Starting phenix.real_space_refine on Tue Dec 12 13:54:14 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8emq_28259/12_2023/8emq_28259.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8emq_28259/12_2023/8emq_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_28259/12_2023/8emq_28259.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8emq_28259/12_2023/8emq_28259.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8emq_28259/12_2023/8emq_28259.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8emq_28259/12_2023/8emq_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: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 28.32, per 1000 atoms: 0.75 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: 14.50 Conformation dependent library (CDL) restraints added in 9.2 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: 2.02 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: 10.20 Time building geometry restraints manager: 15.59 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: 5.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.440 Construct map_model_manager: 0.020 Extract box with map and model: 21.620 Check model and map are aligned: 0.460 Set scattering table: 0.270 Process input model: 103.920 Find NCS groups from input model: 2.280 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 145.660 ------------------------------------------------------------------------------- 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 : 3.749 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 outliers start: 72 outliers final: 24 residues processed: 936 average time/residue: 1.8339 time to fit residues: 1959.3746 Evaluate side-chains 750 residues out of total 3528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 726 time to evaluate : 3.313 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 1.1685 time to fit residues: 38.6191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 0.6980 chunk 309 optimal weight: 0.8980 chunk 171 optimal weight: 0.9990 chunk 105 optimal weight: 0.9980 chunk 208 optimal weight: 0.9980 chunk 165 optimal weight: 10.0000 chunk 319 optimal weight: 0.7980 chunk 123 optimal weight: 0.9980 chunk 194 optimal weight: 2.9990 chunk 238 optimal weight: 0.9990 chunk 370 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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: 0.7892 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 35616 Z= 0.158 Angle : 0.578 5.426 48072 Z= 0.318 Chirality : 0.037 0.121 4992 Planarity : 0.003 0.022 6384 Dihedral : 4.223 17.159 4752 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.64 % Allowed : 4.30 % Favored : 95.06 % 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: 4.86 (0.12), residues: 4440 helix: 3.69 (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 0.015 0.003 TRP E 93 HIS 0.008 0.001 HIS I 60 PHE 0.016 0.002 PHE B 41 TYR 0.020 0.002 TYR A 32 ARG 0.002 0.000 ARG W 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 868 residues out of total 3528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 844 time to evaluate : 3.371 Fit side-chains outliers start: 24 outliers final: 0 residues processed: 844 average time/residue: 1.8765 time to fit residues: 1807.3676 Evaluate side-chains 756 residues out of total 3528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 756 time to evaluate : 3.297 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 308 optimal weight: 5.9990 chunk 252 optimal weight: 6.9990 chunk 102 optimal weight: 10.0000 chunk 371 optimal weight: 0.5980 chunk 400 optimal weight: 3.9990 chunk 330 optimal weight: 4.9990 chunk 368 optimal weight: 10.0000 chunk 126 optimal weight: 1.9990 chunk 297 optimal weight: 2.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- 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 75 GLN 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 75 GLN 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: 74 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 35616 Z= 0.283 Angle : 0.725 5.507 48072 Z= 0.398 Chirality : 0.041 0.131 4992 Planarity : 0.005 0.039 6384 Dihedral : 4.265 16.053 4752 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.27 % Allowed : 6.42 % Favored : 92.30 % 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: 4.90 (0.12), residues: 4440 helix: 3.74 (0.08), residues: 3528 sheet: None (None), residues: 0 loop : 1.02 (0.25), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.004 TRP I 93 HIS 0.003 0.001 HIS N 13 PHE 0.026 0.003 PHE R 41 TYR 0.021 0.004 TYR J 32 ARG 0.005 0.001 ARG I 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 792 residues out of total 3528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 744 time to evaluate : 3.393 Fit side-chains outliers start: 48 outliers final: 16 residues processed: 768 average time/residue: 1.7543 time to fit residues: 1552.5681 Evaluate side-chains 762 residues out of total 3528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 746 time to evaluate : 3.296 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 16 residues processed: 0 time to fit residues: 4.3263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 41 optimal weight: 0.7980 chunk 177 optimal weight: 1.9990 chunk 249 optimal weight: 2.9990 chunk 372 optimal weight: 9.9990 chunk 394 optimal weight: 0.1980 chunk 194 optimal weight: 1.9990 chunk 353 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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: 0.7905 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 35616 Z= 0.178 Angle : 0.587 5.112 48072 Z= 0.321 Chirality : 0.038 0.129 4992 Planarity : 0.004 0.034 6384 Dihedral : 4.231 17.638 4752 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.85 % Allowed : 7.38 % Favored : 91.77 % 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: 5.21 (0.13), residues: 4440 helix: 3.97 (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 0.014 0.003 TRP A 93 HIS 0.003 0.001 HIS E 128 PHE 0.020 0.002 PHE N 41 TYR 0.016 0.002 TYR V 137 ARG 0.003 0.001 ARG O 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 752 residues out of total 3528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 720 time to evaluate : 3.755 Fit side-chains outliers start: 32 outliers final: 24 residues processed: 744 average time/residue: 1.7982 time to fit residues: 1542.2615 Evaluate side-chains 761 residues out of total 3528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 737 time to evaluate : 3.299 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 24 residues processed: 0 time to fit residues: 4.3374 ------------------------------------------------------------------------------- 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: 7.9990 chunk 223 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 chunk 293 optimal weight: 7.9990 chunk 162 optimal weight: 1.9990 chunk 336 optimal weight: 4.9990 chunk 272 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 201 optimal weight: 7.9990 chunk 353 optimal weight: 4.9990 chunk 99 optimal weight: 0.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- 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 112 GLN O 14 GLN O 112 GLN P 14 GLN P 112 GLN Q 14 GLN 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 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: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2347 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= 0.277 Angle : 0.724 8.263 48072 Z= 0.388 Chirality : 0.040 0.133 4992 Planarity : 0.005 0.050 6384 Dihedral : 4.276 16.520 4752 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 3.63 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: 4.92 (0.12), residues: 4440 helix: 3.76 (0.08), residues: 3528 sheet: None (None), residues: 0 loop : 1.01 (0.25), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.004 TRP U 93 HIS 0.003 0.001 HIS G 128 PHE 0.025 0.003 PHE R 41 TYR 0.018 0.003 TYR Q 137 ARG 0.004 0.001 ARG H 79 *********************** 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 794 residues out of total 3528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 770 time to evaluate : 3.731 Fit side-chains outliers start: 24 outliers final: 24 residues processed: 794 average time/residue: 1.7043 time to fit residues: 1564.3098 Evaluate side-chains 790 residues out of total 3528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 766 time to evaluate : 3.343 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 2 residues processed: 22 average time/residue: 0.4211 time to fit residues: 19.6410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 77 optimal weight: 1.9990 chunk 231 optimal weight: 0.9990 chunk 97 optimal weight: 6.9990 chunk 394 optimal weight: 0.3980 chunk 327 optimal weight: 5.9990 chunk 182 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 207 optimal weight: 8.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- 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: 0.7904 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 35616 Z= 0.189 Angle : 0.604 5.266 48072 Z= 0.331 Chirality : 0.038 0.131 4992 Planarity : 0.004 0.035 6384 Dihedral : 4.234 17.748 4752 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.06 % Allowed : 7.86 % Favored : 91.08 % 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: 5.24 (0.13), residues: 4440 helix: 3.99 (0.08), residues: 3528 sheet: None (None), residues: 0 loop : 1.08 (0.25), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP L 93 HIS 0.003 0.001 HIS E 128 PHE 0.021 0.002 PHE A 41 TYR 0.016 0.002 TYR L 137 ARG 0.002 0.001 ARG O 79 *********************** 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 806 residues out of total 3528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 766 time to evaluate : 3.348 Fit side-chains outliers start: 40 outliers final: 24 residues processed: 768 average time/residue: 1.8222 time to fit residues: 1603.8583 Evaluate side-chains 748 residues out of total 3528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 724 time to evaluate : 3.332 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 22 residues processed: 2 average time/residue: 0.4048 time to fit residues: 5.6367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 288 optimal weight: 0.6980 chunk 223 optimal weight: 2.9990 chunk 332 optimal weight: 1.9990 chunk 220 optimal weight: 4.9990 chunk 393 optimal weight: 5.9990 chunk 246 optimal weight: 2.9990 chunk 239 optimal weight: 7.9990 chunk 181 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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: 0.7910 moved from start: 0.2425 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= 0.206 Angle : 0.642 7.448 48072 Z= 0.343 Chirality : 0.038 0.131 4992 Planarity : 0.004 0.038 6384 Dihedral : 4.242 17.614 4752 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.64 % Allowed : 8.28 % Favored : 91.08 % 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: 5.17 (0.13), residues: 4440 helix: 3.94 (0.08), residues: 3528 sheet: None (None), residues: 0 loop : 1.05 (0.25), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP W 93 HIS 0.003 0.001 HIS Q 128 PHE 0.022 0.002 PHE P 41 TYR 0.016 0.002 TYR N 137 ARG 0.003 0.001 ARG N 79 *********************** 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 766 residues out of total 3528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 742 time to evaluate : 3.374 Fit side-chains outliers start: 24 outliers final: 24 residues processed: 764 average time/residue: 1.8266 time to fit residues: 1603.0557 Evaluate side-chains 813 residues out of total 3528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 789 time to evaluate : 3.346 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 1 residues processed: 23 average time/residue: 0.4071 time to fit residues: 19.6772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 10.0000 chunk 157 optimal weight: 8.9990 chunk 234 optimal weight: 0.8980 chunk 118 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 250 optimal weight: 1.9990 chunk 267 optimal weight: 1.9990 chunk 194 optimal weight: 4.9990 chunk 36 optimal weight: 10.0000 chunk 309 optimal weight: 6.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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: 0.7901 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 35616 Z= 0.180 Angle : 0.588 5.146 48072 Z= 0.323 Chirality : 0.038 0.131 4992 Planarity : 0.004 0.033 6384 Dihedral : 4.227 17.918 4752 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.64 % Allowed : 8.28 % Favored : 91.08 % 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: 5.31 (0.13), residues: 4440 helix: 4.04 (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 0.016 0.003 TRP G 93 HIS 0.003 0.001 HIS N 128 PHE 0.020 0.002 PHE G 41 TYR 0.016 0.002 TYR C 137 ARG 0.002 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 771 residues out of total 3528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 747 time to evaluate : 3.329 Fit side-chains outliers start: 24 outliers final: 24 residues processed: 748 average time/residue: 1.8414 time to fit residues: 1588.6506 Evaluate side-chains 745 residues out of total 3528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 721 time to evaluate : 3.471 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 23 residues processed: 1 average time/residue: 0.4723 time to fit residues: 5.2087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 0.0050 chunk 376 optimal weight: 6.9990 chunk 343 optimal weight: 0.4980 chunk 366 optimal weight: 1.9990 chunk 220 optimal weight: 4.9990 chunk 159 optimal weight: 1.9990 chunk 287 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 chunk 331 optimal weight: 7.9990 chunk 346 optimal weight: 1.9990 chunk 365 optimal weight: 2.9990 overall best weight: 1.3000 ------------------------------------------------------------------------------- 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: 0.7902 moved from start: 0.2448 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= 0.182 Angle : 0.615 7.420 48072 Z= 0.327 Chirality : 0.038 0.131 4992 Planarity : 0.004 0.033 6384 Dihedral : 4.197 17.888 4752 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.64 % Allowed : 8.28 % Favored : 91.08 % 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: 5.31 (0.13), residues: 4440 helix: 4.05 (0.08), residues: 3528 sheet: None (None), residues: 0 loop : 1.09 (0.25), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP P 93 HIS 0.003 0.001 HIS O 128 PHE 0.020 0.002 PHE G 41 TYR 0.016 0.002 TYR G 137 ARG 0.002 0.001 ARG T 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 747 residues out of total 3528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 723 time to evaluate : 3.718 Fit side-chains outliers start: 24 outliers final: 23 residues processed: 746 average time/residue: 1.8363 time to fit residues: 1578.0584 Evaluate side-chains 791 residues out of total 3528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 768 time to evaluate : 3.398 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.5195 time to fit residues: 24.3079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 6.9990 chunk 387 optimal weight: 1.9990 chunk 236 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 chunk 269 optimal weight: 0.9990 chunk 406 optimal weight: 7.9990 chunk 374 optimal weight: 0.7980 chunk 323 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 250 optimal weight: 1.9990 chunk 198 optimal weight: 1.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- 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: 0.7901 moved from start: 0.2493 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= 0.185 Angle : 0.600 5.208 48072 Z= 0.327 Chirality : 0.038 0.133 4992 Planarity : 0.004 0.034 6384 Dihedral : 4.192 17.867 4752 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.64 % Allowed : 8.28 % Favored : 91.08 % 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: 5.30 (0.13), residues: 4440 helix: 4.04 (0.08), residues: 3528 sheet: None (None), residues: 0 loop : 1.07 (0.25), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP G 93 HIS 0.003 0.001 HIS H 128 PHE 0.020 0.002 PHE K 41 TYR 0.016 0.002 TYR G 137 ARG 0.002 0.001 ARG L 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 791 residues out of total 3528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 767 time to evaluate : 3.422 Fit side-chains outliers start: 24 outliers final: 22 residues processed: 768 average time/residue: 1.8563 time to fit residues: 1637.8795 Evaluate side-chains 767 residues out of total 3528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 745 time to evaluate : 3.406 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 21 residues processed: 1 average time/residue: 0.4222 time to fit residues: 5.0562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 9.9990 chunk 344 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 chunk 298 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 324 optimal weight: 7.9990 chunk 135 optimal weight: 2.9990 chunk 332 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.145648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.129304 restraints weight = 86676.631| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 0.65 r_work: 0.3015 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work: 0.2749 rms_B_bonded: 3.86 restraints_weight: 0.1250 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2681 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2681 r_free = 0.2681 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 = 0.2680 r_free = 0.2680 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2680 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 35616 Z= 0.178 Angle : 0.585 5.191 48072 Z= 0.321 Chirality : 0.038 0.134 4992 Planarity : 0.004 0.033 6384 Dihedral : 4.192 17.915 4752 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 3.66 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: 5.31 (0.13), residues: 4440 helix: 4.05 (0.08), residues: 3528 sheet: None (None), residues: 0 loop : 1.09 (0.25), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP A 93 HIS 0.003 0.001 HIS L 128 PHE 0.020 0.002 PHE T 41 TYR 0.016 0.002 TYR Q 137 ARG 0.002 0.001 ARG W 63 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22077.54 seconds wall clock time: 382 minutes 44.01 seconds (22964.01 seconds total)