Starting phenix.real_space_refine (version: dev) on Sun Dec 18 15:13:48 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zlg_11265/12_2022/6zlg_11265.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zlg_11265/12_2022/6zlg_11265.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zlg_11265/12_2022/6zlg_11265.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zlg_11265/12_2022/6zlg_11265.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zlg_11265/12_2022/6zlg_11265.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zlg_11265/12_2022/6zlg_11265.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.007 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A GLU 12": "OE1" <-> "OE2" Residue "A ARG 40": "NH1" <-> "NH2" Residue "A GLU 46": "OE1" <-> "OE2" Residue "A GLU 54": "OE1" <-> "OE2" Residue "A GLU 57": "OE1" <-> "OE2" Residue "A GLU 58": "OE1" <-> "OE2" Residue "A ASP 72": "OD1" <-> "OD2" Residue "A PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 88": "OD1" <-> "OD2" Residue "A GLU 89": "OE1" <-> "OE2" Residue "A ASP 113": "OD1" <-> "OD2" Residue "A GLU 131": "OE1" <-> "OE2" Residue "A ASP 136": "OD1" <-> "OD2" Residue "B ARG 40": "NH1" <-> "NH2" Residue "B ASP 41": "OD1" <-> "OD2" Residue "B GLU 54": "OE1" <-> "OE2" Residue "B GLU 57": "OE1" <-> "OE2" Residue "B GLU 68": "OE1" <-> "OE2" Residue "B ASP 72": "OD1" <-> "OD2" Residue "B PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 88": "OD1" <-> "OD2" Residue "B GLU 104": "OE1" <-> "OE2" Residue "B ASP 113": "OD1" <-> "OD2" Residue "B GLU 131": "OE1" <-> "OE2" Residue "B ASP 136": "OD1" <-> "OD2" Residue "C GLU 68": "OE1" <-> "OE2" Residue "C PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 89": "OE1" <-> "OE2" Residue "C GLU 104": "OE1" <-> "OE2" Residue "C ASP 113": "OD1" <-> "OD2" Residue "C GLU 131": "OE1" <-> "OE2" Residue "C ASP 136": "OD1" <-> "OD2" Residue "D ARG 26": "NH1" <-> "NH2" Residue "D GLU 46": "OE1" <-> "OE2" Residue "D GLU 54": "OE1" <-> "OE2" Residue "D GLU 61": "OE1" <-> "OE2" Residue "D GLU 68": "OE1" <-> "OE2" Residue "D PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 88": "OD1" <-> "OD2" Residue "D ARG 121": "NH1" <-> "NH2" Residue "D GLU 131": "OE1" <-> "OE2" Residue "D ASP 136": "OD1" <-> "OD2" Residue "E GLU 46": "OE1" <-> "OE2" Residue "E ARG 53": "NH1" <-> "NH2" Residue "E GLU 54": "OE1" <-> "OE2" Residue "E GLU 57": "OE1" <-> "OE2" Residue "E GLU 58": "OE1" <-> "OE2" Residue "E ARG 60": "NH1" <-> "NH2" Residue "E GLU 68": "OE1" <-> "OE2" Residue "E ASP 72": "OD1" <-> "OD2" Residue "E PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 89": "OE1" <-> "OE2" Residue "E GLU 104": "OE1" <-> "OE2" Residue "E ARG 121": "NH1" <-> "NH2" Residue "E GLU 131": "OE1" <-> "OE2" Residue "E ASP 136": "OD1" <-> "OD2" Residue "F ARG 40": "NH1" <-> "NH2" Residue "F GLU 58": "OE1" <-> "OE2" Residue "F GLU 68": "OE1" <-> "OE2" Residue "F ASP 72": "OD1" <-> "OD2" Residue "F PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 89": "OE1" <-> "OE2" Residue "F GLU 104": "OE1" <-> "OE2" Residue "F GLU 131": "OE1" <-> "OE2" Residue "F ASP 136": "OD1" <-> "OD2" Residue "I GLU 12": "OE1" <-> "OE2" Residue "I ARG 40": "NH1" <-> "NH2" Residue "I ASP 41": "OD1" <-> "OD2" Residue "I GLU 46": "OE1" <-> "OE2" Residue "I GLU 58": "OE1" <-> "OE2" Residue "I ARG 60": "NH1" <-> "NH2" Residue "I GLU 61": "OE1" <-> "OE2" Residue "I ASP 72": "OD1" <-> "OD2" Residue "I PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 89": "OE1" <-> "OE2" Residue "I GLU 95": "OE1" <-> "OE2" Residue "I GLU 131": "OE1" <-> "OE2" Residue "I ASP 136": "OD1" <-> "OD2" Residue "I GLU 138": "OE1" <-> "OE2" Residue "J GLU 12": "OE1" <-> "OE2" Residue "J ARG 40": "NH1" <-> "NH2" Residue "J GLU 54": "OE1" <-> "OE2" Residue "J GLU 68": "OE1" <-> "OE2" Residue "J PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 88": "OD1" <-> "OD2" Residue "J GLU 89": "OE1" <-> "OE2" Residue "J GLU 131": "OE1" <-> "OE2" Residue "J GLU 138": "OE1" <-> "OE2" Residue "K GLU 12": "OE1" <-> "OE2" Residue "K ASP 41": "OD1" <-> "OD2" Residue "K GLU 46": "OE1" <-> "OE2" Residue "K GLU 61": "OE1" <-> "OE2" Residue "K GLU 68": "OE1" <-> "OE2" Residue "K ASP 72": "OD1" <-> "OD2" Residue "K PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 88": "OD1" <-> "OD2" Residue "K GLU 89": "OE1" <-> "OE2" Residue "K GLU 131": "OE1" <-> "OE2" Residue "K ASP 136": "OD1" <-> "OD2" Residue "K GLU 138": "OE1" <-> "OE2" Residue "L ARG 26": "NH1" <-> "NH2" Residue "L ASP 41": "OD1" <-> "OD2" Residue "L GLU 54": "OE1" <-> "OE2" Residue "L GLU 57": "OE1" <-> "OE2" Residue "L ARG 60": "NH1" <-> "NH2" Residue "L GLU 61": "OE1" <-> "OE2" Residue "L ASP 72": "OD1" <-> "OD2" Residue "L PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 81": "OD1" <-> "OD2" Residue "L ASP 88": "OD1" <-> "OD2" Residue "L GLU 89": "OE1" <-> "OE2" Residue "L ASP 113": "OD1" <-> "OD2" Residue "L ARG 121": "NH1" <-> "NH2" Residue "L GLU 131": "OE1" <-> "OE2" Residue "L ASP 136": "OD1" <-> "OD2" Residue "M GLU 12": "OE1" <-> "OE2" Residue "M GLU 46": "OE1" <-> "OE2" Residue "M ARG 53": "NH1" <-> "NH2" Residue "M GLU 58": "OE1" <-> "OE2" Residue "M ARG 60": "NH1" <-> "NH2" Residue "M GLU 68": "OE1" <-> "OE2" Residue "M ASP 72": "OD1" <-> "OD2" Residue "M PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 89": "OE1" <-> "OE2" Residue "M ARG 121": "NH1" <-> "NH2" Residue "M GLU 131": "OE1" <-> "OE2" Residue "M ASP 136": "OD1" <-> "OD2" Residue "N ARG 40": "NH1" <-> "NH2" Residue "N GLU 54": "OE1" <-> "OE2" Residue "N GLU 58": "OE1" <-> "OE2" Residue "N ARG 60": "NH1" <-> "NH2" Residue "N GLU 68": "OE1" <-> "OE2" Residue "N ASP 72": "OD1" <-> "OD2" Residue "N PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 89": "OE1" <-> "OE2" Residue "N GLU 131": "OE1" <-> "OE2" Residue "O ARG 40": "NH1" <-> "NH2" Residue "O ASP 41": "OD1" <-> "OD2" Residue "O ARG 60": "NH1" <-> "NH2" Residue "O GLU 68": "OE1" <-> "OE2" Residue "O PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 88": "OD1" <-> "OD2" Residue "O GLU 89": "OE1" <-> "OE2" Residue "O GLU 131": "OE1" <-> "OE2" Residue "O ASP 136": "OD1" <-> "OD2" Residue "P GLU 12": "OE1" <-> "OE2" Residue "P ARG 40": "NH1" <-> "NH2" Residue "P ASP 41": "OD1" <-> "OD2" Residue "P GLU 54": "OE1" <-> "OE2" Residue "P GLU 57": "OE1" <-> "OE2" Residue "P GLU 58": "OE1" <-> "OE2" Residue "P ARG 60": "NH1" <-> "NH2" Residue "P GLU 61": "OE1" <-> "OE2" Residue "P ASP 72": "OD1" <-> "OD2" Residue "P PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 88": "OD1" <-> "OD2" Residue "P GLU 131": "OE1" <-> "OE2" Residue "Q GLU 12": "OE1" <-> "OE2" Residue "Q GLU 54": "OE1" <-> "OE2" Residue "Q ARG 60": "NH1" <-> "NH2" Residue "Q GLU 61": "OE1" <-> "OE2" Residue "Q GLU 68": "OE1" <-> "OE2" Residue "Q PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 88": "OD1" <-> "OD2" Residue "Q GLU 89": "OE1" <-> "OE2" Residue "Q GLU 131": "OE1" <-> "OE2" Residue "R GLU 12": "OE1" <-> "OE2" Residue "R ARG 26": "NH1" <-> "NH2" Residue "R ASP 41": "OD1" <-> "OD2" Residue "R GLU 54": "OE1" <-> "OE2" Residue "R GLU 68": "OE1" <-> "OE2" Residue "R ASP 72": "OD1" <-> "OD2" Residue "R PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 88": "OD1" <-> "OD2" Residue "R GLU 89": "OE1" <-> "OE2" Residue "R GLU 104": "OE1" <-> "OE2" Residue "R ARG 121": "NH1" <-> "NH2" Residue "R GLU 131": "OE1" <-> "OE2" Residue "R GLU 138": "OE1" <-> "OE2" Residue "S ARG 53": "NH1" <-> "NH2" Residue "S GLU 58": "OE1" <-> "OE2" Residue "S GLU 61": "OE1" <-> "OE2" Residue "S GLU 68": "OE1" <-> "OE2" Residue "S PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 88": "OD1" <-> "OD2" Residue "S GLU 89": "OE1" <-> "OE2" Residue "S ARG 121": "NH1" <-> "NH2" Residue "S GLU 131": "OE1" <-> "OE2" Residue "S ASP 136": "OD1" <-> "OD2" Residue "S GLU 138": "OE1" <-> "OE2" Residue "T ARG 40": "NH1" <-> "NH2" Residue "T GLU 54": "OE1" <-> "OE2" Residue "T GLU 58": "OE1" <-> "OE2" Residue "T GLU 68": "OE1" <-> "OE2" Residue "T ASP 72": "OD1" <-> "OD2" Residue "T PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 88": "OD1" <-> "OD2" Residue "T GLU 89": "OE1" <-> "OE2" Residue "T GLU 104": "OE1" <-> "OE2" Residue "T GLU 131": "OE1" <-> "OE2" Residue "U GLU 12": "OE1" <-> "OE2" Residue "U ARG 40": "NH1" <-> "NH2" Residue "U ASP 41": "OD1" <-> "OD2" Residue "U GLU 57": "OE1" <-> "OE2" Residue "U GLU 58": "OE1" <-> "OE2" Residue "U GLU 68": "OE1" <-> "OE2" Residue "U PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 89": "OE1" <-> "OE2" Residue "U ASP 113": "OD1" <-> "OD2" Residue "U GLU 131": "OE1" <-> "OE2" Residue "U GLU 138": "OE1" <-> "OE2" Residue "V GLU 12": "OE1" <-> "OE2" Residue "V ARG 40": "NH1" <-> "NH2" Residue "V GLU 54": "OE1" <-> "OE2" Residue "V GLU 58": "OE1" <-> "OE2" Residue "V ARG 60": "NH1" <-> "NH2" Residue "V GLU 61": "OE1" <-> "OE2" Residue "V GLU 68": "OE1" <-> "OE2" Residue "V ASP 72": "OD1" <-> "OD2" Residue "V PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 89": "OE1" <-> "OE2" Residue "V GLU 104": "OE1" <-> "OE2" Residue "V GLU 131": "OE1" <-> "OE2" Residue "W ASP 41": "OD1" <-> "OD2" Residue "W GLU 58": "OE1" <-> "OE2" Residue "W GLU 61": "OE1" <-> "OE2" Residue "W GLU 68": "OE1" <-> "OE2" Residue "W PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 88": "OD1" <-> "OD2" Residue "W GLU 89": "OE1" <-> "OE2" Residue "W GLU 131": "OE1" <-> "OE2" Residue "W ASP 136": "OD1" <-> "OD2" Residue "W GLU 138": "OE1" <-> "OE2" Residue "X ARG 26": "NH1" <-> "NH2" Residue "X ARG 60": "NH1" <-> "NH2" Residue "X GLU 68": "OE1" <-> "OE2" Residue "X ASP 72": "OD1" <-> "OD2" Residue "X PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 104": "OE1" <-> "OE2" Residue "X ARG 121": "NH1" <-> "NH2" Residue "X GLU 131": "OE1" <-> "OE2" Residue "Y ARG 53": "NH1" <-> "NH2" Residue "Y GLU 54": "OE1" <-> "OE2" Residue "Y GLU 57": "OE1" <-> "OE2" Residue "Y GLU 61": "OE1" <-> "OE2" Residue "Y GLU 68": "OE1" <-> "OE2" Residue "Y PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 88": "OD1" <-> "OD2" Residue "Y GLU 104": "OE1" <-> "OE2" Residue "Y ARG 121": "NH1" <-> "NH2" Residue "Y GLU 131": "OE1" <-> "OE2" Residue "Y ASP 136": "OD1" <-> "OD2" Residue "Y GLU 138": "OE1" <-> "OE2" Residue "Z GLU 12": "OE1" <-> "OE2" Residue "Z ARG 40": "NH1" <-> "NH2" Residue "Z GLU 54": "OE1" <-> "OE2" Residue "Z ARG 60": "NH1" <-> "NH2" Residue "Z GLU 68": "OE1" <-> "OE2" Residue "Z ASP 72": "OD1" <-> "OD2" Residue "Z PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 88": "OD1" <-> "OD2" Residue "Z GLU 89": "OE1" <-> "OE2" Residue "Z GLU 131": "OE1" <-> "OE2" Residue "Z ASP 136": "OD1" <-> "OD2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 33008 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1370 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 2, 'TRANS': 166} Chain breaks: 1 Chain: "B" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1378 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain breaks: 1 Chain: "C" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1378 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain breaks: 1 Chain: "D" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1378 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain breaks: 1 Chain: "E" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1378 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain breaks: 1 Chain: "F" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1370 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 2, 'TRANS': 166} Chain breaks: 1 Chain: "I" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1370 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 2, 'TRANS': 166} Chain breaks: 1 Chain: "J" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1378 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain breaks: 1 Chain: "K" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1378 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain breaks: 1 Chain: "L" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1378 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain breaks: 1 Chain: "M" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1378 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain breaks: 1 Chain: "N" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1370 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 2, 'TRANS': 166} Chain breaks: 1 Chain: "O" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1370 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 2, 'TRANS': 166} Chain breaks: 1 Chain: "P" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1378 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain breaks: 1 Chain: "Q" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1378 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain breaks: 1 Chain: "R" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1378 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain breaks: 1 Chain: "S" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1378 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain breaks: 1 Chain: "T" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1370 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 2, 'TRANS': 166} Chain breaks: 1 Chain: "U" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1370 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 2, 'TRANS': 166} Chain breaks: 1 Chain: "V" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1378 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain breaks: 1 Chain: "W" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1378 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain breaks: 1 Chain: "X" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1378 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain breaks: 1 Chain: "Y" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1378 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain breaks: 1 Chain: "Z" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1370 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 2, 'TRANS': 166} Chain breaks: 1 Residues with excluded nonbonded symmetry interactions: 24 residue: pdb=" N ARG A 40 " occ=0.50 ... (9 atoms not shown) pdb=" NH2 ARG A 40 " occ=0.50 residue: pdb=" N ARG B 76 " occ=0.50 ... (9 atoms not shown) pdb=" NH2 ARG B 76 " occ=0.50 residue: pdb=" N ARG C 40 " occ=0.50 ... (9 atoms not shown) pdb=" NH2 ARG C 40 " occ=0.50 residue: pdb=" N ARG D 19 " occ=0.50 ... (9 atoms not shown) pdb=" NH2 ARG D 19 " occ=0.50 residue: pdb=" N ARG D 76 " occ=0.50 ... (9 atoms not shown) pdb=" NH2 ARG D 76 " occ=0.50 residue: pdb=" N GLU E 57 " occ=0.50 ... (7 atoms not shown) pdb=" OE2 GLU E 57 " occ=0.50 residue: pdb=" N ARG I 40 " occ=0.50 ... (9 atoms not shown) pdb=" NH2 ARG I 40 " occ=0.50 residue: pdb=" N ARG J 76 " occ=0.50 ... (9 atoms not shown) pdb=" NH2 ARG J 76 " occ=0.50 residue: pdb=" N ARG K 40 " occ=0.50 ... (9 atoms not shown) pdb=" NH2 ARG K 40 " occ=0.50 residue: pdb=" N ARG L 19 " occ=0.50 ... (9 atoms not shown) pdb=" NH2 ARG L 19 " occ=0.50 residue: pdb=" N ARG L 76 " occ=0.50 ... (9 atoms not shown) pdb=" NH2 ARG L 76 " occ=0.50 residue: pdb=" N GLU M 57 " occ=0.50 ... (7 atoms not shown) pdb=" OE2 GLU M 57 " occ=0.50 ... (remaining 12 not shown) Time building chain proxies: 17.09, per 1000 atoms: 0.52 Number of scatterers: 33008 At special positions: 0 Unit cell: (128.7, 128.7, 128.7, 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 112 16.00 O 6208 8.00 N 5968 7.00 C 20720 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: 12.84 Conformation dependent library (CDL) restraints added in 4.6 seconds 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7664 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 0 sheets defined 78.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 10 through 38 Processing helix chain 'A' and resid 45 through 73 Processing helix chain 'A' and resid 92 through 121 Processing helix chain 'A' and resid 123 through 134 Processing helix chain 'A' and resid 134 through 156 Processing helix chain 'A' and resid 170 through 179 Processing helix chain 'B' and resid 10 through 38 Processing helix chain 'B' and resid 45 through 74 Processing helix chain 'B' and resid 92 through 121 Processing helix chain 'B' and resid 123 through 134 Processing helix chain 'B' and resid 134 through 156 Processing helix chain 'B' and resid 170 through 179 Processing helix chain 'C' and resid 10 through 38 Processing helix chain 'C' and resid 45 through 73 Processing helix chain 'C' and resid 92 through 121 Processing helix chain 'C' and resid 123 through 134 Processing helix chain 'C' and resid 134 through 156 Processing helix chain 'C' and resid 170 through 179 Processing helix chain 'D' and resid 10 through 38 Processing helix chain 'D' and resid 45 through 73 Processing helix chain 'D' and resid 92 through 121 Processing helix chain 'D' and resid 123 through 134 Processing helix chain 'D' and resid 134 through 156 Processing helix chain 'D' and resid 170 through 179 Processing helix chain 'E' and resid 10 through 38 Processing helix chain 'E' and resid 45 through 74 Processing helix chain 'E' and resid 92 through 121 Processing helix chain 'E' and resid 123 through 134 Processing helix chain 'E' and resid 134 through 156 Processing helix chain 'E' and resid 170 through 179 Processing helix chain 'F' and resid 10 through 38 Processing helix chain 'F' and resid 45 through 73 Processing helix chain 'F' and resid 92 through 121 Processing helix chain 'F' and resid 123 through 134 Processing helix chain 'F' and resid 134 through 156 Processing helix chain 'F' and resid 170 through 179 Processing helix chain 'I' and resid 10 through 38 Processing helix chain 'I' and resid 45 through 73 Processing helix chain 'I' and resid 92 through 121 Processing helix chain 'I' and resid 123 through 134 Processing helix chain 'I' and resid 134 through 156 Processing helix chain 'I' and resid 170 through 179 Processing helix chain 'J' and resid 10 through 38 Processing helix chain 'J' and resid 45 through 74 Processing helix chain 'J' and resid 92 through 121 Processing helix chain 'J' and resid 123 through 134 Processing helix chain 'J' and resid 134 through 156 Processing helix chain 'J' and resid 170 through 179 Processing helix chain 'K' and resid 10 through 38 Processing helix chain 'K' and resid 45 through 73 removed outlier: 3.506A pdb=" N GLY K 62 " --> pdb=" O GLU K 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 92 through 121 Processing helix chain 'K' and resid 123 through 134 Processing helix chain 'K' and resid 134 through 156 Processing helix chain 'K' and resid 170 through 179 Processing helix chain 'L' and resid 10 through 38 Processing helix chain 'L' and resid 45 through 73 Processing helix chain 'L' and resid 92 through 121 Processing helix chain 'L' and resid 123 through 134 Processing helix chain 'L' and resid 134 through 156 Processing helix chain 'L' and resid 170 through 179 Processing helix chain 'M' and resid 10 through 38 Processing helix chain 'M' and resid 45 through 74 Processing helix chain 'M' and resid 92 through 121 Processing helix chain 'M' and resid 123 through 134 Processing helix chain 'M' and resid 134 through 156 Processing helix chain 'M' and resid 170 through 179 Processing helix chain 'N' and resid 10 through 38 Processing helix chain 'N' and resid 45 through 73 Processing helix chain 'N' and resid 92 through 121 Processing helix chain 'N' and resid 123 through 134 Processing helix chain 'N' and resid 134 through 156 Processing helix chain 'N' and resid 170 through 179 Processing helix chain 'O' and resid 10 through 38 Processing helix chain 'O' and resid 45 through 73 Processing helix chain 'O' and resid 92 through 121 Processing helix chain 'O' and resid 123 through 134 Processing helix chain 'O' and resid 134 through 156 Processing helix chain 'O' and resid 170 through 179 Processing helix chain 'P' and resid 10 through 38 Processing helix chain 'P' and resid 45 through 74 Processing helix chain 'P' and resid 92 through 121 Processing helix chain 'P' and resid 123 through 134 Processing helix chain 'P' and resid 134 through 156 Processing helix chain 'P' and resid 170 through 179 Processing helix chain 'Q' and resid 10 through 38 Processing helix chain 'Q' and resid 45 through 73 Processing helix chain 'Q' and resid 92 through 121 Processing helix chain 'Q' and resid 123 through 134 Processing helix chain 'Q' and resid 134 through 156 Processing helix chain 'Q' and resid 170 through 179 Processing helix chain 'R' and resid 10 through 38 Processing helix chain 'R' and resid 45 through 73 Processing helix chain 'R' and resid 92 through 121 Processing helix chain 'R' and resid 123 through 134 Processing helix chain 'R' and resid 134 through 156 Processing helix chain 'R' and resid 170 through 179 Processing helix chain 'S' and resid 10 through 38 Processing helix chain 'S' and resid 45 through 74 Processing helix chain 'S' and resid 92 through 121 Processing helix chain 'S' and resid 123 through 134 Processing helix chain 'S' and resid 134 through 156 Processing helix chain 'S' and resid 170 through 179 Processing helix chain 'T' and resid 10 through 38 Processing helix chain 'T' and resid 45 through 73 Processing helix chain 'T' and resid 92 through 121 Processing helix chain 'T' and resid 123 through 134 Processing helix chain 'T' and resid 134 through 156 Processing helix chain 'T' and resid 170 through 179 Processing helix chain 'U' and resid 10 through 38 Processing helix chain 'U' and resid 45 through 73 Processing helix chain 'U' and resid 92 through 121 Processing helix chain 'U' and resid 123 through 134 Processing helix chain 'U' and resid 134 through 156 Processing helix chain 'U' and resid 170 through 179 Processing helix chain 'V' and resid 10 through 38 Processing helix chain 'V' and resid 45 through 74 Processing helix chain 'V' and resid 92 through 121 Processing helix chain 'V' and resid 123 through 134 Processing helix chain 'V' and resid 134 through 156 Processing helix chain 'V' and resid 170 through 179 Processing helix chain 'W' and resid 10 through 38 Processing helix chain 'W' and resid 45 through 73 Processing helix chain 'W' and resid 92 through 121 Processing helix chain 'W' and resid 123 through 134 Processing helix chain 'W' and resid 134 through 156 Processing helix chain 'W' and resid 170 through 179 Processing helix chain 'X' and resid 10 through 38 Processing helix chain 'X' and resid 45 through 73 Processing helix chain 'X' and resid 92 through 121 Processing helix chain 'X' and resid 123 through 134 Processing helix chain 'X' and resid 134 through 156 Processing helix chain 'X' and resid 170 through 179 Processing helix chain 'Y' and resid 10 through 38 Processing helix chain 'Y' and resid 45 through 73 Processing helix chain 'Y' and resid 92 through 121 Processing helix chain 'Y' and resid 123 through 134 Processing helix chain 'Y' and resid 134 through 156 Processing helix chain 'Y' and resid 170 through 179 Processing helix chain 'Z' and resid 10 through 38 Processing helix chain 'Z' and resid 45 through 73 Processing helix chain 'Z' and resid 92 through 121 Processing helix chain 'Z' and resid 123 through 134 Processing helix chain 'Z' and resid 134 through 156 Processing helix chain 'Z' and resid 170 through 179 2622 hydrogen bonds defined for protein. 7866 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.91 Time building geometry restraints manager: 13.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 11432 1.34 - 1.46: 6464 1.46 - 1.58: 15464 1.58 - 1.69: 0 1.69 - 1.81: 200 Bond restraints: 33560 Sorted by residual: bond pdb=" CB GLU F 104 " pdb=" CG GLU F 104 " ideal model delta sigma weight residual 1.520 1.489 0.031 3.00e-02 1.11e+03 1.10e+00 bond pdb=" CB GLU E 104 " pdb=" CG GLU E 104 " ideal model delta sigma weight residual 1.520 1.489 0.031 3.00e-02 1.11e+03 1.04e+00 bond pdb=" CB GLU N 104 " pdb=" CG GLU N 104 " ideal model delta sigma weight residual 1.520 1.490 0.030 3.00e-02 1.11e+03 1.00e+00 bond pdb=" CB GLU C 104 " pdb=" CG GLU C 104 " ideal model delta sigma weight residual 1.520 1.492 0.028 3.00e-02 1.11e+03 8.94e-01 bond pdb=" CB GLU I 104 " pdb=" CG GLU I 104 " ideal model delta sigma weight residual 1.520 1.492 0.028 3.00e-02 1.11e+03 8.77e-01 ... (remaining 33555 not shown) Histogram of bond angle deviations from ideal: 99.46 - 106.37: 471 106.37 - 113.27: 18053 113.27 - 120.17: 12568 120.17 - 127.08: 13708 127.08 - 133.98: 264 Bond angle restraints: 45064 Sorted by residual: angle pdb=" N VAL E 43 " pdb=" CA VAL E 43 " pdb=" C VAL E 43 " ideal model delta sigma weight residual 111.48 107.97 3.51 9.40e-01 1.13e+00 1.39e+01 angle pdb=" N VAL C 43 " pdb=" CA VAL C 43 " pdb=" C VAL C 43 " ideal model delta sigma weight residual 111.48 108.04 3.44 9.40e-01 1.13e+00 1.34e+01 angle pdb=" N VAL M 43 " pdb=" CA VAL M 43 " pdb=" C VAL M 43 " ideal model delta sigma weight residual 111.48 108.07 3.41 9.40e-01 1.13e+00 1.32e+01 angle pdb=" N VAL F 43 " pdb=" CA VAL F 43 " pdb=" C VAL F 43 " ideal model delta sigma weight residual 111.48 108.12 3.36 9.40e-01 1.13e+00 1.28e+01 angle pdb=" N VAL J 43 " pdb=" CA VAL J 43 " pdb=" C VAL J 43 " ideal model delta sigma weight residual 111.48 108.15 3.33 9.40e-01 1.13e+00 1.25e+01 ... (remaining 45059 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 17708 17.93 - 35.86: 1938 35.86 - 53.79: 451 53.79 - 71.72: 107 71.72 - 89.65: 52 Dihedral angle restraints: 20256 sinusoidal: 8448 harmonic: 11808 Sorted by residual: dihedral pdb=" CB GLU S 138 " pdb=" CG GLU S 138 " pdb=" CD GLU S 138 " pdb=" OE1 GLU S 138 " ideal model delta sinusoidal sigma weight residual 0.00 89.65 -89.65 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU V 61 " pdb=" CG GLU V 61 " pdb=" CD GLU V 61 " pdb=" OE1 GLU V 61 " ideal model delta sinusoidal sigma weight residual 0.00 89.58 -89.58 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU S 61 " pdb=" CG GLU S 61 " pdb=" CD GLU S 61 " pdb=" OE1 GLU S 61 " ideal model delta sinusoidal sigma weight residual 0.00 89.55 -89.55 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 20253 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 3142 0.024 - 0.049: 1157 0.049 - 0.073: 357 0.073 - 0.097: 123 0.097 - 0.122: 61 Chirality restraints: 4840 Sorted by residual: chirality pdb=" CB VAL U 21 " pdb=" CA VAL U 21 " pdb=" CG1 VAL U 21 " pdb=" CG2 VAL U 21 " both_signs ideal model delta sigma weight residual False -2.63 -2.51 -0.12 2.00e-01 2.50e+01 3.69e-01 chirality pdb=" CB VAL N 21 " pdb=" CA VAL N 21 " pdb=" CG1 VAL N 21 " pdb=" CG2 VAL N 21 " both_signs ideal model delta sigma weight residual False -2.63 -2.51 -0.12 2.00e-01 2.50e+01 3.60e-01 chirality pdb=" CB VAL Z 21 " pdb=" CA VAL Z 21 " pdb=" CG1 VAL Z 21 " pdb=" CG2 VAL Z 21 " both_signs ideal model delta sigma weight residual False -2.63 -2.51 -0.12 2.00e-01 2.50e+01 3.58e-01 ... (remaining 4837 not shown) Planarity restraints: 5944 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP Q 39 " -0.005 2.00e-02 2.50e+03 1.00e-02 1.01e+00 pdb=" CG ASP Q 39 " 0.017 2.00e-02 2.50e+03 pdb=" OD1 ASP Q 39 " -0.006 2.00e-02 2.50e+03 pdb=" OD2 ASP Q 39 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP Y 39 " 0.005 2.00e-02 2.50e+03 9.92e-03 9.83e-01 pdb=" CG ASP Y 39 " -0.017 2.00e-02 2.50e+03 pdb=" OD1 ASP Y 39 " 0.006 2.00e-02 2.50e+03 pdb=" OD2 ASP Y 39 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP W 39 " -0.005 2.00e-02 2.50e+03 9.69e-03 9.40e-01 pdb=" CG ASP W 39 " 0.017 2.00e-02 2.50e+03 pdb=" OD1 ASP W 39 " -0.006 2.00e-02 2.50e+03 pdb=" OD2 ASP W 39 " -0.006 2.00e-02 2.50e+03 ... (remaining 5941 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 1388 2.72 - 3.27: 32885 3.27 - 3.81: 60566 3.81 - 4.36: 71961 4.36 - 4.90: 124485 Nonbonded interactions: 291285 Sorted by model distance: nonbonded pdb=" O GLY O 62 " pdb=" OH TYR O 134 " model vdw 2.180 2.440 nonbonded pdb=" O GLY U 62 " pdb=" OH TYR U 134 " model vdw 2.185 2.440 nonbonded pdb=" O GLY B 62 " pdb=" OH TYR B 134 " model vdw 2.186 2.440 nonbonded pdb=" O GLY J 62 " pdb=" OH TYR J 134 " model vdw 2.188 2.440 nonbonded pdb=" O GLY N 62 " pdb=" OH TYR N 134 " model vdw 2.188 2.440 ... (remaining 291280 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' selection = (chain 'B' and resid 2 through 182) selection = (chain 'C' and resid 2 through 182) selection = (chain 'D' and resid 2 through 182) selection = (chain 'E' and resid 2 through 182) selection = chain 'F' selection = chain 'I' selection = (chain 'J' and resid 2 through 182) selection = (chain 'K' and resid 2 through 182) selection = (chain 'L' and resid 2 through 182) selection = (chain 'M' and resid 2 through 182) selection = chain 'N' selection = chain 'O' selection = (chain 'P' and resid 2 through 182) selection = (chain 'Q' and resid 2 through 182) selection = (chain 'R' and resid 2 through 182) selection = (chain 'S' and resid 2 through 182) selection = chain 'T' selection = chain 'U' selection = (chain 'V' and resid 2 through 182) selection = (chain 'W' and resid 2 through 182) selection = (chain 'X' and resid 2 through 182) selection = (chain 'Y' and resid 2 through 182) selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 112 5.16 5 C 20720 2.51 5 N 5968 2.21 5 O 6208 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.600 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: 6.530 Check model and map are aligned: 0.490 Convert atoms to be neutral: 0.270 Process input model: 78.180 Find NCS groups from input model: 2.400 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:11.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 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 : 0.003 0.031 33560 Z= 0.209 Angle : 0.437 4.072 45064 Z= 0.292 Chirality : 0.031 0.122 4840 Planarity : 0.002 0.024 5944 Dihedral : 16.497 89.647 12592 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Rotamer Outliers : 4.15 % 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: 1.26 (0.12), residues: 3976 helix: 1.53 (0.08), residues: 3144 sheet: None (None), residues: 0 loop : -1.83 (0.17), residues: 832 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 924 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 781 time to evaluate : 3.611 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 143 outliers final: 51 residues processed: 893 average time/residue: 1.3181 time to fit residues: 1413.3498 Evaluate side-chains 719 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 668 time to evaluate : 4.116 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 27 residues processed: 24 average time/residue: 0.3971 time to fit residues: 21.5096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 337 optimal weight: 0.8980 chunk 303 optimal weight: 4.9990 chunk 168 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 chunk 204 optimal weight: 4.9990 chunk 161 optimal weight: 0.9980 chunk 313 optimal weight: 0.8980 chunk 121 optimal weight: 4.9990 chunk 190 optimal weight: 1.9990 chunk 233 optimal weight: 0.0170 chunk 363 optimal weight: 1.9990 overall best weight: 0.9620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 83 GLN A 133 HIS B 7 GLN B 133 HIS C 22 ASN C 83 GLN C 133 HIS D 133 HIS E 83 GLN E 133 HIS F 133 HIS I 133 HIS J 133 HIS K 22 ASN K 83 GLN K 133 HIS L 133 HIS M 83 GLN M 133 HIS N 133 HIS N 182 HIS O 133 HIS P 133 HIS Q 133 HIS R 83 GLN R 133 HIS R 147 ASN S 22 ASN S 83 GLN S 133 HIS T 133 HIS U 22 ASN U 133 HIS V 133 HIS W 133 HIS W 182 HIS X 108 ASN X 133 HIS Y 22 ASN Y 83 GLN Y 133 HIS Z 133 HIS Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 33560 Z= 0.163 Angle : 0.363 4.192 45064 Z= 0.195 Chirality : 0.030 0.116 4840 Planarity : 0.002 0.026 5944 Dihedral : 3.497 11.882 4456 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer Outliers : 5.22 % 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: 3.85 (0.13), residues: 3976 helix: 3.31 (0.09), residues: 3192 sheet: None (None), residues: 0 loop : -1.03 (0.19), residues: 784 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 835 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 655 time to evaluate : 4.119 Fit side-chains revert: symmetry clash outliers start: 180 outliers final: 98 residues processed: 766 average time/residue: 1.3908 time to fit residues: 1270.8868 Evaluate side-chains 705 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 607 time to evaluate : 3.886 Switching outliers to nearest non-outliers outliers start: 98 outliers final: 49 residues processed: 49 average time/residue: 0.4081 time to fit residues: 38.8970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 201 optimal weight: 2.9990 chunk 112 optimal weight: 0.7980 chunk 302 optimal weight: 5.9990 chunk 247 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 chunk 363 optimal weight: 3.9990 chunk 393 optimal weight: 6.9990 chunk 324 optimal weight: 8.9990 chunk 360 optimal weight: 0.7980 chunk 124 optimal weight: 5.9990 chunk 291 optimal weight: 9.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 182 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 33560 Z= 0.282 Angle : 0.401 4.280 45064 Z= 0.213 Chirality : 0.033 0.133 4840 Planarity : 0.003 0.027 5944 Dihedral : 3.521 12.524 4456 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer Outliers : 6.58 % 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: 4.42 (0.13), residues: 3976 helix: 3.70 (0.09), residues: 3192 sheet: None (None), residues: 0 loop : -0.76 (0.20), residues: 784 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 873 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 646 time to evaluate : 3.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 227 outliers final: 129 residues processed: 796 average time/residue: 1.3962 time to fit residues: 1325.5685 Evaluate side-chains 741 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 612 time to evaluate : 3.829 Switching outliers to nearest non-outliers outliers start: 129 outliers final: 81 residues processed: 48 average time/residue: 0.4819 time to fit residues: 40.9757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 359 optimal weight: 2.9990 chunk 273 optimal weight: 3.9990 chunk 188 optimal weight: 0.8980 chunk 40 optimal weight: 7.9990 chunk 173 optimal weight: 6.9990 chunk 244 optimal weight: 2.9990 chunk 365 optimal weight: 3.9990 chunk 386 optimal weight: 1.9990 chunk 190 optimal weight: 0.9980 chunk 346 optimal weight: 0.9990 chunk 104 optimal weight: 5.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 87 GLN I 147 ASN X 87 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 33560 Z= 0.223 Angle : 0.377 4.128 45064 Z= 0.202 Chirality : 0.031 0.123 4840 Planarity : 0.003 0.027 5944 Dihedral : 3.433 12.349 4456 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer Outliers : 5.66 % 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: 4.74 (0.13), residues: 3976 helix: 3.88 (0.09), residues: 3208 sheet: None (None), residues: 0 loop : -0.58 (0.21), residues: 768 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 810 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 615 time to evaluate : 4.077 Fit side-chains revert: symmetry clash outliers start: 195 outliers final: 129 residues processed: 751 average time/residue: 1.3980 time to fit residues: 1253.5053 Evaluate side-chains 712 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 583 time to evaluate : 4.032 Switching outliers to nearest non-outliers outliers start: 129 outliers final: 85 residues processed: 45 average time/residue: 0.7089 time to fit residues: 49.3903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 322 optimal weight: 0.9990 chunk 219 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 287 optimal weight: 0.4980 chunk 159 optimal weight: 0.9990 chunk 329 optimal weight: 0.7980 chunk 267 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 197 optimal weight: 0.8980 chunk 347 optimal weight: 0.9980 chunk 97 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 GLN K 182 HIS L 87 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.023 33560 Z= 0.146 Angle : 0.350 4.389 45064 Z= 0.189 Chirality : 0.030 0.119 4840 Planarity : 0.002 0.028 5944 Dihedral : 3.282 12.047 4456 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer Outliers : 4.47 % 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: 5.02 (0.13), residues: 3976 helix: 4.08 (0.09), residues: 3216 sheet: None (None), residues: 0 loop : -0.51 (0.21), residues: 760 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 788 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 634 time to evaluate : 4.264 Fit side-chains outliers start: 154 outliers final: 116 residues processed: 751 average time/residue: 1.4248 time to fit residues: 1276.1076 Evaluate side-chains 709 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 593 time to evaluate : 3.700 Switching outliers to nearest non-outliers outliers start: 116 outliers final: 90 residues processed: 27 average time/residue: 0.9317 time to fit residues: 37.8689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 130 optimal weight: 0.8980 chunk 348 optimal weight: 0.9990 chunk 76 optimal weight: 7.9990 chunk 227 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 387 optimal weight: 0.6980 chunk 321 optimal weight: 0.8980 chunk 179 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 128 optimal weight: 0.6980 chunk 203 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 GLN D 147 ASN ** J 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 147 ASN ** P 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 147 ASN ** V 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.022 33560 Z= 0.144 Angle : 0.348 4.275 45064 Z= 0.189 Chirality : 0.030 0.117 4840 Planarity : 0.002 0.027 5944 Dihedral : 3.220 12.016 4456 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer Outliers : 4.67 % 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: 5.16 (0.13), residues: 3976 helix: 4.18 (0.09), residues: 3216 sheet: None (None), residues: 0 loop : -0.49 (0.21), residues: 760 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 796 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 635 time to evaluate : 4.043 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 161 outliers final: 124 residues processed: 763 average time/residue: 1.3665 time to fit residues: 1250.3747 Evaluate side-chains 725 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 601 time to evaluate : 4.170 Switching outliers to nearest non-outliers outliers start: 124 outliers final: 98 residues processed: 27 average time/residue: 1.0365 time to fit residues: 40.8080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 373 optimal weight: 5.9990 chunk 43 optimal weight: 0.6980 chunk 220 optimal weight: 6.9990 chunk 282 optimal weight: 3.9990 chunk 218 optimal weight: 0.8980 chunk 325 optimal weight: 0.7980 chunk 216 optimal weight: 4.9990 chunk 385 optimal weight: 2.9990 chunk 241 optimal weight: 2.9990 chunk 235 optimal weight: 0.8980 chunk 177 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 GLN ** J 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 147 ASN ** P 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 147 ASN ** V 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.023 33560 Z= 0.147 Angle : 0.347 4.224 45064 Z= 0.189 Chirality : 0.030 0.118 4840 Planarity : 0.002 0.028 5944 Dihedral : 3.201 11.950 4456 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer Outliers : 4.47 % 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: 5.23 (0.13), residues: 3976 helix: 4.23 (0.09), residues: 3216 sheet: None (None), residues: 0 loop : -0.47 (0.21), residues: 760 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 782 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 628 time to evaluate : 3.837 Fit side-chains revert: symmetry clash outliers start: 154 outliers final: 123 residues processed: 751 average time/residue: 1.3516 time to fit residues: 1221.3878 Evaluate side-chains 724 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 601 time to evaluate : 3.476 Switching outliers to nearest non-outliers outliers start: 123 outliers final: 99 residues processed: 25 average time/residue: 0.8111 time to fit residues: 32.3216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 238 optimal weight: 0.9980 chunk 153 optimal weight: 3.9990 chunk 230 optimal weight: 0.9990 chunk 116 optimal weight: 0.5980 chunk 75 optimal weight: 0.7980 chunk 74 optimal weight: 5.9990 chunk 245 optimal weight: 1.9990 chunk 262 optimal weight: 3.9990 chunk 190 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 303 optimal weight: 5.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 147 ASN ** J 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 147 ASN M 147 ASN ** P 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 147 ASN ** V 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 33560 Z= 0.149 Angle : 0.347 4.209 45064 Z= 0.189 Chirality : 0.030 0.118 4840 Planarity : 0.002 0.027 5944 Dihedral : 3.192 11.980 4456 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer Outliers : 3.39 % 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: 5.27 (0.13), residues: 3976 helix: 4.27 (0.09), residues: 3216 sheet: None (None), residues: 0 loop : -0.48 (0.20), residues: 760 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 739 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 622 time to evaluate : 3.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 117 outliers final: 99 residues processed: 728 average time/residue: 1.3778 time to fit residues: 1202.7520 Evaluate side-chains 697 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 598 time to evaluate : 4.061 Switching outliers to nearest non-outliers outliers start: 99 outliers final: 92 residues processed: 8 average time/residue: 1.5044 time to fit residues: 19.5875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 350 optimal weight: 1.9990 chunk 369 optimal weight: 4.9990 chunk 336 optimal weight: 0.9990 chunk 359 optimal weight: 0.7980 chunk 216 optimal weight: 0.5980 chunk 156 optimal weight: 0.6980 chunk 282 optimal weight: 5.9990 chunk 110 optimal weight: 0.8980 chunk 324 optimal weight: 1.9990 chunk 339 optimal weight: 5.9990 chunk 358 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 147 ASN ** J 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 147 ASN M 147 ASN ** P 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 147 ASN S 147 ASN ** V 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 147 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 33560 Z= 0.143 Angle : 0.349 6.663 45064 Z= 0.190 Chirality : 0.030 0.118 4840 Planarity : 0.002 0.027 5944 Dihedral : 3.186 11.956 4456 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer Outliers : 3.07 % 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: 5.29 (0.13), residues: 3976 helix: 4.29 (0.09), residues: 3216 sheet: None (None), residues: 0 loop : -0.51 (0.20), residues: 760 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 717 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 611 time to evaluate : 4.308 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 106 outliers final: 96 residues processed: 708 average time/residue: 1.3887 time to fit residues: 1180.7226 Evaluate side-chains 674 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 578 time to evaluate : 3.814 Switching outliers to nearest non-outliers outliers start: 96 outliers final: 90 residues processed: 7 average time/residue: 1.1620 time to fit residues: 15.1616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 235 optimal weight: 4.9990 chunk 379 optimal weight: 6.9990 chunk 231 optimal weight: 0.8980 chunk 180 optimal weight: 0.7980 chunk 264 optimal weight: 0.9980 chunk 398 optimal weight: 1.9990 chunk 366 optimal weight: 4.9990 chunk 317 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 245 optimal weight: 3.9990 chunk 194 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 GLN C 50 HIS E 50 HIS I 50 HIS I 147 ASN J 50 HIS ** J 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 147 ASN K 50 HIS M 147 ASN O 50 HIS ** P 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 147 ASN Q 50 HIS R 50 HIS S 50 HIS S 147 ASN U 50 HIS V 50 HIS ** V 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 50 HIS Y 147 ASN Z 50 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 33560 Z= 0.177 Angle : 0.368 7.253 45064 Z= 0.199 Chirality : 0.031 0.118 4840 Planarity : 0.002 0.026 5944 Dihedral : 3.225 12.145 4456 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer Outliers : 2.96 % 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: 5.24 (0.13), residues: 3976 helix: 4.25 (0.09), residues: 3216 sheet: None (None), residues: 0 loop : -0.57 (0.20), residues: 760 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 700 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 598 time to evaluate : 4.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 102 outliers final: 97 residues processed: 691 average time/residue: 1.3380 time to fit residues: 1113.1554 Evaluate side-chains 677 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 580 time to evaluate : 3.846 Switching outliers to nearest non-outliers outliers start: 97 outliers final: 91 residues processed: 7 average time/residue: 1.3679 time to fit residues: 16.5643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 252 optimal weight: 4.9990 chunk 338 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 292 optimal weight: 0.3980 chunk 46 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 317 optimal weight: 5.9990 chunk 133 optimal weight: 1.9990 chunk 326 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS A 147 ASN D 50 HIS F 50 HIS I 147 ASN ** J 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 147 ASN L 50 HIS M 147 ASN N 50 HIS ** O 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 50 HIS ** P 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 147 ASN S 147 ASN T 50 HIS ** V 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 50 HIS Y 50 HIS Y 147 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.101707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.090518 restraints weight = 41470.483| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 1.90 r_work: 0.2940 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3158 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3093 r_free = 0.3093 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3093 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8960 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 33560 Z= 0.164 Angle : 0.362 6.704 45064 Z= 0.196 Chirality : 0.030 0.118 4840 Planarity : 0.002 0.026 5944 Dihedral : 3.209 12.063 4456 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer Outliers : 3.05 % 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: 5.23 (0.13), residues: 3976 helix: 4.29 (0.09), residues: 3200 sheet: None (None), residues: 0 loop : -0.66 (0.19), residues: 776 =============================================================================== Job complete usr+sys time: 15855.67 seconds wall clock time: 277 minutes 44.76 seconds (16664.76 seconds total)