Starting phenix.real_space_refine on Sat Dec 16 13:18:49 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o6e_12738/12_2023/7o6e_12738.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o6e_12738/12_2023/7o6e_12738.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o6e_12738/12_2023/7o6e_12738.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o6e_12738/12_2023/7o6e_12738.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o6e_12738/12_2023/7o6e_12738.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o6e_12738/12_2023/7o6e_12738.pdb" } resolution = 2.1 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= 0.410 sd= 1.618 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 21264 2.51 5 N 6096 2.21 5 O 7824 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 5": "OE1" <-> "OE2" Residue "A GLU 22": "OE1" <-> "OE2" Residue "A GLU 39": "OE1" <-> "OE2" Residue "A GLU 99": "OE1" <-> "OE2" Residue "A ARG 114": "NH1" <-> "NH2" Residue "A GLU 116": "OE1" <-> "OE2" Residue "A GLU 131": "OE1" <-> "OE2" Residue "A GLU 157": "OE1" <-> "OE2" Residue "B GLU 5": "OE1" <-> "OE2" Residue "B GLU 22": "OE1" <-> "OE2" Residue "B GLU 39": "OE1" <-> "OE2" Residue "B GLU 99": "OE1" <-> "OE2" Residue "B ARG 114": "NH1" <-> "NH2" Residue "B GLU 116": "OE1" <-> "OE2" Residue "B GLU 131": "OE1" <-> "OE2" Residue "B GLU 157": "OE1" <-> "OE2" Residue "C GLU 5": "OE1" <-> "OE2" Residue "C GLU 22": "OE1" <-> "OE2" Residue "C GLU 39": "OE1" <-> "OE2" Residue "C GLU 99": "OE1" <-> "OE2" Residue "C ARG 114": "NH1" <-> "NH2" Residue "C GLU 116": "OE1" <-> "OE2" Residue "C GLU 131": "OE1" <-> "OE2" Residue "C GLU 157": "OE1" <-> "OE2" Residue "D GLU 5": "OE1" <-> "OE2" Residue "D GLU 22": "OE1" <-> "OE2" Residue "D GLU 39": "OE1" <-> "OE2" Residue "D GLU 99": "OE1" <-> "OE2" Residue "D ARG 114": "NH1" <-> "NH2" Residue "D GLU 116": "OE1" <-> "OE2" Residue "D GLU 131": "OE1" <-> "OE2" Residue "D GLU 157": "OE1" <-> "OE2" Residue "E GLU 5": "OE1" <-> "OE2" Residue "E GLU 22": "OE1" <-> "OE2" Residue "E GLU 39": "OE1" <-> "OE2" Residue "E GLU 99": "OE1" <-> "OE2" Residue "E ARG 114": "NH1" <-> "NH2" Residue "E GLU 116": "OE1" <-> "OE2" Residue "E GLU 131": "OE1" <-> "OE2" Residue "E GLU 157": "OE1" <-> "OE2" Residue "F GLU 5": "OE1" <-> "OE2" Residue "F GLU 22": "OE1" <-> "OE2" Residue "F GLU 39": "OE1" <-> "OE2" Residue "F GLU 99": "OE1" <-> "OE2" Residue "F ARG 114": "NH1" <-> "NH2" Residue "F GLU 116": "OE1" <-> "OE2" Residue "F GLU 131": "OE1" <-> "OE2" Residue "F GLU 157": "OE1" <-> "OE2" Residue "G GLU 5": "OE1" <-> "OE2" Residue "G GLU 22": "OE1" <-> "OE2" Residue "G GLU 39": "OE1" <-> "OE2" Residue "G GLU 99": "OE1" <-> "OE2" Residue "G ARG 114": "NH1" <-> "NH2" Residue "G GLU 116": "OE1" <-> "OE2" Residue "G GLU 131": "OE1" <-> "OE2" Residue "G GLU 157": "OE1" <-> "OE2" Residue "H GLU 5": "OE1" <-> "OE2" Residue "H GLU 22": "OE1" <-> "OE2" Residue "H GLU 39": "OE1" <-> "OE2" Residue "H GLU 99": "OE1" <-> "OE2" Residue "H ARG 114": "NH1" <-> "NH2" Residue "H GLU 116": "OE1" <-> "OE2" Residue "H GLU 131": "OE1" <-> "OE2" Residue "H GLU 157": "OE1" <-> "OE2" Residue "I GLU 5": "OE1" <-> "OE2" Residue "I GLU 22": "OE1" <-> "OE2" Residue "I GLU 39": "OE1" <-> "OE2" Residue "I GLU 99": "OE1" <-> "OE2" Residue "I ARG 114": "NH1" <-> "NH2" Residue "I GLU 116": "OE1" <-> "OE2" Residue "I GLU 131": "OE1" <-> "OE2" Residue "I GLU 157": "OE1" <-> "OE2" Residue "J GLU 5": "OE1" <-> "OE2" Residue "J GLU 22": "OE1" <-> "OE2" Residue "J GLU 39": "OE1" <-> "OE2" Residue "J GLU 99": "OE1" <-> "OE2" Residue "J ARG 114": "NH1" <-> "NH2" Residue "J GLU 116": "OE1" <-> "OE2" Residue "J GLU 131": "OE1" <-> "OE2" Residue "J GLU 157": "OE1" <-> "OE2" Residue "K GLU 5": "OE1" <-> "OE2" Residue "K GLU 22": "OE1" <-> "OE2" Residue "K GLU 39": "OE1" <-> "OE2" Residue "K GLU 99": "OE1" <-> "OE2" Residue "K ARG 114": "NH1" <-> "NH2" Residue "K GLU 116": "OE1" <-> "OE2" Residue "K GLU 131": "OE1" <-> "OE2" Residue "K GLU 157": "OE1" <-> "OE2" Residue "L GLU 5": "OE1" <-> "OE2" Residue "L GLU 22": "OE1" <-> "OE2" Residue "L GLU 39": "OE1" <-> "OE2" Residue "L GLU 99": "OE1" <-> "OE2" Residue "L ARG 114": "NH1" <-> "NH2" Residue "L GLU 116": "OE1" <-> "OE2" Residue "L GLU 131": "OE1" <-> "OE2" Residue "L GLU 157": "OE1" <-> "OE2" Residue "M GLU 5": "OE1" <-> "OE2" Residue "M GLU 22": "OE1" <-> "OE2" Residue "M GLU 39": "OE1" <-> "OE2" Residue "M GLU 99": "OE1" <-> "OE2" Residue "M ARG 114": "NH1" <-> "NH2" Residue "M GLU 116": "OE1" <-> "OE2" Residue "M GLU 131": "OE1" <-> "OE2" Residue "M GLU 157": "OE1" <-> "OE2" Residue "N GLU 5": "OE1" <-> "OE2" Residue "N GLU 22": "OE1" <-> "OE2" Residue "N GLU 39": "OE1" <-> "OE2" Residue "N GLU 99": "OE1" <-> "OE2" Residue "N ARG 114": "NH1" <-> "NH2" Residue "N GLU 116": "OE1" <-> "OE2" Residue "N GLU 131": "OE1" <-> "OE2" Residue "N GLU 157": "OE1" <-> "OE2" Residue "O GLU 5": "OE1" <-> "OE2" Residue "O GLU 22": "OE1" <-> "OE2" Residue "O GLU 39": "OE1" <-> "OE2" Residue "O GLU 99": "OE1" <-> "OE2" Residue "O ARG 114": "NH1" <-> "NH2" Residue "O GLU 116": "OE1" <-> "OE2" Residue "O GLU 131": "OE1" <-> "OE2" Residue "O GLU 157": "OE1" <-> "OE2" Residue "P GLU 5": "OE1" <-> "OE2" Residue "P GLU 22": "OE1" <-> "OE2" Residue "P GLU 39": "OE1" <-> "OE2" Residue "P GLU 99": "OE1" <-> "OE2" Residue "P ARG 114": "NH1" <-> "NH2" Residue "P GLU 116": "OE1" <-> "OE2" Residue "P GLU 131": "OE1" <-> "OE2" Residue "P GLU 157": "OE1" <-> "OE2" Residue "Q GLU 5": "OE1" <-> "OE2" Residue "Q GLU 22": "OE1" <-> "OE2" Residue "Q GLU 39": "OE1" <-> "OE2" Residue "Q GLU 99": "OE1" <-> "OE2" Residue "Q ARG 114": "NH1" <-> "NH2" Residue "Q GLU 116": "OE1" <-> "OE2" Residue "Q GLU 131": "OE1" <-> "OE2" Residue "Q GLU 157": "OE1" <-> "OE2" Residue "R GLU 5": "OE1" <-> "OE2" Residue "R GLU 22": "OE1" <-> "OE2" Residue "R GLU 39": "OE1" <-> "OE2" Residue "R GLU 99": "OE1" <-> "OE2" Residue "R ARG 114": "NH1" <-> "NH2" Residue "R GLU 116": "OE1" <-> "OE2" Residue "R GLU 131": "OE1" <-> "OE2" Residue "R GLU 157": "OE1" <-> "OE2" Residue "S GLU 5": "OE1" <-> "OE2" Residue "S GLU 22": "OE1" <-> "OE2" Residue "S GLU 39": "OE1" <-> "OE2" Residue "S GLU 99": "OE1" <-> "OE2" Residue "S ARG 114": "NH1" <-> "NH2" Residue "S GLU 116": "OE1" <-> "OE2" Residue "S GLU 131": "OE1" <-> "OE2" Residue "S GLU 157": "OE1" <-> "OE2" Residue "T GLU 5": "OE1" <-> "OE2" Residue "T GLU 22": "OE1" <-> "OE2" Residue "T GLU 39": "OE1" <-> "OE2" Residue "T GLU 99": "OE1" <-> "OE2" Residue "T ARG 114": "NH1" <-> "NH2" Residue "T GLU 116": "OE1" <-> "OE2" Residue "T GLU 131": "OE1" <-> "OE2" Residue "T GLU 157": "OE1" <-> "OE2" Residue "V GLU 5": "OE1" <-> "OE2" Residue "V GLU 22": "OE1" <-> "OE2" Residue "V GLU 39": "OE1" <-> "OE2" Residue "V GLU 99": "OE1" <-> "OE2" Residue "V ARG 114": "NH1" <-> "NH2" Residue "V GLU 116": "OE1" <-> "OE2" Residue "V GLU 131": "OE1" <-> "OE2" Residue "V GLU 157": "OE1" <-> "OE2" Residue "W GLU 5": "OE1" <-> "OE2" Residue "W GLU 22": "OE1" <-> "OE2" Residue "W GLU 39": "OE1" <-> "OE2" Residue "W GLU 99": "OE1" <-> "OE2" Residue "W ARG 114": "NH1" <-> "NH2" Residue "W GLU 116": "OE1" <-> "OE2" Residue "W GLU 131": "OE1" <-> "OE2" Residue "W GLU 157": "OE1" <-> "OE2" Residue "X GLU 5": "OE1" <-> "OE2" Residue "X GLU 22": "OE1" <-> "OE2" Residue "X GLU 39": "OE1" <-> "OE2" Residue "X GLU 99": "OE1" <-> "OE2" Residue "X ARG 114": "NH1" <-> "NH2" Residue "X GLU 116": "OE1" <-> "OE2" Residue "X GLU 131": "OE1" <-> "OE2" Residue "X GLU 157": "OE1" <-> "OE2" Residue "Y GLU 5": "OE1" <-> "OE2" Residue "Y GLU 22": "OE1" <-> "OE2" Residue "Y GLU 39": "OE1" <-> "OE2" Residue "Y GLU 99": "OE1" <-> "OE2" Residue "Y ARG 114": "NH1" <-> "NH2" Residue "Y GLU 116": "OE1" <-> "OE2" Residue "Y GLU 131": "OE1" <-> "OE2" Residue "Y GLU 157": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 35304 Number of models: 1 Model: "" Number of chains: 48 Chain: "A" Number of atoms: 1413 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 177, 1403 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Conformer: "B" Number of residues, atoms: 177, 1403 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} bond proxies already assigned to first conformer: 1417 Chain: "B" Number of atoms: 1413 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 177, 1403 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Conformer: "B" Number of residues, atoms: 177, 1403 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} bond proxies already assigned to first conformer: 1417 Chain: "C" Number of atoms: 1413 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 177, 1403 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Conformer: "B" Number of residues, atoms: 177, 1403 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} bond proxies already assigned to first conformer: 1417 Chain: "D" Number of atoms: 1413 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 177, 1403 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Conformer: "B" Number of residues, atoms: 177, 1403 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} bond proxies already assigned to first conformer: 1417 Chain: "E" Number of atoms: 1413 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 177, 1403 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Conformer: "B" Number of residues, atoms: 177, 1403 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} bond proxies already assigned to first conformer: 1417 Chain: "F" Number of atoms: 1413 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 177, 1403 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Conformer: "B" Number of residues, atoms: 177, 1403 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} bond proxies already assigned to first conformer: 1417 Chain: "G" Number of atoms: 1413 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 177, 1403 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Conformer: "B" Number of residues, atoms: 177, 1403 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} bond proxies already assigned to first conformer: 1417 Chain: "H" Number of atoms: 1413 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 177, 1403 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Conformer: "B" Number of residues, atoms: 177, 1403 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} bond proxies already assigned to first conformer: 1417 Chain: "I" Number of atoms: 1413 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 177, 1403 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Conformer: "B" Number of residues, atoms: 177, 1403 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} bond proxies already assigned to first conformer: 1417 Chain: "J" Number of atoms: 1413 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 177, 1403 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Conformer: "B" Number of residues, atoms: 177, 1403 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} bond proxies already assigned to first conformer: 1417 Chain: "K" Number of atoms: 1413 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 177, 1403 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Conformer: "B" Number of residues, atoms: 177, 1403 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} bond proxies already assigned to first conformer: 1417 Chain: "L" Number of atoms: 1413 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 177, 1403 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Conformer: "B" Number of residues, atoms: 177, 1403 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} bond proxies already assigned to first conformer: 1417 Chain: "M" Number of atoms: 1413 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 177, 1403 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Conformer: "B" Number of residues, atoms: 177, 1403 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} bond proxies already assigned to first conformer: 1417 Chain: "N" Number of atoms: 1413 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 177, 1403 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Conformer: "B" Number of residues, atoms: 177, 1403 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} bond proxies already assigned to first conformer: 1417 Chain: "O" Number of atoms: 1413 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 177, 1403 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Conformer: "B" Number of residues, atoms: 177, 1403 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} bond proxies already assigned to first conformer: 1417 Chain: "P" Number of atoms: 1413 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 177, 1403 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Conformer: "B" Number of residues, atoms: 177, 1403 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} bond proxies already assigned to first conformer: 1417 Chain: "Q" Number of atoms: 1413 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 177, 1403 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Conformer: "B" Number of residues, atoms: 177, 1403 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} bond proxies already assigned to first conformer: 1417 Chain: "R" Number of atoms: 1413 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 177, 1403 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Conformer: "B" Number of residues, atoms: 177, 1403 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} bond proxies already assigned to first conformer: 1417 Chain: "S" Number of atoms: 1413 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 177, 1403 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Conformer: "B" Number of residues, atoms: 177, 1403 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} bond proxies already assigned to first conformer: 1417 Chain: "T" Number of atoms: 1413 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 177, 1403 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Conformer: "B" Number of residues, atoms: 177, 1403 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} bond proxies already assigned to first conformer: 1417 Chain: "V" Number of atoms: 1413 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 177, 1403 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Conformer: "B" Number of residues, atoms: 177, 1403 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} bond proxies already assigned to first conformer: 1417 Chain: "W" Number of atoms: 1413 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 177, 1403 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Conformer: "B" Number of residues, atoms: 177, 1403 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} bond proxies already assigned to first conformer: 1417 Chain: "X" Number of atoms: 1413 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 177, 1403 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Conformer: "B" Number of residues, atoms: 177, 1403 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} bond proxies already assigned to first conformer: 1417 Chain: "Y" Number of atoms: 1413 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 177, 1403 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Conformer: "B" Number of residues, atoms: 177, 1403 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} bond proxies already assigned to first conformer: 1417 Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "B" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "C" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "D" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "E" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "F" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "G" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "H" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "I" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "J" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "K" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "L" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "M" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "N" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "O" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "P" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "Q" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "R" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "S" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "T" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "V" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "W" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "X" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "Y" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Residues with excluded nonbonded symmetry interactions: 24 residue: pdb=" N AHIS A 175 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS A 175 " occ=0.50 residue: pdb=" N AHIS B 175 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS B 175 " occ=0.50 residue: pdb=" N AHIS C 175 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS C 175 " occ=0.50 residue: pdb=" N AHIS D 175 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS D 175 " occ=0.50 residue: pdb=" N AHIS E 175 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS E 175 " occ=0.50 residue: pdb=" N AHIS F 175 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS F 175 " occ=0.50 residue: pdb=" N AHIS G 175 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS G 175 " occ=0.50 residue: pdb=" N AHIS H 175 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS H 175 " occ=0.50 residue: pdb=" N AHIS I 175 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS I 175 " occ=0.50 residue: pdb=" N AHIS J 175 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS J 175 " occ=0.50 residue: pdb=" N AHIS K 175 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS K 175 " occ=0.50 residue: pdb=" N AHIS L 175 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS L 175 " occ=0.50 ... (remaining 12 not shown) Time building chain proxies: 33.41, per 1000 atoms: 0.95 Number of scatterers: 35304 At special positions: 0 Unit cell: (129.629, 129.629, 129.629, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 7824 8.00 N 6096 7.00 C 21264 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: 15.91 Conformation dependent library (CDL) restraints added in 12.0 seconds 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8112 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 0 sheets defined 76.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.71 Creating SS restraints... Processing helix chain 'A' and resid 9 through 38 Processing helix chain 'A' and resid 41 through 69 Processing helix chain 'A' and resid 87 through 117 removed outlier: 3.636A pdb=" N ALA A 91 " --> pdb=" O ARG A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 150 removed outlier: 4.389A pdb=" N TRP A 127 " --> pdb=" O GLN A 123 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N PHE A 128 " --> pdb=" O PHE A 124 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU A 134 " --> pdb=" O GLN A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 164 removed outlier: 3.876A pdb=" N LEU A 156 " --> pdb=" O ASN A 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 38 Processing helix chain 'B' and resid 41 through 69 Processing helix chain 'B' and resid 87 through 117 removed outlier: 3.636A pdb=" N ALA B 91 " --> pdb=" O ARG B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 150 removed outlier: 4.389A pdb=" N TRP B 127 " --> pdb=" O GLN B 123 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N PHE B 128 " --> pdb=" O PHE B 124 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU B 134 " --> pdb=" O GLN B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 164 removed outlier: 3.876A pdb=" N LEU B 156 " --> pdb=" O ASN B 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 38 Processing helix chain 'C' and resid 41 through 69 Processing helix chain 'C' and resid 87 through 117 removed outlier: 3.636A pdb=" N ALA C 91 " --> pdb=" O ARG C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 150 removed outlier: 4.389A pdb=" N TRP C 127 " --> pdb=" O GLN C 123 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N PHE C 128 " --> pdb=" O PHE C 124 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU C 134 " --> pdb=" O GLN C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 164 removed outlier: 3.876A pdb=" N LEU C 156 " --> pdb=" O ASN C 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 38 Processing helix chain 'D' and resid 41 through 69 Processing helix chain 'D' and resid 87 through 117 removed outlier: 3.636A pdb=" N ALA D 91 " --> pdb=" O ARG D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 150 removed outlier: 4.389A pdb=" N TRP D 127 " --> pdb=" O GLN D 123 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N PHE D 128 " --> pdb=" O PHE D 124 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU D 134 " --> pdb=" O GLN D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 164 removed outlier: 3.876A pdb=" N LEU D 156 " --> pdb=" O ASN D 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 38 Processing helix chain 'E' and resid 41 through 69 Processing helix chain 'E' and resid 87 through 117 removed outlier: 3.636A pdb=" N ALA E 91 " --> pdb=" O ARG E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 150 removed outlier: 4.389A pdb=" N TRP E 127 " --> pdb=" O GLN E 123 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N PHE E 128 " --> pdb=" O PHE E 124 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU E 134 " --> pdb=" O GLN E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 164 removed outlier: 3.876A pdb=" N LEU E 156 " --> pdb=" O ASN E 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 38 Processing helix chain 'F' and resid 41 through 69 Processing helix chain 'F' and resid 87 through 117 removed outlier: 3.636A pdb=" N ALA F 91 " --> pdb=" O ARG F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 150 removed outlier: 4.389A pdb=" N TRP F 127 " --> pdb=" O GLN F 123 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N PHE F 128 " --> pdb=" O PHE F 124 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU F 134 " --> pdb=" O GLN F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 164 removed outlier: 3.876A pdb=" N LEU F 156 " --> pdb=" O ASN F 152 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 38 Processing helix chain 'G' and resid 41 through 69 Processing helix chain 'G' and resid 87 through 117 removed outlier: 3.636A pdb=" N ALA G 91 " --> pdb=" O ARG G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 150 removed outlier: 4.389A pdb=" N TRP G 127 " --> pdb=" O GLN G 123 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N PHE G 128 " --> pdb=" O PHE G 124 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU G 134 " --> pdb=" O GLN G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 152 through 164 removed outlier: 3.876A pdb=" N LEU G 156 " --> pdb=" O ASN G 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 38 Processing helix chain 'H' and resid 41 through 69 Processing helix chain 'H' and resid 87 through 117 removed outlier: 3.636A pdb=" N ALA H 91 " --> pdb=" O ARG H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 118 through 150 removed outlier: 4.389A pdb=" N TRP H 127 " --> pdb=" O GLN H 123 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N PHE H 128 " --> pdb=" O PHE H 124 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU H 134 " --> pdb=" O GLN H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 152 through 164 removed outlier: 3.876A pdb=" N LEU H 156 " --> pdb=" O ASN H 152 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 38 Processing helix chain 'I' and resid 41 through 69 Processing helix chain 'I' and resid 87 through 117 removed outlier: 3.636A pdb=" N ALA I 91 " --> pdb=" O ARG I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 118 through 150 removed outlier: 4.389A pdb=" N TRP I 127 " --> pdb=" O GLN I 123 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N PHE I 128 " --> pdb=" O PHE I 124 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU I 134 " --> pdb=" O GLN I 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 152 through 164 removed outlier: 3.876A pdb=" N LEU I 156 " --> pdb=" O ASN I 152 " (cutoff:3.500A) Processing helix chain 'J' and resid 9 through 38 Processing helix chain 'J' and resid 41 through 69 Processing helix chain 'J' and resid 87 through 117 removed outlier: 3.636A pdb=" N ALA J 91 " --> pdb=" O ARG J 87 " (cutoff:3.500A) Processing helix chain 'J' and resid 118 through 150 removed outlier: 4.389A pdb=" N TRP J 127 " --> pdb=" O GLN J 123 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N PHE J 128 " --> pdb=" O PHE J 124 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU J 134 " --> pdb=" O GLN J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 152 through 164 removed outlier: 3.876A pdb=" N LEU J 156 " --> pdb=" O ASN J 152 " (cutoff:3.500A) Processing helix chain 'K' and resid 9 through 38 Processing helix chain 'K' and resid 41 through 69 Processing helix chain 'K' and resid 87 through 117 removed outlier: 3.636A pdb=" N ALA K 91 " --> pdb=" O ARG K 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 118 through 150 removed outlier: 4.389A pdb=" N TRP K 127 " --> pdb=" O GLN K 123 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N PHE K 128 " --> pdb=" O PHE K 124 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU K 134 " --> pdb=" O GLN K 130 " (cutoff:3.500A) Processing helix chain 'K' and resid 152 through 164 removed outlier: 3.876A pdb=" N LEU K 156 " --> pdb=" O ASN K 152 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 38 Processing helix chain 'L' and resid 41 through 69 Processing helix chain 'L' and resid 87 through 117 removed outlier: 3.636A pdb=" N ALA L 91 " --> pdb=" O ARG L 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 118 through 150 removed outlier: 4.389A pdb=" N TRP L 127 " --> pdb=" O GLN L 123 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N PHE L 128 " --> pdb=" O PHE L 124 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU L 134 " --> pdb=" O GLN L 130 " (cutoff:3.500A) Processing helix chain 'L' and resid 152 through 164 removed outlier: 3.876A pdb=" N LEU L 156 " --> pdb=" O ASN L 152 " (cutoff:3.500A) Processing helix chain 'M' and resid 9 through 38 Processing helix chain 'M' and resid 41 through 69 Processing helix chain 'M' and resid 87 through 117 removed outlier: 3.636A pdb=" N ALA M 91 " --> pdb=" O ARG M 87 " (cutoff:3.500A) Processing helix chain 'M' and resid 118 through 150 removed outlier: 4.389A pdb=" N TRP M 127 " --> pdb=" O GLN M 123 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N PHE M 128 " --> pdb=" O PHE M 124 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU M 134 " --> pdb=" O GLN M 130 " (cutoff:3.500A) Processing helix chain 'M' and resid 152 through 164 removed outlier: 3.876A pdb=" N LEU M 156 " --> pdb=" O ASN M 152 " (cutoff:3.500A) Processing helix chain 'N' and resid 9 through 38 Processing helix chain 'N' and resid 41 through 69 Processing helix chain 'N' and resid 87 through 117 removed outlier: 3.636A pdb=" N ALA N 91 " --> pdb=" O ARG N 87 " (cutoff:3.500A) Processing helix chain 'N' and resid 118 through 150 removed outlier: 4.389A pdb=" N TRP N 127 " --> pdb=" O GLN N 123 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N PHE N 128 " --> pdb=" O PHE N 124 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU N 134 " --> pdb=" O GLN N 130 " (cutoff:3.500A) Processing helix chain 'N' and resid 152 through 164 removed outlier: 3.876A pdb=" N LEU N 156 " --> pdb=" O ASN N 152 " (cutoff:3.500A) Processing helix chain 'O' and resid 9 through 38 Processing helix chain 'O' and resid 41 through 69 Processing helix chain 'O' and resid 87 through 117 removed outlier: 3.636A pdb=" N ALA O 91 " --> pdb=" O ARG O 87 " (cutoff:3.500A) Processing helix chain 'O' and resid 118 through 150 removed outlier: 4.389A pdb=" N TRP O 127 " --> pdb=" O GLN O 123 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N PHE O 128 " --> pdb=" O PHE O 124 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU O 134 " --> pdb=" O GLN O 130 " (cutoff:3.500A) Processing helix chain 'O' and resid 152 through 164 removed outlier: 3.876A pdb=" N LEU O 156 " --> pdb=" O ASN O 152 " (cutoff:3.500A) Processing helix chain 'P' and resid 9 through 38 Processing helix chain 'P' and resid 41 through 69 Processing helix chain 'P' and resid 87 through 117 removed outlier: 3.636A pdb=" N ALA P 91 " --> pdb=" O ARG P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 118 through 150 removed outlier: 4.389A pdb=" N TRP P 127 " --> pdb=" O GLN P 123 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N PHE P 128 " --> pdb=" O PHE P 124 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU P 134 " --> pdb=" O GLN P 130 " (cutoff:3.500A) Processing helix chain 'P' and resid 152 through 164 removed outlier: 3.876A pdb=" N LEU P 156 " --> pdb=" O ASN P 152 " (cutoff:3.500A) Processing helix chain 'Q' and resid 9 through 38 Processing helix chain 'Q' and resid 41 through 69 Processing helix chain 'Q' and resid 87 through 117 removed outlier: 3.636A pdb=" N ALA Q 91 " --> pdb=" O ARG Q 87 " (cutoff:3.500A) Processing helix chain 'Q' and resid 118 through 150 removed outlier: 4.389A pdb=" N TRP Q 127 " --> pdb=" O GLN Q 123 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N PHE Q 128 " --> pdb=" O PHE Q 124 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU Q 134 " --> pdb=" O GLN Q 130 " (cutoff:3.500A) Processing helix chain 'Q' and resid 152 through 164 removed outlier: 3.876A pdb=" N LEU Q 156 " --> pdb=" O ASN Q 152 " (cutoff:3.500A) Processing helix chain 'R' and resid 9 through 38 Processing helix chain 'R' and resid 41 through 69 Processing helix chain 'R' and resid 87 through 117 removed outlier: 3.636A pdb=" N ALA R 91 " --> pdb=" O ARG R 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 118 through 150 removed outlier: 4.389A pdb=" N TRP R 127 " --> pdb=" O GLN R 123 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N PHE R 128 " --> pdb=" O PHE R 124 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU R 134 " --> pdb=" O GLN R 130 " (cutoff:3.500A) Processing helix chain 'R' and resid 152 through 164 removed outlier: 3.876A pdb=" N LEU R 156 " --> pdb=" O ASN R 152 " (cutoff:3.500A) Processing helix chain 'S' and resid 9 through 38 Processing helix chain 'S' and resid 41 through 69 Processing helix chain 'S' and resid 87 through 117 removed outlier: 3.636A pdb=" N ALA S 91 " --> pdb=" O ARG S 87 " (cutoff:3.500A) Processing helix chain 'S' and resid 118 through 150 removed outlier: 4.389A pdb=" N TRP S 127 " --> pdb=" O GLN S 123 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N PHE S 128 " --> pdb=" O PHE S 124 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU S 134 " --> pdb=" O GLN S 130 " (cutoff:3.500A) Processing helix chain 'S' and resid 152 through 164 removed outlier: 3.876A pdb=" N LEU S 156 " --> pdb=" O ASN S 152 " (cutoff:3.500A) Processing helix chain 'T' and resid 9 through 38 Processing helix chain 'T' and resid 41 through 69 Processing helix chain 'T' and resid 87 through 117 removed outlier: 3.636A pdb=" N ALA T 91 " --> pdb=" O ARG T 87 " (cutoff:3.500A) Processing helix chain 'T' and resid 118 through 150 removed outlier: 4.389A pdb=" N TRP T 127 " --> pdb=" O GLN T 123 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N PHE T 128 " --> pdb=" O PHE T 124 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU T 134 " --> pdb=" O GLN T 130 " (cutoff:3.500A) Processing helix chain 'T' and resid 152 through 164 removed outlier: 3.876A pdb=" N LEU T 156 " --> pdb=" O ASN T 152 " (cutoff:3.500A) Processing helix chain 'V' and resid 9 through 38 Processing helix chain 'V' and resid 41 through 69 Processing helix chain 'V' and resid 87 through 117 removed outlier: 3.636A pdb=" N ALA V 91 " --> pdb=" O ARG V 87 " (cutoff:3.500A) Processing helix chain 'V' and resid 118 through 150 removed outlier: 4.389A pdb=" N TRP V 127 " --> pdb=" O GLN V 123 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N PHE V 128 " --> pdb=" O PHE V 124 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU V 134 " --> pdb=" O GLN V 130 " (cutoff:3.500A) Processing helix chain 'V' and resid 152 through 164 removed outlier: 3.876A pdb=" N LEU V 156 " --> pdb=" O ASN V 152 " (cutoff:3.500A) Processing helix chain 'W' and resid 9 through 38 Processing helix chain 'W' and resid 41 through 69 Processing helix chain 'W' and resid 87 through 117 removed outlier: 3.636A pdb=" N ALA W 91 " --> pdb=" O ARG W 87 " (cutoff:3.500A) Processing helix chain 'W' and resid 118 through 150 removed outlier: 4.389A pdb=" N TRP W 127 " --> pdb=" O GLN W 123 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N PHE W 128 " --> pdb=" O PHE W 124 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU W 134 " --> pdb=" O GLN W 130 " (cutoff:3.500A) Processing helix chain 'W' and resid 152 through 164 removed outlier: 3.876A pdb=" N LEU W 156 " --> pdb=" O ASN W 152 " (cutoff:3.500A) Processing helix chain 'X' and resid 9 through 38 Processing helix chain 'X' and resid 41 through 69 Processing helix chain 'X' and resid 87 through 117 removed outlier: 3.636A pdb=" N ALA X 91 " --> pdb=" O ARG X 87 " (cutoff:3.500A) Processing helix chain 'X' and resid 118 through 150 removed outlier: 4.389A pdb=" N TRP X 127 " --> pdb=" O GLN X 123 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N PHE X 128 " --> pdb=" O PHE X 124 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU X 134 " --> pdb=" O GLN X 130 " (cutoff:3.500A) Processing helix chain 'X' and resid 152 through 164 removed outlier: 3.876A pdb=" N LEU X 156 " --> pdb=" O ASN X 152 " (cutoff:3.500A) Processing helix chain 'Y' and resid 9 through 38 Processing helix chain 'Y' and resid 41 through 69 Processing helix chain 'Y' and resid 87 through 117 removed outlier: 3.636A pdb=" N ALA Y 91 " --> pdb=" O ARG Y 87 " (cutoff:3.500A) Processing helix chain 'Y' and resid 118 through 150 removed outlier: 4.389A pdb=" N TRP Y 127 " --> pdb=" O GLN Y 123 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N PHE Y 128 " --> pdb=" O PHE Y 124 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU Y 134 " --> pdb=" O GLN Y 130 " (cutoff:3.500A) Processing helix chain 'Y' and resid 152 through 164 removed outlier: 3.876A pdb=" N LEU Y 156 " --> pdb=" O ASN Y 152 " (cutoff:3.500A) 2664 hydrogen bonds defined for protein. 7992 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: 10.44 Time building geometry restraints manager: 16.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 8952 1.32 - 1.44: 6576 1.44 - 1.56: 18816 1.56 - 1.69: 0 1.69 - 1.81: 240 Bond restraints: 34584 Sorted by residual: bond pdb=" C ASN H 57 " pdb=" O ASN H 57 " ideal model delta sigma weight residual 1.237 1.206 0.031 1.17e-02 7.31e+03 6.93e+00 bond pdb=" C ASN D 57 " pdb=" O ASN D 57 " ideal model delta sigma weight residual 1.237 1.206 0.031 1.17e-02 7.31e+03 6.93e+00 bond pdb=" C ASN J 57 " pdb=" O ASN J 57 " ideal model delta sigma weight residual 1.237 1.206 0.031 1.17e-02 7.31e+03 6.93e+00 bond pdb=" C ASN K 57 " pdb=" O ASN K 57 " ideal model delta sigma weight residual 1.237 1.206 0.031 1.17e-02 7.31e+03 6.93e+00 bond pdb=" C ASN R 57 " pdb=" O ASN R 57 " ideal model delta sigma weight residual 1.237 1.206 0.031 1.17e-02 7.31e+03 6.93e+00 ... (remaining 34579 not shown) Histogram of bond angle deviations from ideal: 99.45 - 106.36: 864 106.36 - 113.27: 18432 113.27 - 120.18: 13416 120.18 - 127.09: 13872 127.09 - 134.00: 312 Bond angle restraints: 46896 Sorted by residual: angle pdb=" CA PRO A 168 " pdb=" N PRO A 168 " pdb=" CD PRO A 168 " ideal model delta sigma weight residual 112.00 107.94 4.06 1.40e+00 5.10e-01 8.39e+00 angle pdb=" CA PRO H 168 " pdb=" N PRO H 168 " pdb=" CD PRO H 168 " ideal model delta sigma weight residual 112.00 107.94 4.06 1.40e+00 5.10e-01 8.39e+00 angle pdb=" CA PRO B 168 " pdb=" N PRO B 168 " pdb=" CD PRO B 168 " ideal model delta sigma weight residual 112.00 107.94 4.06 1.40e+00 5.10e-01 8.39e+00 angle pdb=" CA PRO X 168 " pdb=" N PRO X 168 " pdb=" CD PRO X 168 " ideal model delta sigma weight residual 112.00 107.94 4.06 1.40e+00 5.10e-01 8.39e+00 angle pdb=" CA PRO C 168 " pdb=" N PRO C 168 " pdb=" CD PRO C 168 " ideal model delta sigma weight residual 112.00 107.94 4.06 1.40e+00 5.10e-01 8.39e+00 ... (remaining 46891 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 18120 17.72 - 35.43: 1920 35.43 - 53.15: 504 53.15 - 70.86: 144 70.86 - 88.58: 144 Dihedral angle restraints: 20832 sinusoidal: 8376 harmonic: 12456 Sorted by residual: dihedral pdb=" CA PRO R 76 " pdb=" C PRO R 76 " pdb=" N GLY R 77 " pdb=" CA GLY R 77 " ideal model delta harmonic sigma weight residual 180.00 160.38 19.62 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA PRO K 76 " pdb=" C PRO K 76 " pdb=" N GLY K 77 " pdb=" CA GLY K 77 " ideal model delta harmonic sigma weight residual 180.00 160.38 19.62 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA PRO H 76 " pdb=" C PRO H 76 " pdb=" N GLY H 77 " pdb=" CA GLY H 77 " ideal model delta harmonic sigma weight residual 180.00 160.38 19.62 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 20829 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.049: 2400 0.049 - 0.096: 1848 0.096 - 0.143: 768 0.143 - 0.190: 72 0.190 - 0.237: 48 Chirality restraints: 5136 Sorted by residual: chirality pdb=" CA GLU O 74 " pdb=" N GLU O 74 " pdb=" C GLU O 74 " pdb=" CB GLU O 74 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CA GLU L 74 " pdb=" N GLU L 74 " pdb=" C GLU L 74 " pdb=" CB GLU L 74 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CA GLU W 74 " pdb=" N GLU W 74 " pdb=" C GLU W 74 " pdb=" CB GLU W 74 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.41e+00 ... (remaining 5133 not shown) Planarity restraints: 6384 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA N 167 " -0.070 5.00e-02 4.00e+02 1.03e-01 1.71e+01 pdb=" N PRO N 168 " 0.179 5.00e-02 4.00e+02 pdb=" CA PRO N 168 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO N 168 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA T 167 " -0.070 5.00e-02 4.00e+02 1.03e-01 1.71e+01 pdb=" N PRO T 168 " 0.179 5.00e-02 4.00e+02 pdb=" CA PRO T 168 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO T 168 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 167 " -0.070 5.00e-02 4.00e+02 1.03e-01 1.71e+01 pdb=" N PRO B 168 " 0.179 5.00e-02 4.00e+02 pdb=" CA PRO B 168 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO B 168 " -0.057 5.00e-02 4.00e+02 ... (remaining 6381 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 1320 2.67 - 3.23: 36948 3.23 - 3.78: 68328 3.78 - 4.34: 81756 4.34 - 4.90: 128124 Nonbonded interactions: 316476 Sorted by model distance: nonbonded pdb=" O HOH B 212 " pdb=" O HOH B 250 " model vdw 2.110 2.440 nonbonded pdb=" O HOH N 212 " pdb=" O HOH N 250 " model vdw 2.110 2.440 nonbonded pdb=" O HOH T 212 " pdb=" O HOH T 250 " model vdw 2.110 2.440 nonbonded pdb=" O HOH V 212 " pdb=" O HOH V 250 " model vdw 2.110 2.440 nonbonded pdb=" O HOH C 212 " pdb=" O HOH C 250 " model vdw 2.110 2.440 ... (remaining 316471 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 174 or resid 176 through 181)) selection = (chain 'B' and (resid 5 through 174 or resid 176 through 181)) selection = (chain 'C' and (resid 5 through 174 or resid 176 through 181)) selection = (chain 'D' and (resid 5 through 174 or resid 176 through 181)) selection = (chain 'E' and (resid 5 through 174 or resid 176 through 181)) selection = (chain 'F' and (resid 5 through 174 or resid 176 through 181)) selection = (chain 'G' and (resid 5 through 174 or resid 176 through 181)) selection = (chain 'H' and (resid 5 through 174 or resid 176 through 181)) selection = (chain 'I' and (resid 5 through 174 or resid 176 through 181)) selection = (chain 'J' and (resid 5 through 174 or resid 176 through 181)) selection = (chain 'K' and (resid 5 through 174 or resid 176 through 181)) selection = (chain 'L' and (resid 5 through 174 or resid 176 through 181)) selection = (chain 'M' and (resid 5 through 174 or resid 176 through 181)) selection = (chain 'N' and (resid 5 through 174 or resid 176 through 181)) selection = (chain 'O' and (resid 5 through 174 or resid 176 through 181)) selection = (chain 'P' and (resid 5 through 174 or resid 176 through 181)) selection = (chain 'Q' and (resid 5 through 174 or resid 176 through 181)) selection = (chain 'R' and (resid 5 through 174 or resid 176 through 181)) selection = (chain 'S' and (resid 5 through 174 or resid 176 through 181)) selection = (chain 'T' and (resid 5 through 174 or resid 176 through 181)) selection = (chain 'V' and (resid 5 through 174 or resid 176 through 181)) selection = (chain 'W' and (resid 5 through 174 or resid 176 through 181)) selection = (chain 'X' and (resid 5 through 174 or resid 176 through 181)) selection = (chain 'Y' and (resid 5 through 174 or resid 176 through 181)) } 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=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 8.770 Check model and map are aligned: 0.580 Set scattering table: 0.340 Process input model: 111.340 Find NCS groups from input model: 2.410 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 139.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 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 : 0.017 0.078 34584 Z= 1.121 Angle : 1.099 7.286 46896 Z= 0.642 Chirality : 0.070 0.237 5136 Planarity : 0.010 0.103 6384 Dihedral : 18.129 88.578 12720 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.00 % Allowed : 12.50 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.12), residues: 4272 helix: 2.05 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : -0.59 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.006 TRP T 127 HIS 0.016 0.005 HIS T 47 PHE 0.034 0.006 PHE N 128 TYR 0.024 0.006 TYR P 35 ARG 0.006 0.002 ARG S 144 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 694 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 694 time to evaluate : 4.396 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 694 average time/residue: 1.6456 time to fit residues: 1352.3746 Evaluate side-chains 621 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 621 time to evaluate : 4.518 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.7225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 0.8980 chunk 309 optimal weight: 8.9990 chunk 171 optimal weight: 5.9990 chunk 105 optimal weight: 0.7980 chunk 208 optimal weight: 0.9980 chunk 165 optimal weight: 3.9990 chunk 319 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 194 optimal weight: 4.9990 chunk 238 optimal weight: 0.9990 chunk 370 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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: 0.8444 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 34584 Z= 0.160 Angle : 0.436 3.705 46896 Z= 0.240 Chirality : 0.034 0.115 5136 Planarity : 0.006 0.064 6384 Dihedral : 3.561 13.616 4656 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 0.98 % Allowed : 12.38 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.06 (0.12), residues: 4272 helix: 3.55 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : -0.14 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 127 HIS 0.005 0.001 HIS B 47 PHE 0.013 0.002 PHE N 48 TYR 0.009 0.001 TYR W 49 ARG 0.003 0.000 ARG E 72 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 820 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 786 time to evaluate : 4.257 Fit side-chains outliers start: 34 outliers final: 5 residues processed: 810 average time/residue: 1.4967 time to fit residues: 1449.8729 Evaluate side-chains 757 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 752 time to evaluate : 3.948 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 5.2806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 205 optimal weight: 4.9990 chunk 114 optimal weight: 10.0000 chunk 308 optimal weight: 9.9990 chunk 252 optimal weight: 0.6980 chunk 102 optimal weight: 10.0000 chunk 371 optimal weight: 10.0000 chunk 400 optimal weight: 7.9990 chunk 330 optimal weight: 8.9990 chunk 368 optimal weight: 9.9990 chunk 126 optimal weight: 7.9990 chunk 297 optimal weight: 1.9990 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 GLN B 51 GLN D 51 GLN ** E 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 51 GLN H 132 GLN I 51 GLN I 84 GLN J 51 GLN K 51 GLN ** K 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 51 GLN L 132 GLN ** N 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 51 GLN P 51 GLN S 51 GLN T 51 GLN V 51 GLN V 132 GLN W 51 GLN ** X 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 34584 Z= 0.305 Angle : 0.564 7.570 46896 Z= 0.303 Chirality : 0.037 0.138 5136 Planarity : 0.007 0.059 6384 Dihedral : 3.899 16.481 4656 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.95 % Allowed : 13.17 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.92 (0.12), residues: 4272 helix: 3.43 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : -0.17 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP C 127 HIS 0.010 0.003 HIS B 47 PHE 0.021 0.002 PHE G 48 TYR 0.013 0.002 TYR X 35 ARG 0.004 0.001 ARG M 148 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 764 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 731 time to evaluate : 3.792 Fit side-chains outliers start: 33 outliers final: 15 residues processed: 735 average time/residue: 1.5378 time to fit residues: 1348.4237 Evaluate side-chains 737 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 722 time to evaluate : 3.074 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 2 residues processed: 13 average time/residue: 1.8690 time to fit residues: 31.8997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 366 optimal weight: 7.9990 chunk 279 optimal weight: 10.0000 chunk 192 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 177 optimal weight: 9.9990 chunk 249 optimal weight: 9.9990 chunk 372 optimal weight: 0.5980 chunk 394 optimal weight: 0.0980 chunk 194 optimal weight: 9.9990 chunk 353 optimal weight: 6.9990 chunk 106 optimal weight: 4.9990 overall best weight: 3.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: