Starting phenix.real_space_refine on Tue Dec 12 14:47:19 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8en7_28269/12_2023/8en7_28269.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8en7_28269/12_2023/8en7_28269.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8en7_28269/12_2023/8en7_28269.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8en7_28269/12_2023/8en7_28269.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8en7_28269/12_2023/8en7_28269.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8en7_28269/12_2023/8en7_28269.pdb" } resolution = 1.68 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= 0.008 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 35064 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: 5 Type Number sf(0) Gaussians Fe 6 7.16 5 S 192 5.16 5 C 21960 2.51 5 N 6168 2.21 5 O 9288 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 63": "NH1" <-> "NH2" Residue "A ARG 90": "NH1" <-> "NH2" 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 63": "NH1" <-> "NH2" Residue "B ARG 90": "NH1" <-> "NH2" 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 63": "NH1" <-> "NH2" Residue "C ARG 90": "NH1" <-> "NH2" 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 63": "NH1" <-> "NH2" Residue "D ARG 90": "NH1" <-> "NH2" 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 63": "NH1" <-> "NH2" Residue "E ARG 90": "NH1" <-> "NH2" 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 63": "NH1" <-> "NH2" Residue "F ARG 90": "NH1" <-> "NH2" 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 63": "NH1" <-> "NH2" Residue "G ARG 90": "NH1" <-> "NH2" 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 63": "NH1" <-> "NH2" Residue "H ARG 90": "NH1" <-> "NH2" 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 63": "NH1" <-> "NH2" Residue "I ARG 90": "NH1" <-> "NH2" 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 63": "NH1" <-> "NH2" Residue "J ARG 90": "NH1" <-> "NH2" 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 63": "NH1" <-> "NH2" Residue "K ARG 90": "NH1" <-> "NH2" 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 63": "NH1" <-> "NH2" Residue "L ARG 90": "NH1" <-> "NH2" 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 63": "NH1" <-> "NH2" Residue "M ARG 90": "NH1" <-> "NH2" 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 63": "NH1" <-> "NH2" Residue "N ARG 90": "NH1" <-> "NH2" 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 63": "NH1" <-> "NH2" Residue "O ARG 90": "NH1" <-> "NH2" 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 63": "NH1" <-> "NH2" Residue "P ARG 90": "NH1" <-> "NH2" 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 63": "NH1" <-> "NH2" Residue "Q ARG 90": "NH1" <-> "NH2" 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 63": "NH1" <-> "NH2" Residue "R ARG 90": "NH1" <-> "NH2" 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 63": "NH1" <-> "NH2" Residue "S ARG 90": "NH1" <-> "NH2" 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 63": "NH1" <-> "NH2" Residue "T ARG 90": "NH1" <-> "NH2" 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 63": "NH1" <-> "NH2" Residue "U ARG 90": "NH1" <-> "NH2" 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 63": "NH1" <-> "NH2" Residue "V ARG 90": "NH1" <-> "NH2" 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 63": "NH1" <-> "NH2" Residue "W ARG 90": "NH1" <-> "NH2" 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 63": "NH1" <-> "NH2" Residue "X ARG 90": "NH1" <-> "NH2" Residue "X GLU 140": "OE1" <-> "OE2" Residue "X GLU 147": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 37614 Number of models: 1 Model: "" Number of chains: 54 Chain: "A" Number of atoms: 1461 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: 1381 Chain: "B" Number of atoms: 1461 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: 1381 Chain: "C" Number of atoms: 1461 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: 1381 Chain: "D" Number of atoms: 1461 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: 1381 Chain: "E" Number of atoms: 1461 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: 1381 Chain: "F" Number of atoms: 1461 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: 1381 Chain: "G" Number of atoms: 1461 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: 1381 Chain: "H" Number of atoms: 1461 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: 1381 Chain: "I" Number of atoms: 1461 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: 1381 Chain: "J" Number of atoms: 1461 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: 1381 Chain: "K" Number of atoms: 1461 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: 1381 Chain: "L" Number of atoms: 1461 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: 1381 Chain: "M" Number of atoms: 1461 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: 1381 Chain: "N" Number of atoms: 1461 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: 1381 Chain: "O" Number of atoms: 1461 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: 1381 Chain: "P" Number of atoms: 1461 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: 1381 Chain: "Q" Number of atoms: 1461 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: 1381 Chain: "R" Number of atoms: 1461 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: 1381 Chain: "S" Number of atoms: 1461 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: 1381 Chain: "T" Number of atoms: 1461 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: 1381 Chain: "U" Number of atoms: 1461 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: 1381 Chain: "V" Number of atoms: 1461 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: 1381 Chain: "W" Number of atoms: 1461 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: 1381 Chain: "X" Number of atoms: 1461 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: 1381 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "B" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 107 Classifications: {'water': 107} Link IDs: {None: 106} Chain: "C" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "D" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "E" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "F" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "G" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "H" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "I" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "J" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "K" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 105 Classifications: {'water': 105} Link IDs: {None: 104} Chain: "L" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "M" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "N" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "O" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "P" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "Q" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "R" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "S" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "T" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "U" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "V" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "W" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "X" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Residues with excluded nonbonded symmetry interactions: 150 residue: pdb=" N AARG A 63 " occ=0.47 ... (20 atoms not shown) pdb=" NH2BARG A 63 " occ=0.53 residue: pdb=" N AGLU A 64 " occ=0.47 ... (16 atoms not shown) pdb=" OE2BGLU A 64 " occ=0.53 residue: pdb=" N AGLU A 94 " occ=0.59 ... (16 atoms not shown) pdb=" OE2BGLU A 94 " occ=0.41 residue: pdb=" N AILE A 133 " occ=0.60 ... (14 atoms not shown) pdb=" CD1BILE A 133 " occ=0.40 residue: pdb=" N ASER A 144 " occ=0.56 ... (10 atoms not shown) pdb=" OG BSER A 144 " occ=0.44 residue: pdb=" N ALYS A 172 " occ=0.55 ... (16 atoms not shown) pdb=" NZ BLYS A 172 " occ=0.45 residue: pdb=" N AARG B 63 " occ=0.48 ... (20 atoms not shown) pdb=" NH2BARG B 63 " occ=0.52 residue: pdb=" N AGLU B 64 " occ=0.48 ... (16 atoms not shown) pdb=" OE2BGLU B 64 " occ=0.52 residue: pdb=" N AGLU B 94 " occ=0.59 ... (16 atoms not shown) pdb=" OE2BGLU B 94 " occ=0.41 residue: pdb=" N AILE B 133 " occ=0.59 ... (14 atoms not shown) pdb=" CD1BILE B 133 " occ=0.41 residue: pdb=" N ASER B 144 " occ=0.56 ... (10 atoms not shown) pdb=" OG BSER B 144 " occ=0.44 residue: pdb=" N ALYS B 172 " occ=0.55 ... (16 atoms not shown) pdb=" NZ BLYS B 172 " occ=0.45 ... (remaining 138 not shown) Time building chain proxies: 26.01, per 1000 atoms: 0.69 Number of scatterers: 37614 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: 5 Type Number sf(0) Fe 6 26.01 S 192 16.00 O 9288 8.00 N 6168 7.00 C 21960 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.98 Conformation dependent library (CDL) restraints added in 9.0 seconds 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8208 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: 2.13 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: 4.248A 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) 2832 hydrogen bonds defined for protein. 8592 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: 9.83 Time building geometry restraints manager: 14.91 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: 8612 1.33 - 1.45: 8980 1.45 - 1.58: 17976 1.58 - 1.71: 0 1.71 - 1.83: 312 Bond restraints: 35880 Sorted by residual: bond pdb=" C BGLU G 64 " pdb=" N HIS G 65 " ideal model delta sigma weight residual 1.335 1.562 -0.227 1.31e-02 5.83e+03 3.01e+02 bond pdb=" C BGLU F 64 " pdb=" N HIS F 65 " ideal model delta sigma weight residual 1.335 1.562 -0.227 1.31e-02 5.83e+03 3.01e+02 bond pdb=" C BGLU X 64 " pdb=" N HIS X 65 " ideal model delta sigma weight residual 1.335 1.562 -0.227 1.31e-02 5.83e+03 3.01e+02 bond pdb=" C BGLU L 64 " pdb=" N HIS L 65 " ideal model delta sigma weight residual 1.335 1.562 -0.227 1.31e-02 5.83e+03 3.01e+02 bond pdb=" C BGLU V 64 " pdb=" N HIS V 65 " ideal model delta sigma weight residual 1.335 1.562 -0.227 1.31e-02 5.83e+03 3.01e+02 ... (remaining 35875 not shown) Histogram of bond angle deviations from ideal: 97.45 - 104.77: 456 104.77 - 112.09: 15722 112.09 - 119.42: 14439 119.42 - 126.74: 17479 126.74 - 134.06: 312 Bond angle restraints: 48408 Sorted by residual: angle pdb=" CB GLU X 167 " pdb=" CG GLU X 167 " pdb=" CD GLU X 167 " ideal model delta sigma weight residual 112.60 123.27 -10.67 1.70e+00 3.46e-01 3.94e+01 angle pdb=" CB GLU W 167 " pdb=" CG GLU W 167 " pdb=" CD GLU W 167 " ideal model delta sigma weight residual 112.60 123.27 -10.67 1.70e+00 3.46e-01 3.94e+01 angle pdb=" CB GLU I 167 " pdb=" CG GLU I 167 " pdb=" CD GLU I 167 " ideal model delta sigma weight residual 112.60 123.27 -10.67 1.70e+00 3.46e-01 3.94e+01 angle pdb=" CB GLU U 167 " pdb=" CG GLU U 167 " pdb=" CD GLU U 167 " ideal model delta sigma weight residual 112.60 123.27 -10.67 1.70e+00 3.46e-01 3.94e+01 angle pdb=" CB GLU P 167 " pdb=" CG GLU P 167 " pdb=" CD GLU P 167 " ideal model delta sigma weight residual 112.60 123.27 -10.67 1.70e+00 3.46e-01 3.94e+01 ... (remaining 48403 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 21527 35.99 - 71.97: 361 71.97 - 107.96: 72 107.96 - 143.94: 0 143.94 - 179.93: 24 Dihedral angle restraints: 21984 sinusoidal: 9192 harmonic: 12792 Sorted by residual: dihedral pdb=" CD BARG A 63 " pdb=" NE BARG A 63 " pdb=" CZ BARG A 63 " pdb=" NH1BARG A 63 " ideal model delta sinusoidal sigma weight residual 0.00 -179.93 179.93 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CD BARG B 63 " pdb=" NE BARG B 63 " pdb=" CZ BARG B 63 " pdb=" NH1BARG B 63 " ideal model delta sinusoidal sigma weight residual 0.00 -179.93 179.93 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CD BARG D 63 " pdb=" NE BARG D 63 " pdb=" CZ BARG D 63 " pdb=" NH1BARG D 63 " ideal model delta sinusoidal sigma weight residual 0.00 -179.93 179.93 1 1.00e+01 1.00e-02 1.92e+02 ... (remaining 21981 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 3361 0.068 - 0.135: 1414 0.135 - 0.203: 144 0.203 - 0.270: 73 0.270 - 0.338: 24 Chirality restraints: 5016 Sorted by residual: chirality pdb=" CB VAL C 8 " pdb=" CA VAL C 8 " pdb=" CG1 VAL C 8 " pdb=" CG2 VAL C 8 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.85e+00 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 ... (remaining 5013 not shown) Planarity restraints: 6432 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 137 " 0.092 2.00e-02 2.50e+03 4.94e-02 4.88e+01 pdb=" CG TYR C 137 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR C 137 " -0.058 2.00e-02 2.50e+03 pdb=" CD2 TYR C 137 " -0.030 2.00e-02 2.50e+03 pdb=" CE1 TYR C 137 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR C 137 " -0.034 2.00e-02 2.50e+03 pdb=" CZ TYR C 137 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR C 137 " 0.066 2.00e-02 2.50e+03 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 ... (remaining 6429 not shown) Histogram of nonbonded interaction distances: 0.73 - 1.57: 95 1.57 - 2.40: 376 2.40 - 3.23: 42158 3.23 - 4.07: 123097 4.07 - 4.90: 210013 Warning: very small nonbonded interaction distances. Nonbonded interactions: 375739 Sorted by model distance: nonbonded pdb=" NH2AARG C 63 " pdb=" NH2AARG E 63 " model vdw 0.731 3.200 nonbonded pdb=" NH2AARG G 63 " pdb=" NH2AARG U 63 " model vdw 0.733 3.200 nonbonded pdb=" NH2AARG A 63 " pdb=" NH2AARG K 63 " model vdw 0.733 3.200 nonbonded pdb=" NH2AARG D 63 " pdb=" NH2AARG Q 63 " model vdw 0.733 3.200 nonbonded pdb=" NH2AARG F 63 " pdb=" NH2AARG N 63 " model vdw 0.733 3.200 ... (remaining 375734 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 62 or resid 65 through 93 or resid 95 through 13 \ 2 or resid 134 through 143 or resid 145 through 171 or resid 173 through 176)) selection = (chain 'B' and (resid 5 through 62 or resid 65 through 93 or resid 95 through 13 \ 2 or resid 134 through 143 or resid 145 through 171 or resid 173 through 176)) selection = (chain 'C' and (resid 5 through 62 or resid 65 through 93 or resid 95 through 13 \ 2 or resid 134 through 143 or resid 145 through 171 or resid 173 through 176)) selection = (chain 'D' and (resid 5 through 62 or resid 65 through 93 or resid 95 through 13 \ 2 or resid 134 through 143 or resid 145 through 171 or resid 173 through 176)) selection = (chain 'E' and (resid 5 through 62 or resid 65 through 93 or resid 95 through 13 \ 2 or resid 134 through 143 or resid 145 through 171 or resid 173 through 176)) selection = (chain 'F' and (resid 5 through 62 or resid 65 through 93 or resid 95 through 13 \ 2 or resid 134 through 143 or resid 145 through 171 or resid 173 through 176)) selection = (chain 'G' and (resid 5 through 62 or resid 65 through 93 or resid 95 through 13 \ 2 or resid 134 through 143 or resid 145 through 171 or resid 173 through 176)) selection = (chain 'H' and (resid 5 through 62 or resid 65 through 93 or resid 95 through 13 \ 2 or resid 134 through 143 or resid 145 through 171 or resid 173 through 176)) selection = (chain 'I' and (resid 5 through 62 or resid 65 through 93 or resid 95 through 13 \ 2 or resid 134 through 143 or resid 145 through 171 or resid 173 through 176)) selection = (chain 'J' and (resid 5 through 62 or resid 65 through 93 or resid 95 through 13 \ 2 or resid 134 through 143 or resid 145 through 171 or resid 173 through 176)) selection = (chain 'K' and (resid 5 through 62 or resid 65 through 93 or resid 95 through 13 \ 2 or resid 134 through 143 or resid 145 through 171 or resid 173 through 176)) selection = (chain 'L' and (resid 5 through 62 or resid 65 through 93 or resid 95 through 13 \ 2 or resid 134 through 143 or resid 145 through 171 or resid 173 through 176)) selection = (chain 'M' and (resid 5 through 62 or resid 65 through 93 or resid 95 through 13 \ 2 or resid 134 through 143 or resid 145 through 171 or resid 173 through 176)) selection = (chain 'N' and (resid 5 through 62 or resid 65 through 93 or resid 95 through 13 \ 2 or resid 134 through 143 or resid 145 through 171 or resid 173 through 176)) selection = (chain 'O' and (resid 5 through 62 or resid 65 through 93 or resid 95 through 13 \ 2 or resid 134 through 143 or resid 145 through 171 or resid 173 through 176)) selection = (chain 'P' and (resid 5 through 62 or resid 65 through 93 or resid 95 through 13 \ 2 or resid 134 through 143 or resid 145 through 171 or resid 173 through 176)) selection = (chain 'Q' and (resid 5 through 62 or resid 65 through 93 or resid 95 through 13 \ 2 or resid 134 through 143 or resid 145 through 171 or resid 173 through 176)) selection = (chain 'R' and (resid 5 through 62 or resid 65 through 93 or resid 95 through 13 \ 2 or resid 134 through 143 or resid 145 through 171 or resid 173 through 176)) selection = (chain 'S' and (resid 5 through 62 or resid 65 through 93 or resid 95 through 13 \ 2 or resid 134 through 143 or resid 145 through 171 or resid 173 through 176)) selection = (chain 'T' and (resid 5 through 62 or resid 65 through 93 or resid 95 through 13 \ 2 or resid 134 through 143 or resid 145 through 171 or resid 173 through 176)) selection = (chain 'U' and (resid 5 through 62 or resid 65 through 93 or resid 95 through 13 \ 2 or resid 134 through 143 or resid 145 through 171 or resid 173 through 176)) selection = (chain 'V' and (resid 5 through 62 or resid 65 through 93 or resid 95 through 13 \ 2 or resid 134 through 143 or resid 145 through 171 or resid 173 through 176)) selection = (chain 'W' and (resid 5 through 62 or resid 65 through 93 or resid 95 through 13 \ 2 or resid 134 through 143 or resid 145 through 171 or resid 173 through 176)) selection = (chain 'X' and (resid 5 through 62 or resid 65 through 93 or resid 95 through 13 \ 2 or resid 134 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=0.16 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: 5.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.340 Construct map_model_manager: 0.030 Extract box with map and model: 21.460 Check model and map are aligned: 0.420 Set scattering table: 0.270 Process input model: 93.410 Find NCS groups from input model: 2.260 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 134.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 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 : 0.012 0.227 35880 Z= 0.779 Angle : 1.294 13.854 48408 Z= 0.863 Chirality : 0.072 0.338 5016 Planarity : 0.009 0.049 6432 Dihedral : 15.669 179.927 13776 Min Nonbonded Distance : 0.731 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.27 % Allowed : 5.09 % Favored : 93.64 % 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: 2.40 (0.12), residues: 4464 helix: 1.92 (0.08), residues: 3480 sheet: None (None), residues: 0 loop : 0.57 (0.22), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.009 TRP H 93 HIS 0.013 0.003 HIS L 60 PHE 0.028 0.007 PHE V 51 TYR 0.092 0.013 TYR C 137 ARG 0.015 0.002 ARG T 79 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 914 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 866 time to evaluate : 3.216 Fit side-chains outliers start: 48 outliers final: 0 residues processed: 866 average time/residue: 1.7708 time to fit residues: 1761.2046 Evaluate side-chains 617 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 617 time to evaluate : 3.217 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2186 ------------------------------------------------------------------------------- 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: 0.9990 chunk 309 optimal weight: 0.7980 chunk 171 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 208 optimal weight: 2.9990 chunk 165 optimal weight: 6.9990 chunk 319 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 194 optimal weight: 0.6980 chunk 238 optimal weight: 0.9990 chunk 370 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 HIS ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 HIS B 173 HIS C 105 HIS ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 GLN D 105 HIS ** E 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 HIS ** F 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 HIS ** G 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 HIS ** H 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 HIS ** I 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 105 HIS ** J 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 105 HIS ** K 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 105 HIS ** L 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 105 HIS ** M 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 105 HIS ** N 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 105 HIS ** O 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 105 HIS ** P 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 105 HIS ** Q 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 105 HIS ** R 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 105 HIS ** S 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 105 HIS ** T 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 105 HIS ** U 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 105 HIS ** V 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 105 HIS ** W 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 105 HIS ** X 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 105 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 35880 Z= 0.167 Angle : 0.582 5.754 48408 Z= 0.319 Chirality : 0.037 0.122 5016 Planarity : 0.003 0.023 6432 Dihedral : 13.307 178.818 4800 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % 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: 4.87 (0.13), residues: 4464 helix: 3.72 (0.08), residues: 3552 sheet: None (None), residues: 0 loop : 0.99 (0.24), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 93 HIS 0.005 0.001 HIS E 151 PHE 0.013 0.002 PHE W 41 TYR 0.020 0.002 TYR E 32 ARG 0.002 0.000 ARG D 90 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 634 time to evaluate : 3.245 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 634 average time/residue: 1.8859 time to fit residues: 1368.5936 Evaluate side-chains 631 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 631 time to evaluate : 3.258 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2297 ------------------------------------------------------------------------------- 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: 9.9990 chunk 114 optimal weight: 1.9990 chunk 308 optimal weight: 2.9990 chunk 252 optimal weight: 0.5980 chunk 102 optimal weight: 9.9990 chunk 371 optimal weight: 3.9990 chunk 400 optimal weight: 1.9990 chunk 330 optimal weight: 5.9990 chunk 368 optimal weight: 7.9990 chunk 126 optimal weight: 0.8980 chunk 297 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 83 GLN ** H 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 83 GLN ** K 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 83 GLN ** L 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 83 GLN M 83 GLN N 83 GLN ** O 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 83 GLN ** T 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 83 GLN ** U 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 83 GLN ** W 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 83 GLN ** X 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 35880 Z= 0.211 Angle : 0.618 5.868 48408 Z= 0.339 Chirality : 0.038 0.125 5016 Planarity : 0.004 0.022 6432 Dihedral : 13.364 179.360 4800 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.63 % Allowed : 8.20 % Favored : 91.17 % 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: 5.01 (0.12), residues: 4464 helix: 3.87 (0.08), residues: 3552 sheet: None (None), residues: 0 loop : 0.80 (0.24), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP R 93 HIS 0.004 0.002 HIS H 151 PHE 0.017 0.002 PHE P 41 TYR 0.020 0.002 TYR Q 137 ARG 0.003 0.001 ARG U 156 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 662 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 638 time to evaluate : 3.296 Fit side-chains outliers start: 24 outliers final: 0 residues processed: 638 average time/residue: 1.9162 time to fit residues: 1394.5365 Evaluate side-chains 615 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 615 time to evaluate : 3.228 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2485 ------------------------------------------------------------------------------- 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: 3.9990 chunk 192 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 177 optimal weight: 3.9990 chunk 249 optimal weight: 7.9990 chunk 372 optimal weight: 0.8980 chunk 394 optimal weight: 3.9990 chunk 194 optimal weight: 3.9990 chunk 353 optimal weight: 0.9980 chunk 106 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 GLN ** F 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 35880 Z= 0.187 Angle : 0.568 5.127 48408 Z= 0.310 Chirality : 0.036 0.125 5016 Planarity : 0.003 0.020 6432 Dihedral : 13.395 179.880 4800 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.13 % Allowed : 7.49 % Favored : 92.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.13 (0.13), residues: 4464 helix: 3.96 (0.08), residues: 3552 sheet: None (None), residues: 0 loop : 0.83 (0.24), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP X 93 HIS 0.003 0.001 HIS L 151 PHE 0.016 0.002 PHE P 41 TYR 0.018 0.002 TYR P 137 ARG 0.002 0.000 ARG O 90 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 608 time to evaluate : 3.251 Fit side-chains outliers start: 5 outliers final: 0 residues processed: 608 average time/residue: 1.9211 time to fit residues: 1338.7520 Evaluate side-chains 608 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 608 time to evaluate : 3.214 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2258 ------------------------------------------------------------------------------- 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: 5.9990 chunk 223 optimal weight: 8.9990 chunk 5 optimal weight: 5.9990 chunk 293 optimal weight: 6.9990 chunk 162 optimal weight: 1.9990 chunk 336 optimal weight: 5.9990 chunk 272 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 201 optimal weight: 1.9990 chunk 353 optimal weight: 4.9990 chunk 99 optimal weight: 0.7980 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 83 GLN ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 GLN ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 GLN ** F 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 83 GLN ** G 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 83 GLN ** I 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 83 GLN ** J 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 83 GLN ** P 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 83 GLN ** Q 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 83 GLN ** R 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 83 GLN ** S 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 83 GLN ** V 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 83 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 35880 Z= 0.338 Angle : 0.733 6.165 48408 Z= 0.403 Chirality : 0.041 0.125 5016 Planarity : 0.005 0.038 6432 Dihedral : 13.372 178.731 4800 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.53 % Allowed : 6.96 % Favored : 92.51 % 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: 4.56 (0.12), residues: 4464 helix: 3.54 (0.08), residues: 3552 sheet: None (None), residues: 0 loop : 0.70 (0.24), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.003 TRP P 93 HIS 0.007 0.002 HIS T 151 PHE 0.021 0.003 PHE W 41 TYR 0.020 0.003 TYR G 137 ARG 0.004 0.001 ARG O 90 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 638 time to evaluate : 3.183 Fit side-chains outliers start: 20 outliers final: 19 residues processed: 638 average time/residue: 1.8661 time to fit residues: 1363.9967 Evaluate side-chains 634 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 615 time to evaluate : 3.411 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 1.1215 time to fit residues: 30.6323 ------------------------------------------------------------------------------- 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: 6.9990 chunk 355 optimal weight: 0.1980 chunk 77 optimal weight: 0.6980 chunk 231 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 394 optimal weight: 0.8980 chunk 327 optimal weight: 1.9990 chunk 182 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 130 optimal weight: 0.9980 chunk 207 optimal weight: 10.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 35880 Z= 0.155 Angle : 0.516 4.828 48408 Z= 0.282 Chirality : 0.035 0.123 5016 Planarity : 0.003 0.018 6432 Dihedral : 13.391 179.909 4800 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.03 % Allowed : 8.04 % Favored : 91.93 % 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: 5.22 (0.13), residues: 4464 helix: 4.04 (0.08), residues: 3552 sheet: None (None), residues: 0 loop : 0.75 (0.24), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP B 93 HIS 0.002 0.001 HIS P 128 PHE 0.014 0.002 PHE U 41 TYR 0.015 0.002 TYR H 137 ARG 0.001 0.000 ARG S 90 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 640 time to evaluate : 3.314 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 640 average time/residue: 1.8705 time to fit residues: 1372.5214 Evaluate side-chains 615 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 615 time to evaluate : 3.223 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.3203 ------------------------------------------------------------------------------- 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: 3.9990 chunk 44 optimal weight: 0.8980 chunk 224 optimal weight: 0.9990 chunk 288 optimal weight: 0.9980 chunk 223 optimal weight: 2.9990 chunk 332 optimal weight: 1.9990 chunk 220 optimal weight: 0.7980 chunk 393 optimal weight: 8.9990 chunk 246 optimal weight: 0.0050 chunk 239 optimal weight: 8.9990 chunk 181 optimal weight: 3.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 GLN B 141 GLN C 141 GLN D 141 GLN E 141 GLN F 141 GLN G 141 GLN I 141 GLN J 141 GLN K 141 GLN L 141 GLN M 141 GLN N 141 GLN O 141 GLN P 141 GLN Q 141 GLN R 141 GLN S 141 GLN T 141 GLN U 141 GLN V 141 GLN W 141 GLN X 141 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 35880 Z= 0.160 Angle : 0.519 4.826 48408 Z= 0.283 Chirality : 0.036 0.123 5016 Planarity : 0.003 0.020 6432 Dihedral : 13.375 179.836 4800 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.29 (0.13), residues: 4464 helix: 4.08 (0.08), residues: 3552 sheet: None (None), residues: 0 loop : 0.85 (0.25), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP P 93 HIS 0.002 0.001 HIS E 128 PHE 0.015 0.002 PHE D 41 TYR 0.016 0.002 TYR N 137 ARG 0.001 0.000 ARG O 90 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 661 time to evaluate : 3.247 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 661 average time/residue: 1.8578 time to fit residues: 1408.1347 Evaluate side-chains 614 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 614 time to evaluate : 3.243 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2334 ------------------------------------------------------------------------------- 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: 5.9990 chunk 157 optimal weight: 6.9990 chunk 234 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 250 optimal weight: 6.9990 chunk 267 optimal weight: 1.9990 chunk 194 optimal weight: 0.9990 chunk 36 optimal weight: 7.9990 chunk 309 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 GLN B 141 GLN C 141 GLN D 141 GLN E 141 GLN F 141 GLN G 141 GLN I 141 GLN J 141 GLN K 141 GLN L 141 GLN M 141 GLN N 141 GLN O 141 GLN P 141 GLN Q 141 GLN R 141 GLN S 141 GLN T 141 GLN U 141 GLN V 141 GLN W 141 GLN X 141 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 35880 Z= 0.176 Angle : 0.528 4.958 48408 Z= 0.291 Chirality : 0.036 0.123 5016 Planarity : 0.003 0.019 6432 Dihedral : 13.371 179.562 4800 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.21 (0.13), residues: 4464 helix: 4.01 (0.08), residues: 3552 sheet: None (None), residues: 0 loop : 0.87 (0.24), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP C 93 HIS 0.003 0.001 HIS H 128 PHE 0.016 0.002 PHE A 41 TYR 0.017 0.002 TYR C 137 ARG 0.001 0.000 ARG O 90 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 622 time to evaluate : 3.241 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 622 average time/residue: 1.9293 time to fit residues: 1368.1245 Evaluate side-chains 608 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 608 time to evaluate : 3.194 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1538 ------------------------------------------------------------------------------- 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: 5.9990 chunk 376 optimal weight: 7.9990 chunk 343 optimal weight: 0.9990 chunk 366 optimal weight: 0.8980 chunk 220 optimal weight: 0.7980 chunk 159 optimal weight: 7.9990 chunk 287 optimal weight: 0.0970 chunk 112 optimal weight: 0.9990 chunk 331 optimal weight: 0.9980 chunk 346 optimal weight: 6.9990 chunk 365 optimal weight: 0.0980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 35880 Z= 0.146 Angle : 0.488 4.615 48408 Z= 0.270 Chirality : 0.035 0.123 5016 Planarity : 0.003 0.020 6432 Dihedral : 13.361 179.809 4800 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.44 (0.13), residues: 4464 helix: 4.17 (0.08), residues: 3552 sheet: None (None), residues: 0 loop : 0.98 (0.25), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP O 93 HIS 0.002 0.001 HIS S 151 PHE 0.013 0.002 PHE T 41 TYR 0.015 0.001 TYR C 137 ARG 0.001 0.000 ARG M 90 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 654 time to evaluate : 3.285 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 654 average time/residue: 1.8545 time to fit residues: 1393.7609 Evaluate side-chains 654 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 654 time to evaluate : 3.324 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.3530 ------------------------------------------------------------------------------- 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: 2.9990 chunk 387 optimal weight: 5.9990 chunk 236 optimal weight: 0.7980 chunk 183 optimal weight: 0.6980 chunk 269 optimal weight: 5.9990 chunk 406 optimal weight: 0.7980 chunk 374 optimal weight: 5.9990 chunk 323 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 250 optimal weight: 6.9990 chunk 198 optimal weight: 0.9980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 35880 Z= 0.205 Angle : 0.564 5.233 48408 Z= 0.312 Chirality : 0.037 0.123 5016 Planarity : 0.003 0.019 6432 Dihedral : 13.371 179.445 4800 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.15 (0.13), residues: 4464 helix: 3.96 (0.08), residues: 3552 sheet: None (None), residues: 0 loop : 0.90 (0.25), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP D 93 HIS 0.015 0.002 HIS J 60 PHE 0.017 0.002 PHE T 41 TYR 0.017 0.002 TYR C 137 ARG 0.002 0.000 ARG E 90 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 629 time to evaluate : 3.648 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 629 average time/residue: 1.9012 time to fit residues: 1368.8905 Evaluate side-chains 629 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 629 time to evaluate : 3.313 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2748 ------------------------------------------------------------------------------- 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: 7.9990 chunk 344 optimal weight: 0.7980 chunk 99 optimal weight: 6.9990 chunk 298 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 324 optimal weight: 0.6980 chunk 135 optimal weight: 2.9990 chunk 332 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.150095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.137543 restraints weight = 163066.693| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.60 r_work: 0.3134 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work: 0.2893 rms_B_bonded: 4.29 restraints_weight: 0.1250 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2834 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2834 r_free = 0.2834 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2833 r_free = 0.2833 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2833 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 35880 Z= 0.170 Angle : 0.523 4.960 48408 Z= 0.289 Chirality : 0.036 0.124 5016 Planarity : 0.003 0.019 6432 Dihedral : 13.375 179.742 4800 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.33 (0.13), residues: 4464 helix: 4.08 (0.08), residues: 3552 sheet: None (None), residues: 0 loop : 0.96 (0.24), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP D 93 HIS 0.012 0.001 HIS U 60 PHE 0.015 0.002 PHE X 41 TYR 0.016 0.002 TYR C 137 ARG 0.001 0.000 ARG O 90 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19525.67 seconds wall clock time: 338 minutes 52.69 seconds (20332.69 seconds total)