Starting phenix.real_space_refine on Wed Apr 10 19:39:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8en7_28269/04_2024/8en7_28269.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8en7_28269/04_2024/8en7_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_28269/04_2024/8en7_28269.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8en7_28269/04_2024/8en7_28269.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8en7_28269/04_2024/8en7_28269.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8en7_28269/04_2024/8en7_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-dev-5288/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: 25.81, 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: 14.21 Conformation dependent library (CDL) restraints added in 8.9 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: 2.10 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: 10.18 Time building geometry restraints manager: 15.21 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: 6.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.330 Construct map_model_manager: 0.040 Extract box with map and model: 21.670 Check model and map are aligned: 0.420 Set scattering table: 0.260 Process input model: 94.590 Find NCS groups from input model: 2.230 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 137.890 ------------------------------------------------------------------------------- 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 : 3.286 Fit side-chains REVERT: A 49 LYS cc_start: 0.7727 (mttm) cc_final: 0.7289 (mppt) REVERT: A 53 LYS cc_start: 0.7529 (ttpp) cc_final: 0.7159 (ttpp) REVERT: A 68 LYS cc_start: 0.7631 (OUTLIER) cc_final: 0.7327 (tttm) REVERT: A 75 GLN cc_start: 0.7707 (mt0) cc_final: 0.7488 (tt0) REVERT: A 139 SER cc_start: 0.7859 (m) cc_final: 0.7658 (t) REVERT: A 143 LYS cc_start: 0.7842 (ttmm) cc_final: 0.7520 (mttt) REVERT: B 49 LYS cc_start: 0.7729 (mttm) cc_final: 0.7289 (mppt) REVERT: B 53 LYS cc_start: 0.7530 (ttpp) cc_final: 0.7161 (ttpp) REVERT: B 68 LYS cc_start: 0.7627 (OUTLIER) cc_final: 0.7322 (tttm) REVERT: B 75 GLN cc_start: 0.7707 (mt0) cc_final: 0.7486 (tt0) REVERT: B 139 SER cc_start: 0.7859 (m) cc_final: 0.7654 (t) REVERT: B 143 LYS cc_start: 0.7834 (ttmm) cc_final: 0.7510 (mttt) REVERT: C 14 GLN cc_start: 0.7360 (mm-40) cc_final: 0.6975 (mt0) REVERT: C 49 LYS cc_start: 0.7714 (mttm) cc_final: 0.7283 (mppt) REVERT: C 53 LYS cc_start: 0.7487 (ttpp) cc_final: 0.7112 (ttpp) REVERT: C 68 LYS cc_start: 0.7655 (OUTLIER) cc_final: 0.7353 (tttm) REVERT: C 75 GLN cc_start: 0.7756 (mt0) cc_final: 0.7545 (tt0) REVERT: C 143 LYS cc_start: 0.7865 (ttmm) cc_final: 0.7580 (mttp) REVERT: D 49 LYS cc_start: 0.7728 (mttm) cc_final: 0.7292 (mppt) REVERT: D 53 LYS cc_start: 0.7530 (ttpp) cc_final: 0.7158 (ttpp) REVERT: D 68 LYS cc_start: 0.7634 (OUTLIER) cc_final: 0.7330 (tttm) REVERT: D 75 GLN cc_start: 0.7703 (mt0) cc_final: 0.7488 (tt0) REVERT: D 139 SER cc_start: 0.7860 (m) cc_final: 0.7658 (t) REVERT: D 143 LYS cc_start: 0.7843 (ttmm) cc_final: 0.7520 (mttt) REVERT: E 49 LYS cc_start: 0.7731 (mttm) cc_final: 0.7294 (mppt) REVERT: E 53 LYS cc_start: 0.7532 (ttpp) cc_final: 0.7161 (ttpp) REVERT: E 68 LYS cc_start: 0.7630 (OUTLIER) cc_final: 0.7327 (tttm) REVERT: E 75 GLN cc_start: 0.7702 (mt0) cc_final: 0.7486 (tt0) REVERT: E 139 SER cc_start: 0.7860 (m) cc_final: 0.7660 (t) REVERT: E 143 LYS cc_start: 0.7844 (ttmm) cc_final: 0.7520 (mttt) REVERT: F 49 LYS cc_start: 0.7727 (mttm) cc_final: 0.7291 (mppt) REVERT: F 53 LYS cc_start: 0.7528 (ttpp) cc_final: 0.7158 (ttpp) REVERT: F 68 LYS cc_start: 0.7634 (OUTLIER) cc_final: 0.7328 (tttm) REVERT: F 75 GLN cc_start: 0.7701 (mt0) cc_final: 0.7486 (tt0) REVERT: F 139 SER cc_start: 0.7863 (m) cc_final: 0.7660 (t) REVERT: F 143 LYS cc_start: 0.7846 (ttmm) cc_final: 0.7520 (mttt) REVERT: G 49 LYS cc_start: 0.7727 (mttm) cc_final: 0.7291 (mppt) REVERT: G 53 LYS cc_start: 0.7527 (ttpp) cc_final: 0.7157 (ttpp) REVERT: G 68 LYS cc_start: 0.7631 (OUTLIER) cc_final: 0.7326 (tttm) REVERT: G 75 GLN cc_start: 0.7703 (mt0) cc_final: 0.7488 (tt0) REVERT: G 139 SER cc_start: 0.7862 (m) cc_final: 0.7659 (t) REVERT: G 143 LYS cc_start: 0.7843 (ttmm) cc_final: 0.7520 (mttt) REVERT: H 49 LYS cc_start: 0.7730 (mttm) cc_final: 0.7293 (mppt) REVERT: H 53 LYS cc_start: 0.7531 (ttpp) cc_final: 0.7161 (ttpp) REVERT: H 68 LYS cc_start: 0.7630 (OUTLIER) cc_final: 0.7326 (tttm) REVERT: H 75 GLN cc_start: 0.7705 (mt0) cc_final: 0.7485 (tt0) REVERT: H 139 SER cc_start: 0.7859 (m) cc_final: 0.7658 (t) REVERT: H 143 LYS cc_start: 0.7843 (ttmm) cc_final: 0.7518 (mttt) REVERT: I 49 LYS cc_start: 0.7727 (mttm) cc_final: 0.7288 (mppt) REVERT: I 53 LYS cc_start: 0.7526 (ttpp) cc_final: 0.7155 (ttpp) REVERT: I 68 LYS cc_start: 0.7629 (OUTLIER) cc_final: 0.7323 (tttm) REVERT: I 75 GLN cc_start: 0.7706 (mt0) cc_final: 0.7485 (tt0) REVERT: I 139 SER cc_start: 0.7864 (m) cc_final: 0.7662 (t) REVERT: I 143 LYS cc_start: 0.7844 (ttmm) cc_final: 0.7520 (mttt) REVERT: J 49 LYS cc_start: 0.7727 (mttm) cc_final: 0.7289 (mppt) REVERT: J 53 LYS cc_start: 0.7527 (ttpp) cc_final: 0.7157 (ttpp) REVERT: J 68 LYS cc_start: 0.7631 (OUTLIER) cc_final: 0.7327 (tttm) REVERT: J 75 GLN cc_start: 0.7707 (mt0) cc_final: 0.7489 (tt0) REVERT: J 139 SER cc_start: 0.7862 (m) cc_final: 0.7659 (t) REVERT: J 143 LYS cc_start: 0.7841 (ttmm) cc_final: 0.7519 (mttt) REVERT: K 49 LYS cc_start: 0.7730 (mttm) cc_final: 0.7291 (mppt) REVERT: K 53 LYS cc_start: 0.7529 (ttpp) cc_final: 0.7158 (ttpp) REVERT: K 68 LYS cc_start: 0.7630 (OUTLIER) cc_final: 0.7325 (tttm) REVERT: K 75 GLN cc_start: 0.7707 (mt0) cc_final: 0.7485 (tt0) REVERT: K 139 SER cc_start: 0.7864 (m) cc_final: 0.7662 (t) REVERT: K 143 LYS cc_start: 0.7844 (ttmm) cc_final: 0.7519 (mttt) REVERT: L 49 LYS cc_start: 0.7729 (mttm) cc_final: 0.7290 (mppt) REVERT: L 53 LYS cc_start: 0.7529 (ttpp) cc_final: 0.7159 (ttpp) REVERT: L 68 LYS cc_start: 0.7633 (OUTLIER) cc_final: 0.7328 (tttm) REVERT: L 75 GLN cc_start: 0.7706 (mt0) cc_final: 0.7488 (tt0) REVERT: L 139 SER cc_start: 0.7862 (m) cc_final: 0.7660 (t) REVERT: L 143 LYS cc_start: 0.7845 (ttmm) cc_final: 0.7521 (mttt) REVERT: M 49 LYS cc_start: 0.7725 (mttm) cc_final: 0.7291 (mppt) REVERT: M 53 LYS cc_start: 0.7528 (ttpp) cc_final: 0.7157 (ttpp) REVERT: M 68 LYS cc_start: 0.7632 (OUTLIER) cc_final: 0.7327 (tttm) REVERT: M 75 GLN cc_start: 0.7702 (mt0) cc_final: 0.7487 (tt0) REVERT: M 139 SER cc_start: 0.7859 (m) cc_final: 0.7657 (t) REVERT: M 143 LYS cc_start: 0.7844 (ttmm) cc_final: 0.7520 (mttt) REVERT: N 49 LYS cc_start: 0.7728 (mttm) cc_final: 0.7293 (mppt) REVERT: N 53 LYS cc_start: 0.7531 (ttpp) cc_final: 0.7161 (ttpp) REVERT: N 68 LYS cc_start: 0.7631 (OUTLIER) cc_final: 0.7326 (tttm) REVERT: N 75 GLN cc_start: 0.7701 (mt0) cc_final: 0.7485 (tt0) REVERT: N 139 SER cc_start: 0.7860 (m) cc_final: 0.7659 (t) REVERT: N 143 LYS cc_start: 0.7845 (ttmm) cc_final: 0.7520 (mttt) REVERT: O 49 LYS cc_start: 0.7731 (mttm) cc_final: 0.7292 (mppt) REVERT: O 53 LYS cc_start: 0.7529 (ttpp) cc_final: 0.7159 (ttpp) REVERT: O 68 LYS cc_start: 0.7629 (OUTLIER) cc_final: 0.7324 (tttm) REVERT: O 75 GLN cc_start: 0.7704 (mt0) cc_final: 0.7482 (tt0) REVERT: O 139 SER cc_start: 0.7860 (m) cc_final: 0.7660 (t) REVERT: O 143 LYS cc_start: 0.7843 (ttmm) cc_final: 0.7519 (mttt) REVERT: P 49 LYS cc_start: 0.7727 (mttm) cc_final: 0.7289 (mppt) REVERT: P 53 LYS cc_start: 0.7528 (ttpp) cc_final: 0.7157 (ttpp) REVERT: P 68 LYS cc_start: 0.7628 (OUTLIER) cc_final: 0.7324 (tttm) REVERT: P 75 GLN cc_start: 0.7706 (mt0) cc_final: 0.7483 (tt0) REVERT: P 139 SER cc_start: 0.7859 (m) cc_final: 0.7658 (t) REVERT: P 143 LYS cc_start: 0.7843 (ttmm) cc_final: 0.7518 (mttt) REVERT: Q 49 LYS cc_start: 0.7732 (mttm) cc_final: 0.7293 (mppt) REVERT: Q 53 LYS cc_start: 0.7531 (ttpp) cc_final: 0.7161 (ttpp) REVERT: Q 68 LYS cc_start: 0.7628 (OUTLIER) cc_final: 0.7323 (tttm) REVERT: Q 75 GLN cc_start: 0.7705 (mt0) cc_final: 0.7483 (tt0) REVERT: Q 139 SER cc_start: 0.7861 (m) cc_final: 0.7660 (t) REVERT: Q 143 LYS cc_start: 0.7846 (ttmm) cc_final: 0.7520 (mttt) REVERT: R 49 LYS cc_start: 0.7728 (mttm) cc_final: 0.7291 (mppt) REVERT: R 53 LYS cc_start: 0.7526 (ttpp) cc_final: 0.7156 (ttpp) REVERT: R 68 LYS cc_start: 0.7632 (OUTLIER) cc_final: 0.7328 (tttm) REVERT: R 75 GLN cc_start: 0.7700 (mt0) cc_final: 0.7482 (tt0) REVERT: R 139 SER cc_start: 0.7861 (m) cc_final: 0.7660 (t) REVERT: R 143 LYS cc_start: 0.7843 (ttmm) cc_final: 0.7519 (mttt) REVERT: S 49 LYS cc_start: 0.7728 (mttm) cc_final: 0.7291 (mppt) REVERT: S 53 LYS cc_start: 0.7527 (ttpp) cc_final: 0.7158 (ttpp) REVERT: S 68 LYS cc_start: 0.7630 (OUTLIER) cc_final: 0.7325 (tttm) REVERT: S 75 GLN cc_start: 0.7703 (mt0) cc_final: 0.7486 (tt0) REVERT: S 139 SER cc_start: 0.7863 (m) cc_final: 0.7661 (t) REVERT: S 143 LYS cc_start: 0.7843 (ttmm) cc_final: 0.7519 (mttt) REVERT: T 49 LYS cc_start: 0.7729 (mttm) cc_final: 0.7293 (mppt) REVERT: T 53 LYS cc_start: 0.7529 (ttpp) cc_final: 0.7159 (ttpp) REVERT: T 68 LYS cc_start: 0.7629 (OUTLIER) cc_final: 0.7324 (tttm) REVERT: T 75 GLN cc_start: 0.7701 (mt0) cc_final: 0.7483 (tt0) REVERT: T 139 SER cc_start: 0.7862 (m) cc_final: 0.7661 (t) REVERT: T 143 LYS cc_start: 0.7845 (ttmm) cc_final: 0.7520 (mttt) REVERT: U 49 LYS cc_start: 0.7728 (mttm) cc_final: 0.7292 (mppt) REVERT: U 53 LYS cc_start: 0.7527 (ttpp) cc_final: 0.7157 (ttpp) REVERT: U 68 LYS cc_start: 0.7629 (OUTLIER) cc_final: 0.7324 (tttm) REVERT: U 75 GLN cc_start: 0.7698 (mt0) cc_final: 0.7479 (tt0) REVERT: U 139 SER cc_start: 0.7862 (m) cc_final: 0.7661 (t) REVERT: U 143 LYS cc_start: 0.7845 (ttmm) cc_final: 0.7519 (mttt) REVERT: V 49 LYS cc_start: 0.7727 (mttm) cc_final: 0.7292 (mppt) REVERT: V 53 LYS cc_start: 0.7529 (ttpp) cc_final: 0.7159 (ttpp) REVERT: V 68 LYS cc_start: 0.7630 (OUTLIER) cc_final: 0.7326 (tttm) REVERT: V 75 GLN cc_start: 0.7702 (mt0) cc_final: 0.7483 (tt0) REVERT: V 143 LYS cc_start: 0.7842 (ttmm) cc_final: 0.7518 (mttt) REVERT: W 49 LYS cc_start: 0.7729 (mttm) cc_final: 0.7291 (mppt) REVERT: W 53 LYS cc_start: 0.7526 (ttpp) cc_final: 0.7157 (ttpp) REVERT: W 68 LYS cc_start: 0.7628 (OUTLIER) cc_final: 0.7323 (tttm) REVERT: W 75 GLN cc_start: 0.7706 (mt0) cc_final: 0.7485 (tt0) REVERT: W 139 SER cc_start: 0.7861 (m) cc_final: 0.7659 (t) REVERT: W 143 LYS cc_start: 0.7842 (ttmm) cc_final: 0.7518 (mttt) REVERT: X 49 LYS cc_start: 0.7731 (mttm) cc_final: 0.7294 (mppt) REVERT: X 53 LYS cc_start: 0.7531 (ttpp) cc_final: 0.7159 (ttpp) REVERT: X 68 LYS cc_start: 0.7632 (OUTLIER) cc_final: 0.7328 (tttm) REVERT: X 75 GLN cc_start: 0.7700 (mt0) cc_final: 0.7486 (tt0) REVERT: X 143 LYS cc_start: 0.7845 (ttmm) cc_final: 0.7519 (mttt) outliers start: 48 outliers final: 0 residues processed: 866 average time/residue: 1.7110 time to fit residues: 1698.6331 Evaluate side-chains 760 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 736 time to evaluate : 3.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain C residue 68 LYS Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain G residue 68 LYS Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain I residue 68 LYS Chi-restraints excluded: chain J residue 68 LYS Chi-restraints excluded: chain K residue 68 LYS Chi-restraints excluded: chain L residue 68 LYS Chi-restraints excluded: chain M residue 68 LYS Chi-restraints excluded: chain N residue 68 LYS Chi-restraints excluded: chain O residue 68 LYS Chi-restraints excluded: chain P residue 68 LYS Chi-restraints excluded: chain Q residue 68 LYS Chi-restraints excluded: chain R residue 68 LYS Chi-restraints excluded: chain S residue 68 LYS Chi-restraints excluded: chain T residue 68 LYS Chi-restraints excluded: chain U residue 68 LYS Chi-restraints excluded: chain V residue 68 LYS Chi-restraints excluded: chain W residue 68 LYS Chi-restraints excluded: chain X residue 68 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 0.7980 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: 0.7980 chunk 319 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 194 optimal weight: 0.8980 chunk 238 optimal weight: 0.9990 chunk 370 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.7634 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 35880 Z= 0.156 Angle : 0.566 5.651 48408 Z= 0.312 Chirality : 0.037 0.121 5016 Planarity : 0.003 0.023 6432 Dihedral : 13.316 179.135 4896 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.63 % Allowed : 7.04 % Favored : 92.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.86 (0.13), residues: 4464 helix: 3.70 (0.08), residues: 3552 sheet: None (None), residues: 0 loop : 1.02 (0.24), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 93 HIS 0.004 0.001 HIS C 105 PHE 0.013 0.002 PHE A 41 TYR 0.021 0.002 TYR B 32 ARG 0.001 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 681 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 657 time to evaluate : 3.193 Fit side-chains REVERT: A 53 LYS cc_start: 0.7683 (ttpp) cc_final: 0.7302 (ttpp) REVERT: A 68 LYS cc_start: 0.7734 (OUTLIER) cc_final: 0.7470 (tttm) REVERT: A 139 SER cc_start: 0.7913 (m) cc_final: 0.7711 (t) REVERT: A 143 LYS cc_start: 0.7947 (ttmm) cc_final: 0.7647 (mttm) REVERT: B 53 LYS cc_start: 0.7685 (ttpp) cc_final: 0.7305 (ttpp) REVERT: B 68 LYS cc_start: 0.7735 (OUTLIER) cc_final: 0.7471 (tttm) REVERT: B 139 SER cc_start: 0.7910 (m) cc_final: 0.7707 (t) REVERT: B 143 LYS cc_start: 0.7946 (ttmm) cc_final: 0.7646 (mttm) REVERT: C 49 LYS cc_start: 0.7710 (mttm) cc_final: 0.7277 (mppt) REVERT: C 53 LYS cc_start: 0.7695 (ttpp) cc_final: 0.7312 (ttpp) REVERT: C 68 LYS cc_start: 0.7738 (OUTLIER) cc_final: 0.7474 (tttm) REVERT: C 143 LYS cc_start: 0.7947 (ttmm) cc_final: 0.7643 (mttm) REVERT: D 53 LYS cc_start: 0.7683 (ttpp) cc_final: 0.7302 (ttpp) REVERT: D 68 LYS cc_start: 0.7735 (OUTLIER) cc_final: 0.7472 (tttm) REVERT: D 139 SER cc_start: 0.7914 (m) cc_final: 0.7713 (t) REVERT: D 143 LYS cc_start: 0.7946 (ttmm) cc_final: 0.7644 (mttm) REVERT: E 53 LYS cc_start: 0.7683 (ttpp) cc_final: 0.7302 (ttpp) REVERT: E 68 LYS cc_start: 0.7734 (OUTLIER) cc_final: 0.7471 (tttm) REVERT: E 139 SER cc_start: 0.7912 (m) cc_final: 0.7710 (t) REVERT: E 143 LYS cc_start: 0.7945 (ttmm) cc_final: 0.7644 (mttm) REVERT: F 53 LYS cc_start: 0.7684 (ttpp) cc_final: 0.7302 (ttpp) REVERT: F 68 LYS cc_start: 0.7737 (OUTLIER) cc_final: 0.7473 (tttm) REVERT: F 139 SER cc_start: 0.7911 (m) cc_final: 0.7709 (t) REVERT: F 143 LYS cc_start: 0.7946 (ttmm) cc_final: 0.7646 (mttm) REVERT: G 53 LYS cc_start: 0.7689 (ttpp) cc_final: 0.7308 (ttpp) REVERT: G 68 LYS cc_start: 0.7736 (OUTLIER) cc_final: 0.7471 (tttm) REVERT: G 139 SER cc_start: 0.7911 (m) cc_final: 0.7709 (t) REVERT: G 143 LYS cc_start: 0.7946 (ttmm) cc_final: 0.7645 (mttm) REVERT: H 53 LYS cc_start: 0.7684 (ttpp) cc_final: 0.7302 (ttpp) REVERT: H 68 LYS cc_start: 0.7735 (OUTLIER) cc_final: 0.7472 (tttm) REVERT: H 139 SER cc_start: 0.7914 (m) cc_final: 0.7712 (t) REVERT: H 143 LYS cc_start: 0.7946 (ttmm) cc_final: 0.7644 (mttm) REVERT: I 53 LYS cc_start: 0.7690 (ttpp) cc_final: 0.7308 (ttpp) REVERT: I 68 LYS cc_start: 0.7737 (OUTLIER) cc_final: 0.7473 (tttm) REVERT: I 139 SER cc_start: 0.7913 (m) cc_final: 0.7711 (t) REVERT: I 143 LYS cc_start: 0.7947 (ttmm) cc_final: 0.7647 (mttm) REVERT: J 53 LYS cc_start: 0.7690 (ttpp) cc_final: 0.7307 (ttpp) REVERT: J 68 LYS cc_start: 0.7735 (OUTLIER) cc_final: 0.7472 (tttm) REVERT: J 139 SER cc_start: 0.7912 (m) cc_final: 0.7711 (t) REVERT: J 143 LYS cc_start: 0.7946 (ttmm) cc_final: 0.7645 (mttm) REVERT: K 53 LYS cc_start: 0.7686 (ttpp) cc_final: 0.7304 (ttpp) REVERT: K 68 LYS cc_start: 0.7735 (OUTLIER) cc_final: 0.7471 (tttm) REVERT: K 139 SER cc_start: 0.7912 (m) cc_final: 0.7710 (t) REVERT: K 143 LYS cc_start: 0.7948 (ttmm) cc_final: 0.7647 (mttm) REVERT: L 53 LYS cc_start: 0.7682 (ttpp) cc_final: 0.7302 (ttpp) REVERT: L 68 LYS cc_start: 0.7734 (OUTLIER) cc_final: 0.7471 (tttm) REVERT: L 139 SER cc_start: 0.7912 (m) cc_final: 0.7710 (t) REVERT: L 143 LYS cc_start: 0.7947 (ttmm) cc_final: 0.7647 (mttm) REVERT: M 53 LYS cc_start: 0.7684 (ttpp) cc_final: 0.7302 (ttpp) REVERT: M 68 LYS cc_start: 0.7737 (OUTLIER) cc_final: 0.7473 (tttm) REVERT: M 139 SER cc_start: 0.7912 (m) cc_final: 0.7709 (t) REVERT: M 143 LYS cc_start: 0.7946 (ttmm) cc_final: 0.7646 (mttm) REVERT: N 53 LYS cc_start: 0.7683 (ttpp) cc_final: 0.7303 (ttpp) REVERT: N 68 LYS cc_start: 0.7736 (OUTLIER) cc_final: 0.7472 (tttm) REVERT: N 139 SER cc_start: 0.7914 (m) cc_final: 0.7712 (t) REVERT: N 143 LYS cc_start: 0.7945 (ttmm) cc_final: 0.7645 (mttm) REVERT: O 53 LYS cc_start: 0.7682 (ttpp) cc_final: 0.7302 (ttpp) REVERT: O 68 LYS cc_start: 0.7734 (OUTLIER) cc_final: 0.7471 (tttm) REVERT: O 139 SER cc_start: 0.7915 (m) cc_final: 0.7713 (t) REVERT: O 143 LYS cc_start: 0.7945 (ttmm) cc_final: 0.7644 (mttm) REVERT: P 53 LYS cc_start: 0.7684 (ttpp) cc_final: 0.7303 (ttpp) REVERT: P 68 LYS cc_start: 0.7737 (OUTLIER) cc_final: 0.7473 (tttm) REVERT: P 139 SER cc_start: 0.7910 (m) cc_final: 0.7709 (t) REVERT: P 143 LYS cc_start: 0.7947 (ttmm) cc_final: 0.7647 (mttm) REVERT: Q 53 LYS cc_start: 0.7683 (ttpp) cc_final: 0.7303 (ttpp) REVERT: Q 68 LYS cc_start: 0.7736 (OUTLIER) cc_final: 0.7472 (tttm) REVERT: Q 139 SER cc_start: 0.7912 (m) cc_final: 0.7710 (t) REVERT: Q 143 LYS cc_start: 0.7946 (ttmm) cc_final: 0.7646 (mttm) REVERT: R 53 LYS cc_start: 0.7684 (ttpp) cc_final: 0.7301 (ttpp) REVERT: R 68 LYS cc_start: 0.7735 (OUTLIER) cc_final: 0.7472 (tttm) REVERT: R 139 SER cc_start: 0.7915 (m) cc_final: 0.7704 (t) REVERT: R 143 LYS cc_start: 0.7946 (ttmm) cc_final: 0.7634 (mttp) REVERT: S 53 LYS cc_start: 0.7689 (ttpp) cc_final: 0.7307 (ttpp) REVERT: S 68 LYS cc_start: 0.7734 (OUTLIER) cc_final: 0.7471 (tttm) REVERT: S 139 SER cc_start: 0.7914 (m) cc_final: 0.7711 (t) REVERT: S 143 LYS cc_start: 0.7945 (ttmm) cc_final: 0.7644 (mttm) REVERT: T 53 LYS cc_start: 0.7685 (ttpp) cc_final: 0.7305 (ttpp) REVERT: T 68 LYS cc_start: 0.7736 (OUTLIER) cc_final: 0.7472 (tttm) REVERT: T 139 SER cc_start: 0.7912 (m) cc_final: 0.7709 (t) REVERT: T 143 LYS cc_start: 0.7946 (ttmm) cc_final: 0.7645 (mttm) REVERT: U 53 LYS cc_start: 0.7684 (ttpp) cc_final: 0.7302 (ttpp) REVERT: U 68 LYS cc_start: 0.7736 (OUTLIER) cc_final: 0.7472 (tttm) REVERT: U 139 SER cc_start: 0.7914 (m) cc_final: 0.7710 (t) REVERT: U 143 LYS cc_start: 0.7946 (ttmm) cc_final: 0.7646 (mttm) REVERT: V 53 LYS cc_start: 0.7682 (ttpp) cc_final: 0.7301 (ttpp) REVERT: V 68 LYS cc_start: 0.7734 (OUTLIER) cc_final: 0.7471 (tttm) REVERT: V 143 LYS cc_start: 0.7946 (ttmm) cc_final: 0.7643 (mttm) REVERT: W 53 LYS cc_start: 0.7683 (ttpp) cc_final: 0.7303 (ttpp) REVERT: W 68 LYS cc_start: 0.7736 (OUTLIER) cc_final: 0.7472 (tttm) REVERT: W 139 SER cc_start: 0.7914 (m) cc_final: 0.7703 (t) REVERT: W 143 LYS cc_start: 0.7945 (ttmm) cc_final: 0.7634 (mttp) REVERT: X 53 LYS cc_start: 0.7684 (ttpp) cc_final: 0.7302 (ttpp) REVERT: X 68 LYS cc_start: 0.7735 (OUTLIER) cc_final: 0.7472 (tttm) REVERT: X 143 LYS cc_start: 0.7947 (ttmm) cc_final: 0.7642 (mttm) outliers start: 24 outliers final: 0 residues processed: 657 average time/residue: 1.7756 time to fit residues: 1333.1462 Evaluate side-chains 654 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 630 time to evaluate : 3.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain C residue 68 LYS Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain G residue 68 LYS Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain I residue 68 LYS Chi-restraints excluded: chain J residue 68 LYS Chi-restraints excluded: chain K residue 68 LYS Chi-restraints excluded: chain L residue 68 LYS Chi-restraints excluded: chain M residue 68 LYS Chi-restraints excluded: chain N residue 68 LYS Chi-restraints excluded: chain O residue 68 LYS Chi-restraints excluded: chain P residue 68 LYS Chi-restraints excluded: chain Q residue 68 LYS Chi-restraints excluded: chain R residue 68 LYS Chi-restraints excluded: chain S residue 68 LYS Chi-restraints excluded: chain T residue 68 LYS Chi-restraints excluded: chain U residue 68 LYS Chi-restraints excluded: chain V residue 68 LYS Chi-restraints excluded: chain W residue 68 LYS Chi-restraints excluded: chain X residue 68 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 205 optimal weight: 10.0000 chunk 114 optimal weight: 2.9990 chunk 308 optimal weight: 2.9990 chunk 252 optimal weight: 4.9990 chunk 102 optimal weight: 10.0000 chunk 371 optimal weight: 4.9990 chunk 400 optimal weight: 1.9990 chunk 330 optimal weight: 3.9990 chunk 368 optimal weight: 0.6980 chunk 126 optimal weight: 0.7980 chunk 297 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 GLN C 83 GLN ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 GLN ** E 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN E 83 GLN ** F 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 GLN ** G 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 83 GLN ** H 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 75 GLN H 83 GLN ** I 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 75 GLN 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 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 75 GLN ** N 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 75 GLN N 83 GLN ** O 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 75 GLN ** P 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 75 GLN ** Q 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 75 GLN ** R 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 83 GLN ** T 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 75 GLN ** U 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 75 GLN W 83 GLN ** X 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 75 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 35880 Z= 0.210 Angle : 0.632 5.921 48408 Z= 0.346 Chirality : 0.038 0.124 5016 Planarity : 0.004 0.022 6432 Dihedral : 13.355 179.262 4896 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.27 % Allowed : 7.28 % Favored : 91.46 % 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: 4.89 (0.12), residues: 4464 helix: 3.77 (0.08), residues: 3552 sheet: None (None), residues: 0 loop : 0.85 (0.24), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP D 93 HIS 0.005 0.002 HIS L 151 PHE 0.017 0.002 PHE N 41 TYR 0.020 0.002 TYR T 137 ARG 0.002 0.000 ARG O 90 *********************** 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 708 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 660 time to evaluate : 3.195 Fit side-chains REVERT: A 53 LYS cc_start: 0.7689 (ttpp) cc_final: 0.7294 (ttpp) REVERT: A 68 LYS cc_start: 0.7726 (OUTLIER) cc_final: 0.7463 (tttm) REVERT: A 139 SER cc_start: 0.7926 (m) cc_final: 0.7723 (t) REVERT: A 143 LYS cc_start: 0.7948 (ttmm) cc_final: 0.7646 (mttp) REVERT: B 53 LYS cc_start: 0.7688 (ttpp) cc_final: 0.7293 (ttpp) REVERT: B 68 LYS cc_start: 0.7729 (OUTLIER) cc_final: 0.7466 (tttm) REVERT: B 139 SER cc_start: 0.7925 (m) cc_final: 0.7722 (t) REVERT: B 143 LYS cc_start: 0.7947 (ttmm) cc_final: 0.7645 (mttp) REVERT: C 49 LYS cc_start: 0.7789 (mttm) cc_final: 0.7343 (mppt) REVERT: C 53 LYS cc_start: 0.7688 (ttpp) cc_final: 0.7295 (ttpp) REVERT: C 68 LYS cc_start: 0.7731 (OUTLIER) cc_final: 0.7468 (tttm) REVERT: C 143 LYS cc_start: 0.7949 (ttmm) cc_final: 0.7652 (mttm) REVERT: D 53 LYS cc_start: 0.7690 (ttpp) cc_final: 0.7293 (ttpp) REVERT: D 68 LYS cc_start: 0.7727 (OUTLIER) cc_final: 0.7465 (tttm) REVERT: D 139 SER cc_start: 0.7928 (m) cc_final: 0.7724 (t) REVERT: D 143 LYS cc_start: 0.7948 (ttmm) cc_final: 0.7643 (mttp) REVERT: E 53 LYS cc_start: 0.7689 (ttpp) cc_final: 0.7294 (ttpp) REVERT: E 68 LYS cc_start: 0.7727 (OUTLIER) cc_final: 0.7464 (tttm) REVERT: E 139 SER cc_start: 0.7927 (m) cc_final: 0.7724 (t) REVERT: E 143 LYS cc_start: 0.7949 (ttmm) cc_final: 0.7644 (mttp) REVERT: F 53 LYS cc_start: 0.7690 (ttpp) cc_final: 0.7293 (ttpp) REVERT: F 68 LYS cc_start: 0.7730 (OUTLIER) cc_final: 0.7468 (tttm) REVERT: F 139 SER cc_start: 0.7928 (m) cc_final: 0.7724 (t) REVERT: F 143 LYS cc_start: 0.7947 (ttmm) cc_final: 0.7644 (mttp) REVERT: G 53 LYS cc_start: 0.7689 (ttpp) cc_final: 0.7293 (ttpp) REVERT: G 68 LYS cc_start: 0.7728 (OUTLIER) cc_final: 0.7466 (tttm) REVERT: G 139 SER cc_start: 0.7927 (m) cc_final: 0.7723 (t) REVERT: G 143 LYS cc_start: 0.7948 (ttmm) cc_final: 0.7644 (mttp) REVERT: H 53 LYS cc_start: 0.7691 (ttpp) cc_final: 0.7294 (ttpp) REVERT: H 68 LYS cc_start: 0.7727 (OUTLIER) cc_final: 0.7465 (tttm) REVERT: H 139 SER cc_start: 0.7928 (m) cc_final: 0.7725 (t) REVERT: H 143 LYS cc_start: 0.7949 (ttmm) cc_final: 0.7644 (mttp) REVERT: I 53 LYS cc_start: 0.7690 (ttpp) cc_final: 0.7294 (ttpp) REVERT: I 68 LYS cc_start: 0.7729 (OUTLIER) cc_final: 0.7467 (tttm) REVERT: I 139 SER cc_start: 0.7927 (m) cc_final: 0.7724 (t) REVERT: I 143 LYS cc_start: 0.7948 (ttmm) cc_final: 0.7645 (mttp) REVERT: J 53 LYS cc_start: 0.7691 (ttpp) cc_final: 0.7294 (ttpp) REVERT: J 68 LYS cc_start: 0.7727 (OUTLIER) cc_final: 0.7465 (tttm) REVERT: J 139 SER cc_start: 0.7928 (m) cc_final: 0.7725 (t) REVERT: J 143 LYS cc_start: 0.7947 (ttmm) cc_final: 0.7644 (mttp) REVERT: K 53 LYS cc_start: 0.7691 (ttpp) cc_final: 0.7294 (ttpp) REVERT: K 68 LYS cc_start: 0.7727 (OUTLIER) cc_final: 0.7465 (tttm) REVERT: K 139 SER cc_start: 0.7926 (m) cc_final: 0.7724 (t) REVERT: K 143 LYS cc_start: 0.7949 (ttmm) cc_final: 0.7646 (mttp) REVERT: L 53 LYS cc_start: 0.7689 (ttpp) cc_final: 0.7294 (ttpp) REVERT: L 68 LYS cc_start: 0.7726 (OUTLIER) cc_final: 0.7464 (tttm) REVERT: L 139 SER cc_start: 0.7928 (m) cc_final: 0.7725 (t) REVERT: L 143 LYS cc_start: 0.7950 (ttmm) cc_final: 0.7646 (mttp) REVERT: M 53 LYS cc_start: 0.7689 (ttpp) cc_final: 0.7293 (ttpp) REVERT: M 68 LYS cc_start: 0.7730 (OUTLIER) cc_final: 0.7468 (tttm) REVERT: M 139 SER cc_start: 0.7926 (m) cc_final: 0.7723 (t) REVERT: M 143 LYS cc_start: 0.7949 (ttmm) cc_final: 0.7644 (mttp) REVERT: N 53 LYS cc_start: 0.7689 (ttpp) cc_final: 0.7293 (ttpp) REVERT: N 68 LYS cc_start: 0.7728 (OUTLIER) cc_final: 0.7466 (tttm) REVERT: N 139 SER cc_start: 0.7927 (m) cc_final: 0.7723 (t) REVERT: N 143 LYS cc_start: 0.7948 (ttmm) cc_final: 0.7644 (mttp) REVERT: O 53 LYS cc_start: 0.7689 (ttpp) cc_final: 0.7293 (ttpp) REVERT: O 68 LYS cc_start: 0.7726 (OUTLIER) cc_final: 0.7464 (tttm) REVERT: O 139 SER cc_start: 0.7928 (m) cc_final: 0.7725 (t) REVERT: O 143 LYS cc_start: 0.7949 (ttmm) cc_final: 0.7646 (mttp) REVERT: P 53 LYS cc_start: 0.7690 (ttpp) cc_final: 0.7294 (ttpp) REVERT: P 68 LYS cc_start: 0.7729 (OUTLIER) cc_final: 0.7467 (tttm) REVERT: P 139 SER cc_start: 0.7927 (m) cc_final: 0.7724 (t) REVERT: P 143 LYS cc_start: 0.7949 (ttmm) cc_final: 0.7645 (mttp) REVERT: Q 53 LYS cc_start: 0.7688 (ttpp) cc_final: 0.7293 (ttpp) REVERT: Q 68 LYS cc_start: 0.7728 (OUTLIER) cc_final: 0.7466 (tttm) REVERT: Q 139 SER cc_start: 0.7927 (m) cc_final: 0.7724 (t) REVERT: Q 143 LYS cc_start: 0.7949 (ttmm) cc_final: 0.7644 (mttp) REVERT: R 53 LYS cc_start: 0.7690 (ttpp) cc_final: 0.7293 (ttpp) REVERT: R 68 LYS cc_start: 0.7727 (OUTLIER) cc_final: 0.7465 (tttm) REVERT: R 139 SER cc_start: 0.7928 (m) cc_final: 0.7725 (t) REVERT: R 143 LYS cc_start: 0.7947 (ttmm) cc_final: 0.7643 (mttp) REVERT: S 53 LYS cc_start: 0.7690 (ttpp) cc_final: 0.7294 (ttpp) REVERT: S 68 LYS cc_start: 0.7726 (OUTLIER) cc_final: 0.7464 (tttm) REVERT: S 139 SER cc_start: 0.7928 (m) cc_final: 0.7724 (t) REVERT: S 143 LYS cc_start: 0.7949 (ttmm) cc_final: 0.7644 (mttp) REVERT: T 53 LYS cc_start: 0.7689 (ttpp) cc_final: 0.7293 (ttpp) REVERT: T 68 LYS cc_start: 0.7728 (OUTLIER) cc_final: 0.7466 (tttm) REVERT: T 139 SER cc_start: 0.7927 (m) cc_final: 0.7723 (t) REVERT: T 143 LYS cc_start: 0.7948 (ttmm) cc_final: 0.7644 (mttp) REVERT: U 53 LYS cc_start: 0.7689 (ttpp) cc_final: 0.7293 (ttpp) REVERT: U 68 LYS cc_start: 0.7730 (OUTLIER) cc_final: 0.7467 (tttm) REVERT: U 139 SER cc_start: 0.7928 (m) cc_final: 0.7724 (t) REVERT: U 143 LYS cc_start: 0.7949 (ttmm) cc_final: 0.7644 (mttp) REVERT: V 53 LYS cc_start: 0.7690 (ttpp) cc_final: 0.7294 (ttpp) REVERT: V 68 LYS cc_start: 0.7727 (OUTLIER) cc_final: 0.7464 (tttm) REVERT: V 143 LYS cc_start: 0.7949 (ttmm) cc_final: 0.7654 (mttm) REVERT: W 53 LYS cc_start: 0.7688 (ttpp) cc_final: 0.7293 (ttpp) REVERT: W 68 LYS cc_start: 0.7729 (OUTLIER) cc_final: 0.7466 (tttm) REVERT: W 139 SER cc_start: 0.7927 (m) cc_final: 0.7724 (t) REVERT: W 143 LYS cc_start: 0.7947 (ttmm) cc_final: 0.7645 (mttp) REVERT: X 53 LYS cc_start: 0.7690 (ttpp) cc_final: 0.7293 (ttpp) REVERT: X 68 LYS cc_start: 0.7727 (OUTLIER) cc_final: 0.7465 (tttm) REVERT: X 143 LYS cc_start: 0.7950 (ttmm) cc_final: 0.7653 (mttm) outliers start: 48 outliers final: 0 residues processed: 660 average time/residue: 1.7991 time to fit residues: 1354.7490 Evaluate side-chains 684 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 660 time to evaluate : 3.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain C residue 68 LYS Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain G residue 68 LYS Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain I residue 68 LYS Chi-restraints excluded: chain J residue 68 LYS Chi-restraints excluded: chain K residue 68 LYS Chi-restraints excluded: chain L residue 68 LYS Chi-restraints excluded: chain M residue 68 LYS Chi-restraints excluded: chain N residue 68 LYS Chi-restraints excluded: chain O residue 68 LYS Chi-restraints excluded: chain P residue 68 LYS Chi-restraints excluded: chain Q residue 68 LYS Chi-restraints excluded: chain R residue 68 LYS Chi-restraints excluded: chain S residue 68 LYS Chi-restraints excluded: chain T residue 68 LYS Chi-restraints excluded: chain U residue 68 LYS Chi-restraints excluded: chain V residue 68 LYS Chi-restraints excluded: chain W residue 68 LYS Chi-restraints excluded: chain X residue 68 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 366 optimal weight: 1.9990 chunk 279 optimal weight: 3.9990 chunk 192 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 177 optimal weight: 3.9990 chunk 249 optimal weight: 7.9990 chunk 372 optimal weight: 3.9990 chunk 394 optimal weight: 3.9990 chunk 194 optimal weight: 3.9990 chunk 353 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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** ** 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** ** 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** M 83 GLN ** 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** T 83 GLN ** U 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 83 GLN ** V 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 83 GLN ** 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: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 35880 Z= 0.302 Angle : 0.726 6.218 48408 Z= 0.399 Chirality : 0.041 0.124 5016 Planarity : 0.005 0.038 6432 Dihedral : 13.412 179.508 4896 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.66 % Allowed : 6.41 % Favored : 92.93 % 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: 4.51 (0.12), residues: 4464 helix: 3.50 (0.08), residues: 3552 sheet: None (None), residues: 0 loop : 0.71 (0.24), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP L 93 HIS 0.007 0.002 HIS L 151 PHE 0.021 0.003 PHE V 41 TYR 0.021 0.003 TYR C 137 ARG 0.004 0.001 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 685 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 660 time to evaluate : 3.216 Fit side-chains REVERT: A 53 LYS cc_start: 0.7672 (ttpp) cc_final: 0.7244 (ttpp) REVERT: A 68 LYS cc_start: 0.7729 (ttmp) cc_final: 0.7462 (tttm) REVERT: A 143 LYS cc_start: 0.7970 (ttmm) cc_final: 0.7661 (mttm) REVERT: B 53 LYS cc_start: 0.7672 (ttpp) cc_final: 0.7243 (ttpp) REVERT: B 68 LYS cc_start: 0.7731 (ttmp) cc_final: 0.7465 (tttm) REVERT: B 143 LYS cc_start: 0.7968 (ttmm) cc_final: 0.7660 (mttm) REVERT: C 49 LYS cc_start: 0.7784 (mttm) cc_final: 0.7335 (mppt) REVERT: C 53 LYS cc_start: 0.7673 (ttpp) cc_final: 0.7246 (ttpp) REVERT: C 68 LYS cc_start: 0.7733 (ttmp) cc_final: 0.7467 (tttm) REVERT: C 143 LYS cc_start: 0.7969 (ttmm) cc_final: 0.7662 (mttm) REVERT: D 53 LYS cc_start: 0.7673 (ttpp) cc_final: 0.7246 (ttpp) REVERT: D 68 LYS cc_start: 0.7730 (ttmp) cc_final: 0.7463 (tttm) REVERT: D 143 LYS cc_start: 0.7967 (ttmm) cc_final: 0.7659 (mttm) REVERT: E 53 LYS cc_start: 0.7671 (ttpp) cc_final: 0.7244 (ttpp) REVERT: E 68 LYS cc_start: 0.7730 (ttmp) cc_final: 0.7463 (tttm) REVERT: E 143 LYS cc_start: 0.7967 (ttmm) cc_final: 0.7659 (mttm) REVERT: F 53 LYS cc_start: 0.7672 (ttpp) cc_final: 0.7245 (ttpp) REVERT: F 68 LYS cc_start: 0.7732 (ttmp) cc_final: 0.7467 (tttm) REVERT: F 143 LYS cc_start: 0.7967 (ttmm) cc_final: 0.7660 (mttm) REVERT: G 53 LYS cc_start: 0.7672 (ttpp) cc_final: 0.7244 (ttpp) REVERT: G 68 LYS cc_start: 0.7731 (ttmp) cc_final: 0.7465 (tttm) REVERT: G 143 LYS cc_start: 0.7967 (ttmm) cc_final: 0.7659 (mttm) REVERT: H 53 LYS cc_start: 0.7673 (ttpp) cc_final: 0.7246 (ttpp) REVERT: H 68 LYS cc_start: 0.7730 (ttmp) cc_final: 0.7463 (tttm) REVERT: H 143 LYS cc_start: 0.7969 (ttmm) cc_final: 0.7661 (mttm) REVERT: I 53 LYS cc_start: 0.7673 (ttpp) cc_final: 0.7245 (ttpp) REVERT: I 68 LYS cc_start: 0.7732 (ttmp) cc_final: 0.7466 (tttm) REVERT: I 143 LYS cc_start: 0.7968 (ttmm) cc_final: 0.7660 (mttm) REVERT: J 53 LYS cc_start: 0.7673 (ttpp) cc_final: 0.7245 (ttpp) REVERT: J 68 LYS cc_start: 0.7730 (ttmp) cc_final: 0.7464 (tttm) REVERT: J 143 LYS cc_start: 0.7969 (ttmm) cc_final: 0.7661 (mttm) REVERT: K 53 LYS cc_start: 0.7672 (ttpp) cc_final: 0.7245 (ttpp) REVERT: K 68 LYS cc_start: 0.7730 (ttmp) cc_final: 0.7464 (tttm) REVERT: K 143 LYS cc_start: 0.7969 (ttmm) cc_final: 0.7661 (mttm) REVERT: L 53 LYS cc_start: 0.7672 (ttpp) cc_final: 0.7244 (ttpp) REVERT: L 68 LYS cc_start: 0.7730 (ttmp) cc_final: 0.7463 (tttm) REVERT: L 143 LYS cc_start: 0.7970 (ttmm) cc_final: 0.7662 (mttm) REVERT: M 53 LYS cc_start: 0.7672 (ttpp) cc_final: 0.7245 (ttpp) REVERT: M 68 LYS cc_start: 0.7732 (ttmp) cc_final: 0.7467 (tttm) REVERT: M 143 LYS cc_start: 0.7967 (ttmm) cc_final: 0.7659 (mttm) REVERT: N 53 LYS cc_start: 0.7672 (ttpp) cc_final: 0.7244 (ttpp) REVERT: N 68 LYS cc_start: 0.7731 (ttmp) cc_final: 0.7465 (tttm) REVERT: N 143 LYS cc_start: 0.7967 (ttmm) cc_final: 0.7660 (mttm) REVERT: O 53 LYS cc_start: 0.7672 (ttpp) cc_final: 0.7244 (ttpp) REVERT: O 68 LYS cc_start: 0.7730 (ttmp) cc_final: 0.7463 (tttm) REVERT: O 143 LYS cc_start: 0.7970 (ttmm) cc_final: 0.7662 (mttm) REVERT: P 53 LYS cc_start: 0.7673 (ttpp) cc_final: 0.7245 (ttpp) REVERT: P 68 LYS cc_start: 0.7731 (ttmp) cc_final: 0.7465 (tttm) REVERT: P 143 LYS cc_start: 0.7968 (ttmm) cc_final: 0.7660 (mttm) REVERT: Q 53 LYS cc_start: 0.7672 (ttpp) cc_final: 0.7243 (ttpp) REVERT: Q 68 LYS cc_start: 0.7731 (ttmp) cc_final: 0.7466 (tttm) REVERT: Q 143 LYS cc_start: 0.7968 (ttmm) cc_final: 0.7660 (mttm) REVERT: R 53 LYS cc_start: 0.7672 (ttpp) cc_final: 0.7246 (ttpp) REVERT: R 68 LYS cc_start: 0.7731 (ttmp) cc_final: 0.7465 (tttm) REVERT: R 143 LYS cc_start: 0.7967 (ttmm) cc_final: 0.7659 (mttm) REVERT: S 53 LYS cc_start: 0.7671 (ttpp) cc_final: 0.7244 (ttpp) REVERT: S 68 LYS cc_start: 0.7730 (ttmp) cc_final: 0.7464 (tttm) REVERT: S 143 LYS cc_start: 0.7967 (ttmm) cc_final: 0.7659 (mttm) REVERT: T 53 LYS cc_start: 0.7672 (ttpp) cc_final: 0.7244 (ttpp) REVERT: T 68 LYS cc_start: 0.7731 (ttmp) cc_final: 0.7465 (tttm) REVERT: T 143 LYS cc_start: 0.7967 (ttmm) cc_final: 0.7660 (mttm) REVERT: U 53 LYS cc_start: 0.7672 (ttpp) cc_final: 0.7245 (ttpp) REVERT: U 68 LYS cc_start: 0.7731 (ttmp) cc_final: 0.7466 (tttm) REVERT: U 143 LYS cc_start: 0.7967 (ttmm) cc_final: 0.7660 (mttm) REVERT: V 53 LYS cc_start: 0.7671 (ttpp) cc_final: 0.7244 (ttpp) REVERT: V 68 LYS cc_start: 0.7730 (ttmp) cc_final: 0.7463 (tttm) REVERT: V 143 LYS cc_start: 0.7971 (ttmm) cc_final: 0.7659 (mttm) REVERT: W 53 LYS cc_start: 0.7672 (ttpp) cc_final: 0.7243 (ttpp) REVERT: W 68 LYS cc_start: 0.7731 (ttmp) cc_final: 0.7466 (tttm) REVERT: W 143 LYS cc_start: 0.7968 (ttmm) cc_final: 0.7660 (mttm) REVERT: X 53 LYS cc_start: 0.7673 (ttpp) cc_final: 0.7246 (ttpp) REVERT: X 68 LYS cc_start: 0.7731 (ttmp) cc_final: 0.7465 (tttm) REVERT: X 143 LYS cc_start: 0.7971 (ttmm) cc_final: 0.7659 (mttm) outliers start: 25 outliers final: 24 residues processed: 660 average time/residue: 1.8282 time to fit residues: 1379.9510 Evaluate side-chains 663 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 639 time to evaluate : 3.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 MET Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain F residue 165 MET Chi-restraints excluded: chain G residue 165 MET Chi-restraints excluded: chain H residue 165 MET Chi-restraints excluded: chain I residue 165 MET Chi-restraints excluded: chain J residue 165 MET Chi-restraints excluded: chain K residue 165 MET Chi-restraints excluded: chain L residue 165 MET Chi-restraints excluded: chain M residue 165 MET Chi-restraints excluded: chain N residue 165 MET Chi-restraints excluded: chain O residue 165 MET Chi-restraints excluded: chain P residue 165 MET Chi-restraints excluded: chain Q residue 165 MET Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain S residue 165 MET Chi-restraints excluded: chain T residue 165 MET Chi-restraints excluded: chain U residue 165 MET Chi-restraints excluded: chain V residue 165 MET Chi-restraints excluded: chain W residue 165 MET Chi-restraints excluded: chain X residue 165 MET 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: 9.9990 chunk 5 optimal weight: 5.9990 chunk 293 optimal weight: 0.9990 chunk 162 optimal weight: 0.6980 chunk 336 optimal weight: 0.9980 chunk 272 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 201 optimal weight: 0.6980 chunk 353 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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** ** H 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 35880 Z= 0.146 Angle : 0.520 4.873 48408 Z= 0.283 Chirality : 0.035 0.123 5016 Planarity : 0.003 0.018 6432 Dihedral : 13.393 179.974 4800 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.63 % Allowed : 7.09 % Favored : 92.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.24 (0.13), residues: 4464 helix: 4.05 (0.08), residues: 3552 sheet: None (None), residues: 0 loop : 0.79 (0.25), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP B 93 HIS 0.002 0.001 HIS V 151 PHE 0.014 0.002 PHE K 41 TYR 0.016 0.002 TYR M 137 ARG 0.001 0.000 ARG L 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 687 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 663 time to evaluate : 3.181 Fit side-chains REVERT: A 53 LYS cc_start: 0.7707 (ttpp) cc_final: 0.7309 (ttpp) REVERT: A 68 LYS cc_start: 0.7710 (ttmp) cc_final: 0.7426 (tttm) REVERT: A 143 LYS cc_start: 0.7976 (ttmm) cc_final: 0.7668 (mttm) REVERT: A 165 MET cc_start: 0.7396 (OUTLIER) cc_final: 0.6916 (tpp) REVERT: B 53 LYS cc_start: 0.7708 (ttpp) cc_final: 0.7311 (ttpp) REVERT: B 68 LYS cc_start: 0.7713 (ttmp) cc_final: 0.7428 (tttm) REVERT: B 143 LYS cc_start: 0.7975 (ttmm) cc_final: 0.7668 (mttm) REVERT: B 165 MET cc_start: 0.7396 (OUTLIER) cc_final: 0.6918 (tpp) REVERT: C 53 LYS cc_start: 0.7703 (ttpp) cc_final: 0.7308 (ttpp) REVERT: C 68 LYS cc_start: 0.7714 (ttmp) cc_final: 0.7429 (tttm) REVERT: C 143 LYS cc_start: 0.7975 (ttmm) cc_final: 0.7671 (mttm) REVERT: C 165 MET cc_start: 0.7395 (OUTLIER) cc_final: 0.6915 (tpp) REVERT: D 53 LYS cc_start: 0.7721 (ttpp) cc_final: 0.7323 (ttpp) REVERT: D 68 LYS cc_start: 0.7711 (ttmp) cc_final: 0.7427 (tttm) REVERT: D 143 LYS cc_start: 0.7974 (ttmm) cc_final: 0.7667 (mttm) REVERT: D 165 MET cc_start: 0.7396 (OUTLIER) cc_final: 0.6915 (tpp) REVERT: E 53 LYS cc_start: 0.7719 (ttpp) cc_final: 0.7320 (ttpp) REVERT: E 68 LYS cc_start: 0.7710 (ttmp) cc_final: 0.7427 (tttm) REVERT: E 143 LYS cc_start: 0.7974 (ttmm) cc_final: 0.7667 (mttm) REVERT: F 53 LYS cc_start: 0.7721 (ttpp) cc_final: 0.7323 (ttpp) REVERT: F 68 LYS cc_start: 0.7714 (ttmp) cc_final: 0.7430 (tttm) REVERT: F 143 LYS cc_start: 0.7974 (ttmm) cc_final: 0.7667 (mttm) REVERT: F 165 MET cc_start: 0.7395 (OUTLIER) cc_final: 0.6916 (tpp) REVERT: G 53 LYS cc_start: 0.7721 (ttpp) cc_final: 0.7321 (ttpp) REVERT: G 68 LYS cc_start: 0.7711 (ttmp) cc_final: 0.7426 (tttm) REVERT: G 143 LYS cc_start: 0.7973 (ttmm) cc_final: 0.7667 (mttm) REVERT: G 165 MET cc_start: 0.7396 (OUTLIER) cc_final: 0.6916 (tpp) REVERT: H 53 LYS cc_start: 0.7721 (ttpp) cc_final: 0.7323 (ttpp) REVERT: H 68 LYS cc_start: 0.7710 (ttmp) cc_final: 0.7426 (tttm) REVERT: H 143 LYS cc_start: 0.7974 (ttmm) cc_final: 0.7667 (mttm) REVERT: H 165 MET cc_start: 0.7395 (OUTLIER) cc_final: 0.6914 (tpp) REVERT: I 53 LYS cc_start: 0.7721 (ttpp) cc_final: 0.7322 (ttpp) REVERT: I 68 LYS cc_start: 0.7714 (ttmp) cc_final: 0.7430 (tttm) REVERT: I 143 LYS cc_start: 0.7973 (ttmm) cc_final: 0.7668 (mttm) REVERT: I 165 MET cc_start: 0.7395 (OUTLIER) cc_final: 0.6914 (tpp) REVERT: J 53 LYS cc_start: 0.7721 (ttpp) cc_final: 0.7323 (ttpp) REVERT: J 68 LYS cc_start: 0.7710 (ttmp) cc_final: 0.7426 (tttm) REVERT: J 143 LYS cc_start: 0.7975 (ttmm) cc_final: 0.7668 (mttm) REVERT: J 165 MET cc_start: 0.7395 (OUTLIER) cc_final: 0.6915 (tpp) REVERT: K 53 LYS cc_start: 0.7709 (ttpp) cc_final: 0.7312 (ttpp) REVERT: K 68 LYS cc_start: 0.7711 (ttmp) cc_final: 0.7427 (tttm) REVERT: K 143 LYS cc_start: 0.7976 (ttmm) cc_final: 0.7669 (mttm) REVERT: K 165 MET cc_start: 0.7395 (OUTLIER) cc_final: 0.6915 (tpp) REVERT: L 53 LYS cc_start: 0.7720 (ttpp) cc_final: 0.7321 (ttpp) REVERT: L 68 LYS cc_start: 0.7710 (ttmp) cc_final: 0.7427 (tttm) REVERT: L 143 LYS cc_start: 0.7976 (ttmm) cc_final: 0.7668 (mttm) REVERT: L 165 MET cc_start: 0.7396 (OUTLIER) cc_final: 0.6915 (tpp) REVERT: M 53 LYS cc_start: 0.7721 (ttpp) cc_final: 0.7323 (ttpp) REVERT: M 68 LYS cc_start: 0.7714 (ttmp) cc_final: 0.7430 (tttm) REVERT: M 143 LYS cc_start: 0.7974 (ttmm) cc_final: 0.7667 (mttm) REVERT: M 165 MET cc_start: 0.7395 (OUTLIER) cc_final: 0.6915 (tpp) REVERT: N 53 LYS cc_start: 0.7720 (ttpp) cc_final: 0.7320 (ttpp) REVERT: N 68 LYS cc_start: 0.7712 (ttmp) cc_final: 0.7427 (tttm) REVERT: N 143 LYS cc_start: 0.7973 (ttmm) cc_final: 0.7667 (mttm) REVERT: N 165 MET cc_start: 0.7395 (OUTLIER) cc_final: 0.6919 (tpp) REVERT: O 53 LYS cc_start: 0.7709 (ttpp) cc_final: 0.7311 (ttpp) REVERT: O 68 LYS cc_start: 0.7711 (ttmp) cc_final: 0.7427 (tttm) REVERT: O 143 LYS cc_start: 0.7974 (ttmm) cc_final: 0.7666 (mttm) REVERT: O 165 MET cc_start: 0.7396 (OUTLIER) cc_final: 0.6916 (tpp) REVERT: P 53 LYS cc_start: 0.7708 (ttpp) cc_final: 0.7312 (ttpp) REVERT: P 68 LYS cc_start: 0.7714 (ttmp) cc_final: 0.7429 (tttm) REVERT: P 143 LYS cc_start: 0.7973 (ttmm) cc_final: 0.7668 (mttm) REVERT: P 165 MET cc_start: 0.7395 (OUTLIER) cc_final: 0.6915 (tpp) REVERT: Q 53 LYS cc_start: 0.7721 (ttpp) cc_final: 0.7321 (ttpp) REVERT: Q 68 LYS cc_start: 0.7712 (ttmp) cc_final: 0.7428 (tttm) REVERT: Q 143 LYS cc_start: 0.7975 (ttmm) cc_final: 0.7668 (mttm) REVERT: Q 165 MET cc_start: 0.7395 (OUTLIER) cc_final: 0.6916 (tpp) REVERT: R 53 LYS cc_start: 0.7721 (ttpp) cc_final: 0.7322 (ttpp) REVERT: R 68 LYS cc_start: 0.7712 (ttmp) cc_final: 0.7428 (tttm) REVERT: R 143 LYS cc_start: 0.7974 (ttmm) cc_final: 0.7667 (mttm) REVERT: R 165 MET cc_start: 0.7396 (OUTLIER) cc_final: 0.6916 (tpp) REVERT: S 53 LYS cc_start: 0.7720 (ttpp) cc_final: 0.7320 (ttpp) REVERT: S 68 LYS cc_start: 0.7711 (ttmp) cc_final: 0.7427 (tttm) REVERT: S 143 LYS cc_start: 0.7974 (ttmm) cc_final: 0.7667 (mttm) REVERT: S 165 MET cc_start: 0.7396 (OUTLIER) cc_final: 0.6916 (tpp) REVERT: T 53 LYS cc_start: 0.7708 (ttpp) cc_final: 0.7310 (ttpp) REVERT: T 68 LYS cc_start: 0.7713 (ttmp) cc_final: 0.7428 (tttm) REVERT: T 143 LYS cc_start: 0.7973 (ttmm) cc_final: 0.7667 (mttm) REVERT: T 165 MET cc_start: 0.7395 (OUTLIER) cc_final: 0.6917 (tpp) REVERT: U 53 LYS cc_start: 0.7708 (ttpp) cc_final: 0.7312 (ttpp) REVERT: U 68 LYS cc_start: 0.7715 (ttmp) cc_final: 0.7430 (tttm) REVERT: U 143 LYS cc_start: 0.7974 (ttmm) cc_final: 0.7667 (mttm) REVERT: U 165 MET cc_start: 0.7395 (OUTLIER) cc_final: 0.6916 (tpp) REVERT: V 53 LYS cc_start: 0.7707 (ttpp) cc_final: 0.7309 (ttpp) REVERT: V 68 LYS cc_start: 0.7710 (ttmp) cc_final: 0.7427 (tttm) REVERT: V 143 LYS cc_start: 0.7972 (ttmm) cc_final: 0.7664 (mttm) REVERT: V 165 MET cc_start: 0.7396 (OUTLIER) cc_final: 0.6916 (tpp) REVERT: W 53 LYS cc_start: 0.7721 (ttpp) cc_final: 0.7321 (ttpp) REVERT: W 68 LYS cc_start: 0.7712 (ttmp) cc_final: 0.7427 (tttm) REVERT: W 143 LYS cc_start: 0.7975 (ttmm) cc_final: 0.7668 (mttm) REVERT: W 165 MET cc_start: 0.7396 (OUTLIER) cc_final: 0.6916 (tpp) REVERT: X 53 LYS cc_start: 0.7708 (ttpp) cc_final: 0.7312 (ttpp) REVERT: X 68 LYS cc_start: 0.7711 (ttmp) cc_final: 0.7427 (tttm) REVERT: X 143 LYS cc_start: 0.7971 (ttmm) cc_final: 0.7664 (mttm) REVERT: X 165 MET cc_start: 0.7396 (OUTLIER) cc_final: 0.6916 (tpp) outliers start: 24 outliers final: 0 residues processed: 663 average time/residue: 1.7818 time to fit residues: 1349.7245 Evaluate side-chains 662 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 639 time to evaluate : 3.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 MET Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain F residue 165 MET Chi-restraints excluded: chain G residue 165 MET Chi-restraints excluded: chain H residue 165 MET Chi-restraints excluded: chain I residue 165 MET Chi-restraints excluded: chain J residue 165 MET Chi-restraints excluded: chain K residue 165 MET Chi-restraints excluded: chain L residue 165 MET Chi-restraints excluded: chain M residue 165 MET Chi-restraints excluded: chain N residue 165 MET Chi-restraints excluded: chain O residue 165 MET Chi-restraints excluded: chain P residue 165 MET Chi-restraints excluded: chain Q residue 165 MET Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain S residue 165 MET Chi-restraints excluded: chain T residue 165 MET Chi-restraints excluded: chain U residue 165 MET Chi-restraints excluded: chain V residue 165 MET Chi-restraints excluded: chain W residue 165 MET Chi-restraints excluded: chain X residue 165 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 5.9990 chunk 355 optimal weight: 0.3980 chunk 77 optimal weight: 1.9990 chunk 231 optimal weight: 0.5980 chunk 97 optimal weight: 2.9990 chunk 394 optimal weight: 3.9990 chunk 327 optimal weight: 6.9990 chunk 182 optimal weight: 6.9990 chunk 32 optimal weight: 0.7980 chunk 130 optimal weight: 0.9990 chunk 207 optimal weight: 9.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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: 0.7639 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 35880 Z= 0.170 Angle : 0.542 4.998 48408 Z= 0.295 Chirality : 0.036 0.122 5016 Planarity : 0.003 0.020 6432 Dihedral : 13.382 179.740 4800 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.66 % Allowed : 7.28 % Favored : 92.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.17 (0.13), residues: 4464 helix: 3.99 (0.08), residues: 3552 sheet: None (None), residues: 0 loop : 0.83 (0.25), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP M 93 HIS 0.003 0.001 HIS G 128 PHE 0.016 0.002 PHE E 41 TYR 0.017 0.002 TYR J 137 ARG 0.001 0.000 ARG O 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 664 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 639 time to evaluate : 3.169 Fit side-chains REVERT: A 53 LYS cc_start: 0.7737 (ttpp) cc_final: 0.7334 (ttpp) REVERT: A 68 LYS cc_start: 0.7704 (ttmp) cc_final: 0.7420 (tttm) REVERT: A 143 LYS cc_start: 0.7968 (ttmm) cc_final: 0.7655 (mttm) REVERT: A 165 MET cc_start: 0.7398 (OUTLIER) cc_final: 0.6932 (tpp) REVERT: B 53 LYS cc_start: 0.7736 (ttpp) cc_final: 0.7333 (ttpp) REVERT: B 68 LYS cc_start: 0.7707 (ttmp) cc_final: 0.7421 (tttm) REVERT: B 143 LYS cc_start: 0.7966 (ttmm) cc_final: 0.7657 (mttm) REVERT: B 165 MET cc_start: 0.7399 (OUTLIER) cc_final: 0.6934 (tpp) REVERT: C 53 LYS cc_start: 0.7735 (ttpp) cc_final: 0.7334 (ttpp) REVERT: C 68 LYS cc_start: 0.7709 (ttmp) cc_final: 0.7424 (tttm) REVERT: C 143 LYS cc_start: 0.7965 (ttmm) cc_final: 0.7655 (mttm) REVERT: C 165 MET cc_start: 0.7398 (OUTLIER) cc_final: 0.6932 (tpp) REVERT: D 53 LYS cc_start: 0.7737 (ttpp) cc_final: 0.7336 (ttpp) REVERT: D 68 LYS cc_start: 0.7707 (ttmp) cc_final: 0.7422 (tttm) REVERT: D 143 LYS cc_start: 0.7968 (ttmm) cc_final: 0.7657 (mttm) REVERT: D 165 MET cc_start: 0.7399 (OUTLIER) cc_final: 0.6933 (tpp) REVERT: E 53 LYS cc_start: 0.7736 (ttpp) cc_final: 0.7334 (ttpp) REVERT: E 68 LYS cc_start: 0.7705 (ttmp) cc_final: 0.7421 (tttm) REVERT: E 143 LYS cc_start: 0.7969 (ttmm) cc_final: 0.7657 (mttm) REVERT: E 165 MET cc_start: 0.7391 (OUTLIER) cc_final: 0.6939 (tpp) REVERT: F 53 LYS cc_start: 0.7736 (ttpp) cc_final: 0.7334 (ttpp) REVERT: F 68 LYS cc_start: 0.7709 (ttmp) cc_final: 0.7424 (tttm) REVERT: F 143 LYS cc_start: 0.7969 (ttmm) cc_final: 0.7658 (mttm) REVERT: F 165 MET cc_start: 0.7398 (OUTLIER) cc_final: 0.6932 (tpp) REVERT: G 53 LYS cc_start: 0.7736 (ttpp) cc_final: 0.7333 (ttpp) REVERT: G 68 LYS cc_start: 0.7706 (ttmp) cc_final: 0.7421 (tttm) REVERT: G 143 LYS cc_start: 0.7968 (ttmm) cc_final: 0.7657 (mttm) REVERT: G 165 MET cc_start: 0.7398 (OUTLIER) cc_final: 0.6932 (tpp) REVERT: H 53 LYS cc_start: 0.7737 (ttpp) cc_final: 0.7335 (ttpp) REVERT: H 68 LYS cc_start: 0.7705 (ttmp) cc_final: 0.7420 (tttm) REVERT: H 143 LYS cc_start: 0.7966 (ttmm) cc_final: 0.7655 (mttm) REVERT: H 165 MET cc_start: 0.7398 (OUTLIER) cc_final: 0.6931 (tpp) REVERT: I 53 LYS cc_start: 0.7739 (ttpp) cc_final: 0.7336 (ttpp) REVERT: I 68 LYS cc_start: 0.7708 (ttmp) cc_final: 0.7424 (tttm) REVERT: I 143 LYS cc_start: 0.7967 (ttmm) cc_final: 0.7659 (mttm) REVERT: I 165 MET cc_start: 0.7397 (OUTLIER) cc_final: 0.6931 (tpp) REVERT: J 53 LYS cc_start: 0.7739 (ttpp) cc_final: 0.7337 (ttpp) REVERT: J 68 LYS cc_start: 0.7705 (ttmp) cc_final: 0.7421 (tttm) REVERT: J 143 LYS cc_start: 0.7969 (ttmm) cc_final: 0.7658 (mttm) REVERT: J 165 MET cc_start: 0.7398 (OUTLIER) cc_final: 0.6932 (tpp) REVERT: K 53 LYS cc_start: 0.7737 (ttpp) cc_final: 0.7335 (ttpp) REVERT: K 68 LYS cc_start: 0.7706 (ttmp) cc_final: 0.7422 (tttm) REVERT: K 143 LYS cc_start: 0.7971 (ttmm) cc_final: 0.7660 (mttm) REVERT: K 165 MET cc_start: 0.7398 (OUTLIER) cc_final: 0.6932 (tpp) REVERT: L 53 LYS cc_start: 0.7737 (ttpp) cc_final: 0.7334 (ttpp) REVERT: L 68 LYS cc_start: 0.7705 (ttmp) cc_final: 0.7422 (tttm) REVERT: L 143 LYS cc_start: 0.7971 (ttmm) cc_final: 0.7659 (mttm) REVERT: L 165 MET cc_start: 0.7398 (OUTLIER) cc_final: 0.6933 (tpp) REVERT: M 53 LYS cc_start: 0.7736 (ttpp) cc_final: 0.7334 (ttpp) REVERT: M 68 LYS cc_start: 0.7708 (ttmp) cc_final: 0.7423 (tttm) REVERT: M 143 LYS cc_start: 0.7966 (ttmm) cc_final: 0.7654 (mttm) REVERT: M 165 MET cc_start: 0.7398 (OUTLIER) cc_final: 0.6933 (tpp) REVERT: N 53 LYS cc_start: 0.7735 (ttpp) cc_final: 0.7332 (ttpp) REVERT: N 68 LYS cc_start: 0.7706 (ttmp) cc_final: 0.7421 (tttm) REVERT: N 143 LYS cc_start: 0.7965 (ttmm) cc_final: 0.7653 (mttm) REVERT: N 165 MET cc_start: 0.7398 (OUTLIER) cc_final: 0.6932 (tpp) REVERT: O 53 LYS cc_start: 0.7736 (ttpp) cc_final: 0.7333 (ttpp) REVERT: O 68 LYS cc_start: 0.7706 (ttmp) cc_final: 0.7421 (tttm) REVERT: O 143 LYS cc_start: 0.7969 (ttmm) cc_final: 0.7657 (mttm) REVERT: O 165 MET cc_start: 0.7398 (OUTLIER) cc_final: 0.6933 (tpp) REVERT: P 53 LYS cc_start: 0.7736 (ttpp) cc_final: 0.7334 (ttpp) REVERT: P 68 LYS cc_start: 0.7709 (ttmp) cc_final: 0.7424 (tttm) REVERT: P 143 LYS cc_start: 0.7967 (ttmm) cc_final: 0.7659 (mttm) REVERT: P 165 MET cc_start: 0.7398 (OUTLIER) cc_final: 0.6933 (tpp) REVERT: Q 53 LYS cc_start: 0.7736 (ttpp) cc_final: 0.7333 (ttpp) REVERT: Q 68 LYS cc_start: 0.7707 (ttmp) cc_final: 0.7423 (tttm) REVERT: Q 143 LYS cc_start: 0.7966 (ttmm) cc_final: 0.7658 (mttm) REVERT: Q 165 MET cc_start: 0.7398 (OUTLIER) cc_final: 0.6933 (tpp) REVERT: R 53 LYS cc_start: 0.7737 (ttpp) cc_final: 0.7335 (ttpp) REVERT: R 68 LYS cc_start: 0.7706 (ttmp) cc_final: 0.7422 (tttm) REVERT: R 143 LYS cc_start: 0.7968 (ttmm) cc_final: 0.7657 (mttm) REVERT: R 165 MET cc_start: 0.7399 (OUTLIER) cc_final: 0.6933 (tpp) REVERT: S 53 LYS cc_start: 0.7737 (ttpp) cc_final: 0.7334 (ttpp) REVERT: S 68 LYS cc_start: 0.7705 (ttmp) cc_final: 0.7421 (tttm) REVERT: S 143 LYS cc_start: 0.7969 (ttmm) cc_final: 0.7658 (mttm) REVERT: S 165 MET cc_start: 0.7399 (OUTLIER) cc_final: 0.6933 (tpp) REVERT: T 53 LYS cc_start: 0.7735 (ttpp) cc_final: 0.7332 (ttpp) REVERT: T 68 LYS cc_start: 0.7707 (ttmp) cc_final: 0.7422 (tttm) REVERT: T 143 LYS cc_start: 0.7968 (ttmm) cc_final: 0.7657 (mttm) REVERT: T 165 MET cc_start: 0.7398 (OUTLIER) cc_final: 0.6932 (tpp) REVERT: U 53 LYS cc_start: 0.7736 (ttpp) cc_final: 0.7334 (ttpp) REVERT: U 68 LYS cc_start: 0.7708 (ttmp) cc_final: 0.7423 (tttm) REVERT: U 143 LYS cc_start: 0.7969 (ttmm) cc_final: 0.7658 (mttm) REVERT: U 165 MET cc_start: 0.7398 (OUTLIER) cc_final: 0.6932 (tpp) REVERT: V 53 LYS cc_start: 0.7736 (ttpp) cc_final: 0.7333 (ttpp) REVERT: V 68 LYS cc_start: 0.7705 (ttmp) cc_final: 0.7421 (tttm) REVERT: V 143 LYS cc_start: 0.7967 (ttmm) cc_final: 0.7654 (mttm) REVERT: V 165 MET cc_start: 0.7399 (OUTLIER) cc_final: 0.6933 (tpp) REVERT: W 53 LYS cc_start: 0.7736 (ttpp) cc_final: 0.7333 (ttpp) REVERT: W 68 LYS cc_start: 0.7708 (ttmp) cc_final: 0.7423 (tttm) REVERT: W 143 LYS cc_start: 0.7966 (ttmm) cc_final: 0.7657 (mttm) REVERT: W 165 MET cc_start: 0.7398 (OUTLIER) cc_final: 0.6934 (tpp) REVERT: X 53 LYS cc_start: 0.7736 (ttpp) cc_final: 0.7334 (ttpp) REVERT: X 68 LYS cc_start: 0.7706 (ttmp) cc_final: 0.7421 (tttm) REVERT: X 143 LYS cc_start: 0.7966 (ttmm) cc_final: 0.7654 (mttm) REVERT: X 165 MET cc_start: 0.7399 (OUTLIER) cc_final: 0.6932 (tpp) outliers start: 25 outliers final: 0 residues processed: 639 average time/residue: 1.8622 time to fit residues: 1365.4934 Evaluate side-chains 663 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 639 time to evaluate : 3.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 MET Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain F residue 165 MET Chi-restraints excluded: chain G residue 165 MET Chi-restraints excluded: chain H residue 165 MET Chi-restraints excluded: chain I residue 165 MET Chi-restraints excluded: chain J residue 165 MET Chi-restraints excluded: chain K residue 165 MET Chi-restraints excluded: chain L residue 165 MET Chi-restraints excluded: chain M residue 165 MET Chi-restraints excluded: chain N residue 165 MET Chi-restraints excluded: chain O residue 165 MET Chi-restraints excluded: chain P residue 165 MET Chi-restraints excluded: chain Q residue 165 MET Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain S residue 165 MET Chi-restraints excluded: chain T residue 165 MET Chi-restraints excluded: chain U residue 165 MET Chi-restraints excluded: chain V residue 165 MET Chi-restraints excluded: chain W residue 165 MET Chi-restraints excluded: chain X residue 165 MET 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: 0.6980 chunk 224 optimal weight: 0.9980 chunk 288 optimal weight: 0.9990 chunk 223 optimal weight: 1.9990 chunk 332 optimal weight: 1.9990 chunk 220 optimal weight: 0.6980 chunk 393 optimal weight: 7.9990 chunk 246 optimal weight: 0.6980 chunk 239 optimal weight: 7.9990 chunk 181 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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: 0.7630 moved from start: 0.2455 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= 0.162 Angle : 0.523 4.899 48408 Z= 0.285 Chirality : 0.036 0.122 5016 Planarity : 0.003 0.020 6432 Dihedral : 13.382 179.913 4800 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.63 % Allowed : 7.23 % Favored : 92.14 % 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: 5.26 (0.13), residues: 4464 helix: 4.04 (0.08), residues: 3552 sheet: None (None), residues: 0 loop : 0.93 (0.25), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP W 93 HIS 0.003 0.001 HIS W 128 PHE 0.014 0.002 PHE O 41 TYR 0.016 0.002 TYR Q 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 663 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 639 time to evaluate : 3.233 Fit side-chains REVERT: A 53 LYS cc_start: 0.7724 (ttpp) cc_final: 0.7321 (ttpp) REVERT: A 68 LYS cc_start: 0.7703 (ttmp) cc_final: 0.7420 (tttm) REVERT: A 143 LYS cc_start: 0.7953 (ttmm) cc_final: 0.7646 (mttm) REVERT: A 165 MET cc_start: 0.7391 (OUTLIER) cc_final: 0.6930 (tpp) REVERT: B 53 LYS cc_start: 0.7724 (ttpp) cc_final: 0.7321 (ttpp) REVERT: B 68 LYS cc_start: 0.7705 (ttmp) cc_final: 0.7422 (tttm) REVERT: B 143 LYS cc_start: 0.7951 (ttmm) cc_final: 0.7646 (mttm) REVERT: B 165 MET cc_start: 0.7396 (OUTLIER) cc_final: 0.6936 (tpp) REVERT: C 53 LYS cc_start: 0.7723 (ttpp) cc_final: 0.7323 (ttpp) REVERT: C 68 LYS cc_start: 0.7707 (ttmp) cc_final: 0.7423 (tttm) REVERT: C 143 LYS cc_start: 0.7951 (ttmm) cc_final: 0.7645 (mttm) REVERT: C 165 MET cc_start: 0.7390 (OUTLIER) cc_final: 0.6930 (tpp) REVERT: D 53 LYS cc_start: 0.7724 (ttpp) cc_final: 0.7323 (ttpp) REVERT: D 68 LYS cc_start: 0.7704 (ttmp) cc_final: 0.7422 (tttm) REVERT: D 143 LYS cc_start: 0.7950 (ttmm) cc_final: 0.7645 (mttm) REVERT: D 165 MET cc_start: 0.7391 (OUTLIER) cc_final: 0.6929 (tpp) REVERT: E 53 LYS cc_start: 0.7723 (ttpp) cc_final: 0.7321 (ttpp) REVERT: E 68 LYS cc_start: 0.7704 (ttmp) cc_final: 0.7421 (tttm) REVERT: E 143 LYS cc_start: 0.7951 (ttmm) cc_final: 0.7645 (mttm) REVERT: E 165 MET cc_start: 0.7386 (OUTLIER) cc_final: 0.6938 (tpp) REVERT: F 53 LYS cc_start: 0.7724 (ttpp) cc_final: 0.7322 (ttpp) REVERT: F 68 LYS cc_start: 0.7706 (ttmp) cc_final: 0.7471 (tttm) REVERT: F 143 LYS cc_start: 0.7951 (ttmm) cc_final: 0.7646 (mttm) REVERT: F 165 MET cc_start: 0.7390 (OUTLIER) cc_final: 0.6930 (tpp) REVERT: G 53 LYS cc_start: 0.7723 (ttpp) cc_final: 0.7320 (ttpp) REVERT: G 68 LYS cc_start: 0.7704 (ttmp) cc_final: 0.7469 (tttm) REVERT: G 143 LYS cc_start: 0.7950 (ttmm) cc_final: 0.7644 (mttm) REVERT: G 165 MET cc_start: 0.7396 (OUTLIER) cc_final: 0.6934 (tpp) REVERT: H 53 LYS cc_start: 0.7723 (ttpp) cc_final: 0.7322 (ttpp) REVERT: H 68 LYS cc_start: 0.7703 (ttmp) cc_final: 0.7421 (tttm) REVERT: H 143 LYS cc_start: 0.7951 (ttmm) cc_final: 0.7646 (mttm) REVERT: H 165 MET cc_start: 0.7390 (OUTLIER) cc_final: 0.6928 (tpp) REVERT: I 53 LYS cc_start: 0.7725 (ttpp) cc_final: 0.7323 (ttpp) REVERT: I 68 LYS cc_start: 0.7706 (ttmp) cc_final: 0.7423 (tttm) REVERT: I 143 LYS cc_start: 0.7951 (ttmm) cc_final: 0.7646 (mttm) REVERT: I 165 MET cc_start: 0.7390 (OUTLIER) cc_final: 0.6929 (tpp) REVERT: J 53 LYS cc_start: 0.7725 (ttpp) cc_final: 0.7323 (ttpp) REVERT: J 68 LYS cc_start: 0.7703 (ttmp) cc_final: 0.7468 (tttm) REVERT: J 143 LYS cc_start: 0.7951 (ttmm) cc_final: 0.7646 (mttm) REVERT: J 165 MET cc_start: 0.7390 (OUTLIER) cc_final: 0.6929 (tpp) REVERT: K 53 LYS cc_start: 0.7723 (ttpp) cc_final: 0.7322 (ttpp) REVERT: K 68 LYS cc_start: 0.7703 (ttmp) cc_final: 0.7468 (tttm) REVERT: K 143 LYS cc_start: 0.7953 (ttmm) cc_final: 0.7648 (mttm) REVERT: K 165 MET cc_start: 0.7390 (OUTLIER) cc_final: 0.6929 (tpp) REVERT: L 53 LYS cc_start: 0.7723 (ttpp) cc_final: 0.7320 (ttpp) REVERT: L 68 LYS cc_start: 0.7703 (ttmp) cc_final: 0.7467 (tttm) REVERT: L 143 LYS cc_start: 0.7953 (ttmm) cc_final: 0.7646 (mttm) REVERT: L 165 MET cc_start: 0.7391 (OUTLIER) cc_final: 0.6930 (tpp) REVERT: M 53 LYS cc_start: 0.7725 (ttpp) cc_final: 0.7323 (ttpp) REVERT: M 68 LYS cc_start: 0.7707 (ttmp) cc_final: 0.7423 (tttm) REVERT: M 143 LYS cc_start: 0.7951 (ttmm) cc_final: 0.7645 (mttm) REVERT: M 165 MET cc_start: 0.7390 (OUTLIER) cc_final: 0.6930 (tpp) REVERT: N 53 LYS cc_start: 0.7722 (ttpp) cc_final: 0.7320 (ttpp) REVERT: N 68 LYS cc_start: 0.7705 (ttmp) cc_final: 0.7422 (tttm) REVERT: N 143 LYS cc_start: 0.7950 (ttmm) cc_final: 0.7645 (mttm) REVERT: N 165 MET cc_start: 0.7390 (OUTLIER) cc_final: 0.6930 (tpp) REVERT: O 53 LYS cc_start: 0.7722 (ttpp) cc_final: 0.7319 (ttpp) REVERT: O 68 LYS cc_start: 0.7703 (ttmp) cc_final: 0.7420 (tttm) REVERT: O 143 LYS cc_start: 0.7951 (ttmm) cc_final: 0.7644 (mttm) REVERT: O 165 MET cc_start: 0.7391 (OUTLIER) cc_final: 0.6930 (tpp) REVERT: P 53 LYS cc_start: 0.7724 (ttpp) cc_final: 0.7322 (ttpp) REVERT: P 68 LYS cc_start: 0.7707 (ttmp) cc_final: 0.7423 (tttm) REVERT: P 143 LYS cc_start: 0.7951 (ttmm) cc_final: 0.7645 (mttm) REVERT: P 165 MET cc_start: 0.7390 (OUTLIER) cc_final: 0.6930 (tpp) REVERT: Q 53 LYS cc_start: 0.7724 (ttpp) cc_final: 0.7320 (ttpp) REVERT: Q 68 LYS cc_start: 0.7704 (ttmp) cc_final: 0.7468 (tttm) REVERT: Q 143 LYS cc_start: 0.7951 (ttmm) cc_final: 0.7646 (mttm) REVERT: Q 165 MET cc_start: 0.7390 (OUTLIER) cc_final: 0.6929 (tpp) REVERT: R 53 LYS cc_start: 0.7724 (ttpp) cc_final: 0.7322 (ttpp) REVERT: R 68 LYS cc_start: 0.7705 (ttmp) cc_final: 0.7422 (tttm) REVERT: R 143 LYS cc_start: 0.7950 (ttmm) cc_final: 0.7645 (mttm) REVERT: R 165 MET cc_start: 0.7397 (OUTLIER) cc_final: 0.6935 (tpp) REVERT: S 53 LYS cc_start: 0.7724 (ttpp) cc_final: 0.7321 (ttpp) REVERT: S 68 LYS cc_start: 0.7703 (ttmp) cc_final: 0.7468 (tttm) REVERT: S 143 LYS cc_start: 0.7951 (ttmm) cc_final: 0.7645 (mttm) REVERT: S 165 MET cc_start: 0.7391 (OUTLIER) cc_final: 0.6929 (tpp) REVERT: T 53 LYS cc_start: 0.7722 (ttpp) cc_final: 0.7319 (ttpp) REVERT: T 68 LYS cc_start: 0.7704 (ttmp) cc_final: 0.7421 (tttm) REVERT: T 143 LYS cc_start: 0.7950 (ttmm) cc_final: 0.7644 (mttm) REVERT: T 165 MET cc_start: 0.7390 (OUTLIER) cc_final: 0.6929 (tpp) REVERT: U 53 LYS cc_start: 0.7723 (ttpp) cc_final: 0.7321 (ttpp) REVERT: U 68 LYS cc_start: 0.7705 (ttmp) cc_final: 0.7470 (tttm) REVERT: U 143 LYS cc_start: 0.7951 (ttmm) cc_final: 0.7646 (mttm) REVERT: U 165 MET cc_start: 0.7396 (OUTLIER) cc_final: 0.6935 (tpp) REVERT: V 53 LYS cc_start: 0.7722 (ttpp) cc_final: 0.7320 (ttpp) REVERT: V 68 LYS cc_start: 0.7703 (ttmp) cc_final: 0.7421 (tttm) REVERT: V 143 LYS cc_start: 0.7953 (ttmm) cc_final: 0.7646 (mttm) REVERT: V 165 MET cc_start: 0.7396 (OUTLIER) cc_final: 0.6934 (tpp) REVERT: W 53 LYS cc_start: 0.7724 (ttpp) cc_final: 0.7321 (ttpp) REVERT: W 68 LYS cc_start: 0.7704 (ttmp) cc_final: 0.7468 (tttm) REVERT: W 143 LYS cc_start: 0.7951 (ttmm) cc_final: 0.7645 (mttm) REVERT: W 165 MET cc_start: 0.7396 (OUTLIER) cc_final: 0.6934 (tpp) REVERT: X 53 LYS cc_start: 0.7723 (ttpp) cc_final: 0.7321 (ttpp) REVERT: X 68 LYS cc_start: 0.7704 (ttmp) cc_final: 0.7469 (tttm) REVERT: X 143 LYS cc_start: 0.7953 (ttmm) cc_final: 0.7648 (mttm) REVERT: X 165 MET cc_start: 0.7392 (OUTLIER) cc_final: 0.6930 (tpp) outliers start: 24 outliers final: 0 residues processed: 639 average time/residue: 1.8338 time to fit residues: 1333.5989 Evaluate side-chains 663 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 639 time to evaluate : 3.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 MET Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain F residue 165 MET Chi-restraints excluded: chain G residue 165 MET Chi-restraints excluded: chain H residue 165 MET Chi-restraints excluded: chain I residue 165 MET Chi-restraints excluded: chain J residue 165 MET Chi-restraints excluded: chain K residue 165 MET Chi-restraints excluded: chain L residue 165 MET Chi-restraints excluded: chain M residue 165 MET Chi-restraints excluded: chain N residue 165 MET Chi-restraints excluded: chain O residue 165 MET Chi-restraints excluded: chain P residue 165 MET Chi-restraints excluded: chain Q residue 165 MET Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain S residue 165 MET Chi-restraints excluded: chain T residue 165 MET Chi-restraints excluded: chain U residue 165 MET Chi-restraints excluded: chain V residue 165 MET Chi-restraints excluded: chain W residue 165 MET Chi-restraints excluded: chain X residue 165 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 3.9990 chunk 157 optimal weight: 1.9990 chunk 234 optimal weight: 2.9990 chunk 118 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 250 optimal weight: 6.9990 chunk 267 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 309 optimal weight: 2.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 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** ** O 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 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** ** W 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 35880 Z= 0.216 Angle : 0.586 5.429 48408 Z= 0.321 Chirality : 0.037 0.124 5016 Planarity : 0.003 0.020 6432 Dihedral : 13.370 179.265 4800 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.63 % Allowed : 7.52 % Favored : 91.85 % 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: 4.93 (0.13), residues: 4464 helix: 3.81 (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 0.013 0.003 TRP F 93 HIS 0.004 0.001 HIS U 128 PHE 0.018 0.002 PHE V 41 TYR 0.017 0.002 TYR K 137 ARG 0.002 0.000 ARG T 156 *********************** 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 663 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 639 time to evaluate : 3.236 Fit side-chains REVERT: A 53 LYS cc_start: 0.7683 (ttpp) cc_final: 0.7262 (ttpp) REVERT: A 68 LYS cc_start: 0.7719 (ttmp) cc_final: 0.7462 (tttm) REVERT: A 143 LYS cc_start: 0.7960 (ttmm) cc_final: 0.7653 (mttm) REVERT: A 165 MET cc_start: 0.7428 (OUTLIER) cc_final: 0.6967 (tpp) REVERT: B 53 LYS cc_start: 0.7684 (ttpp) cc_final: 0.7263 (ttpp) REVERT: B 68 LYS cc_start: 0.7721 (ttmp) cc_final: 0.7463 (tttm) REVERT: B 143 LYS cc_start: 0.7955 (ttmm) cc_final: 0.7653 (mttm) REVERT: B 165 MET cc_start: 0.7427 (OUTLIER) cc_final: 0.6968 (tpp) REVERT: C 53 LYS cc_start: 0.7690 (ttpp) cc_final: 0.7272 (ttpp) REVERT: C 68 LYS cc_start: 0.7720 (ttmp) cc_final: 0.7462 (tttm) REVERT: C 143 LYS cc_start: 0.7956 (ttmm) cc_final: 0.7652 (mttm) REVERT: C 165 MET cc_start: 0.7426 (OUTLIER) cc_final: 0.6966 (tpp) REVERT: D 53 LYS cc_start: 0.7684 (ttpp) cc_final: 0.7265 (ttpp) REVERT: D 68 LYS cc_start: 0.7721 (ttmp) cc_final: 0.7463 (tttm) REVERT: D 143 LYS cc_start: 0.7957 (ttmm) cc_final: 0.7651 (mttm) REVERT: D 165 MET cc_start: 0.7427 (OUTLIER) cc_final: 0.6965 (tpp) REVERT: E 53 LYS cc_start: 0.7683 (ttpp) cc_final: 0.7262 (ttpp) REVERT: E 68 LYS cc_start: 0.7720 (ttmp) cc_final: 0.7462 (tttm) REVERT: E 143 LYS cc_start: 0.7957 (ttmm) cc_final: 0.7650 (mttm) REVERT: E 165 MET cc_start: 0.7423 (OUTLIER) cc_final: 0.6976 (tpp) REVERT: F 53 LYS cc_start: 0.7682 (ttpp) cc_final: 0.7262 (ttpp) REVERT: F 68 LYS cc_start: 0.7723 (ttmp) cc_final: 0.7466 (tttm) REVERT: F 143 LYS cc_start: 0.7950 (ttmm) cc_final: 0.7646 (mttm) REVERT: F 165 MET cc_start: 0.7426 (OUTLIER) cc_final: 0.6966 (tpp) REVERT: G 53 LYS cc_start: 0.7682 (ttpp) cc_final: 0.7261 (ttpp) REVERT: G 68 LYS cc_start: 0.7722 (ttmp) cc_final: 0.7463 (tttm) REVERT: G 143 LYS cc_start: 0.7957 (ttmm) cc_final: 0.7651 (mttm) REVERT: G 165 MET cc_start: 0.7426 (OUTLIER) cc_final: 0.6966 (tpp) REVERT: H 53 LYS cc_start: 0.7685 (ttpp) cc_final: 0.7265 (ttpp) REVERT: H 68 LYS cc_start: 0.7721 (ttmp) cc_final: 0.7463 (tttm) REVERT: H 143 LYS cc_start: 0.7959 (ttmm) cc_final: 0.7653 (mttm) REVERT: H 165 MET cc_start: 0.7427 (OUTLIER) cc_final: 0.6966 (tpp) REVERT: I 53 LYS cc_start: 0.7684 (ttpp) cc_final: 0.7263 (ttpp) REVERT: I 68 LYS cc_start: 0.7719 (ttmp) cc_final: 0.7461 (tttm) REVERT: I 143 LYS cc_start: 0.7955 (ttmm) cc_final: 0.7652 (mttm) REVERT: I 165 MET cc_start: 0.7427 (OUTLIER) cc_final: 0.6966 (tpp) REVERT: J 53 LYS cc_start: 0.7683 (ttpp) cc_final: 0.7263 (ttpp) REVERT: J 68 LYS cc_start: 0.7721 (ttmp) cc_final: 0.7463 (tttm) REVERT: J 143 LYS cc_start: 0.7958 (ttmm) cc_final: 0.7654 (mttm) REVERT: J 165 MET cc_start: 0.7427 (OUTLIER) cc_final: 0.6966 (tpp) REVERT: K 53 LYS cc_start: 0.7682 (ttpp) cc_final: 0.7263 (ttpp) REVERT: K 68 LYS cc_start: 0.7721 (ttmp) cc_final: 0.7463 (tttm) REVERT: K 143 LYS cc_start: 0.7958 (ttmm) cc_final: 0.7654 (mttm) REVERT: K 165 MET cc_start: 0.7427 (OUTLIER) cc_final: 0.6966 (tpp) REVERT: L 53 LYS cc_start: 0.7685 (ttpp) cc_final: 0.7264 (ttpp) REVERT: L 68 LYS cc_start: 0.7720 (ttmp) cc_final: 0.7462 (tttm) REVERT: L 143 LYS cc_start: 0.7959 (ttmm) cc_final: 0.7653 (mttm) REVERT: L 165 MET cc_start: 0.7427 (OUTLIER) cc_final: 0.6967 (tpp) REVERT: M 53 LYS cc_start: 0.7682 (ttpp) cc_final: 0.7262 (ttpp) REVERT: M 68 LYS cc_start: 0.7723 (ttmp) cc_final: 0.7465 (tttm) REVERT: M 143 LYS cc_start: 0.7958 (ttmm) cc_final: 0.7652 (mttm) REVERT: M 165 MET cc_start: 0.7426 (OUTLIER) cc_final: 0.6967 (tpp) REVERT: N 53 LYS cc_start: 0.7684 (ttpp) cc_final: 0.7263 (ttpp) REVERT: N 68 LYS cc_start: 0.7722 (ttmp) cc_final: 0.7464 (tttm) REVERT: N 143 LYS cc_start: 0.7958 (ttmm) cc_final: 0.7652 (mttm) REVERT: N 165 MET cc_start: 0.7426 (OUTLIER) cc_final: 0.6967 (tpp) REVERT: O 53 LYS cc_start: 0.7683 (ttpp) cc_final: 0.7262 (ttpp) REVERT: O 68 LYS cc_start: 0.7716 (ttmp) cc_final: 0.7458 (tttm) REVERT: O 143 LYS cc_start: 0.7959 (ttmm) cc_final: 0.7653 (mttm) REVERT: O 165 MET cc_start: 0.7427 (OUTLIER) cc_final: 0.6967 (tpp) REVERT: P 53 LYS cc_start: 0.7683 (ttpp) cc_final: 0.7263 (ttpp) REVERT: P 68 LYS cc_start: 0.7723 (ttmp) cc_final: 0.7465 (tttm) REVERT: P 143 LYS cc_start: 0.7955 (ttmm) cc_final: 0.7653 (mttm) REVERT: P 165 MET cc_start: 0.7427 (OUTLIER) cc_final: 0.6967 (tpp) REVERT: Q 53 LYS cc_start: 0.7682 (ttpp) cc_final: 0.7261 (ttpp) REVERT: Q 68 LYS cc_start: 0.7722 (ttmp) cc_final: 0.7464 (tttm) REVERT: Q 143 LYS cc_start: 0.7955 (ttmm) cc_final: 0.7653 (mttm) REVERT: Q 165 MET cc_start: 0.7427 (OUTLIER) cc_final: 0.6966 (tpp) REVERT: R 53 LYS cc_start: 0.7682 (ttpp) cc_final: 0.7262 (ttpp) REVERT: R 68 LYS cc_start: 0.7720 (ttmp) cc_final: 0.7462 (tttm) REVERT: R 143 LYS cc_start: 0.7957 (ttmm) cc_final: 0.7651 (mttm) REVERT: R 165 MET cc_start: 0.7427 (OUTLIER) cc_final: 0.6966 (tpp) REVERT: S 53 LYS cc_start: 0.7682 (ttpp) cc_final: 0.7262 (ttpp) REVERT: S 68 LYS cc_start: 0.7717 (ttmp) cc_final: 0.7458 (tttm) REVERT: S 143 LYS cc_start: 0.7957 (ttmm) cc_final: 0.7651 (mttm) REVERT: S 165 MET cc_start: 0.7427 (OUTLIER) cc_final: 0.6966 (tpp) REVERT: T 53 LYS cc_start: 0.7682 (ttpp) cc_final: 0.7260 (ttpp) REVERT: T 68 LYS cc_start: 0.7718 (ttmp) cc_final: 0.7459 (tttm) REVERT: T 143 LYS cc_start: 0.7956 (ttmm) cc_final: 0.7651 (mttm) REVERT: T 165 MET cc_start: 0.7426 (OUTLIER) cc_final: 0.6966 (tpp) REVERT: U 53 LYS cc_start: 0.7682 (ttpp) cc_final: 0.7262 (ttpp) REVERT: U 68 LYS cc_start: 0.7719 (ttmp) cc_final: 0.7461 (tttm) REVERT: U 143 LYS cc_start: 0.7957 (ttmm) cc_final: 0.7652 (mttm) REVERT: U 165 MET cc_start: 0.7426 (OUTLIER) cc_final: 0.6966 (tpp) REVERT: V 53 LYS cc_start: 0.7683 (ttpp) cc_final: 0.7262 (ttpp) REVERT: V 68 LYS cc_start: 0.7720 (ttmp) cc_final: 0.7462 (tttm) REVERT: V 143 LYS cc_start: 0.7954 (ttmm) cc_final: 0.7648 (mttm) REVERT: V 165 MET cc_start: 0.7427 (OUTLIER) cc_final: 0.6966 (tpp) REVERT: W 53 LYS cc_start: 0.7682 (ttpp) cc_final: 0.7261 (ttpp) REVERT: W 68 LYS cc_start: 0.7721 (ttmp) cc_final: 0.7464 (tttm) REVERT: W 143 LYS cc_start: 0.7956 (ttmm) cc_final: 0.7653 (mttm) REVERT: W 165 MET cc_start: 0.7426 (OUTLIER) cc_final: 0.6967 (tpp) REVERT: X 53 LYS cc_start: 0.7681 (ttpp) cc_final: 0.7262 (ttpp) REVERT: X 68 LYS cc_start: 0.7720 (ttmp) cc_final: 0.7463 (tttm) REVERT: X 143 LYS cc_start: 0.7954 (ttmm) cc_final: 0.7648 (mttm) REVERT: X 165 MET cc_start: 0.7427 (OUTLIER) cc_final: 0.6965 (tpp) outliers start: 24 outliers final: 0 residues processed: 639 average time/residue: 1.9214 time to fit residues: 1421.8773 Evaluate side-chains 639 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 615 time to evaluate : 3.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 MET Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain F residue 165 MET Chi-restraints excluded: chain G residue 165 MET Chi-restraints excluded: chain H residue 165 MET Chi-restraints excluded: chain I residue 165 MET Chi-restraints excluded: chain J residue 165 MET Chi-restraints excluded: chain K residue 165 MET Chi-restraints excluded: chain L residue 165 MET Chi-restraints excluded: chain M residue 165 MET Chi-restraints excluded: chain N residue 165 MET Chi-restraints excluded: chain O residue 165 MET Chi-restraints excluded: chain P residue 165 MET Chi-restraints excluded: chain Q residue 165 MET Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain S residue 165 MET Chi-restraints excluded: chain T residue 165 MET Chi-restraints excluded: chain U residue 165 MET Chi-restraints excluded: chain V residue 165 MET Chi-restraints excluded: chain W residue 165 MET Chi-restraints excluded: chain X residue 165 MET 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: 3.9990 chunk 366 optimal weight: 1.9990 chunk 220 optimal weight: 0.5980 chunk 159 optimal weight: 7.9990 chunk 287 optimal weight: 0.7980 chunk 112 optimal weight: 0.7980 chunk 331 optimal weight: 0.0370 chunk 346 optimal weight: 3.9990 chunk 365 optimal weight: 0.8980 overall best weight: 0.6258 ------------------------------------------------------------------------------- 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: 0.7620 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 35880 Z= 0.149 Angle : 0.503 4.660 48408 Z= 0.274 Chirality : 0.035 0.124 5016 Planarity : 0.003 0.020 6432 Dihedral : 13.372 179.871 4800 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.63 % Allowed : 6.65 % Favored : 92.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.32 (0.13), residues: 4464 helix: 4.08 (0.08), residues: 3552 sheet: None (None), residues: 0 loop : 0.96 (0.25), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP D 93 HIS 0.002 0.001 HIS A 128 PHE 0.013 0.002 PHE D 41 TYR 0.015 0.001 TYR W 137 ARG 0.001 0.000 ARG G 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 687 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 663 time to evaluate : 3.387 Fit side-chains REVERT: A 53 LYS cc_start: 0.7714 (ttpp) cc_final: 0.7312 (ttpp) REVERT: A 68 LYS cc_start: 0.7700 (ttmp) cc_final: 0.7418 (tttm) REVERT: A 143 LYS cc_start: 0.7951 (ttmm) cc_final: 0.7644 (mttm) REVERT: A 165 MET cc_start: 0.7388 (OUTLIER) cc_final: 0.6936 (tpp) REVERT: B 53 LYS cc_start: 0.7712 (ttpp) cc_final: 0.7311 (ttpp) REVERT: B 68 LYS cc_start: 0.7702 (ttmp) cc_final: 0.7420 (tttm) REVERT: B 143 LYS cc_start: 0.7949 (ttmm) cc_final: 0.7642 (mttm) REVERT: B 165 MET cc_start: 0.7389 (OUTLIER) cc_final: 0.6938 (tpp) REVERT: C 53 LYS cc_start: 0.7714 (ttpp) cc_final: 0.7315 (ttpp) REVERT: C 68 LYS cc_start: 0.7703 (ttmp) cc_final: 0.7421 (tttm) REVERT: C 143 LYS cc_start: 0.7949 (ttmm) cc_final: 0.7642 (mttm) REVERT: C 165 MET cc_start: 0.7388 (OUTLIER) cc_final: 0.6936 (tpp) REVERT: D 53 LYS cc_start: 0.7712 (ttpp) cc_final: 0.7312 (ttpp) REVERT: D 68 LYS cc_start: 0.7701 (ttmp) cc_final: 0.7419 (tttm) REVERT: D 143 LYS cc_start: 0.7948 (ttmm) cc_final: 0.7641 (mttm) REVERT: D 165 MET cc_start: 0.7389 (OUTLIER) cc_final: 0.6936 (tpp) REVERT: E 53 LYS cc_start: 0.7714 (ttpp) cc_final: 0.7312 (ttpp) REVERT: E 68 LYS cc_start: 0.7700 (ttmp) cc_final: 0.7419 (tttm) REVERT: E 143 LYS cc_start: 0.7948 (ttmm) cc_final: 0.7642 (mttm) REVERT: E 165 MET cc_start: 0.7368 (OUTLIER) cc_final: 0.6928 (tpp) REVERT: F 53 LYS cc_start: 0.7714 (ttpp) cc_final: 0.7314 (ttpp) REVERT: F 68 LYS cc_start: 0.7705 (ttmp) cc_final: 0.7422 (tttm) REVERT: F 143 LYS cc_start: 0.7949 (ttmm) cc_final: 0.7641 (mttm) REVERT: F 165 MET cc_start: 0.7388 (OUTLIER) cc_final: 0.6936 (tpp) REVERT: G 53 LYS cc_start: 0.7713 (ttpp) cc_final: 0.7311 (ttpp) REVERT: G 68 LYS cc_start: 0.7702 (ttmp) cc_final: 0.7420 (tttm) REVERT: G 143 LYS cc_start: 0.7949 (ttmm) cc_final: 0.7642 (mttm) REVERT: G 165 MET cc_start: 0.7388 (OUTLIER) cc_final: 0.6936 (tpp) REVERT: H 53 LYS cc_start: 0.7713 (ttpp) cc_final: 0.7313 (ttpp) REVERT: H 68 LYS cc_start: 0.7701 (ttmp) cc_final: 0.7419 (tttm) REVERT: H 143 LYS cc_start: 0.7949 (ttmm) cc_final: 0.7642 (mttm) REVERT: H 165 MET cc_start: 0.7388 (OUTLIER) cc_final: 0.6935 (tpp) REVERT: I 53 LYS cc_start: 0.7713 (ttpp) cc_final: 0.7313 (ttpp) REVERT: I 68 LYS cc_start: 0.7704 (ttmp) cc_final: 0.7422 (tttm) REVERT: I 143 LYS cc_start: 0.7949 (ttmm) cc_final: 0.7642 (mttm) REVERT: I 165 MET cc_start: 0.7388 (OUTLIER) cc_final: 0.6936 (tpp) REVERT: J 53 LYS cc_start: 0.7712 (ttpp) cc_final: 0.7312 (ttpp) REVERT: J 68 LYS cc_start: 0.7701 (ttmp) cc_final: 0.7419 (tttm) REVERT: J 143 LYS cc_start: 0.7949 (ttmm) cc_final: 0.7642 (mttm) REVERT: J 165 MET cc_start: 0.7388 (OUTLIER) cc_final: 0.6936 (tpp) REVERT: K 53 LYS cc_start: 0.7713 (ttpp) cc_final: 0.7313 (ttpp) REVERT: K 68 LYS cc_start: 0.7701 (ttmp) cc_final: 0.7419 (tttm) REVERT: K 143 LYS cc_start: 0.7951 (ttmm) cc_final: 0.7644 (mttm) REVERT: K 165 MET cc_start: 0.7388 (OUTLIER) cc_final: 0.6936 (tpp) REVERT: L 53 LYS cc_start: 0.7712 (ttpp) cc_final: 0.7311 (ttpp) REVERT: L 68 LYS cc_start: 0.7701 (ttmp) cc_final: 0.7419 (tttm) REVERT: L 143 LYS cc_start: 0.7951 (ttmm) cc_final: 0.7644 (mttm) REVERT: L 165 MET cc_start: 0.7388 (OUTLIER) cc_final: 0.6936 (tpp) REVERT: M 53 LYS cc_start: 0.7712 (ttpp) cc_final: 0.7312 (ttpp) REVERT: M 68 LYS cc_start: 0.7704 (ttmp) cc_final: 0.7421 (tttm) REVERT: M 143 LYS cc_start: 0.7949 (ttmm) cc_final: 0.7641 (mttm) REVERT: M 165 MET cc_start: 0.7388 (OUTLIER) cc_final: 0.6937 (tpp) REVERT: N 53 LYS cc_start: 0.7713 (ttpp) cc_final: 0.7311 (ttpp) REVERT: N 68 LYS cc_start: 0.7702 (ttmp) cc_final: 0.7420 (tttm) REVERT: N 143 LYS cc_start: 0.7949 (ttmm) cc_final: 0.7642 (mttm) REVERT: N 165 MET cc_start: 0.7388 (OUTLIER) cc_final: 0.6936 (tpp) REVERT: O 53 LYS cc_start: 0.7714 (ttpp) cc_final: 0.7312 (ttpp) REVERT: O 68 LYS cc_start: 0.7701 (ttmp) cc_final: 0.7419 (tttm) REVERT: O 143 LYS cc_start: 0.7949 (ttmm) cc_final: 0.7642 (mttm) REVERT: O 165 MET cc_start: 0.7388 (OUTLIER) cc_final: 0.6936 (tpp) REVERT: P 53 LYS cc_start: 0.7713 (ttpp) cc_final: 0.7313 (ttpp) REVERT: P 68 LYS cc_start: 0.7703 (ttmp) cc_final: 0.7421 (tttm) REVERT: P 143 LYS cc_start: 0.7949 (ttmm) cc_final: 0.7642 (mttm) REVERT: P 165 MET cc_start: 0.7388 (OUTLIER) cc_final: 0.6937 (tpp) REVERT: Q 53 LYS cc_start: 0.7712 (ttpp) cc_final: 0.7311 (ttpp) REVERT: Q 68 LYS cc_start: 0.7702 (ttmp) cc_final: 0.7420 (tttm) REVERT: Q 143 LYS cc_start: 0.7949 (ttmm) cc_final: 0.7642 (mttm) REVERT: Q 165 MET cc_start: 0.7388 (OUTLIER) cc_final: 0.6936 (tpp) REVERT: R 53 LYS cc_start: 0.7712 (ttpp) cc_final: 0.7312 (ttpp) REVERT: R 68 LYS cc_start: 0.7701 (ttmp) cc_final: 0.7420 (tttm) REVERT: R 143 LYS cc_start: 0.7948 (ttmm) cc_final: 0.7641 (mttm) REVERT: R 165 MET cc_start: 0.7388 (OUTLIER) cc_final: 0.6936 (tpp) REVERT: S 53 LYS cc_start: 0.7711 (ttpp) cc_final: 0.7310 (ttpp) REVERT: S 68 LYS cc_start: 0.7700 (ttmp) cc_final: 0.7419 (tttm) REVERT: S 143 LYS cc_start: 0.7949 (ttmm) cc_final: 0.7642 (mttm) REVERT: S 165 MET cc_start: 0.7389 (OUTLIER) cc_final: 0.6936 (tpp) REVERT: T 53 LYS cc_start: 0.7713 (ttpp) cc_final: 0.7311 (ttpp) REVERT: T 68 LYS cc_start: 0.7702 (ttmp) cc_final: 0.7419 (tttm) REVERT: T 143 LYS cc_start: 0.7949 (ttmm) cc_final: 0.7642 (mttm) REVERT: T 165 MET cc_start: 0.7388 (OUTLIER) cc_final: 0.6936 (tpp) REVERT: U 53 LYS cc_start: 0.7713 (ttpp) cc_final: 0.7313 (ttpp) REVERT: U 68 LYS cc_start: 0.7704 (ttmp) cc_final: 0.7421 (tttm) REVERT: U 143 LYS cc_start: 0.7948 (ttmm) cc_final: 0.7641 (mttm) REVERT: U 165 MET cc_start: 0.7388 (OUTLIER) cc_final: 0.6936 (tpp) REVERT: V 53 LYS cc_start: 0.7712 (ttpp) cc_final: 0.7311 (ttpp) REVERT: V 68 LYS cc_start: 0.7700 (ttmp) cc_final: 0.7419 (tttm) REVERT: V 143 LYS cc_start: 0.7946 (ttmm) cc_final: 0.7639 (mttm) REVERT: V 165 MET cc_start: 0.7389 (OUTLIER) cc_final: 0.6936 (tpp) REVERT: W 53 LYS cc_start: 0.7712 (ttpp) cc_final: 0.7310 (ttpp) REVERT: W 68 LYS cc_start: 0.7702 (ttmp) cc_final: 0.7420 (tttm) REVERT: W 143 LYS cc_start: 0.7949 (ttmm) cc_final: 0.7641 (mttm) REVERT: W 165 MET cc_start: 0.7388 (OUTLIER) cc_final: 0.6936 (tpp) REVERT: X 53 LYS cc_start: 0.7713 (ttpp) cc_final: 0.7313 (ttpp) REVERT: X 68 LYS cc_start: 0.7701 (ttmp) cc_final: 0.7419 (tttm) REVERT: X 143 LYS cc_start: 0.7946 (ttmm) cc_final: 0.7639 (mttm) REVERT: X 165 MET cc_start: 0.7389 (OUTLIER) cc_final: 0.6936 (tpp) outliers start: 24 outliers final: 0 residues processed: 663 average time/residue: 1.7789 time to fit residues: 1346.5179 Evaluate side-chains 687 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 663 time to evaluate : 3.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 MET Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain F residue 165 MET Chi-restraints excluded: chain G residue 165 MET Chi-restraints excluded: chain H residue 165 MET Chi-restraints excluded: chain I residue 165 MET Chi-restraints excluded: chain J residue 165 MET Chi-restraints excluded: chain K residue 165 MET Chi-restraints excluded: chain L residue 165 MET Chi-restraints excluded: chain M residue 165 MET Chi-restraints excluded: chain N residue 165 MET Chi-restraints excluded: chain O residue 165 MET Chi-restraints excluded: chain P residue 165 MET Chi-restraints excluded: chain Q residue 165 MET Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain S residue 165 MET Chi-restraints excluded: chain T residue 165 MET Chi-restraints excluded: chain U residue 165 MET Chi-restraints excluded: chain V residue 165 MET Chi-restraints excluded: chain W residue 165 MET Chi-restraints excluded: chain X residue 165 MET 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: 7.9990 chunk 236 optimal weight: 0.6980 chunk 183 optimal weight: 1.9990 chunk 269 optimal weight: 5.9990 chunk 406 optimal weight: 0.8980 chunk 374 optimal weight: 5.9990 chunk 323 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 250 optimal weight: 0.9990 chunk 198 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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: 0.7632 moved from start: 0.2447 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= 0.168 Angle : 0.530 4.900 48408 Z= 0.289 Chirality : 0.036 0.125 5016 Planarity : 0.003 0.019 6432 Dihedral : 13.367 179.619 4800 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.63 % Allowed : 6.65 % Favored : 92.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.21 (0.13), residues: 4464 helix: 3.99 (0.08), residues: 3552 sheet: None (None), residues: 0 loop : 0.95 (0.25), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP D 93 HIS 0.003 0.001 HIS M 128 PHE 0.015 0.002 PHE N 41 TYR 0.016 0.002 TYR X 137 ARG 0.001 0.000 ARG C 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 663 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 639 time to evaluate : 3.178 Fit side-chains REVERT: A 53 LYS cc_start: 0.7733 (ttpp) cc_final: 0.7331 (ttpp) REVERT: A 68 LYS cc_start: 0.7705 (ttmp) cc_final: 0.7423 (tttm) REVERT: A 143 LYS cc_start: 0.7951 (ttmm) cc_final: 0.7645 (mttm) REVERT: A 165 MET cc_start: 0.7390 (OUTLIER) cc_final: 0.6956 (tpp) REVERT: B 53 LYS cc_start: 0.7731 (ttpp) cc_final: 0.7330 (ttpp) REVERT: B 68 LYS cc_start: 0.7706 (ttmp) cc_final: 0.7424 (tttm) REVERT: B 143 LYS cc_start: 0.7950 (ttmm) cc_final: 0.7646 (mttm) REVERT: B 165 MET cc_start: 0.7390 (OUTLIER) cc_final: 0.6956 (tpp) REVERT: C 53 LYS cc_start: 0.7734 (ttpp) cc_final: 0.7333 (ttpp) REVERT: C 68 LYS cc_start: 0.7708 (ttmp) cc_final: 0.7425 (tttm) REVERT: C 143 LYS cc_start: 0.7950 (ttmm) cc_final: 0.7644 (mttm) REVERT: C 165 MET cc_start: 0.7389 (OUTLIER) cc_final: 0.6955 (tpp) REVERT: D 53 LYS cc_start: 0.7732 (ttpp) cc_final: 0.7338 (ttpp) REVERT: D 68 LYS cc_start: 0.7705 (ttmp) cc_final: 0.7424 (tttm) REVERT: D 143 LYS cc_start: 0.7949 (ttmm) cc_final: 0.7644 (mttm) REVERT: D 165 MET cc_start: 0.7390 (OUTLIER) cc_final: 0.6955 (tpp) REVERT: E 53 LYS cc_start: 0.7734 (ttpp) cc_final: 0.7331 (ttpp) REVERT: E 68 LYS cc_start: 0.7705 (ttmp) cc_final: 0.7424 (tttm) REVERT: E 143 LYS cc_start: 0.7949 (ttmm) cc_final: 0.7643 (mttm) REVERT: E 165 MET cc_start: 0.7396 (OUTLIER) cc_final: 0.6961 (tpp) REVERT: F 53 LYS cc_start: 0.7734 (ttpp) cc_final: 0.7332 (ttpp) REVERT: F 68 LYS cc_start: 0.7708 (ttmp) cc_final: 0.7426 (tttm) REVERT: F 143 LYS cc_start: 0.7949 (ttmm) cc_final: 0.7644 (mttm) REVERT: F 165 MET cc_start: 0.7389 (OUTLIER) cc_final: 0.6955 (tpp) REVERT: G 53 LYS cc_start: 0.7732 (ttpp) cc_final: 0.7330 (ttpp) REVERT: G 68 LYS cc_start: 0.7706 (ttmp) cc_final: 0.7424 (tttm) REVERT: G 143 LYS cc_start: 0.7949 (ttmm) cc_final: 0.7644 (mttm) REVERT: G 165 MET cc_start: 0.7389 (OUTLIER) cc_final: 0.6956 (tpp) REVERT: H 53 LYS cc_start: 0.7733 (ttpp) cc_final: 0.7339 (ttpp) REVERT: H 68 LYS cc_start: 0.7705 (ttmp) cc_final: 0.7424 (tttm) REVERT: H 143 LYS cc_start: 0.7949 (ttmm) cc_final: 0.7644 (mttm) REVERT: H 165 MET cc_start: 0.7389 (OUTLIER) cc_final: 0.6955 (tpp) REVERT: I 53 LYS cc_start: 0.7733 (ttpp) cc_final: 0.7332 (ttpp) REVERT: I 68 LYS cc_start: 0.7707 (ttmp) cc_final: 0.7425 (tttm) REVERT: I 143 LYS cc_start: 0.7950 (ttmm) cc_final: 0.7644 (mttm) REVERT: I 165 MET cc_start: 0.7389 (OUTLIER) cc_final: 0.6955 (tpp) REVERT: J 53 LYS cc_start: 0.7733 (ttpp) cc_final: 0.7333 (ttpp) REVERT: J 68 LYS cc_start: 0.7705 (ttmp) cc_final: 0.7423 (tttm) REVERT: J 143 LYS cc_start: 0.7949 (ttmm) cc_final: 0.7645 (mttm) REVERT: J 165 MET cc_start: 0.7389 (OUTLIER) cc_final: 0.6955 (tpp) REVERT: K 53 LYS cc_start: 0.7734 (ttpp) cc_final: 0.7340 (ttpp) REVERT: K 68 LYS cc_start: 0.7704 (ttmp) cc_final: 0.7423 (tttm) REVERT: K 143 LYS cc_start: 0.7951 (ttmm) cc_final: 0.7646 (mttm) REVERT: K 165 MET cc_start: 0.7389 (OUTLIER) cc_final: 0.6955 (tpp) REVERT: L 53 LYS cc_start: 0.7732 (ttpp) cc_final: 0.7337 (ttpp) REVERT: L 68 LYS cc_start: 0.7704 (ttmp) cc_final: 0.7423 (tttm) REVERT: L 143 LYS cc_start: 0.7951 (ttmm) cc_final: 0.7646 (mttm) REVERT: L 165 MET cc_start: 0.7390 (OUTLIER) cc_final: 0.6956 (tpp) REVERT: M 53 LYS cc_start: 0.7732 (ttpp) cc_final: 0.7331 (ttpp) REVERT: M 68 LYS cc_start: 0.7708 (ttmp) cc_final: 0.7426 (tttm) REVERT: M 143 LYS cc_start: 0.7949 (ttmm) cc_final: 0.7644 (mttm) REVERT: M 165 MET cc_start: 0.7390 (OUTLIER) cc_final: 0.6955 (tpp) REVERT: N 53 LYS cc_start: 0.7733 (ttpp) cc_final: 0.7331 (ttpp) REVERT: N 68 LYS cc_start: 0.7706 (ttmp) cc_final: 0.7424 (tttm) REVERT: N 143 LYS cc_start: 0.7949 (ttmm) cc_final: 0.7644 (mttm) REVERT: N 165 MET cc_start: 0.7394 (OUTLIER) cc_final: 0.6961 (tpp) REVERT: O 53 LYS cc_start: 0.7734 (ttpp) cc_final: 0.7332 (ttpp) REVERT: O 68 LYS cc_start: 0.7704 (ttmp) cc_final: 0.7423 (tttm) REVERT: O 143 LYS cc_start: 0.7949 (ttmm) cc_final: 0.7643 (mttm) REVERT: O 165 MET cc_start: 0.7389 (OUTLIER) cc_final: 0.6956 (tpp) REVERT: P 53 LYS cc_start: 0.7734 (ttpp) cc_final: 0.7333 (ttpp) REVERT: P 68 LYS cc_start: 0.7707 (ttmp) cc_final: 0.7425 (tttm) REVERT: P 143 LYS cc_start: 0.7950 (ttmm) cc_final: 0.7644 (mttm) REVERT: P 165 MET cc_start: 0.7389 (OUTLIER) cc_final: 0.6955 (tpp) REVERT: Q 53 LYS cc_start: 0.7732 (ttpp) cc_final: 0.7330 (ttpp) REVERT: Q 68 LYS cc_start: 0.7705 (ttmp) cc_final: 0.7423 (tttm) REVERT: Q 143 LYS cc_start: 0.7950 (ttmm) cc_final: 0.7646 (mttm) REVERT: Q 165 MET cc_start: 0.7389 (OUTLIER) cc_final: 0.6955 (tpp) REVERT: R 53 LYS cc_start: 0.7733 (ttpp) cc_final: 0.7332 (ttpp) REVERT: R 68 LYS cc_start: 0.7705 (ttmp) cc_final: 0.7424 (tttm) REVERT: R 143 LYS cc_start: 0.7949 (ttmm) cc_final: 0.7644 (mttm) REVERT: R 165 MET cc_start: 0.7390 (OUTLIER) cc_final: 0.6955 (tpp) REVERT: S 53 LYS cc_start: 0.7732 (ttpp) cc_final: 0.7330 (ttpp) REVERT: S 68 LYS cc_start: 0.7704 (ttmp) cc_final: 0.7423 (tttm) REVERT: S 143 LYS cc_start: 0.7949 (ttmm) cc_final: 0.7644 (mttm) REVERT: S 165 MET cc_start: 0.7391 (OUTLIER) cc_final: 0.6957 (tpp) REVERT: T 53 LYS cc_start: 0.7733 (ttpp) cc_final: 0.7331 (ttpp) REVERT: T 68 LYS cc_start: 0.7706 (ttmp) cc_final: 0.7424 (tttm) REVERT: T 143 LYS cc_start: 0.7949 (ttmm) cc_final: 0.7644 (mttm) REVERT: T 165 MET cc_start: 0.7389 (OUTLIER) cc_final: 0.6956 (tpp) REVERT: U 53 LYS cc_start: 0.7733 (ttpp) cc_final: 0.7339 (ttpp) REVERT: U 68 LYS cc_start: 0.7707 (ttmp) cc_final: 0.7425 (tttm) REVERT: U 143 LYS cc_start: 0.7949 (ttmm) cc_final: 0.7644 (mttm) REVERT: U 165 MET cc_start: 0.7390 (OUTLIER) cc_final: 0.6955 (tpp) REVERT: V 53 LYS cc_start: 0.7733 (ttpp) cc_final: 0.7332 (ttpp) REVERT: V 68 LYS cc_start: 0.7705 (ttmp) cc_final: 0.7424 (tttm) REVERT: V 143 LYS cc_start: 0.7946 (ttmm) cc_final: 0.7640 (mttm) REVERT: V 165 MET cc_start: 0.7391 (OUTLIER) cc_final: 0.6956 (tpp) REVERT: W 53 LYS cc_start: 0.7732 (ttpp) cc_final: 0.7330 (ttpp) REVERT: W 68 LYS cc_start: 0.7706 (ttmp) cc_final: 0.7423 (tttm) REVERT: W 143 LYS cc_start: 0.7950 (ttmm) cc_final: 0.7646 (mttm) REVERT: W 165 MET cc_start: 0.7389 (OUTLIER) cc_final: 0.6955 (tpp) REVERT: X 53 LYS cc_start: 0.7734 (ttpp) cc_final: 0.7334 (ttpp) REVERT: X 68 LYS cc_start: 0.7705 (ttmp) cc_final: 0.7424 (tttm) REVERT: X 143 LYS cc_start: 0.7946 (ttmm) cc_final: 0.7641 (mttm) REVERT: X 165 MET cc_start: 0.7390 (OUTLIER) cc_final: 0.6955 (tpp) outliers start: 24 outliers final: 0 residues processed: 639 average time/residue: 1.8405 time to fit residues: 1337.4614 Evaluate side-chains 663 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 639 time to evaluate : 3.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 MET Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain F residue 165 MET Chi-restraints excluded: chain G residue 165 MET Chi-restraints excluded: chain H residue 165 MET Chi-restraints excluded: chain I residue 165 MET Chi-restraints excluded: chain J residue 165 MET Chi-restraints excluded: chain K residue 165 MET Chi-restraints excluded: chain L residue 165 MET Chi-restraints excluded: chain M residue 165 MET Chi-restraints excluded: chain N residue 165 MET Chi-restraints excluded: chain O residue 165 MET Chi-restraints excluded: chain P residue 165 MET Chi-restraints excluded: chain Q residue 165 MET Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain S residue 165 MET Chi-restraints excluded: chain T residue 165 MET Chi-restraints excluded: chain U residue 165 MET Chi-restraints excluded: chain V residue 165 MET Chi-restraints excluded: chain W residue 165 MET Chi-restraints excluded: chain X residue 165 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 8.9990 chunk 344 optimal weight: 0.5980 chunk 99 optimal weight: 6.9990 chunk 298 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 324 optimal weight: 6.9990 chunk 135 optimal weight: 0.0980 chunk 332 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3568 r_free = 0.3568 target = 0.150872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.138976 restraints weight = 164561.570| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.47 r_work: 0.3143 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work: 0.2917 rms_B_bonded: 4.18 restraints_weight: 0.1250 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2861 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2861 r_free = 0.2861 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2860 r_free = 0.2860 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2860 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 35880 Z= 0.154 Angle : 0.510 4.730 48408 Z= 0.278 Chirality : 0.035 0.124 5016 Planarity : 0.003 0.020 6432 Dihedral : 13.377 179.957 4800 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.63 % Allowed : 6.65 % Favored : 92.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.30 (0.13), residues: 4464 helix: 4.06 (0.08), residues: 3552 sheet: None (None), residues: 0 loop : 0.96 (0.25), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP D 93 HIS 0.002 0.001 HIS U 128 PHE 0.014 0.002 PHE S 41 TYR 0.015 0.001 TYR X 137 ARG 0.001 0.000 ARG N 156 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19442.97 seconds wall clock time: 338 minutes 53.67 seconds (20333.67 seconds total)