 3.23: 43119 3.23 - 4.07: 122976 4.07 - 4.90: 212416 Warning: very small nonbonded interaction distances. Nonbonded interactions: 378931 Sorted by model distance: nonbonded pdb=" NH2 ARG C 63 " pdb=" NH2 ARG E 63 " model vdw 0.733 3.200 nonbonded pdb=" NH2 ARG G 63 " pdb=" NH2 ARG U 63 " model vdw 0.733 3.200 nonbonded pdb=" NH2 ARG A 63 " pdb=" NH2 ARG K 63 " model vdw 0.733 3.200 nonbonded pdb=" NH2 ARG D 63 " pdb=" NH2 ARG Q 63 " model vdw 0.733 3.200 nonbonded pdb=" NH2 ARG F 63 " pdb=" NH2 ARG N 63 " model vdw 0.733 3.200 ... (remaining 378926 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 93 or resid 95 through 132 or resid 134 through \ 139 or resid 141 through 143 or resid 145 through 171 or resid 173 through 176)) \ selection = (chain 'B' and (resid 5 through 93 or resid 95 through 132 or resid 134 through \ 139 or resid 141 through 143 or resid 145 through 171 or resid 173 through 176)) \ selection = (chain 'C' and (resid 5 through 93 or resid 95 through 132 or resid 134 through \ 139 or resid 141 through 143 or resid 145 through 171 or resid 173 through 176)) \ selection = (chain 'D' and (resid 5 through 93 or resid 95 through 132 or resid 134 through \ 139 or resid 141 through 143 or resid 145 through 171 or resid 173 through 176)) \ selection = (chain 'E' and (resid 5 through 93 or resid 95 through 132 or resid 134 through \ 139 or resid 141 through 143 or resid 145 through 171 or resid 173 through 176)) \ selection = (chain 'F' and (resid 5 through 93 or resid 95 through 132 or resid 134 through \ 139 or resid 141 through 143 or resid 145 through 171 or resid 173 through 176)) \ selection = (chain 'G' and (resid 5 through 93 or resid 95 through 132 or resid 134 through \ 139 or resid 141 through 143 or resid 145 through 171 or resid 173 through 176)) \ selection = (chain 'H' and (resid 5 through 93 or resid 95 through 132 or resid 134 through \ 139 or resid 141 through 143 or resid 145 through 171 or resid 173 through 176)) \ selection = (chain 'I' and (resid 5 through 93 or resid 95 through 132 or resid 134 through \ 139 or resid 141 through 143 or resid 145 through 171 or resid 173 through 176)) \ selection = (chain 'J' and (resid 5 through 93 or resid 95 through 132 or resid 134 through \ 139 or resid 141 through 143 or resid 145 through 171 or resid 173 through 176)) \ selection = (chain 'K' and (resid 5 through 93 or resid 95 through 132 or resid 134 through \ 139 or resid 141 through 143 or resid 145 through 171 or resid 173 through 176)) \ selection = (chain 'L' and (resid 5 through 93 or resid 95 through 132 or resid 134 through \ 139 or resid 141 through 143 or resid 145 through 171 or resid 173 through 176)) \ selection = (chain 'M' and (resid 5 through 93 or resid 95 through 132 or resid 134 through \ 139 or resid 141 through 143 or resid 145 through 171 or resid 173 through 176)) \ selection = (chain 'N' and (resid 5 through 93 or resid 95 through 132 or resid 134 through \ 139 or resid 141 through 143 or resid 145 through 171 or resid 173 through 176)) \ selection = (chain 'O' and (resid 5 through 93 or resid 95 through 132 or resid 134 through \ 139 or resid 141 through 143 or resid 145 through 171 or resid 173 through 176)) \ selection = (chain 'P' and (resid 5 through 93 or resid 95 through 132 or resid 134 through \ 139 or resid 141 through 143 or resid 145 through 171 or resid 173 through 176)) \ selection = (chain 'Q' and (resid 5 through 93 or resid 95 through 132 or resid 134 through \ 139 or resid 141 through 143 or resid 145 through 171 or resid 173 through 176)) \ selection = (chain 'R' and (resid 5 through 93 or resid 95 through 132 or resid 134 through \ 139 or resid 141 through 143 or resid 145 through 171 or resid 173 through 176)) \ selection = (chain 'S' and (resid 5 through 93 or resid 95 through 132 or resid 134 through \ 139 or resid 141 through 143 or resid 145 through 171 or resid 173 through 176)) \ selection = (chain 'T' and (resid 5 through 93 or resid 95 through 132 or resid 134 through \ 139 or resid 141 through 143 or resid 145 through 171 or resid 173 through 176)) \ selection = (chain 'U' and (resid 5 through 93 or resid 95 through 132 or resid 134 through \ 139 or resid 141 through 143 or resid 145 through 171 or resid 173 through 176)) \ selection = (chain 'V' and (resid 5 through 93 or resid 95 through 132 or resid 134 through \ 139 or resid 141 through 143 or resid 145 through 171 or resid 173 through 176)) \ selection = (chain 'W' and (resid 5 through 93 or resid 95 through 132 or resid 134 through \ 139 or resid 141 through 143 or resid 145 through 171 or resid 173 through 176)) \ selection = (chain 'X' and (resid 5 through 93 or resid 95 through 132 or resid 134 through \ 139 or resid 141 through 143 or resid 145 through 171 or resid 173 through 176)) \ } 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=0.22 max=1.00 mean=0.97 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: 4.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.330 Construct map_model_manager: 0.030 Extract box with map and model: 21.290 Check model and map are aligned: 0.520 Set scattering table: 0.270 Process input model: 98.390 Find NCS groups from input model: 2.250 Set up NCS constraints: 0.190 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:10.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 138.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 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 : 0.011 0.110 35616 Z= 0.705 Angle : 1.312 10.670 48072 Z= 0.887 Chirality : 0.072 0.337 4992 Planarity : 0.009 0.049 6384 Dihedral : 15.252 140.203 13632 Min Nonbonded Distance : 0.733 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 1.91 % Allowed : 3.18 % Favored : 94.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 2.37 (0.12), residues: 4440 helix: 1.86 (0.08), residues: 3480 sheet: None (None), residues: 0 loop : 0.72 (0.23), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.009 TRP H 93 HIS 0.013 0.002 HIS L 60 PHE 0.028 0.007 PHE V 51 TYR 0.092 0.013 TYR O 137 ARG 0.015 0.002 ARG T 79 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1008 residues out of total 3528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 936 time to evaluate : 3.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLN cc_start: 0.7751 (mm-40) cc_final: 0.6946 (mp10) REVERT: A 49 LYS cc_start: 0.8089 (mttm) cc_final: 0.7849 (mtmm) REVERT: A 53 LYS cc_start: 0.8155 (ttpp) cc_final: 0.7755 (ttpp) REVERT: A 68 LYS cc_start: 0.7807 (OUTLIER) cc_final: 0.7572 (ttmm) REVERT: A 92 ASP cc_start: 0.7575 (t0) cc_final: 0.7197 (t0) REVERT: A 119 LYS cc_start: 0.7397 (ttmp) cc_final: 0.7143 (ttpt) REVERT: B 14 GLN cc_start: 0.7742 (mm-40) cc_final: 0.6934 (mp10) REVERT: B 49 LYS cc_start: 0.8092 (mttm) cc_final: 0.7852 (mtmm) REVERT: B 53 LYS cc_start: 0.8154 (ttpp) cc_final: 0.7755 (ttpp) REVERT: B 68 LYS cc_start: 0.7808 (OUTLIER) cc_final: 0.7573 (ttmm) REVERT: B 92 ASP cc_start: 0.7577 (t0) cc_final: 0.7199 (t0) REVERT: B 119 LYS cc_start: 0.7400 (ttmp) cc_final: 0.7145 (ttpt) REVERT: C 14 GLN cc_start: 0.7741 (mm-40) cc_final: 0.6935 (mp10) REVERT: C 49 LYS cc_start: 0.8092 (mttm) cc_final: 0.7852 (mtmm) REVERT: C 53 LYS cc_start: 0.8155 (ttpp) cc_final: 0.7754 (ttpp) REVERT: C 68 LYS cc_start: 0.7805 (OUTLIER) cc_final: 0.7569 (ttmm) REVERT: C 92 ASP cc_start: 0.7585 (t0) cc_final: 0.7211 (t0) REVERT: C 119 LYS cc_start: 0.7396 (ttmp) cc_final: 0.7142 (ttpt) REVERT: D 14 GLN cc_start: 0.7743 (mm-40) cc_final: 0.6937 (mp10) REVERT: D 49 LYS cc_start: 0.8089 (mttm) cc_final: 0.7850 (mtmm) REVERT: D 53 LYS cc_start: 0.8155 (ttpp) cc_final: 0.7755 (ttpp) REVERT: D 68 LYS cc_start: 0.7810 (OUTLIER) cc_final: 0.7576 (ttmm) REVERT: D 92 ASP cc_start: 0.7578 (t0) cc_final: 0.7200 (t0) REVERT: D 119 LYS cc_start: 0.7398 (ttmp) cc_final: 0.7145 (ttpt) REVERT: E 14 GLN cc_start: 0.7743 (mm-40) cc_final: 0.6936 (mp10) REVERT: E 49 LYS cc_start: 0.8093 (mttm) cc_final: 0.7853 (mtmm) REVERT: E 53 LYS cc_start: 0.8157 (ttpp) cc_final: 0.7757 (ttpp) REVERT: E 68 LYS cc_start: 0.7806 (OUTLIER) cc_final: 0.7571 (ttmm) REVERT: E 92 ASP cc_start: 0.7583 (t0) cc_final: 0.7210 (t0) REVERT: E 119 LYS cc_start: 0.7393 (ttmp) cc_final: 0.7140 (ttpt) REVERT: F 14 GLN cc_start: 0.7762 (mm-40) cc_final: 0.6957 (mp10) REVERT: F 49 LYS cc_start: 0.8089 (mttm) cc_final: 0.7850 (mtmm) REVERT: F 53 LYS cc_start: 0.8154 (ttpp) cc_final: 0.7754 (ttpp) REVERT: F 68 LYS cc_start: 0.7806 (OUTLIER) cc_final: 0.7572 (ttmm) REVERT: F 92 ASP cc_start: 0.7584 (t0) cc_final: 0.7210 (t0) REVERT: F 119 LYS cc_start: 0.7398 (ttmp) cc_final: 0.7144 (ttpt) REVERT: G 14 GLN cc_start: 0.7744 (mm-40) cc_final: 0.6937 (mp10) REVERT: G 49 LYS cc_start: 0.8090 (mttm) cc_final: 0.7851 (mtmm) REVERT: G 53 LYS cc_start: 0.8153 (ttpp) cc_final: 0.7754 (ttpp) REVERT: G 68 LYS cc_start: 0.7808 (OUTLIER) cc_final: 0.7574 (ttmm) REVERT: G 92 ASP cc_start: 0.7576 (t0) cc_final: 0.7197 (t0) REVERT: G 119 LYS cc_start: 0.7401 (ttmp) cc_final: 0.7147 (ttpt) REVERT: H 14 GLN cc_start: 0.7748 (mm-40) cc_final: 0.6945 (mp10) REVERT: H 49 LYS cc_start: 0.8091 (mttm) cc_final: 0.7853 (mtmm) REVERT: H 53 LYS cc_start: 0.8156 (ttpp) cc_final: 0.7755 (ttpp) REVERT: H 68 LYS cc_start: 0.7805 (OUTLIER) cc_final: 0.7558 (tttm) REVERT: H 92 ASP cc_start: 0.7584 (t0) cc_final: 0.7208 (t0) REVERT: H 119 LYS cc_start: 0.7394 (ttmp) cc_final: 0.7139 (ttpt) REVERT: I 14 GLN cc_start: 0.7742 (mm-40) cc_final: 0.6936 (mp10) REVERT: I 49 LYS cc_start: 0.8089 (mttm) cc_final: 0.7850 (mtmm) REVERT: I 53 LYS cc_start: 0.8152 (ttpp) cc_final: 0.7752 (ttpp) REVERT: I 68 LYS cc_start: 0.7803 (OUTLIER) cc_final: 0.7569 (ttmm) REVERT: I 92 ASP cc_start: 0.7581 (t0) cc_final: 0.7205 (t0) REVERT: I 119 LYS cc_start: 0.7400 (ttmp) cc_final: 0.7146 (ttpt) REVERT: J 14 GLN cc_start: 0.7745 (mm-40) cc_final: 0.6937 (mp10) REVERT: J 49 LYS cc_start: 0.8090 (mttm) cc_final: 0.7849 (mtmm) REVERT: J 53 LYS cc_start: 0.8153 (ttpp) cc_final: 0.7753 (ttpp) REVERT: J 68 LYS cc_start: 0.7807 (OUTLIER) cc_final: 0.7572 (ttmm) REVERT: J 92 ASP cc_start: 0.7577 (t0) cc_final: 0.7200 (t0) REVERT: J 119 LYS cc_start: 0.7401 (ttmp) cc_final: 0.7146 (ttpt) REVERT: K 14 GLN cc_start: 0.7763 (mm-40) cc_final: 0.6957 (mp10) REVERT: K 49 LYS cc_start: 0.8093 (mttm) cc_final: 0.7852 (mtmm) REVERT: K 53 LYS cc_start: 0.8155 (ttpp) cc_final: 0.7754 (ttpp) REVERT: K 68 LYS cc_start: 0.7800 (OUTLIER) cc_final: 0.7565 (ttmm) REVERT: K 92 ASP cc_start: 0.7584 (t0) cc_final: 0.7211 (t0) REVERT: K 119 LYS cc_start: 0.7396 (ttmp) cc_final: 0.7141 (ttpt) REVERT: L 14 GLN cc_start: 0.7764 (mm-40) cc_final: 0.6957 (mp10) REVERT: L 49 LYS cc_start: 0.8091 (mttm) cc_final: 0.7849 (mtmm) REVERT: L 53 LYS cc_start: 0.8155 (ttpp) cc_final: 0.7755 (ttpp) REVERT: L 68 LYS cc_start: 0.7804 (OUTLIER) cc_final: 0.7569 (ttmm) REVERT: L 92 ASP cc_start: 0.7584 (t0) cc_final: 0.7211 (t0) REVERT: L 119 LYS cc_start: 0.7397 (ttmp) cc_final: 0.7143 (ttpt) REVERT: M 14 GLN cc_start: 0.7749 (mm-40) cc_final: 0.6946 (mp10) REVERT: M 49 LYS cc_start: 0.8087 (mttm) cc_final: 0.7850 (mtmm) REVERT: M 53 LYS cc_start: 0.8153 (ttpp) cc_final: 0.7754 (ttpp) REVERT: M 68 LYS cc_start: 0.7809 (OUTLIER) cc_final: 0.7574 (ttmm) REVERT: M 92 ASP cc_start: 0.7574 (t0) cc_final: 0.7196 (t0) REVERT: M 119 LYS cc_start: 0.7398 (ttmp) cc_final: 0.7144 (ttpt) REVERT: N 14 GLN cc_start: 0.7748 (mm-40) cc_final: 0.6944 (mp10) REVERT: N 49 LYS cc_start: 0.8091 (mttm) cc_final: 0.7854 (mtmm) REVERT: N 53 LYS cc_start: 0.8156 (ttpp) cc_final: 0.7756 (ttpp) REVERT: N 68 LYS cc_start: 0.7806 (OUTLIER) cc_final: 0.7560 (tttm) REVERT: N 92 ASP cc_start: 0.7583 (t0) cc_final: 0.7204 (t0) REVERT: N 119 LYS cc_start: 0.7393 (ttmp) cc_final: 0.7139 (ttpt) REVERT: O 14 GLN cc_start: 0.7744 (mm-40) cc_final: 0.6935 (mp10) REVERT: O 49 LYS cc_start: 0.8093 (mttm) cc_final: 0.7851 (mtmm) REVERT: O 53 LYS cc_start: 0.8155 (ttpp) cc_final: 0.7755 (ttpp) REVERT: O 68 LYS cc_start: 0.7801 (OUTLIER) cc_final: 0.7566 (ttmm) REVERT: O 92 ASP cc_start: 0.7582 (t0) cc_final: 0.7205 (t0) REVERT: O 119 LYS cc_start: 0.7394 (ttmp) cc_final: 0.7139 (ttpt) REVERT: P 14 GLN cc_start: 0.7749 (mm-40) cc_final: 0.6946 (mp10) REVERT: P 49 LYS cc_start: 0.8090 (mttm) cc_final: 0.7852 (mtmm) REVERT: P 53 LYS cc_start: 0.8153 (ttpp) cc_final: 0.7752 (ttpp) REVERT: P 68 LYS cc_start: 0.7805 (OUTLIER) cc_final: 0.7558 (tttm) REVERT: P 92 ASP cc_start: 0.7583 (t0) cc_final: 0.7206 (t0) REVERT: P 119 LYS cc_start: 0.7396 (ttmp) cc_final: 0.7142 (ttpt) REVERT: Q 14 GLN cc_start: 0.7741 (mm-40) cc_final: 0.6933 (mp10) REVERT: Q 49 LYS cc_start: 0.8097 (mttm) cc_final: 0.7856 (mtmm) REVERT: Q 53 LYS cc_start: 0.8155 (ttpp) cc_final: 0.7756 (ttpp) REVERT: Q 68 LYS cc_start: 0.7803 (OUTLIER) cc_final: 0.7556 (tttm) REVERT: Q 92 ASP cc_start: 0.7582 (t0) cc_final: 0.7207 (t0) REVERT: Q 119 LYS cc_start: 0.7393 (ttmp) cc_final: 0.7139 (ttpt) REVERT: R 14 GLN cc_start: 0.7745 (mm-40) cc_final: 0.6938 (mp10) REVERT: R 49 LYS cc_start: 0.8090 (mttm) cc_final: 0.7850 (mtmm) REVERT: R 53 LYS cc_start: 0.8154 (ttpp) cc_final: 0.7753 (ttpp) REVERT: R 68 LYS cc_start: 0.7804 (OUTLIER) cc_final: 0.7570 (ttmm) REVERT: R 92 ASP cc_start: 0.7581 (t0) cc_final: 0.7204 (t0) REVERT: R 119 LYS cc_start: 0.7399 (ttmp) cc_final: 0.7145 (ttpt) REVERT: S 14 GLN cc_start: 0.7745 (mm-40) cc_final: 0.6938 (mp10) REVERT: S 49 LYS cc_start: 0.8091 (mttm) cc_final: 0.7851 (mtmm) REVERT: S 53 LYS cc_start: 0.8153 (ttpp) cc_final: 0.7754 (ttpp) REVERT: S 68 LYS cc_start: 0.7804 (OUTLIER) cc_final: 0.7570 (ttmm) REVERT: S 92 ASP cc_start: 0.7580 (t0) cc_final: 0.7203 (t0) REVERT: S 119 LYS cc_start: 0.7398 (ttmp) cc_final: 0.7145 (ttpt) REVERT: T 14 GLN cc_start: 0.7762 (mm-40) cc_final: 0.6956 (mp10) REVERT: T 49 LYS cc_start: 0.8093 (mttm) cc_final: 0.7853 (mtmm) REVERT: T 53 LYS cc_start: 0.8154 (ttpp) cc_final: 0.7755 (ttpp) REVERT: T 68 LYS cc_start: 0.7802 (OUTLIER) cc_final: 0.7568 (ttmm) REVERT: T 92 ASP cc_start: 0.7583 (t0) cc_final: 0.7209 (t0) REVERT: T 119 LYS cc_start: 0.7395 (ttmp) cc_final: 0.7141 (ttpt) REVERT: U 14 GLN cc_start: 0.7742 (mm-40) cc_final: 0.6935 (mp10) REVERT: U 49 LYS cc_start: 0.8091 (mttm) cc_final: 0.7852 (mtmm) REVERT: U 53 LYS cc_start: 0.8154 (ttpp) cc_final: 0.7753 (ttpp) REVERT: U 68 LYS cc_start: 0.7802 (OUTLIER) cc_final: 0.7568 (ttmm) REVERT: U 92 ASP cc_start: 0.7583 (t0) cc_final: 0.7205 (t0) REVERT: U 119 LYS cc_start: 0.7394 (ttmp) cc_final: 0.7139 (ttpt) REVERT: V 14 GLN cc_start: 0.7750 (mm-40) cc_final: 0.6947 (mp10) REVERT: V 49 LYS cc_start: 0.8091 (mttm) cc_final: 0.7852 (mtmm) REVERT: V 53 LYS cc_start: 0.8155 (ttpp) cc_final: 0.7755 (ttpp) REVERT: V 68 LYS cc_start: 0.7805 (OUTLIER) cc_final: 0.7559 (tttm) REVERT: V 92 ASP cc_start: 0.7582 (t0) cc_final: 0.7205 (t0) REVERT: V 119 LYS cc_start: 0.7394 (ttmp) cc_final: 0.7140 (ttpt) REVERT: W 14 GLN cc_start: 0.7744 (mm-40) cc_final: 0.6935 (mp10) REVERT: W 49 LYS cc_start: 0.8093 (mttm) cc_final: 0.7853 (mtmm) REVERT: W 53 LYS cc_start: 0.8153 (ttpp) cc_final: 0.7754 (ttpp) REVERT: W 68 LYS cc_start: 0.7805 (OUTLIER) cc_final: 0.7570 (ttmm) REVERT: W 92 ASP cc_start: 0.7581 (t0) cc_final: 0.7203 (t0) REVERT: W 119 LYS cc_start: 0.7399 (ttmp) cc_final: 0.7144 (ttpt) REVERT: X 14 GLN cc_start: 0.7742 (mm-40) cc_final: 0.6935 (mp10) REVERT: X 49 LYS cc_start: 0.8093 (mttm) cc_final: 0.7853 (mtmm) REVERT: X 53 LYS cc_start: 0.8156 (ttpp) cc_final: 0.7756 (ttpp) REVERT: X 68 LYS cc_start: 0.7805 (OUTLIER) cc_final: 0.7559 (tttm) REVERT: X 92 ASP cc_start: 0.7583 (t0) cc_final: 0.7210 (t0) REVERT: X 119 LYS cc_start: 0.7392 (ttmp) cc_final: 0.7138 (ttpt) outliers start: 72 outliers final: 24 residues processed: 936 average time/residue: 1.7784 time to fit residues: 1900.8412 Evaluate side-chains 834 residues out of total 3528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 786 time to evaluate : 3.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 165 MET Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain C residue 68 LYS Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 165 MET Chi-restraints excluded: chain G residue 68 LYS Chi-restraints excluded: chain G residue 165 MET Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 165 MET Chi-restraints excluded: chain I residue 68 LYS Chi-restraints excluded: chain I residue 165 MET Chi-restraints excluded: chain J residue 68 LYS Chi-restraints excluded: chain J residue 165 MET Chi-restraints excluded: chain K residue 68 LYS Chi-restraints excluded: chain K residue 165 MET Chi-restraints excluded: chain L residue 68 LYS Chi-restraints excluded: chain L residue 165 MET Chi-restraints excluded: chain M residue 68 LYS Chi-restraints excluded: chain M residue 165 MET Chi-restraints excluded: chain N residue 68 LYS Chi-restraints excluded: chain N residue 165 MET Chi-restraints excluded: chain O residue 68 LYS Chi-restraints excluded: chain O residue 165 MET Chi-restraints excluded: chain P residue 68 LYS Chi-restraints excluded: chain P residue 165 MET Chi-restraints excluded: chain Q residue 68 LYS Chi-restraints excluded: chain Q residue 165 MET Chi-restraints excluded: chain R residue 68 LYS Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain S residue 68 LYS Chi-restraints excluded: chain S residue 165 MET Chi-restraints excluded: chain T residue 68 LYS Chi-restraints excluded: chain T residue 165 MET Chi-restraints excluded: chain U residue 68 LYS Chi-restraints excluded: chain U residue 165 MET Chi-restraints excluded: chain V residue 68 LYS Chi-restraints excluded: chain V residue 165 MET Chi-restraints excluded: chain W residue 68 LYS Chi-restraints excluded: chain W residue 165 MET Chi-restraints excluded: chain X residue 68 LYS Chi-restraints excluded: chain X residue 165 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 0.8980 chunk 309 optimal weight: 0.9990 chunk 171 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 chunk 208 optimal weight: 0.9980 chunk 165 optimal weight: 0.6980 chunk 319 optimal weight: 5.9990 chunk 123 optimal weight: 0.9990 chunk 194 optimal weight: 2.9990 chunk 238 optimal weight: 0.7980 chunk 370 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 83 GLN A 112 GLN B 58 GLN B 83 GLN B 112 GLN C 58 GLN C 83 GLN C 112 GLN D 58 GLN D 83 GLN D 112 GLN E 58 GLN E 83 GLN E 112 GLN F 58 GLN F 83 GLN F 112 GLN G 58 GLN G 83 GLN G 112 GLN H 58 GLN H 83 GLN H 112 GLN I 58 GLN I 83 GLN I 112 GLN J 58 GLN J 83 GLN J 112 GLN K 58 GLN K 83 GLN K 112 GLN L 58 GLN L 83 GLN L 112 GLN M 58 GLN M 83 GLN M 112 GLN N 58 GLN N 83 GLN N 112 GLN O 58 GLN O 83 GLN O 112 GLN P 58 GLN P 83 GLN P 112 GLN Q 58 GLN Q 83 GLN Q 112 GLN R 58 GLN R 83 GLN R 112 GLN S 58 GLN S 83 GLN S 112 GLN T 58 GLN T 83 GLN T 112 GLN U 58 GLN U 83 GLN U 112 GLN V 58 GLN V 83 GLN V 112 GLN W 58 GLN W 83 GLN W 112 GLN X 58 GLN X 83 GLN X 112 GLN Total number of N/Q/H flips: 72 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 35616 Z= 0.153 Angle : 0.573 5.524 48072 Z= 0.315 Chirality : 0.037 0.119 4992 Planarity : 0.003 0.022 6384 Dihedral : 5.488 40.766 4920 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.27 % Allowed : 3.82 % Favored : 94.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 4.92 (0.13), residues: 4440 helix: 3.74 (0.08), residues: 3528 sheet: None (None), residues: 0 loop : 1.11 (0.25), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP D 93 HIS 0.008 0.001 HIS D 60 PHE 0.016 0.002 PHE S 41 TYR 0.020 0.002 TYR W 32 ARG 0.003 0.000 ARG I 79 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 960 residues out of total 3528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 912 time to evaluate : 3.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LYS cc_start: 0.8086 (mttm) cc_final: 0.7582 (mmpt) REVERT: A 68 LYS cc_start: 0.7968 (OUTLIER) cc_final: 0.7767 (tttm) REVERT: A 92 ASP cc_start: 0.7802 (t0) cc_final: 0.7578 (t0) REVERT: A 119 LYS cc_start: 0.7953 (ttmp) cc_final: 0.7636 (tttm) REVERT: B 49 LYS cc_start: 0.8085 (mttm) cc_final: 0.7588 (mmpt) REVERT: B 68 LYS cc_start: 0.7969 (OUTLIER) cc_final: 0.7767 (tttm) REVERT: B 92 ASP cc_start: 0.7801 (t0) cc_final: 0.7578 (t0) REVERT: B 119 LYS cc_start: 0.7952 (ttmp) cc_final: 0.7636 (tttm) REVERT: C 49 LYS cc_start: 0.8084 (mttm) cc_final: 0.7586 (mmpt) REVERT: C 68 LYS cc_start: 0.7969 (OUTLIER) cc_final: 0.7767 (tttm) REVERT: C 92 ASP cc_start: 0.7803 (t0) cc_final: 0.7579 (t0) REVERT: C 119 LYS cc_start: 0.7950 (ttmp) cc_final: 0.7634 (tttm) REVERT: D 49 LYS cc_start: 0.8086 (mttm) cc_final: 0.7588 (mmpt) REVERT: D 68 LYS cc_start: 0.7968 (OUTLIER) cc_final: 0.7766 (tttm) REVERT: D 92 ASP cc_start: 0.7801 (t0) cc_final: 0.7579 (t0) REVERT: D 119 LYS cc_start: 0.7952 (ttmp) cc_final: 0.7636 (tttm) REVERT: E 49 LYS cc_start: 0.8086 (mttm) cc_final: 0.7587 (mmpt) REVERT: E 68 LYS cc_start: 0.7967 (OUTLIER) cc_final: 0.7766 (tttm) REVERT: E 92 ASP cc_start: 0.7801 (t0) cc_final: 0.7577 (t0) REVERT: E 119 LYS cc_start: 0.7955 (ttmp) cc_final: 0.7638 (tttm) REVERT: F 49 LYS cc_start: 0.8086 (mttm) cc_final: 0.7588 (mmpt) REVERT: F 68 LYS cc_start: 0.7965 (OUTLIER) cc_final: 0.7762 (tttm) REVERT: F 92 ASP cc_start: 0.7803 (t0) cc_final: 0.7580 (t0) REVERT: F 119 LYS cc_start: 0.7951 (ttmp) cc_final: 0.7635 (tttm) REVERT: G 49 LYS cc_start: 0.8086 (mttm) cc_final: 0.7583 (mmpt) REVERT: G 68 LYS cc_start: 0.7964 (OUTLIER) cc_final: 0.7762 (tttm) REVERT: G 92 ASP cc_start: 0.7802 (t0) cc_final: 0.7579 (t0) REVERT: G 119 LYS cc_start: 0.7954 (ttmp) cc_final: 0.7638 (tttm) REVERT: H 49 LYS cc_start: 0.8084 (mttm) cc_final: 0.7580 (mmpt) REVERT: H 68 LYS cc_start: 0.7963 (OUTLIER) cc_final: 0.7699 (ttmm) REVERT: H 92 ASP cc_start: 0.7803 (t0) cc_final: 0.7579 (t0) REVERT: H 119 LYS cc_start: 0.7951 (ttmp) cc_final: 0.7634 (tttm) REVERT: I 49 LYS cc_start: 0.8084 (mttm) cc_final: 0.7580 (mmpt) REVERT: I 68 LYS cc_start: 0.7966 (OUTLIER) cc_final: 0.7763 (tttm) REVERT: I 92 ASP cc_start: 0.7804 (t0) cc_final: 0.7580 (t0) REVERT: I 119 LYS cc_start: 0.7950 (ttmp) cc_final: 0.7634 (tttm) REVERT: J 49 LYS cc_start: 0.8084 (mttm) cc_final: 0.7581 (mmpt) REVERT: J 68 LYS cc_start: 0.7964 (OUTLIER) cc_final: 0.7762 (tttm) REVERT: J 92 ASP cc_start: 0.7803 (t0) cc_final: 0.7580 (t0) REVERT: J 119 LYS cc_start: 0.7951 (ttmp) cc_final: 0.7634 (tttm) REVERT: K 49 LYS cc_start: 0.8085 (mttm) cc_final: 0.7586 (mmpt) REVERT: K 68 LYS cc_start: 0.7965 (OUTLIER) cc_final: 0.7762 (tttm) REVERT: K 92 ASP cc_start: 0.7803 (t0) cc_final: 0.7580 (t0) REVERT: K 119 LYS cc_start: 0.7951 (ttmp) cc_final: 0.7634 (tttm) REVERT: L 49 LYS cc_start: 0.8087 (mttm) cc_final: 0.7588 (mmpt) REVERT: L 68 LYS cc_start: 0.7964 (OUTLIER) cc_final: 0.7762 (tttm) REVERT: L 92 ASP cc_start: 0.7802 (t0) cc_final: 0.7578 (t0) REVERT: L 119 LYS cc_start: 0.7953 (ttmp) cc_final: 0.7636 (tttm) REVERT: M 49 LYS cc_start: 0.8085 (mttm) cc_final: 0.7582 (mmpt) REVERT: M 68 LYS cc_start: 0.7969 (OUTLIER) cc_final: 0.7767 (tttm) REVERT: M 92 ASP cc_start: 0.7803 (t0) cc_final: 0.7579 (t0) REVERT: M 119 LYS cc_start: 0.7951 (ttmp) cc_final: 0.7634 (tttm) REVERT: N 49 LYS cc_start: 0.8086 (mttm) cc_final: 0.7583 (mmpt) REVERT: N 68 LYS cc_start: 0.7964 (OUTLIER) cc_final: 0.7700 (ttmm) REVERT: N 92 ASP cc_start: 0.7802 (t0) cc_final: 0.7578 (t0) REVERT: N 119 LYS cc_start: 0.7954 (ttmp) cc_final: 0.7638 (tttm) REVERT: O 49 LYS cc_start: 0.8087 (mttm) cc_final: 0.7583 (mmpt) REVERT: O 68 LYS cc_start: 0.7963 (OUTLIER) cc_final: 0.7699 (ttmm) REVERT: O 92 ASP cc_start: 0.7802 (t0) cc_final: 0.7578 (t0) REVERT: O 119 LYS cc_start: 0.7953 (ttmp) cc_final: 0.7636 (tttm) REVERT: P 49 LYS cc_start: 0.8084 (mttm) cc_final: 0.7580 (mmpt) REVERT: P 68 LYS cc_start: 0.7965 (OUTLIER) cc_final: 0.7700 (ttmm) REVERT: P 92 ASP cc_start: 0.7803 (t0) cc_final: 0.7579 (t0) REVERT: P 119 LYS cc_start: 0.7951 (ttmp) cc_final: 0.7635 (tttm) REVERT: Q 49 LYS cc_start: 0.8087 (mttm) cc_final: 0.7582 (mmpt) REVERT: Q 68 LYS cc_start: 0.7964 (OUTLIER) cc_final: 0.7701 (ttmm) REVERT: Q 92 ASP cc_start: 0.7802 (t0) cc_final: 0.7579 (t0) REVERT: Q 119 LYS cc_start: 0.7952 (ttmp) cc_final: 0.7636 (tttm) REVERT: R 49 LYS cc_start: 0.8087 (mttm) cc_final: 0.7583 (mmpt) REVERT: R 68 LYS cc_start: 0.7963 (OUTLIER) cc_final: 0.7762 (tttm) REVERT: R 92 ASP cc_start: 0.7801 (t0) cc_final: 0.7578 (t0) REVERT: R 119 LYS cc_start: 0.7952 (ttmp) cc_final: 0.7635 (tttm) REVERT: S 49 LYS cc_start: 0.8086 (mttm) cc_final: 0.7582 (mmpt) REVERT: S 68 LYS cc_start: 0.7963 (OUTLIER) cc_final: 0.7761 (tttm) REVERT: S 92 ASP cc_start: 0.7802 (t0) cc_final: 0.7578 (t0) REVERT: S 119 LYS cc_start: 0.7955 (ttmp) cc_final: 0.7639 (tttm) REVERT: T 49 LYS cc_start: 0.8087 (mttm) cc_final: 0.7583 (mmpt) REVERT: T 68 LYS cc_start: 0.7964 (OUTLIER) cc_final: 0.7762 (tttm) REVERT: T 92 ASP cc_start: 0.7802 (t0) cc_final: 0.7578 (t0) REVERT: T 119 LYS cc_start: 0.7954 (ttmp) cc_final: 0.7638 (tttm) REVERT: U 49 LYS cc_start: 0.8086 (mttm) cc_final: 0.7582 (mmpt) REVERT: U 68 LYS cc_start: 0.7965 (OUTLIER) cc_final: 0.7700 (ttmm) REVERT: U 92 ASP cc_start: 0.7803 (t0) cc_final: 0.7579 (t0) REVERT: U 119 LYS cc_start: 0.7951 (ttmp) cc_final: 0.7634 (tttm) REVERT: V 49 LYS cc_start: 0.8086 (mttm) cc_final: 0.7582 (mmpt) REVERT: V 68 LYS cc_start: 0.7962 (OUTLIER) cc_final: 0.7698 (ttmm) REVERT: V 92 ASP cc_start: 0.7801 (t0) cc_final: 0.7578 (t0) REVERT: V 119 LYS cc_start: 0.7955 (ttmp) cc_final: 0.7639 (tttm) REVERT: W 49 LYS cc_start: 0.8086 (mttm) cc_final: 0.7582 (mmpt) REVERT: W 68 LYS cc_start: 0.7965 (OUTLIER) cc_final: 0.7762 (tttm) REVERT: W 92 ASP cc_start: 0.7802 (t0) cc_final: 0.7578 (t0) REVERT: W 119 LYS cc_start: 0.7952 (ttmp) cc_final: 0.7636 (tttm) REVERT: X 49 LYS cc_start: 0.8087 (mttm) cc_final: 0.7583 (mmpt) REVERT: X 68 LYS cc_start: 0.7963 (OUTLIER) cc_final: 0.7698 (ttmm) REVERT: X 92 ASP cc_start: 0.7802 (t0) cc_final: 0.7579 (t0) REVERT: X 119 LYS cc_start: 0.7952 (ttmp) cc_final: 0.7635 (tttm) outliers start: 48 outliers final: 0 residues processed: 912 average time/residue: 1.8013 time to fit residues: 1872.7591 Evaluate side-chains 816 residues out of total 3528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 792 time to evaluate : 3.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain C residue 68 LYS Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain G residue 68 LYS Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain I residue 68 LYS Chi-restraints excluded: chain J residue 68 LYS Chi-restraints excluded: chain K residue 68 LYS Chi-restraints excluded: chain L residue 68 LYS Chi-restraints excluded: chain M residue 68 LYS Chi-restraints excluded: chain N residue 68 LYS Chi-restraints excluded: chain O residue 68 LYS Chi-restraints excluded: chain P residue 68 LYS Chi-restraints excluded: chain Q residue 68 LYS Chi-restraints excluded: chain R residue 68 LYS Chi-restraints excluded: chain S residue 68 LYS Chi-restraints excluded: chain T residue 68 LYS Chi-restraints excluded: chain U residue 68 LYS Chi-restraints excluded: chain V residue 68 LYS Chi-restraints excluded: chain W residue 68 LYS Chi-restraints excluded: chain X residue 68 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 205 optimal weight: 8.9990 chunk 114 optimal weight: 0.9980 chunk 308 optimal weight: 5.9990 chunk 252 optimal weight: 0.5980 chunk 102 optimal weight: 10.0000 chunk 371 optimal weight: 6.9990 chunk 400 optimal weight: 0.9990 chunk 330 optimal weight: 5.9990 chunk 368 optimal weight: 10.0000 chunk 126 optimal weight: 1.9990 chunk 297 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 75 GLN A 112 GLN B 14 GLN B 75 GLN B 112 GLN C 14 GLN C 75 GLN C 112 GLN D 14 GLN D 75 GLN D 112 GLN E 14 GLN E 60 HIS E 75 GLN E 112 GLN F 14 GLN F 75 GLN F 112 GLN G 14 GLN G 75 GLN G 112 GLN H 14 GLN H 75 GLN H 112 GLN I 14 GLN I 75 GLN I 112 GLN J 14 GLN J 75 GLN J 112 GLN K 14 GLN K 60 HIS K 75 GLN K 112 GLN L 14 GLN L 60 HIS L 75 GLN L 112 GLN M 14 GLN M 75 GLN M 112 GLN N 14 GLN N 60 HIS N 75 GLN N 112 GLN O 14 GLN O 60 HIS O 75 GLN O 112 GLN P 14 GLN P 75 GLN P 112 GLN Q 14 GLN Q 60 HIS Q 75 GLN Q 112 GLN R 14 GLN R 75 GLN R 112 GLN S 14 GLN S 60 HIS S 75 GLN S 112 GLN T 14 GLN T 60 HIS T 75 GLN T 112 GLN U 14 GLN U 60 HIS U 75 GLN U 112 GLN V 14 GLN V 60 HIS V 75 GLN V 112 GLN W 14 GLN W 60 HIS W 75 GLN W 112 GLN X 14 GLN X 60 HIS X 75 GLN X 112 GLN Total number of N/Q/H flips: 84 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 35616 Z= 0.162 Angle : 0.584 5.163 48072 Z= 0.317 Chirality : 0.037 0.126 4992 Planarity : 0.003 0.021 6384 Dihedral : 4.512 17.836 4848 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.64 % Allowed : 7.32 % Favored : 92.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 5.29 (0.13), residues: 4440 helix: 4.05 (0.08), residues: 3528 sheet: None (None), residues: 0 loop : 1.03 (0.25), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP P 93 HIS 0.003 0.001 HIS H 60 PHE 0.017 0.002 PHE K 41 TYR 0.016 0.002 TYR A 32 ARG 0.003 0.001 ARG T 79 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 816 residues out of total 3528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 792 time to evaluate : 3.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LYS cc_start: 0.8110 (mttm) cc_final: 0.7897 (mtpm) REVERT: A 68 LYS cc_start: 0.7934 (OUTLIER) cc_final: 0.7663 (ttmm) REVERT: A 92 ASP cc_start: 0.7848 (t0) cc_final: 0.7613 (t0) REVERT: B 49 LYS cc_start: 0.8111 (mttm) cc_final: 0.7897 (mtpm) REVERT: B 68 LYS cc_start: 0.7935 (OUTLIER) cc_final: 0.7664 (ttmm) REVERT: B 92 ASP cc_start: 0.7848 (t0) cc_final: 0.7612 (t0) REVERT: C 49 LYS cc_start: 0.8110 (mttm) cc_final: 0.7895 (mtpm) REVERT: C 68 LYS cc_start: 0.7934 (OUTLIER) cc_final: 0.7662 (ttmm) REVERT: C 92 ASP cc_start: 0.7849 (t0) cc_final: 0.7613 (t0) REVERT: D 49 LYS cc_start: 0.8109 (mttm) cc_final: 0.7895 (mtpm) REVERT: D 68 LYS cc_start: 0.7932 (OUTLIER) cc_final: 0.7661 (ttmm) REVERT: D 92 ASP cc_start: 0.7849 (t0) cc_final: 0.7613 (t0) REVERT: E 49 LYS cc_start: 0.8109 (mttm) cc_final: 0.7896 (mtpm) REVERT: E 68 LYS cc_start: 0.7932 (OUTLIER) cc_final: 0.7664 (ttmm) REVERT: E 92 ASP cc_start: 0.7848 (t0) cc_final: 0.7612 (t0) REVERT: F 49 LYS cc_start: 0.8111 (mttm) cc_final: 0.7896 (mtpm) REVERT: F 68 LYS cc_start: 0.7934 (OUTLIER) cc_final: 0.7662 (ttmm) REVERT: F 92 ASP cc_start: 0.7849 (t0) cc_final: 0.7614 (t0) REVERT: G 49 LYS cc_start: 0.8112 (mttm) cc_final: 0.7897 (mtpm) REVERT: G 68 LYS cc_start: 0.7934 (OUTLIER) cc_final: 0.7663 (ttmm) REVERT: G 92 ASP cc_start: 0.7848 (t0) cc_final: 0.7613 (t0) REVERT: H 49 LYS cc_start: 0.8109 (mttm) cc_final: 0.7896 (mtpm) REVERT: H 68 LYS cc_start: 0.7933 (OUTLIER) cc_final: 0.7662 (ttmm) REVERT: H 92 ASP cc_start: 0.7848 (t0) cc_final: 0.7612 (t0) REVERT: I 49 LYS cc_start: 0.8110 (mttm) cc_final: 0.7895 (mtpm) REVERT: I 68 LYS cc_start: 0.7934 (OUTLIER) cc_final: 0.7662 (ttmm) REVERT: I 92 ASP cc_start: 0.7851 (t0) cc_final: 0.7615 (t0) REVERT: J 49 LYS cc_start: 0.8109 (mttm) cc_final: 0.7896 (mtpm) REVERT: J 68 LYS cc_start: 0.7933 (OUTLIER) cc_final: 0.7662 (ttmm) REVERT: J 92 ASP cc_start: 0.7850 (t0) cc_final: 0.7614 (t0) REVERT: K 49 LYS cc_start: 0.8108 (mttm) cc_final: 0.7895 (mtpm) REVERT: K 68 LYS cc_start: 0.7935 (OUTLIER) cc_final: 0.7665 (ttmm) REVERT: K 92 ASP cc_start: 0.7849 (t0) cc_final: 0.7612 (t0) REVERT: L 49 LYS cc_start: 0.8109 (mttm) cc_final: 0.7896 (mtpm) REVERT: L 68 LYS cc_start: 0.7935 (OUTLIER) cc_final: 0.7665 (ttmm) REVERT: L 92 ASP cc_start: 0.7849 (t0) cc_final: 0.7613 (t0) REVERT: M 49 LYS cc_start: 0.8111 (mttm) cc_final: 0.7896 (mtpm) REVERT: M 68 LYS cc_start: 0.7934 (OUTLIER) cc_final: 0.7662 (ttmm) REVERT: M 92 ASP cc_start: 0.7848 (t0) cc_final: 0.7613 (t0) REVERT: N 49 LYS cc_start: 0.8111 (mttm) cc_final: 0.7896 (mtpm) REVERT: N 68 LYS cc_start: 0.7933 (OUTLIER) cc_final: 0.7664 (ttmm) REVERT: N 92 ASP cc_start: 0.7846 (t0) cc_final: 0.7611 (t0) REVERT: O 49 LYS cc_start: 0.8109 (mttm) cc_final: 0.7896 (mtpm) REVERT: O 68 LYS cc_start: 0.7934 (OUTLIER) cc_final: 0.7665 (ttmm) REVERT: O 92 ASP cc_start: 0.7847 (t0) cc_final: 0.7612 (t0) REVERT: P 49 LYS cc_start: 0.8110 (mttm) cc_final: 0.7895 (mtpm) REVERT: P 68 LYS cc_start: 0.7934 (OUTLIER) cc_final: 0.7662 (ttmm) REVERT: P 92 ASP cc_start: 0.7849 (t0) cc_final: 0.7613 (t0) REVERT: Q 49 LYS cc_start: 0.8111 (mttm) cc_final: 0.7896 (mtpm) REVERT: Q 68 LYS cc_start: 0.7936 (OUTLIER) cc_final: 0.7666 (ttmm) REVERT: Q 92 ASP cc_start: 0.7847 (t0) cc_final: 0.7611 (t0) REVERT: R 49 LYS cc_start: 0.8109 (mttm) cc_final: 0.7895 (mtpm) REVERT: R 68 LYS cc_start: 0.7933 (OUTLIER) cc_final: 0.7661 (ttmm) REVERT: R 92 ASP cc_start: 0.7848 (t0) cc_final: 0.7612 (t0) REVERT: S 49 LYS cc_start: 0.8110 (mttm) cc_final: 0.7896 (mtpm) REVERT: S 68 LYS cc_start: 0.7934 (OUTLIER) cc_final: 0.7665 (ttmm) REVERT: S 92 ASP cc_start: 0.7849 (t0) cc_final: 0.7612 (t0) REVERT: T 49 LYS cc_start: 0.8111 (mttm) cc_final: 0.7896 (mtpm) REVERT: T 68 LYS cc_start: 0.7935 (OUTLIER) cc_final: 0.7666 (ttmm) REVERT: T 92 ASP cc_start: 0.7846 (t0) cc_final: 0.7611 (t0) REVERT: U 49 LYS cc_start: 0.8110 (mttm) cc_final: 0.7895 (mtpm) REVERT: U 68 LYS cc_start: 0.7934 (OUTLIER) cc_final: 0.7665 (ttmm) REVERT: U 92 ASP cc_start: 0.7847 (t0) cc_final: 0.7613 (t0) REVERT: V 49 LYS cc_start: 0.8110 (mttm) cc_final: 0.7895 (mtpm) REVERT: V 68 LYS cc_start: 0.7933 (OUTLIER) cc_final: 0.7664 (ttmm) REVERT: V 92 ASP cc_start: 0.7847 (t0) cc_final: 0.7612 (t0) REVERT: W 49 LYS cc_start: 0.8111 (mttm) cc_final: 0.7896 (mtpm) REVERT: W 68 LYS cc_start: 0.7936 (OUTLIER) cc_final: 0.7666 (ttmm) REVERT: W 92 ASP cc_start: 0.7846 (t0) cc_final: 0.7611 (t0) REVERT: X 49 LYS cc_start: 0.8109 (mttm) cc_final: 0.7894 (mtpm) REVERT: X 68 LYS cc_start: 0.7934 (OUTLIER) cc_final: 0.7664 (ttmm) REVERT: X 92 ASP cc_start: 0.7849 (t0) cc_final: 0.7613 (t0) outliers start: 24 outliers final: 0 residues processed: 792 average time/residue: 1.8195 time to fit residues: 1644.5674 Evaluate side-chains 816 residues out of total 3528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 792 time to evaluate : 3.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain C residue 68 LYS Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain G residue 68 LYS Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain I residue 68 LYS Chi-restraints excluded: chain J residue 68 LYS Chi-restraints excluded: chain K residue 68 LYS Chi-restraints excluded: chain L residue 68 LYS Chi-restraints excluded: chain M residue 68 LYS Chi-restraints excluded: chain N residue 68 LYS Chi-restraints excluded: chain O residue 68 LYS Chi-restraints excluded: chain P residue 68 LYS Chi-restraints excluded: chain Q residue 68 LYS Chi-restraints excluded: chain R residue 68 LYS Chi-restraints excluded: chain S residue 68 LYS Chi-restraints excluded: chain T residue 68 LYS Chi-restraints excluded: chain U residue 68 LYS Chi-restraints excluded: chain V residue 68 LYS Chi-restraints excluded: chain W residue 68 LYS Chi-restraints excluded: chain X residue 68 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 366 optimal weight: 1.9990 chunk 279 optimal weight: 1.9990 chunk 192 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 177 optimal weight: 3.9990 chunk 249 optimal weight: 6.9990 chunk 372 optimal weight: 0.5980 chunk 394 optimal weight: 3.9990 chunk 194 optimal weight: 3.9990 chunk 353 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 112 GLN B 14 GLN B 112 GLN C 14 GLN C 112 GLN D 14 GLN D 112 GLN E 14 GLN E 60 HIS E 112 GLN F 14 GLN F 112 GLN G 14 GLN G 112 GLN H 14 GLN H 112 GLN I 14 GLN I 112 GLN J 14 GLN J 112 GLN K 14 GLN K 60 HIS K 112 GLN L 14 GLN L 60 HIS L 112 GLN M 14 GLN M 112 GLN N 14 GLN N 60 HIS N 112 GLN O 14 GLN O 60 HIS O 112 GLN P 14 GLN P 112 GLN Q 14 GLN Q 60 HIS Q 112 GLN R 14 GLN R 112 GLN S 14 GLN S 60 HIS S 112 GLN T 14 GLN T 60 HIS T 112 GLN U 14 GLN U 60 HIS U 112 GLN V 14 GLN V 60 HIS V 112 GLN W 14 GLN W 60 HIS W 112 GLN X 14 GLN X 60 HIS X 112 GLN Total number of N/Q/H flips: 60 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 35616 Z= 0.187 Angle : 0.611 5.331 48072 Z= 0.333 Chirality : 0.038 0.125 4992 Planarity : 0.004 0.021 6384 Dihedral : 4.500 17.529 4848 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.27 % Allowed : 7.32 % Favored : 91.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 5.29 (0.13), residues: 4440 helix: 4.03 (0.08), residues: 3528 sheet: None (None), residues: 0 loop : 1.10 (0.25), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP N 93 HIS 0.002 0.001 HIS K 128 PHE 0.019 0.002 PHE M 41 TYR 0.016 0.002 TYR A 137 ARG 0.003 0.001 ARG P 79 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 840 residues out of total 3528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 792 time to evaluate : 4.029 Fit side-chains REVERT: A 49 LYS cc_start: 0.8128 (mttm) cc_final: 0.7912 (mtpm) REVERT: A 92 ASP cc_start: 0.7876 (t0) cc_final: 0.7637 (t0) REVERT: A 162 GLU cc_start: 0.6612 (mp0) cc_final: 0.6353 (mm-30) REVERT: B 49 LYS cc_start: 0.8131 (mttm) cc_final: 0.7914 (mtpm) REVERT: B 92 ASP cc_start: 0.7877 (t0) cc_final: 0.7638 (t0) REVERT: B 162 GLU cc_start: 0.6612 (mp0) cc_final: 0.6354 (mm-30) REVERT: C 49 LYS cc_start: 0.8129 (mttm) cc_final: 0.7911 (mtpm) REVERT: C 92 ASP cc_start: 0.7877 (t0) cc_final: 0.7628 (t0) REVERT: C 162 GLU cc_start: 0.6611 (mp0) cc_final: 0.6353 (mm-30) REVERT: D 49 LYS cc_start: 0.8128 (mttm) cc_final: 0.7911 (mtpm) REVERT: D 92 ASP cc_start: 0.7877 (t0) cc_final: 0.7638 (t0) REVERT: D 162 GLU cc_start: 0.6611 (mp0) cc_final: 0.6352 (mm-30) REVERT: E 49 LYS cc_start: 0.8129 (mttm) cc_final: 0.7912 (mtpm) REVERT: E 62 GLU cc_start: 0.7382 (mm-30) cc_final: 0.7029 (mm-30) REVERT: E 92 ASP cc_start: 0.7876 (t0) cc_final: 0.7627 (t0) REVERT: E 162 GLU cc_start: 0.6612 (mp0) cc_final: 0.6353 (mm-30) REVERT: F 49 LYS cc_start: 0.8130 (mttm) cc_final: 0.7913 (mtpm) REVERT: F 92 ASP cc_start: 0.7877 (t0) cc_final: 0.7639 (t0) REVERT: F 162 GLU cc_start: 0.6610 (mp0) cc_final: 0.6353 (mm-30) REVERT: G 49 LYS cc_start: 0.8131 (mttm) cc_final: 0.7913 (mtpm) REVERT: G 92 ASP cc_start: 0.7876 (t0) cc_final: 0.7628 (t0) REVERT: G 162 GLU cc_start: 0.6611 (mp0) cc_final: 0.6353 (mm-30) REVERT: H 49 LYS cc_start: 0.8128 (mttm) cc_final: 0.7912 (mtpm) REVERT: H 92 ASP cc_start: 0.7876 (t0) cc_final: 0.7627 (t0) REVERT: H 162 GLU cc_start: 0.6610 (mp0) cc_final: 0.6351 (mm-30) REVERT: I 49 LYS cc_start: 0.8129 (mttm) cc_final: 0.7911 (mtpm) REVERT: I 92 ASP cc_start: 0.7878 (t0) cc_final: 0.7639 (t0) REVERT: I 162 GLU cc_start: 0.6611 (mp0) cc_final: 0.6353 (mm-30) REVERT: J 49 LYS cc_start: 0.8128 (mttm) cc_final: 0.7912 (mtpm) REVERT: J 92 ASP cc_start: 0.7878 (t0) cc_final: 0.7639 (t0) REVERT: J 162 GLU cc_start: 0.6611 (mp0) cc_final: 0.6352 (mm-30) REVERT: K 49 LYS cc_start: 0.8128 (mttm) cc_final: 0.7911 (mtpm) REVERT: K 62 GLU cc_start: 0.7384 (mm-30) cc_final: 0.7030 (mm-30) REVERT: K 92 ASP cc_start: 0.7877 (t0) cc_final: 0.7628 (t0) REVERT: K 162 GLU cc_start: 0.6611 (mp0) cc_final: 0.6351 (mm-30) REVERT: L 49 LYS cc_start: 0.8128 (mttm) cc_final: 0.7912 (mtpm) REVERT: L 62 GLU cc_start: 0.7382 (mm-30) cc_final: 0.7029 (mm-30) REVERT: L 92 ASP cc_start: 0.7877 (t0) cc_final: 0.7639 (t0) REVERT: L 162 GLU cc_start: 0.6612 (mp0) cc_final: 0.6353 (mm-30) REVERT: M 49 LYS cc_start: 0.8130 (mttm) cc_final: 0.7912 (mtpm) REVERT: M 92 ASP cc_start: 0.7876 (t0) cc_final: 0.7638 (t0) REVERT: M 162 GLU cc_start: 0.6610 (mp0) cc_final: 0.6353 (mm-30) REVERT: N 49 LYS cc_start: 0.8131 (mttm) cc_final: 0.7913 (mtpm) REVERT: N 92 ASP cc_start: 0.7875 (t0) cc_final: 0.7637 (t0) REVERT: N 162 GLU cc_start: 0.6610 (mp0) cc_final: 0.6353 (mm-30) REVERT: O 49 LYS cc_start: 0.8128 (mttm) cc_final: 0.7912 (mtpm) REVERT: O 92 ASP cc_start: 0.7876 (t0) cc_final: 0.7627 (t0) REVERT: O 162 GLU cc_start: 0.6612 (mp0) cc_final: 0.6353 (mm-30) REVERT: P 49 LYS cc_start: 0.8129 (mttm) cc_final: 0.7911 (mtpm) REVERT: P 92 ASP cc_start: 0.7876 (t0) cc_final: 0.7639 (t0) REVERT: P 162 GLU cc_start: 0.6610 (mp0) cc_final: 0.6353 (mm-30) REVERT: Q 49 LYS cc_start: 0.8131 (mttm) cc_final: 0.7913 (mtpm) REVERT: Q 62 GLU cc_start: 0.7381 (mm-30) cc_final: 0.7028 (mm-30) REVERT: Q 92 ASP cc_start: 0.7876 (t0) cc_final: 0.7637 (t0) REVERT: Q 162 GLU cc_start: 0.6612 (mp0) cc_final: 0.6354 (mm-30) REVERT: R 49 LYS cc_start: 0.8128 (mttm) cc_final: 0.7911 (mtpm) REVERT: R 92 ASP cc_start: 0.7876 (t0) cc_final: 0.7637 (t0) REVERT: R 162 GLU cc_start: 0.6610 (mp0) cc_final: 0.6352 (mm-30) REVERT: S 49 LYS cc_start: 0.8129 (mttm) cc_final: 0.7912 (mtpm) REVERT: S 62 GLU cc_start: 0.7383 (mm-30) cc_final: 0.7029 (mm-30) REVERT: S 92 ASP cc_start: 0.7876 (t0) cc_final: 0.7638 (t0) REVERT: S 162 GLU cc_start: 0.6612 (mp0) cc_final: 0.6353 (mm-30) REVERT: T 49 LYS cc_start: 0.8131 (mttm) cc_final: 0.7913 (mtpm) REVERT: T 62 GLU cc_start: 0.7385 (mm-30) cc_final: 0.7031 (mm-30) REVERT: T 92 ASP cc_start: 0.7875 (t0) cc_final: 0.7627 (t0) REVERT: T 162 GLU cc_start: 0.6610 (mp0) cc_final: 0.6353 (mm-30) REVERT: U 49 LYS cc_start: 0.8130 (mttm) cc_final: 0.7912 (mtpm) REVERT: U 62 GLU cc_start: 0.7382 (mm-30) cc_final: 0.7028 (mm-30) REVERT: U 92 ASP cc_start: 0.7876 (t0) cc_final: 0.7627 (t0) REVERT: U 162 GLU cc_start: 0.6610 (mp0) cc_final: 0.6353 (mm-30) REVERT: V 49 LYS cc_start: 0.8129 (mttm) cc_final: 0.7912 (mtpm) REVERT: V 62 GLU cc_start: 0.7381 (mm-30) cc_final: 0.7027 (mm-30) REVERT: V 92 ASP cc_start: 0.7876 (t0) cc_final: 0.7638 (t0) REVERT: V 162 GLU cc_start: 0.6612 (mp0) cc_final: 0.6353 (mm-30) REVERT: W 49 LYS cc_start: 0.8131 (mttm) cc_final: 0.7913 (mtpm) REVERT: W 62 GLU cc_start: 0.7382 (mm-30) cc_final: 0.7029 (mm-30) REVERT: W 92 ASP cc_start: 0.7876 (t0) cc_final: 0.7637 (t0) REVERT: W 162 GLU cc_start: 0.6612 (mp0) cc_final: 0.6354 (mm-30) REVERT: X 49 LYS cc_start: 0.8128 (mttm) cc_final: 0.7910 (mtpm) REVERT: X 92 ASP cc_start: 0.7877 (t0) cc_final: 0.7638 (t0) REVERT: X 162 GLU cc_start: 0.6610 (mp0) cc_final: 0.6352 (mm-30) outliers start: 48 outliers final: 0 residues processed: 816 average time/residue: 1.7803 time to fit residues: 1664.1635 Evaluate side-chains 776 residues out of total 3528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 776 time to evaluate : 3.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 10.0000 chunk 223 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 293 optimal weight: 8.9990 chunk 162 optimal weight: 1.9990 chunk 336 optimal weight: 4.9990 chunk 272 optimal weight: 0.0770 chunk 0 optimal weight: 10.0000 chunk 201 optimal weight: 20.0000 chunk 353 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 overall best weight: 2.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 60 HIS A 112 GLN B 14 GLN B 60 HIS B 112 GLN C 14 GLN C 60 HIS C 112 GLN D 14 GLN D 60 HIS D 112 GLN E 14 GLN E 112 GLN F 14 GLN F 60 HIS F 112 GLN G 14 GLN G 60 HIS G 112 GLN H 14 GLN H 60 HIS H 112 GLN I 14 GLN I 60 HIS I 112 GLN J 14 GLN J 60 HIS J 112 GLN K 14 GLN K 112 GLN L 14 GLN L 112 GLN M 14 GLN M 60 HIS M 112 GLN N 14 GLN N 112 GLN O 14 GLN O 112 GLN P 14 GLN P 60 HIS P 112 GLN Q 14 GLN Q 112 GLN R 14 GLN R 60 HIS R 112 GLN S 14 GLN S 112 GLN T 14 GLN T 112 GLN U 14 GLN U 112 GLN V 14 GLN V 112 GLN W 14 GLN W 112 GLN X 14 GLN X 112 GLN Total number of N/Q/H flips: 60 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 35616 Z= 0.222 Angle : 0.649 5.339 48072 Z= 0.355 Chirality : 0.039 0.129 4992 Planarity : 0.004 0.036 6384 Dihedral : 4.214 17.006 4752 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.64 % Allowed : 7.64 % Favored : 91.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 5.12 (0.13), residues: 4440 helix: 3.91 (0.08), residues: 3528 sheet: None (None), residues: 0 loop : 1.04 (0.25), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.004 TRP O 93 HIS 0.003 0.001 HIS J 128 PHE 0.022 0.003 PHE J 41 TYR 0.016 0.003 TYR W 137 ARG 0.010 0.001 ARG P 63 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 816 residues out of total 3528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 792 time to evaluate : 3.141 Fit side-chains REVERT: A 49 LYS cc_start: 0.8134 (mttm) cc_final: 0.7918 (mtpm) REVERT: A 62 GLU cc_start: 0.7373 (mm-30) cc_final: 0.7051 (mm-30) REVERT: A 92 ASP cc_start: 0.7891 (t0) cc_final: 0.7648 (t0) REVERT: A 162 GLU cc_start: 0.6609 (mp0) cc_final: 0.6368 (mm-30) REVERT: B 49 LYS cc_start: 0.8135 (mttm) cc_final: 0.7920 (mtpm) REVERT: B 92 ASP cc_start: 0.7890 (t0) cc_final: 0.7648 (t0) REVERT: B 162 GLU cc_start: 0.6608 (mp0) cc_final: 0.6369 (mm-30) REVERT: C 49 LYS cc_start: 0.8135 (mttm) cc_final: 0.7919 (mtpm) REVERT: C 62 GLU cc_start: 0.7393 (mm-30) cc_final: 0.7080 (mm-30) REVERT: C 92 ASP cc_start: 0.7891 (t0) cc_final: 0.7649 (t0) REVERT: C 162 GLU cc_start: 0.6608 (mp0) cc_final: 0.6368 (mm-30) REVERT: D 49 LYS cc_start: 0.8133 (mttm) cc_final: 0.7916 (mtpm) REVERT: D 92 ASP cc_start: 0.7892 (t0) cc_final: 0.7649 (t0) REVERT: D 162 GLU cc_start: 0.6607 (mp0) cc_final: 0.6367 (mm-30) REVERT: E 49 LYS cc_start: 0.8134 (mttm) cc_final: 0.7918 (mtpm) REVERT: E 62 GLU cc_start: 0.7359 (mm-30) cc_final: 0.7067 (mm-30) REVERT: E 92 ASP cc_start: 0.7891 (t0) cc_final: 0.7649 (t0) REVERT: E 162 GLU cc_start: 0.6608 (mp0) cc_final: 0.6368 (mm-30) REVERT: F 49 LYS cc_start: 0.8136 (mttm) cc_final: 0.7919 (mtpm) REVERT: F 92 ASP cc_start: 0.7892 (t0) cc_final: 0.7650 (t0) REVERT: F 162 GLU cc_start: 0.6607 (mp0) cc_final: 0.6368 (mm-30) REVERT: G 49 LYS cc_start: 0.8137 (mttm) cc_final: 0.7921 (mtpm) REVERT: G 92 ASP cc_start: 0.7889 (t0) cc_final: 0.7647 (t0) REVERT: G 162 GLU cc_start: 0.6608 (mp0) cc_final: 0.6369 (mm-30) REVERT: H 49 LYS cc_start: 0.8133 (mttm) cc_final: 0.7917 (mtpm) REVERT: H 92 ASP cc_start: 0.7892 (t0) cc_final: 0.7649 (t0) REVERT: H 162 GLU cc_start: 0.6607 (mp0) cc_final: 0.6366 (mm-30) REVERT: I 49 LYS cc_start: 0.8135 (mttm) cc_final: 0.7919 (mtpm) REVERT: I 92 ASP cc_start: 0.7891 (t0) cc_final: 0.7649 (t0) REVERT: I 162 GLU cc_start: 0.6608 (mp0) cc_final: 0.6369 (mm-30) REVERT: J 49 LYS cc_start: 0.8133 (mttm) cc_final: 0.7917 (mtpm) REVERT: J 92 ASP cc_start: 0.7892 (t0) cc_final: 0.7649 (t0) REVERT: J 162 GLU cc_start: 0.6607 (mp0) cc_final: 0.6366 (mm-30) REVERT: K 49 LYS cc_start: 0.8133 (mttm) cc_final: 0.7917 (mtpm) REVERT: K 62 GLU cc_start: 0.7355 (mm-30) cc_final: 0.7063 (mm-30) REVERT: K 92 ASP cc_start: 0.7892 (t0) cc_final: 0.7649 (t0) REVERT: K 162 GLU cc_start: 0.6607 (mp0) cc_final: 0.6366 (mm-30) REVERT: L 49 LYS cc_start: 0.8134 (mttm) cc_final: 0.7918 (mtpm) REVERT: L 62 GLU cc_start: 0.7361 (mm-30) cc_final: 0.7036 (mm-30) REVERT: L 92 ASP cc_start: 0.7891 (t0) cc_final: 0.7648 (t0) REVERT: L 162 GLU cc_start: 0.6609 (mp0) cc_final: 0.6368 (mm-30) REVERT: M 49 LYS cc_start: 0.8136 (mttm) cc_final: 0.7919 (mtpm) REVERT: M 62 GLU cc_start: 0.7378 (mm-30) cc_final: 0.7063 (mm-30) REVERT: M 92 ASP cc_start: 0.7892 (t0) cc_final: 0.7650 (t0) REVERT: M 162 GLU cc_start: 0.6607 (mp0) cc_final: 0.6367 (mm-30) REVERT: N 49 LYS cc_start: 0.8137 (mttm) cc_final: 0.7921 (mtpm) REVERT: N 62 GLU cc_start: 0.7355 (mm-30) cc_final: 0.7031 (mm-30) REVERT: N 92 ASP cc_start: 0.7889 (t0) cc_final: 0.7648 (t0) REVERT: N 162 GLU cc_start: 0.6608 (mp0) cc_final: 0.6369 (mm-30) REVERT: O 49 LYS cc_start: 0.8134 (mttm) cc_final: 0.7918 (mtpm) REVERT: O 62 GLU cc_start: 0.7364 (mm-30) cc_final: 0.7039 (mm-30) REVERT: O 92 ASP cc_start: 0.7890 (t0) cc_final: 0.7648 (t0) REVERT: O 162 GLU cc_start: 0.6609 (mp0) cc_final: 0.6368 (mm-30) REVERT: P 49 LYS cc_start: 0.8135 (mttm) cc_final: 0.7919 (mtpm) REVERT: P 92 ASP cc_start: 0.7891 (t0) cc_final: 0.7648 (t0) REVERT: P 162 GLU cc_start: 0.6608 (mp0) cc_final: 0.6368 (mm-30) REVERT: Q 49 LYS cc_start: 0.8136 (mttm) cc_final: 0.7920 (mtpm) REVERT: Q 62 GLU cc_start: 0.7360 (mm-30) cc_final: 0.7036 (mm-30) REVERT: Q 92 ASP cc_start: 0.7890 (t0) cc_final: 0.7648 (t0) REVERT: Q 162 GLU cc_start: 0.6608 (mp0) cc_final: 0.6368 (mm-30) REVERT: R 49 LYS cc_start: 0.8133 (mttm) cc_final: 0.7916 (mtpm) REVERT: R 92 ASP cc_start: 0.7892 (t0) cc_final: 0.7649 (t0) REVERT: R 162 GLU cc_start: 0.6607 (mp0) cc_final: 0.6367 (mm-30) REVERT: S 49 LYS cc_start: 0.8134 (mttm) cc_final: 0.7918 (mtpm) REVERT: S 62 GLU cc_start: 0.7361 (mm-30) cc_final: 0.7036 (mm-30) REVERT: S 92 ASP cc_start: 0.7891 (t0) cc_final: 0.7649 (t0) REVERT: S 162 GLU cc_start: 0.6608 (mp0) cc_final: 0.6368 (mm-30) REVERT: T 49 LYS cc_start: 0.8137 (mttm) cc_final: 0.7921 (mtpm) REVERT: T 62 GLU cc_start: 0.7357 (mm-30) cc_final: 0.7065 (mm-30) REVERT: T 92 ASP cc_start: 0.7889 (t0) cc_final: 0.7647 (t0) REVERT: T 162 GLU cc_start: 0.6608 (mp0) cc_final: 0.6369 (mm-30) REVERT: U 49 LYS cc_start: 0.8136 (mttm) cc_final: 0.7919 (mtpm) REVERT: U 62 GLU cc_start: 0.7362 (mm-30) cc_final: 0.7036 (mm-30) REVERT: U 92 ASP cc_start: 0.7892 (t0) cc_final: 0.7650 (t0) REVERT: U 162 GLU cc_start: 0.6607 (mp0) cc_final: 0.6367 (mm-30) REVERT: V 49 LYS cc_start: 0.8135 (mttm) cc_final: 0.7918 (mtpm) REVERT: V 62 GLU cc_start: 0.7357 (mm-30) cc_final: 0.7033 (mm-30) REVERT: V 92 ASP cc_start: 0.7891 (t0) cc_final: 0.7649 (t0) REVERT: V 162 GLU cc_start: 0.6608 (mp0) cc_final: 0.6368 (mm-30) REVERT: W 49 LYS cc_start: 0.8136 (mttm) cc_final: 0.7920 (mtpm) REVERT: W 62 GLU cc_start: 0.7359 (mm-30) cc_final: 0.7034 (mm-30) REVERT: W 92 ASP cc_start: 0.7889 (t0) cc_final: 0.7648 (t0) REVERT: W 162 GLU cc_start: 0.6608 (mp0) cc_final: 0.6369 (mm-30) REVERT: X 49 LYS cc_start: 0.8133 (mttm) cc_final: 0.7916 (mtpm) REVERT: X 62 GLU cc_start: 0.7356 (mm-30) cc_final: 0.7031 (mm-30) REVERT: X 92 ASP cc_start: 0.7892 (t0) cc_final: 0.7649 (t0) REVERT: X 162 GLU cc_start: 0.6607 (mp0) cc_final: 0.6367 (mm-30) outliers start: 24 outliers final: 24 residues processed: 816 average time/residue: 1.7247 time to fit residues: 1614.3750 Evaluate side-chains 804 residues out of total 3528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 780 time to evaluate : 3.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain F residue 91 ASP Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain H residue 91 ASP Chi-restraints excluded: chain I residue 91 ASP Chi-restraints excluded: chain J residue 91 ASP Chi-restraints excluded: chain K residue 91 ASP Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain M residue 91 ASP Chi-restraints excluded: chain N residue 91 ASP Chi-restraints excluded: chain O residue 91 ASP Chi-restraints excluded: chain P residue 91 ASP Chi-restraints excluded: chain Q residue 91 ASP Chi-restraints excluded: chain R residue 91 ASP Chi-restraints excluded: chain S residue 91 ASP Chi-restraints excluded: chain T residue 91 ASP Chi-restraints excluded: chain U residue 91 ASP Chi-restraints excluded: chain V residue 91 ASP Chi-restraints excluded: chain W residue 91 ASP Chi-restraints excluded: chain X residue 91 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 1.9990 chunk 355 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 231 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 394 optimal weight: 3.9990 chunk 327 optimal weight: 0.8980 chunk 182 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 130 optimal weight: 2.9990 chunk 207 optimal weight: 8.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 60 HIS A 112 GLN B 14 GLN B 60 HIS B 112 GLN C 14 GLN C 60 HIS C 112 GLN D 14 GLN D 60 HIS D 112 GLN E 14 GLN E 60 HIS E 112 GLN F 14 GLN F 60 HIS F 112 GLN G 14 GLN G 60 HIS G 112 GLN H 14 GLN H 60 HIS H 112 GLN I 14 GLN I 60 HIS I 112 GLN J 14 GLN J 60 HIS J 112 GLN K 14 GLN K 60 HIS K 112 GLN L 14 GLN L 60 HIS L 112 GLN M 14 GLN M 60 HIS M 112 GLN N 14 GLN N 60 HIS N 112 GLN O 14 GLN O 60 HIS O 112 GLN P 14 GLN P 60 HIS P 112 GLN Q 14 GLN Q 60 HIS Q 112 GLN R 14 GLN R 60 HIS R 112 GLN S 14 GLN S 60 HIS S 112 GLN T 14 GLN T 60 HIS T 112 GLN U 14 GLN U 60 HIS U 112 GLN V 14 GLN V 60 HIS V 112 GLN W 14 GLN W 60 HIS W 112 GLN X 14 GLN X 60 HIS X 112 GLN Total number of N/Q/H flips: 72 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 35616 Z= 0.202 Angle : 0.620 5.328 48072 Z= 0.339 Chirality : 0.038 0.128 4992 Planarity : 0.004 0.045 6384 Dihedral : 4.219 17.559 4752 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.64 % Allowed : 7.64 % Favored : 91.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 5.19 (0.13), residues: 4440 helix: 3.96 (0.08), residues: 3528 sheet: None (None), residues: 0 loop : 1.04 (0.25), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP J 93 HIS 0.003 0.001 HIS R 128 PHE 0.021 0.002 PHE O 41 TYR 0.016 0.002 TYR O 137 ARG 0.013 0.001 ARG M 63 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 792 residues out of total 3528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 768 time to evaluate : 3.379 Fit side-chains REVERT: A 49 LYS cc_start: 0.8125 (mttm) cc_final: 0.7912 (mtpm) REVERT: A 92 ASP cc_start: 0.7878 (t0) cc_final: 0.7647 (t0) REVERT: A 162 GLU cc_start: 0.6606 (mp0) cc_final: 0.6349 (mm-30) REVERT: B 49 LYS cc_start: 0.8127 (mttm) cc_final: 0.7913 (mtpm) REVERT: B 92 ASP cc_start: 0.7878 (t0) cc_final: 0.7640 (t0) REVERT: B 162 GLU cc_start: 0.6606 (mp0) cc_final: 0.6350 (mm-30) REVERT: C 49 LYS cc_start: 0.8126 (mttm) cc_final: 0.7912 (mtpm) REVERT: C 92 ASP cc_start: 0.7879 (t0) cc_final: 0.7649 (t0) REVERT: C 162 GLU cc_start: 0.6605 (mp0) cc_final: 0.6348 (mm-30) REVERT: D 49 LYS cc_start: 0.8125 (mttm) cc_final: 0.7911 (mtpm) REVERT: D 92 ASP cc_start: 0.7881 (t0) cc_final: 0.7642 (t0) REVERT: D 162 GLU cc_start: 0.6604 (mp0) cc_final: 0.6347 (mm-30) REVERT: E 49 LYS cc_start: 0.8126 (mttm) cc_final: 0.7913 (mtpm) REVERT: E 92 ASP cc_start: 0.7879 (t0) cc_final: 0.7648 (t0) REVERT: E 162 GLU cc_start: 0.6605 (mp0) cc_final: 0.6349 (mm-30) REVERT: F 49 LYS cc_start: 0.8126 (mttm) cc_final: 0.7913 (mtpm) REVERT: F 92 ASP cc_start: 0.7880 (t0) cc_final: 0.7641 (t0) REVERT: F 162 GLU cc_start: 0.6604 (mp0) cc_final: 0.6348 (mm-30) REVERT: G 49 LYS cc_start: 0.8127 (mttm) cc_final: 0.7914 (mtpm) REVERT: G 92 ASP cc_start: 0.7877 (t0) cc_final: 0.7639 (t0) REVERT: G 162 GLU cc_start: 0.6605 (mp0) cc_final: 0.6349 (mm-30) REVERT: H 49 LYS cc_start: 0.8125 (mttm) cc_final: 0.7912 (mtpm) REVERT: H 92 ASP cc_start: 0.7879 (t0) cc_final: 0.7648 (t0) REVERT: H 162 GLU cc_start: 0.6605 (mp0) cc_final: 0.6348 (mm-30) REVERT: I 49 LYS cc_start: 0.8126 (mttm) cc_final: 0.7912 (mtpm) REVERT: I 92 ASP cc_start: 0.7879 (t0) cc_final: 0.7641 (t0) REVERT: I 162 GLU cc_start: 0.6605 (mp0) cc_final: 0.6349 (mm-30) REVERT: J 49 LYS cc_start: 0.8125 (mttm) cc_final: 0.7912 (mtpm) REVERT: J 92 ASP cc_start: 0.7880 (t0) cc_final: 0.7641 (t0) REVERT: J 162 GLU cc_start: 0.6605 (mp0) cc_final: 0.6348 (mm-30) REVERT: K 49 LYS cc_start: 0.8124 (mttm) cc_final: 0.7912 (mtpm) REVERT: K 92 ASP cc_start: 0.7879 (t0) cc_final: 0.7649 (t0) REVERT: K 162 GLU cc_start: 0.6605 (mp0) cc_final: 0.6348 (mm-30) REVERT: L 49 LYS cc_start: 0.8125 (mttm) cc_final: 0.7912 (mtpm) REVERT: L 62 GLU cc_start: 0.7355 (mm-30) cc_final: 0.7036 (mm-30) REVERT: L 92 ASP cc_start: 0.7880 (t0) cc_final: 0.7641 (t0) REVERT: L 162 GLU cc_start: 0.6606 (mp0) cc_final: 0.6349 (mm-30) REVERT: M 49 LYS cc_start: 0.8126 (mttm) cc_final: 0.7912 (mtpm) REVERT: M 92 ASP cc_start: 0.7879 (t0) cc_final: 0.7649 (t0) REVERT: M 162 GLU cc_start: 0.6604 (mp0) cc_final: 0.6348 (mm-30) REVERT: N 49 LYS cc_start: 0.8127 (mttm) cc_final: 0.7914 (mtpm) REVERT: N 62 GLU cc_start: 0.7356 (mm-30) cc_final: 0.7037 (mm-30) REVERT: N 92 ASP cc_start: 0.7877 (t0) cc_final: 0.7646 (t0) REVERT: N 162 GLU cc_start: 0.6605 (mp0) cc_final: 0.6349 (mm-30) REVERT: O 49 LYS cc_start: 0.8125 (mttm) cc_final: 0.7912 (mtpm) REVERT: O 62 GLU cc_start: 0.7355 (mm-30) cc_final: 0.7036 (mm-30) REVERT: O 92 ASP cc_start: 0.7879 (t0) cc_final: 0.7640 (t0) REVERT: O 162 GLU cc_start: 0.6606 (mp0) cc_final: 0.6349 (mm-30) REVERT: P 49 LYS cc_start: 0.8126 (mttm) cc_final: 0.7912 (mtpm) REVERT: P 92 ASP cc_start: 0.7879 (t0) cc_final: 0.7649 (t0) REVERT: P 162 GLU cc_start: 0.6604 (mp0) cc_final: 0.6348 (mm-30) REVERT: Q 49 LYS cc_start: 0.8127 (mttm) cc_final: 0.7914 (mtpm) REVERT: Q 62 GLU cc_start: 0.7356 (mm-30) cc_final: 0.7038 (mm-30) REVERT: Q 92 ASP cc_start: 0.7877 (t0) cc_final: 0.7647 (t0) REVERT: Q 162 GLU cc_start: 0.6606 (mp0) cc_final: 0.6350 (mm-30) REVERT: R 49 LYS cc_start: 0.8125 (mttm) cc_final: 0.7911 (mtpm) REVERT: R 92 ASP cc_start: 0.7880 (t0) cc_final: 0.7649 (t0) REVERT: R 162 GLU cc_start: 0.6604 (mp0) cc_final: 0.6347 (mm-30) REVERT: S 49 LYS cc_start: 0.8126 (mttm) cc_final: 0.7913 (mtpm) REVERT: S 62 GLU cc_start: 0.7356 (mm-30) cc_final: 0.7037 (mm-30) REVERT: S 92 ASP cc_start: 0.7879 (t0) cc_final: 0.7640 (t0) REVERT: S 162 GLU cc_start: 0.6605 (mp0) cc_final: 0.6349 (mm-30) REVERT: T 49 LYS cc_start: 0.8128 (mttm) cc_final: 0.7914 (mtpm) REVERT: T 92 ASP cc_start: 0.7877 (t0) cc_final: 0.7639 (t0) REVERT: T 162 GLU cc_start: 0.6605 (mp0) cc_final: 0.6349 (mm-30) REVERT: U 49 LYS cc_start: 0.8126 (mttm) cc_final: 0.7913 (mtpm) REVERT: U 62 GLU cc_start: 0.7355 (mm-30) cc_final: 0.7036 (mm-30) REVERT: U 92 ASP cc_start: 0.7880 (t0) cc_final: 0.7641 (t0) REVERT: U 162 GLU cc_start: 0.6604 (mp0) cc_final: 0.6348 (mm-30) REVERT: V 49 LYS cc_start: 0.8126 (mttm) cc_final: 0.7912 (mtpm) REVERT: V 62 GLU cc_start: 0.7355 (mm-30) cc_final: 0.7036 (mm-30) REVERT: V 92 ASP cc_start: 0.7878 (t0) cc_final: 0.7648 (t0) REVERT: V 162 GLU cc_start: 0.6605 (mp0) cc_final: 0.6349 (mm-30) REVERT: W 49 LYS cc_start: 0.8127 (mttm) cc_final: 0.7913 (mtpm) REVERT: W 62 GLU cc_start: 0.7359 (mm-30) cc_final: 0.7041 (mm-30) REVERT: W 92 ASP cc_start: 0.7877 (t0) cc_final: 0.7647 (t0) REVERT: W 162 GLU cc_start: 0.6606 (mp0) cc_final: 0.6350 (mm-30) REVERT: X 49 LYS cc_start: 0.8125 (mttm) cc_final: 0.7911 (mtpm) REVERT: X 62 GLU cc_start: 0.7355 (mm-30) cc_final: 0.7035 (mm-30) REVERT: X 92 ASP cc_start: 0.7880 (t0) cc_final: 0.7649 (t0) REVERT: X 162 GLU cc_start: 0.6604 (mp0) cc_final: 0.6347 (mm-30) outliers start: 24 outliers final: 24 residues processed: 792 average time/residue: 1.7499 time to fit residues: 1586.8453 Evaluate side-chains 792 residues out of total 3528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 768 time to evaluate : 3.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain F residue 91 ASP Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain H residue 91 ASP Chi-restraints excluded: chain I residue 91 ASP Chi-restraints excluded: chain J residue 91 ASP Chi-restraints excluded: chain K residue 91 ASP Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain M residue 91 ASP Chi-restraints excluded: chain N residue 91 ASP Chi-restraints excluded: chain O residue 91 ASP Chi-restraints excluded: chain P residue 91 ASP Chi-restraints excluded: chain Q residue 91 ASP Chi-restraints excluded: chain R residue 91 ASP Chi-restraints excluded: chain S residue 91 ASP Chi-restraints excluded: chain T residue 91 ASP Chi-restraints excluded: chain U residue 91 ASP Chi-restraints excluded: chain V residue 91 ASP Chi-restraints excluded: chain W residue 91 ASP Chi-restraints excluded: chain X residue 91 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 224 optimal weight: 3.9990 chunk 288 optimal weight: 0.7980 chunk 223 optimal weight: 2.9990 chunk 332 optimal weight: 1.9990 chunk 220 optimal weight: 4.9990 chunk 393 optimal weight: 4.9990 chunk 246 optimal weight: 2.9990 chunk 239 optimal weight: 7.9990 chunk 181 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 60 HIS A 112 GLN B 14 GLN B 60 HIS B 112 GLN C 14 GLN C 60 HIS C 112 GLN D 14 GLN D 60 HIS D 112 GLN E 14 GLN E 60 HIS E 112 GLN F 14 GLN F 60 HIS F 112 GLN G 14 GLN G 60 HIS G 112 GLN H 14 GLN H 60 HIS H 112 GLN I 14 GLN I 60 HIS I 112 GLN J 14 GLN J 60 HIS J 112 GLN K 14 GLN K 60 HIS K 112 GLN L 14 GLN L 60 HIS L 112 GLN M 14 GLN M 60 HIS M 112 GLN N 14 GLN N 60 HIS N 112 GLN O 14 GLN O 60 HIS O 112 GLN P 14 GLN P 60 HIS P 112 GLN Q 14 GLN Q 60 HIS Q 112 GLN R 14 GLN R 60 HIS R 112 GLN S 14 GLN S 60 HIS S 112 GLN T 14 GLN T 60 HIS T 112 GLN U 14 GLN U 60 HIS U 112 GLN V 14 GLN V 60 HIS V 112 GLN W 14 GLN W 60 HIS W 112 GLN X 14 GLN X 60 HIS X 112 GLN Total number of N/Q/H flips: 72 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 35616 Z= 0.233 Angle : 0.662 5.614 48072 Z= 0.362 Chirality : 0.039 0.130 4992 Planarity : 0.005 0.049 6384 Dihedral : 4.224 17.085 4752 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.64 % Allowed : 7.64 % Favored : 91.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 5.05 (0.12), residues: 4440 helix: 3.86 (0.08), residues: 3528 sheet: None (None), residues: 0 loop : 1.00 (0.25), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.004 TRP S 93 HIS 0.003 0.001 HIS R 128 PHE 0.024 0.003 PHE J 41 TYR 0.017 0.003 TYR K 137 ARG 0.014 0.001 ARG C 63 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 816 residues out of total 3528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 792 time to evaluate : 3.196 Fit side-chains REVERT: A 49 LYS cc_start: 0.8130 (mttm) cc_final: 0.7915 (mtpm) REVERT: A 92 ASP cc_start: 0.7891 (t0) cc_final: 0.7659 (t0) REVERT: A 162 GLU cc_start: 0.6603 (mp0) cc_final: 0.6340 (mm-30) REVERT: B 49 LYS cc_start: 0.8132 (mttm) cc_final: 0.7917 (mtpm) REVERT: B 63 ARG cc_start: 0.7641 (ttp-170) cc_final: 0.7141 (ttt90) REVERT: B 92 ASP cc_start: 0.7892 (t0) cc_final: 0.7660 (t0) REVERT: B 162 GLU cc_start: 0.6603 (mp0) cc_final: 0.6341 (mm-30) REVERT: C 49 LYS cc_start: 0.8130 (mttm) cc_final: 0.7915 (mtpm) REVERT: C 92 ASP cc_start: 0.7891 (t0) cc_final: 0.7659 (t0) REVERT: C 162 GLU cc_start: 0.6602 (mp0) cc_final: 0.6341 (mm-30) REVERT: D 49 LYS cc_start: 0.8129 (mttm) cc_final: 0.7913 (mtpm) REVERT: D 63 ARG cc_start: 0.7641 (ttp-170) cc_final: 0.7140 (ttt90) REVERT: D 92 ASP cc_start: 0.7894 (t0) cc_final: 0.7660 (t0) REVERT: D 162 GLU cc_start: 0.6601 (mp0) cc_final: 0.6338 (mm-30) REVERT: E 49 LYS cc_start: 0.8129 (mttm) cc_final: 0.7914 (mtpm) REVERT: E 92 ASP cc_start: 0.7891 (t0) cc_final: 0.7659 (t0) REVERT: E 162 GLU cc_start: 0.6602 (mp0) cc_final: 0.6340 (mm-30) REVERT: F 49 LYS cc_start: 0.8130 (mttm) cc_final: 0.7915 (mtpm) REVERT: F 63 ARG cc_start: 0.7640 (ttp-170) cc_final: 0.7140 (ttt90) REVERT: F 92 ASP cc_start: 0.7893 (t0) cc_final: 0.7662 (t0) REVERT: F 162 GLU cc_start: 0.6601 (mp0) cc_final: 0.6339 (mm-30) REVERT: G 49 LYS cc_start: 0.8132 (mttm) cc_final: 0.7916 (mtpm) REVERT: G 63 ARG cc_start: 0.7641 (ttp-170) cc_final: 0.7140 (ttt90) REVERT: G 92 ASP cc_start: 0.7891 (t0) cc_final: 0.7659 (t0) REVERT: G 162 GLU cc_start: 0.6602 (mp0) cc_final: 0.6341 (mm-30) REVERT: H 49 LYS cc_start: 0.8129 (mttm) cc_final: 0.7914 (mtpm) REVERT: H 63 ARG cc_start: 0.7640 (ttp-170) cc_final: 0.7140 (ttt90) REVERT: H 92 ASP cc_start: 0.7893 (t0) cc_final: 0.7660 (t0) REVERT: H 162 GLU cc_start: 0.6602 (mp0) cc_final: 0.6339 (mm-30) REVERT: I 49 LYS cc_start: 0.8130 (mttm) cc_final: 0.7915 (mtpm) REVERT: I 63 ARG cc_start: 0.7640 (ttp-170) cc_final: 0.7140 (ttt90) REVERT: I 92 ASP cc_start: 0.7893 (t0) cc_final: 0.7661 (t0) REVERT: I 162 GLU cc_start: 0.6602 (mp0) cc_final: 0.6341 (mm-30) REVERT: J 49 LYS cc_start: 0.8129 (mttm) cc_final: 0.7914 (mtpm) REVERT: J 63 ARG cc_start: 0.7640 (ttp-170) cc_final: 0.7141 (ttt90) REVERT: J 92 ASP cc_start: 0.7895 (t0) cc_final: 0.7661 (t0) REVERT: J 162 GLU cc_start: 0.6602 (mp0) cc_final: 0.6339 (mm-30) REVERT: K 49 LYS cc_start: 0.8128 (mttm) cc_final: 0.7913 (mtpm) REVERT: K 92 ASP cc_start: 0.7893 (t0) cc_final: 0.7660 (t0) REVERT: K 162 GLU cc_start: 0.6602 (mp0) cc_final: 0.6339 (mm-30) REVERT: L 49 LYS cc_start: 0.8128 (mttm) cc_final: 0.7914 (mtpm) REVERT: L 92 ASP cc_start: 0.7893 (t0) cc_final: 0.7660 (t0) REVERT: L 162 GLU cc_start: 0.6603 (mp0) cc_final: 0.6340 (mm-30) REVERT: M 49 LYS cc_start: 0.8130 (mttm) cc_final: 0.7914 (mtpm) REVERT: M 92 ASP cc_start: 0.7892 (t0) cc_final: 0.7661 (t0) REVERT: M 162 GLU cc_start: 0.6600 (mp0) cc_final: 0.6339 (mm-30) REVERT: N 49 LYS cc_start: 0.8132 (mttm) cc_final: 0.7916 (mtpm) REVERT: N 92 ASP cc_start: 0.7889 (t0) cc_final: 0.7658 (t0) REVERT: N 162 GLU cc_start: 0.6602 (mp0) cc_final: 0.6341 (mm-30) REVERT: O 49 LYS cc_start: 0.8128 (mttm) cc_final: 0.7914 (mtpm) REVERT: O 92 ASP cc_start: 0.7892 (t0) cc_final: 0.7660 (t0) REVERT: O 162 GLU cc_start: 0.6603 (mp0) cc_final: 0.6340 (mm-30) REVERT: P 49 LYS cc_start: 0.8130 (mttm) cc_final: 0.7915 (mtpm) REVERT: P 63 ARG cc_start: 0.7641 (ttp-170) cc_final: 0.7139 (ttt90) REVERT: P 92 ASP cc_start: 0.7891 (t0) cc_final: 0.7659 (t0) REVERT: P 162 GLU cc_start: 0.6602 (mp0) cc_final: 0.6340 (mm-30) REVERT: Q 49 LYS cc_start: 0.8132 (mttm) cc_final: 0.7916 (mtpm) REVERT: Q 92 ASP cc_start: 0.7890 (t0) cc_final: 0.7659 (t0) REVERT: Q 162 GLU cc_start: 0.6603 (mp0) cc_final: 0.6341 (mm-30) REVERT: R 49 LYS cc_start: 0.8129 (mttm) cc_final: 0.7913 (mtpm) REVERT: R 63 ARG cc_start: 0.7640 (ttp-170) cc_final: 0.7140 (ttt90) REVERT: R 92 ASP cc_start: 0.7892 (t0) cc_final: 0.7659 (t0) REVERT: R 162 GLU cc_start: 0.6601 (mp0) cc_final: 0.6338 (mm-30) REVERT: S 49 LYS cc_start: 0.8129 (mttm) cc_final: 0.7914 (mtpm) REVERT: S 92 ASP cc_start: 0.7893 (t0) cc_final: 0.7661 (t0) REVERT: S 162 GLU cc_start: 0.6602 (mp0) cc_final: 0.6340 (mm-30) REVERT: T 49 LYS cc_start: 0.8132 (mttm) cc_final: 0.7916 (mtpm) REVERT: T 92 ASP cc_start: 0.7891 (t0) cc_final: 0.7660 (t0) REVERT: T 162 GLU cc_start: 0.6602 (mp0) cc_final: 0.6341 (mm-30) REVERT: U 49 LYS cc_start: 0.8129 (mttm) cc_final: 0.7914 (mtpm) REVERT: U 92 ASP cc_start: 0.7893 (t0) cc_final: 0.7661 (t0) REVERT: U 162 GLU cc_start: 0.6601 (mp0) cc_final: 0.6339 (mm-30) REVERT: V 49 LYS cc_start: 0.8129 (mttm) cc_final: 0.7914 (mtpm) REVERT: V 92 ASP cc_start: 0.7891 (t0) cc_final: 0.7659 (t0) REVERT: V 162 GLU cc_start: 0.6602 (mp0) cc_final: 0.6340 (mm-30) REVERT: W 49 LYS cc_start: 0.8131 (mttm) cc_final: 0.7916 (mtpm) REVERT: W 92 ASP cc_start: 0.7890 (t0) cc_final: 0.7659 (t0) REVERT: W 162 GLU cc_start: 0.6603 (mp0) cc_final: 0.6341 (mm-30) REVERT: X 49 LYS cc_start: 0.8128 (mttm) cc_final: 0.7912 (mtpm) REVERT: X 92 ASP cc_start: 0.7892 (t0) cc_final: 0.7660 (t0) REVERT: X 162 GLU cc_start: 0.6601 (mp0) cc_final: 0.6339 (mm-30) outliers start: 24 outliers final: 24 residues processed: 816 average time/residue: 1.7311 time to fit residues: 1619.8627 Evaluate side-chains 816 residues out of total 3528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 792 time to evaluate : 3.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain F residue 91 ASP Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain H residue 91 ASP Chi-restraints excluded: chain I residue 91 ASP Chi-restraints excluded: chain J residue 91 ASP Chi-restraints excluded: chain K residue 91 ASP Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain M residue 91 ASP Chi-restraints excluded: chain N residue 91 ASP Chi-restraints excluded: chain O residue 91 ASP Chi-restraints excluded: chain P residue 91 ASP Chi-restraints excluded: chain Q residue 91 ASP Chi-restraints excluded: chain R residue 91 ASP Chi-restraints excluded: chain S residue 91 ASP Chi-restraints excluded: chain T residue 91 ASP Chi-restraints excluded: chain U residue 91 ASP Chi-restraints excluded: chain V residue 91 ASP Chi-restraints excluded: chain W residue 91 ASP Chi-restraints excluded: chain X residue 91 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 6.9990 chunk 157 optimal weight: 7.9990 chunk 234 optimal weight: 0.5980 chunk 118 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 250 optimal weight: 2.9990 chunk 267 optimal weight: 6.9990 chunk 194 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 309 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 60 HIS A 112 GLN B 14 GLN B 60 HIS B 112 GLN C 14 GLN C 60 HIS C 112 GLN D 14 GLN D 60 HIS D 112 GLN E 14 GLN E 60 HIS E 112 GLN F 14 GLN F 60 HIS F 112 GLN G 14 GLN G 60 HIS G 112 GLN H 14 GLN H 60 HIS H 112 GLN I 14 GLN I 60 HIS I 112 GLN J 14 GLN J 60 HIS J 112 GLN K 14 GLN K 60 HIS K 112 GLN L 14 GLN L 60 HIS L 112 GLN M 14 GLN M 60 HIS M 112 GLN N 14 GLN N 60 HIS N 112 GLN O 14 GLN O 60 HIS O 112 GLN P 14 GLN P 60 HIS P 112 GLN Q 14 GLN Q 60 HIS Q 112 GLN R 14 GLN R 60 HIS R 112 GLN S 14 GLN S 60 HIS S 112 GLN T 14 GLN T 60 HIS T 112 GLN U 14 GLN U 60 HIS U 112 GLN V 14 GLN V 60 HIS V 112 GLN W 14 GLN W 60 HIS W 112 GLN X 14 GLN X 60 HIS X 112 GLN Total number of N/Q/H flips: 72 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 35616 Z= 0.154 Angle : 0.562 6.502 48072 Z= 0.305 Chirality : 0.037 0.130 4992 Planarity : 0.004 0.054 6384 Dihedral : 4.168 18.073 4752 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.64 % Allowed : 7.64 % Favored : 91.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 5.34 (0.13), residues: 4440 helix: 4.07 (0.08), residues: 3552 sheet: None (None), residues: 0 loop : 0.99 (0.26), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP L 93 HIS 0.003 0.001 HIS R 128 PHE 0.018 0.002 PHE X 41 TYR 0.015 0.002 TYR K 137 ARG 0.013 0.001 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 792 residues out of total 3528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 768 time to evaluate : 3.325 Fit side-chains REVERT: A 49 LYS cc_start: 0.8091 (mttm) cc_final: 0.7879 (mtpm) REVERT: A 62 GLU cc_start: 0.7304 (mm-30) cc_final: 0.7027 (mm-30) REVERT: A 92 ASP cc_start: 0.7817 (t0) cc_final: 0.7588 (t0) REVERT: A 162 GLU cc_start: 0.6646 (mp0) cc_final: 0.6371 (mm-30) REVERT: B 49 LYS cc_start: 0.8092 (mttm) cc_final: 0.7880 (mtpm) REVERT: B 63 ARG cc_start: 0.7606 (ttp-170) cc_final: 0.7121 (ttt90) REVERT: B 92 ASP cc_start: 0.7816 (t0) cc_final: 0.7587 (t0) REVERT: B 162 GLU cc_start: 0.6645 (mp0) cc_final: 0.6372 (mm-30) REVERT: C 49 LYS cc_start: 0.8092 (mttm) cc_final: 0.7880 (mtpm) REVERT: C 62 GLU cc_start: 0.7310 (mm-30) cc_final: 0.7003 (mm-30) REVERT: C 92 ASP cc_start: 0.7817 (t0) cc_final: 0.7588 (t0) REVERT: C 162 GLU cc_start: 0.6645 (mp0) cc_final: 0.6371 (mm-30) REVERT: D 49 LYS cc_start: 0.8092 (mttm) cc_final: 0.7878 (mtpm) REVERT: D 63 ARG cc_start: 0.7605 (ttp-170) cc_final: 0.7121 (ttt90) REVERT: D 92 ASP cc_start: 0.7817 (t0) cc_final: 0.7588 (t0) REVERT: D 162 GLU cc_start: 0.6645 (mp0) cc_final: 0.6371 (mm-30) REVERT: E 49 LYS cc_start: 0.8095 (mttm) cc_final: 0.7881 (mtpm) REVERT: E 92 ASP cc_start: 0.7817 (t0) cc_final: 0.7587 (t0) REVERT: E 162 GLU cc_start: 0.6646 (mp0) cc_final: 0.6371 (mm-30) REVERT: F 49 LYS cc_start: 0.8092 (mttm) cc_final: 0.7880 (mtpm) REVERT: F 63 ARG cc_start: 0.7605 (ttp-170) cc_final: 0.7120 (ttt90) REVERT: F 92 ASP cc_start: 0.7815 (t0) cc_final: 0.7586 (t0) REVERT: F 162 GLU cc_start: 0.6645 (mp0) cc_final: 0.6370 (mm-30) REVERT: G 49 LYS cc_start: 0.8093 (mttm) cc_final: 0.7881 (mtpm) REVERT: G 63 ARG cc_start: 0.7606 (ttp-170) cc_final: 0.7121 (ttt90) REVERT: G 92 ASP cc_start: 0.7814 (t0) cc_final: 0.7585 (t0) REVERT: G 162 GLU cc_start: 0.6646 (mp0) cc_final: 0.6372 (mm-30) REVERT: H 49 LYS cc_start: 0.8091 (mttm) cc_final: 0.7878 (mtpm) REVERT: H 63 ARG cc_start: 0.7605 (ttp-170) cc_final: 0.7121 (ttt90) REVERT: H 92 ASP cc_start: 0.7819 (t0) cc_final: 0.7589 (t0) REVERT: H 162 GLU cc_start: 0.6646 (mp0) cc_final: 0.6370 (mm-30) REVERT: I 49 LYS cc_start: 0.8092 (mttm) cc_final: 0.7880 (mtpm) REVERT: I 63 ARG cc_start: 0.7605 (ttp-170) cc_final: 0.7121 (ttt90) REVERT: I 92 ASP cc_start: 0.7817 (t0) cc_final: 0.7587 (t0) REVERT: I 162 GLU cc_start: 0.6645 (mp0) cc_final: 0.6371 (mm-30) REVERT: J 49 LYS cc_start: 0.8090 (mttm) cc_final: 0.7877 (mtpm) REVERT: J 63 ARG cc_start: 0.7606 (ttp-170) cc_final: 0.7122 (ttt90) REVERT: J 92 ASP cc_start: 0.7818 (t0) cc_final: 0.7588 (t0) REVERT: J 162 GLU cc_start: 0.6646 (mp0) cc_final: 0.6370 (mm-30) REVERT: K 49 LYS cc_start: 0.8093 (mttm) cc_final: 0.7880 (mtpm) REVERT: K 92 ASP cc_start: 0.7819 (t0) cc_final: 0.7589 (t0) REVERT: K 162 GLU cc_start: 0.6646 (mp0) cc_final: 0.6370 (mm-30) REVERT: L 49 LYS cc_start: 0.8094 (mttm) cc_final: 0.7881 (mtpm) REVERT: L 92 ASP cc_start: 0.7817 (t0) cc_final: 0.7587 (t0) REVERT: L 162 GLU cc_start: 0.6646 (mp0) cc_final: 0.6371 (mm-30) REVERT: M 49 LYS cc_start: 0.8092 (mttm) cc_final: 0.7880 (mtpm) REVERT: M 62 GLU cc_start: 0.7306 (mm-30) cc_final: 0.6999 (mm-30) REVERT: M 92 ASP cc_start: 0.7816 (t0) cc_final: 0.7587 (t0) REVERT: M 162 GLU cc_start: 0.6645 (mp0) cc_final: 0.6370 (mm-30) REVERT: N 49 LYS cc_start: 0.8096 (mttm) cc_final: 0.7883 (mtpm) REVERT: N 92 ASP cc_start: 0.7815 (t0) cc_final: 0.7586 (t0) REVERT: N 162 GLU cc_start: 0.6646 (mp0) cc_final: 0.6372 (mm-30) REVERT: O 49 LYS cc_start: 0.8094 (mttm) cc_final: 0.7881 (mtpm) REVERT: O 92 ASP cc_start: 0.7816 (t0) cc_final: 0.7587 (t0) REVERT: O 162 GLU cc_start: 0.6646 (mp0) cc_final: 0.6371 (mm-30) REVERT: P 49 LYS cc_start: 0.8091 (mttm) cc_final: 0.7879 (mtpm) REVERT: P 63 ARG cc_start: 0.7605 (ttp-170) cc_final: 0.7121 (ttt90) REVERT: P 92 ASP cc_start: 0.7817 (t0) cc_final: 0.7588 (t0) REVERT: P 162 GLU cc_start: 0.6644 (mp0) cc_final: 0.6371 (mm-30) REVERT: Q 49 LYS cc_start: 0.8095 (mttm) cc_final: 0.7882 (mtpm) REVERT: Q 92 ASP cc_start: 0.7816 (t0) cc_final: 0.7587 (t0) REVERT: Q 162 GLU cc_start: 0.6645 (mp0) cc_final: 0.6372 (mm-30) REVERT: R 49 LYS cc_start: 0.8092 (mttm) cc_final: 0.7879 (mtpm) REVERT: R 63 ARG cc_start: 0.7605 (ttp-170) cc_final: 0.7121 (ttt90) REVERT: R 92 ASP cc_start: 0.7817 (t0) cc_final: 0.7587 (t0) REVERT: R 162 GLU cc_start: 0.6645 (mp0) cc_final: 0.6371 (mm-30) REVERT: S 49 LYS cc_start: 0.8095 (mttm) cc_final: 0.7882 (mtpm) REVERT: S 92 ASP cc_start: 0.7816 (t0) cc_final: 0.7587 (t0) REVERT: S 162 GLU cc_start: 0.6645 (mp0) cc_final: 0.6371 (mm-30) REVERT: T 49 LYS cc_start: 0.8095 (mttm) cc_final: 0.7883 (mtpm) REVERT: T 92 ASP cc_start: 0.7814 (t0) cc_final: 0.7585 (t0) REVERT: T 162 GLU cc_start: 0.6646 (mp0) cc_final: 0.6372 (mm-30) REVERT: U 49 LYS cc_start: 0.8095 (mttm) cc_final: 0.7881 (mtpm) REVERT: U 92 ASP cc_start: 0.7815 (t0) cc_final: 0.7587 (t0) REVERT: U 162 GLU cc_start: 0.6645 (mp0) cc_final: 0.6370 (mm-30) REVERT: V 49 LYS cc_start: 0.8095 (mttm) cc_final: 0.7881 (mtpm) REVERT: V 92 ASP cc_start: 0.7817 (t0) cc_final: 0.7587 (t0) REVERT: V 162 GLU cc_start: 0.6645 (mp0) cc_final: 0.6371 (mm-30) REVERT: W 49 LYS cc_start: 0.8095 (mttm) cc_final: 0.7882 (mtpm) REVERT: W 92 ASP cc_start: 0.7816 (t0) cc_final: 0.7587 (t0) REVERT: W 162 GLU cc_start: 0.6645 (mp0) cc_final: 0.6372 (mm-30) REVERT: X 49 LYS cc_start: 0.8094 (mttm) cc_final: 0.7880 (mtpm) REVERT: X 92 ASP cc_start: 0.7817 (t0) cc_final: 0.7587 (t0) REVERT: X 162 GLU cc_start: 0.6646 (mp0) cc_final: 0.6371 (mm-30) outliers start: 24 outliers final: 24 residues processed: 792 average time/residue: 1.7621 time to fit residues: 1597.5020 Evaluate side-chains 792 residues out of total 3528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 768 time to evaluate : 3.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain F residue 91 ASP Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain H residue 91 ASP Chi-restraints excluded: chain I residue 91 ASP Chi-restraints excluded: chain J residue 91 ASP Chi-restraints excluded: chain K residue 91 ASP Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain M residue 91 ASP Chi-restraints excluded: chain N residue 91 ASP Chi-restraints excluded: chain O residue 91 ASP Chi-restraints excluded: chain P residue 91 ASP Chi-restraints excluded: chain Q residue 91 ASP Chi-restraints excluded: chain R residue 91 ASP Chi-restraints excluded: chain S residue 91 ASP Chi-restraints excluded: chain T residue 91 ASP Chi-restraints excluded: chain U residue 91 ASP Chi-restraints excluded: chain V residue 91 ASP Chi-restraints excluded: chain W residue 91 ASP Chi-restraints excluded: chain X residue 91 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 0.5980 chunk 376 optimal weight: 4.9990 chunk 343 optimal weight: 3.9990 chunk 366 optimal weight: 2.9990 chunk 220 optimal weight: 4.9990 chunk 159 optimal weight: 4.9990 chunk 287 optimal weight: 0.9990 chunk 112 optimal weight: 5.9990 chunk 331 optimal weight: 8.9990 chunk 346 optimal weight: 1.9990 chunk 365 optimal weight: 4.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 112 GLN B 14 GLN B 112 GLN C 14 GLN C 112 GLN D 14 GLN D 112 GLN E 14 GLN E 112 GLN F 14 GLN F 112 GLN G 14 GLN G 112 GLN H 14 GLN H 112 GLN I 14 GLN I 112 GLN J 14 GLN J 112 GLN K 14 GLN K 112 GLN L 14 GLN L 112 GLN M 14 GLN M 112 GLN N 14 GLN N 60 HIS N 112 GLN O 14 GLN O 60 HIS O 112 GLN P 14 GLN P 112 GLN Q 14 GLN Q 60 HIS Q 112 GLN R 14 GLN R 112 GLN S 14 GLN S 112 GLN T 14 GLN T 112 GLN U 14 GLN U 60 HIS U 112 GLN V 14 GLN V 60 HIS V 112 GLN W 14 GLN W 112 GLN X 14 GLN X 60 HIS X 112 GLN Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 35616 Z= 0.232 Angle : 0.654 5.974 48072 Z= 0.358 Chirality : 0.039 0.136 4992 Planarity : 0.005 0.059 6384 Dihedral : 4.219 17.219 4752 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.64 % Allowed : 7.64 % Favored : 91.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 5.14 (0.13), residues: 4440 helix: 3.92 (0.08), residues: 3528 sheet: None (None), residues: 0 loop : 1.04 (0.25), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.004 TRP R 93 HIS 0.003 0.001 HIS S 128 PHE 0.022 0.003 PHE I 41 TYR 0.016 0.003 TYR F 137 ARG 0.015 0.001 ARG C 63 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 816 residues out of total 3528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 792 time to evaluate : 3.258 Fit side-chains REVERT: A 49 LYS cc_start: 0.8131 (mttm) cc_final: 0.7915 (mtpm) REVERT: A 92 ASP cc_start: 0.7900 (t0) cc_final: 0.7666 (t0) REVERT: A 162 GLU cc_start: 0.6596 (mp0) cc_final: 0.6355 (mm-30) REVERT: B 49 LYS cc_start: 0.8132 (mttm) cc_final: 0.7916 (mtpm) REVERT: B 92 ASP cc_start: 0.7900 (t0) cc_final: 0.7667 (t0) REVERT: B 162 GLU cc_start: 0.6596 (mp0) cc_final: 0.6356 (mm-30) REVERT: C 49 LYS cc_start: 0.8131 (mttm) cc_final: 0.7915 (mtpm) REVERT: C 92 ASP cc_start: 0.7900 (t0) cc_final: 0.7667 (t0) REVERT: C 162 GLU cc_start: 0.6597 (mp0) cc_final: 0.6356 (mm-30) REVERT: D 49 LYS cc_start: 0.8130 (mttm) cc_final: 0.7913 (mtpm) REVERT: D 92 ASP cc_start: 0.7901 (t0) cc_final: 0.7667 (t0) REVERT: D 162 GLU cc_start: 0.6595 (mp0) cc_final: 0.6354 (mm-30) REVERT: E 49 LYS cc_start: 0.8131 (mttm) cc_final: 0.7915 (mtpm) REVERT: E 92 ASP cc_start: 0.7901 (t0) cc_final: 0.7667 (t0) REVERT: E 162 GLU cc_start: 0.6597 (mp0) cc_final: 0.6356 (mm-30) REVERT: F 49 LYS cc_start: 0.8132 (mttm) cc_final: 0.7915 (mtpm) REVERT: F 92 ASP cc_start: 0.7901 (t0) cc_final: 0.7668 (t0) REVERT: F 162 GLU cc_start: 0.6594 (mp0) cc_final: 0.6355 (mm-30) REVERT: G 49 LYS cc_start: 0.8133 (mttm) cc_final: 0.7917 (mtpm) REVERT: G 92 ASP cc_start: 0.7899 (t0) cc_final: 0.7666 (t0) REVERT: G 162 GLU cc_start: 0.6594 (mp0) cc_final: 0.6355 (mm-30) REVERT: H 49 LYS cc_start: 0.8130 (mttm) cc_final: 0.7914 (mtpm) REVERT: H 92 ASP cc_start: 0.7901 (t0) cc_final: 0.7667 (t0) REVERT: H 162 GLU cc_start: 0.6596 (mp0) cc_final: 0.6355 (mm-30) REVERT: I 49 LYS cc_start: 0.8131 (mttm) cc_final: 0.7915 (mtpm) REVERT: I 92 ASP cc_start: 0.7901 (t0) cc_final: 0.7667 (t0) REVERT: I 162 GLU cc_start: 0.6597 (mp0) cc_final: 0.6356 (mm-30) REVERT: J 49 LYS cc_start: 0.8129 (mttm) cc_final: 0.7914 (mtpm) REVERT: J 92 ASP cc_start: 0.7901 (t0) cc_final: 0.7667 (t0) REVERT: J 162 GLU cc_start: 0.6596 (mp0) cc_final: 0.6354 (mm-30) REVERT: K 49 LYS cc_start: 0.8130 (mttm) cc_final: 0.7914 (mtpm) REVERT: K 92 ASP cc_start: 0.7902 (t0) cc_final: 0.7668 (t0) REVERT: K 162 GLU cc_start: 0.6596 (mp0) cc_final: 0.6355 (mm-30) REVERT: L 49 LYS cc_start: 0.8131 (mttm) cc_final: 0.7915 (mtpm) REVERT: L 92 ASP cc_start: 0.7901 (t0) cc_final: 0.7666 (t0) REVERT: L 162 GLU cc_start: 0.6596 (mp0) cc_final: 0.6355 (mm-30) REVERT: M 49 LYS cc_start: 0.8132 (mttm) cc_final: 0.7915 (mtpm) REVERT: M 92 ASP cc_start: 0.7901 (t0) cc_final: 0.7667 (t0) REVERT: M 162 GLU cc_start: 0.6594 (mp0) cc_final: 0.6355 (mm-30) REVERT: N 49 LYS cc_start: 0.8133 (mttm) cc_final: 0.7917 (mtpm) REVERT: N 92 ASP cc_start: 0.7899 (t0) cc_final: 0.7666 (t0) REVERT: N 162 GLU cc_start: 0.6594 (mp0) cc_final: 0.6355 (mm-30) REVERT: O 49 LYS cc_start: 0.8131 (mttm) cc_final: 0.7915 (mtpm) REVERT: O 92 ASP cc_start: 0.7901 (t0) cc_final: 0.7666 (t0) REVERT: O 162 GLU cc_start: 0.6596 (mp0) cc_final: 0.6355 (mm-30) REVERT: P 49 LYS cc_start: 0.8131 (mttm) cc_final: 0.7915 (mtpm) REVERT: P 92 ASP cc_start: 0.7900 (t0) cc_final: 0.7667 (t0) REVERT: P 162 GLU cc_start: 0.6597 (mp0) cc_final: 0.6356 (mm-30) REVERT: Q 49 LYS cc_start: 0.8132 (mttm) cc_final: 0.7916 (mtpm) REVERT: Q 92 ASP cc_start: 0.7899 (t0) cc_final: 0.7666 (t0) REVERT: Q 162 GLU cc_start: 0.6596 (mp0) cc_final: 0.6356 (mm-30) REVERT: R 49 LYS cc_start: 0.8130 (mttm) cc_final: 0.7913 (mtpm) REVERT: R 92 ASP cc_start: 0.7901 (t0) cc_final: 0.7667 (t0) REVERT: R 162 GLU cc_start: 0.6595 (mp0) cc_final: 0.6354 (mm-30) REVERT: S 49 LYS cc_start: 0.8131 (mttm) cc_final: 0.7915 (mtpm) REVERT: S 92 ASP cc_start: 0.7901 (t0) cc_final: 0.7667 (t0) REVERT: S 162 GLU cc_start: 0.6597 (mp0) cc_final: 0.6356 (mm-30) REVERT: T 49 LYS cc_start: 0.8133 (mttm) cc_final: 0.7917 (mtpm) REVERT: T 92 ASP cc_start: 0.7899 (t0) cc_final: 0.7666 (t0) REVERT: T 162 GLU cc_start: 0.6595 (mp0) cc_final: 0.6355 (mm-30) REVERT: U 49 LYS cc_start: 0.8132 (mttm) cc_final: 0.7915 (mtpm) REVERT: U 92 ASP cc_start: 0.7903 (t0) cc_final: 0.7671 (t0) REVERT: U 162 GLU cc_start: 0.6594 (mp0) cc_final: 0.6355 (mm-30) REVERT: V 49 LYS cc_start: 0.8131 (mttm) cc_final: 0.7915 (mtpm) REVERT: V 92 ASP cc_start: 0.7901 (t0) cc_final: 0.7667 (t0) REVERT: V 162 GLU cc_start: 0.6597 (mp0) cc_final: 0.6356 (mm-30) REVERT: W 49 LYS cc_start: 0.8132 (mttm) cc_final: 0.7916 (mtpm) REVERT: W 92 ASP cc_start: 0.7899 (t0) cc_final: 0.7666 (t0) REVERT: W 162 GLU cc_start: 0.6596 (mp0) cc_final: 0.6356 (mm-30) REVERT: X 49 LYS cc_start: 0.8130 (mttm) cc_final: 0.7913 (mtpm) REVERT: X 92 ASP cc_start: 0.7901 (t0) cc_final: 0.7667 (t0) REVERT: X 162 GLU cc_start: 0.6595 (mp0) cc_final: 0.6354 (mm-30) outliers start: 24 outliers final: 24 residues processed: 816 average time/residue: 1.7210 time to fit residues: 1611.2504 Evaluate side-chains 810 residues out of total 3528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 786 time to evaluate : 3.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain F residue 91 ASP Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain H residue 91 ASP Chi-restraints excluded: chain I residue 91 ASP Chi-restraints excluded: chain J residue 91 ASP Chi-restraints excluded: chain K residue 91 ASP Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain M residue 91 ASP Chi-restraints excluded: chain N residue 91 ASP Chi-restraints excluded: chain O residue 91 ASP Chi-restraints excluded: chain P residue 91 ASP Chi-restraints excluded: chain Q residue 91 ASP Chi-restraints excluded: chain R residue 91 ASP Chi-restraints excluded: chain S residue 91 ASP Chi-restraints excluded: chain T residue 91 ASP Chi-restraints excluded: chain U residue 91 ASP Chi-restraints excluded: chain V residue 91 ASP Chi-restraints excluded: chain W residue 91 ASP Chi-restraints excluded: chain X residue 91 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 4.9990 chunk 387 optimal weight: 4.9990 chunk 236 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 269 optimal weight: 6.9990 chunk 406 optimal weight: 2.9990 chunk 374 optimal weight: 5.9990 chunk 323 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 250 optimal weight: 0.8980 chunk 198 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN B 14 GLN C 14 GLN D 14 GLN E 14 GLN E 60 HIS F 14 GLN G 14 GLN H 14 GLN I 14 GLN J 14 GLN K 14 GLN K 60 HIS L 14 GLN L 60 HIS M 14 GLN N 14 GLN N 60 HIS O 14 GLN O 60 HIS P 14 GLN Q 14 GLN Q 60 HIS R 14 GLN S 14 GLN S 60 HIS T 14 GLN T 60 HIS U 14 GLN U 60 HIS V 14 GLN V 60 HIS W 14 GLN W 60 HIS X 14 GLN X 60 HIS Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 35616 Z= 0.203 Angle : 0.621 6.053 48072 Z= 0.339 Chirality : 0.038 0.141 4992 Planarity : 0.004 0.056 6384 Dihedral : 4.210 17.626 4752 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.64 % Allowed : 7.64 % Favored : 91.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 5.13 (0.13), residues: 4440 helix: 3.91 (0.08), residues: 3552 sheet: None (None), residues: 0 loop : 1.01 (0.26), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.004 TRP S 93 HIS 0.003 0.001 HIS F 128 PHE 0.021 0.003 PHE P 41 TYR 0.016 0.002 TYR T 137 ARG 0.014 0.001 ARG C 63 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 792 residues out of total 3528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 768 time to evaluate : 3.194 Fit side-chains REVERT: A 49 LYS cc_start: 0.8125 (mttm) cc_final: 0.7910 (mtpm) REVERT: A 92 ASP cc_start: 0.7872 (t0) cc_final: 0.7642 (t0) REVERT: A 162 GLU cc_start: 0.6601 (mp0) cc_final: 0.6353 (mm-30) REVERT: B 49 LYS cc_start: 0.8127 (mttm) cc_final: 0.7912 (mtpm) REVERT: B 92 ASP cc_start: 0.7874 (t0) cc_final: 0.7645 (t0) REVERT: B 162 GLU cc_start: 0.6601 (mp0) cc_final: 0.6354 (mm-30) REVERT: C 49 LYS cc_start: 0.8123 (mttm) cc_final: 0.7909 (mtpm) REVERT: C 92 ASP cc_start: 0.7872 (t0) cc_final: 0.7643 (t0) REVERT: C 162 GLU cc_start: 0.6600 (mp0) cc_final: 0.6353 (mm-30) REVERT: D 49 LYS cc_start: 0.8122 (mttm) cc_final: 0.7906 (mtpm) REVERT: D 92 ASP cc_start: 0.7876 (t0) cc_final: 0.7647 (t0) REVERT: D 162 GLU cc_start: 0.6600 (mp0) cc_final: 0.6352 (mm-30) REVERT: E 49 LYS cc_start: 0.8124 (mttm) cc_final: 0.7907 (mtpm) REVERT: E 92 ASP cc_start: 0.7872 (t0) cc_final: 0.7642 (t0) REVERT: E 162 GLU cc_start: 0.6602 (mp0) cc_final: 0.6354 (mm-30) REVERT: F 49 LYS cc_start: 0.8124 (mttm) cc_final: 0.7909 (mtpm) REVERT: F 92 ASP cc_start: 0.7877 (t0) cc_final: 0.7648 (t0) REVERT: F 162 GLU cc_start: 0.6600 (mp0) cc_final: 0.6352 (mm-30) REVERT: G 49 LYS cc_start: 0.8125 (mttm) cc_final: 0.7909 (mtpm) REVERT: G 92 ASP cc_start: 0.7874 (t0) cc_final: 0.7644 (t0) REVERT: G 162 GLU cc_start: 0.6600 (mp0) cc_final: 0.6353 (mm-30) REVERT: H 49 LYS cc_start: 0.8123 (mttm) cc_final: 0.7907 (mtpm) REVERT: H 92 ASP cc_start: 0.7873 (t0) cc_final: 0.7643 (t0) REVERT: H 162 GLU cc_start: 0.6601 (mp0) cc_final: 0.6352 (mm-30) REVERT: I 49 LYS cc_start: 0.8123 (mttm) cc_final: 0.7908 (mtpm) REVERT: I 92 ASP cc_start: 0.7876 (t0) cc_final: 0.7647 (t0) REVERT: I 162 GLU cc_start: 0.6601 (mp0) cc_final: 0.6353 (mm-30) REVERT: J 49 LYS cc_start: 0.8122 (mttm) cc_final: 0.7907 (mtpm) REVERT: J 92 ASP cc_start: 0.7876 (t0) cc_final: 0.7646 (t0) REVERT: J 162 GLU cc_start: 0.6602 (mp0) cc_final: 0.6352 (mm-30) REVERT: K 49 LYS cc_start: 0.8122 (mttm) cc_final: 0.7906 (mtpm) REVERT: K 92 ASP cc_start: 0.7874 (t0) cc_final: 0.7643 (t0) REVERT: K 162 GLU cc_start: 0.6602 (mp0) cc_final: 0.6352 (mm-30) REVERT: L 49 LYS cc_start: 0.8122 (mttm) cc_final: 0.7907 (mtpm) REVERT: L 92 ASP cc_start: 0.7875 (t0) cc_final: 0.7645 (t0) REVERT: L 162 GLU cc_start: 0.6602 (mp0) cc_final: 0.6353 (mm-30) REVERT: M 49 LYS cc_start: 0.8126 (mttm) cc_final: 0.7910 (mtpm) REVERT: M 92 ASP cc_start: 0.7873 (t0) cc_final: 0.7644 (t0) REVERT: M 162 GLU cc_start: 0.6599 (mp0) cc_final: 0.6352 (mm-30) REVERT: N 49 LYS cc_start: 0.8127 (mttm) cc_final: 0.7912 (mtpm) REVERT: N 92 ASP cc_start: 0.7871 (t0) cc_final: 0.7641 (t0) REVERT: N 162 GLU cc_start: 0.6600 (mp0) cc_final: 0.6353 (mm-30) REVERT: O 49 LYS cc_start: 0.8123 (mttm) cc_final: 0.7907 (mtpm) REVERT: O 92 ASP cc_start: 0.7875 (t0) cc_final: 0.7646 (t0) REVERT: O 162 GLU cc_start: 0.6602 (mp0) cc_final: 0.6353 (mm-30) REVERT: P 49 LYS cc_start: 0.8124 (mttm) cc_final: 0.7909 (mtpm) REVERT: P 92 ASP cc_start: 0.7873 (t0) cc_final: 0.7643 (t0) REVERT: P 162 GLU cc_start: 0.6600 (mp0) cc_final: 0.6353 (mm-30) REVERT: Q 49 LYS cc_start: 0.8125 (mttm) cc_final: 0.7910 (mtpm) REVERT: Q 92 ASP cc_start: 0.7871 (t0) cc_final: 0.7641 (t0) REVERT: Q 162 GLU cc_start: 0.6601 (mp0) cc_final: 0.6354 (mm-30) REVERT: R 49 LYS cc_start: 0.8122 (mttm) cc_final: 0.7906 (mtpm) REVERT: R 92 ASP cc_start: 0.7873 (t0) cc_final: 0.7644 (t0) REVERT: R 162 GLU cc_start: 0.6600 (mp0) cc_final: 0.6352 (mm-30) REVERT: S 49 LYS cc_start: 0.8124 (mttm) cc_final: 0.7907 (mtpm) REVERT: S 92 ASP cc_start: 0.7875 (t0) cc_final: 0.7646 (t0) REVERT: S 162 GLU cc_start: 0.6601 (mp0) cc_final: 0.6353 (mm-30) REVERT: T 49 LYS cc_start: 0.8125 (mttm) cc_final: 0.7909 (mtpm) REVERT: T 92 ASP cc_start: 0.7874 (t0) cc_final: 0.7644 (t0) REVERT: T 162 GLU cc_start: 0.6600 (mp0) cc_final: 0.6353 (mm-30) REVERT: U 49 LYS cc_start: 0.8126 (mttm) cc_final: 0.7911 (mtpm) REVERT: U 92 ASP cc_start: 0.7876 (t0) cc_final: 0.7648 (t0) REVERT: U 162 GLU cc_start: 0.6600 (mp0) cc_final: 0.6352 (mm-30) REVERT: V 49 LYS cc_start: 0.8126 (mttm) cc_final: 0.7910 (mtpm) REVERT: V 92 ASP cc_start: 0.7873 (t0) cc_final: 0.7642 (t0) REVERT: V 162 GLU cc_start: 0.6601 (mp0) cc_final: 0.6353 (mm-30) REVERT: W 49 LYS cc_start: 0.8125 (mttm) cc_final: 0.7910 (mtpm) REVERT: W 92 ASP cc_start: 0.7871 (t0) cc_final: 0.7641 (t0) REVERT: W 162 GLU cc_start: 0.6601 (mp0) cc_final: 0.6354 (mm-30) REVERT: X 49 LYS cc_start: 0.8122 (mttm) cc_final: 0.7906 (mtpm) REVERT: X 92 ASP cc_start: 0.7874 (t0) cc_final: 0.7644 (t0) REVERT: X 162 GLU cc_start: 0.6600 (mp0) cc_final: 0.6352 (mm-30) outliers start: 24 outliers final: 24 residues processed: 792 average time/residue: 1.8086 time to fit residues: 1636.6831 Evaluate side-chains 780 residues out of total 3528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 756 time to evaluate : 3.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain F residue 91 ASP Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain H residue 91 ASP Chi-restraints excluded: chain I residue 91 ASP Chi-restraints excluded: chain J residue 91 ASP Chi-restraints excluded: chain K residue 91 ASP Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain M residue 91 ASP Chi-restraints excluded: chain N residue 91 ASP Chi-restraints excluded: chain O residue 91 ASP Chi-restraints excluded: chain P residue 91 ASP Chi-restraints excluded: chain Q residue 91 ASP Chi-restraints excluded: chain R residue 91 ASP Chi-restraints excluded: chain S residue 91 ASP Chi-restraints excluded: chain T residue 91 ASP Chi-restraints excluded: chain U residue 91 ASP Chi-restraints excluded: chain V residue 91 ASP Chi-restraints excluded: chain W residue 91 ASP Chi-restraints excluded: chain X residue 91 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 10.0000 chunk 344 optimal weight: 0.9980 chunk 99 optimal weight: 6.9990 chunk 298 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 89 optimal weight: 7.9990 chunk 324 optimal weight: 7.9990 chunk 135 optimal weight: 0.7980 chunk 332 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 59 optimal weight: 6.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 60 HIS B 14 GLN B 60 HIS C 14 GLN C 60 HIS D 14 GLN D 60 HIS E 14 GLN E 60 HIS F 14 GLN F 60 HIS G 14 GLN G 60 HIS H 14 GLN H 60 HIS I 14 GLN I 60 HIS J 14 GLN J 60 HIS K 14 GLN K 60 HIS L 14 GLN L 60 HIS M 14 GLN M 60 HIS N 14 GLN N 60 HIS O 14 GLN O 60 HIS P 14 GLN P 60 HIS Q 14 GLN Q 60 HIS R 14 GLN R 60 HIS S 14 GLN S 60 HIS T 14 GLN T 60 HIS U 14 GLN U 60 HIS V 14 GLN V 60 HIS W 14 GLN W 60 HIS X 14 GLN X 60 HIS Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.145750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.131261 restraints weight = 78759.293| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 0.58 r_work: 0.3002 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work: 0.2762 rms_B_bonded: 3.94 restraints_weight: 0.1250 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2685 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2685 r_free = 0.2685 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2684 r_free = 0.2684 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2684 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 35616 Z= 0.165 Angle : 0.579 6.812 48072 Z= 0.314 Chirality : 0.037 0.136 4992 Planarity : 0.004 0.056 6384 Dihedral : 4.169 17.980 4752 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.64 % Allowed : 7.64 % Favored : 91.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 5.32 (0.13), residues: 4440 helix: 4.04 (0.08), residues: 3552 sheet: None (None), residues: 0 loop : 1.03 (0.26), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP C 93 HIS 0.002 0.001 HIS R 128 PHE 0.019 0.002 PHE Q 41 TYR 0.015 0.002 TYR D 137 ARG 0.015 0.001 ARG A 63 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22083.60 seconds wall clock time: 382 minutes 7.90 seconds (22927.90 seconds total)