Starting phenix.real_space_refine (version: 1.21rc1) on Sat Jul 15 17:32:03 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zlg_11265/07_2023/6zlg_11265.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zlg_11265/07_2023/6zlg_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_11265/07_2023/6zlg_11265.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zlg_11265/07_2023/6zlg_11265.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zlg_11265/07_2023/6zlg_11265.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zlg_11265/07_2023/6zlg_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 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. 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-1.21rc1-5013/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: 14.76, per 1000 atoms: 0.45 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: 13.82 Conformation dependent library (CDL) restraints added in 5.1 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: 0.89 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: 11.19 Time building geometry restraints manager: 14.74 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 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: 0.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 6.600 Check model and map are aligned: 0.470 Set scattering table: 0.280 Process input model: 79.400 Find NCS groups from input model: 2.610 Set up NCS constraints: 0.150 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:13.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 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 : 4.193 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 143 outliers final: 51 residues processed: 893 average time/residue: 1.4536 time to fit residues: 1546.2705 Evaluate side-chains 719 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 668 time to evaluate : 3.859 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 27 residues processed: 24 average time/residue: 0.3904 time to fit residues: 20.9445 ------------------------------------------------------------------------------- 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: 0.8403 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 : 4.081 Fit side-chains revert: symmetry clash outliers start: 180 outliers final: 98 residues processed: 766 average time/residue: 1.5313 time to fit residues: 1387.2174 Evaluate side-chains 705 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 607 time to evaluate : 3.813 Switching outliers to nearest non-outliers outliers start: 98 outliers final: 49 residues processed: 49 average time/residue: 0.3908 time to fit residues: 37.4381 ------------------------------------------------------------------------------- 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: 3.9990 chunk 112 optimal weight: 0.5980 chunk 302 optimal weight: 6.9990 chunk 247 optimal weight: 0.7980 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: 0.9990 chunk 124 optimal weight: 5.9990 chunk 291 optimal weight: 10.0000 overall best weight: 2.0786 ------------------------------------------------------------------------------- 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: 0.8433 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 33560 Z= 0.278 Angle : 0.399 4.259 45064 Z= 0.212 Chirality : 0.033 0.132 4840 Planarity : 0.003 0.027 5944 Dihedral : 3.512 12.489 4456 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer Outliers : 6.55 % 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: 4.43 (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 869 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 643 time to evaluate : 4.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 226 outliers final: 130 residues processed: 793 average time/residue: 1.4728 time to fit residues: 1384.8054 Evaluate side-chains 743 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 613 time to evaluate : 3.655 Switching outliers to nearest non-outliers outliers start: 130 outliers final: 82 residues processed: 48 average time/residue: 0.5076 time to fit residues: 43.2246 ------------------------------------------------------------------------------- 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: 0.9990 chunk 273 optimal weight: 3.9990 chunk 188 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 chunk 173 optimal weight: 6.9990 chunk 244 optimal weight: 2.9990 chunk 365 optimal weight: 4.9990 chunk 386 optimal weight: 0.9990 chunk 190 optimal weight: 0.9980 chunk 346 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 87 GLN K 182 HIS X 87 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 33560 Z= 0.183 Angle : 0.363 4.263 45064 Z= 0.195 Chirality : 0.031 0.118 4840 Planarity : 0.002 0.026 5944 Dihedral : 3.370 12.081 4456 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer Outliers : 5.05 % 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: 4.86 (0.13), residues: 3976 helix: 4.00 (0.09), residues: 3192 sheet: None (None), residues: 0 loop : -0.62 (0.20), residues: 784 *********************** 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 801 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 627 time to evaluate : 3.837 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 174 outliers final: 120 residues processed: 757 average time/residue: 1.5297 time to fit residues: 1367.5433 Evaluate side-chains 711 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 591 time to evaluate : 3.936 Switching outliers to nearest non-outliers outliers start: 120 outliers final: 84 residues processed: 36 average time/residue: 0.9611 time to fit residues: 49.5895 ------------------------------------------------------------------------------- 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: 0.8980 chunk 219 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 287 optimal weight: 4.9990 chunk 159 optimal weight: 6.9990 chunk 329 optimal weight: 2.9990 chunk 267 optimal weight: 0.2980 chunk 0 optimal weight: 10.0000 chunk 197 optimal weight: 0.9990 chunk 347 optimal weight: 0.9980 chunk 97 optimal weight: 6.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 147 ASN P 147 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1598 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= 0.165 Angle : 0.356 4.218 45064 Z= 0.192 Chirality : 0.030 0.119 4840 Planarity : 0.002 0.027 5944 Dihedral : 3.294 12.092 4456 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer Outliers : 5.13 % 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: 5.03 (0.13), residues: 3976 helix: 4.09 (0.09), residues: 3216 sheet: None (None), residues: 0 loop : -0.52 (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 815 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 638 time to evaluate : 3.910 Fit side-chains outliers start: 177 outliers final: 137 residues processed: 759 average time/residue: 1.4804 time to fit residues: 1333.7110 Evaluate side-chains 745 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 608 time to evaluate : 3.899 Switching outliers to nearest non-outliers outliers start: 137 outliers final: 88 residues processed: 49 average time/residue: 0.7202 time to fit residues: 53.8127 ------------------------------------------------------------------------------- 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: 4.9990 chunk 348 optimal weight: 0.8980 chunk 76 optimal weight: 0.8980 chunk 227 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 387 optimal weight: 0.6980 chunk 321 optimal weight: 0.8980 chunk 179 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 chunk 203 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 147 ASN L 87 GLN ** 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: 0.8395 moved from start: 0.1694 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= 0.150 Angle : 0.349 4.262 45064 Z= 0.189 Chirality : 0.030 0.117 4840 Planarity : 0.002 0.027 5944 Dihedral : 3.235 12.094 4456 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer Outliers : 4.12 % 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: 5.14 (0.13), residues: 3976 helix: 4.17 (0.09), residues: 3216 sheet: None (None), residues: 0 loop : -0.50 (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 784 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 642 time to evaluate : 3.797 Fit side-chains revert: symmetry clash outliers start: 142 outliers final: 112 residues processed: 763 average time/residue: 1.4878 time to fit residues: 1348.4427 Evaluate side-chains 720 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 608 time to evaluate : 3.696 Switching outliers to nearest non-outliers outliers start: 112 outliers final: 96 residues processed: 16 average time/residue: 1.5003 time to fit residues: 33.3710 ------------------------------------------------------------------------------- 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: 0.9980 chunk 220 optimal weight: 4.9990 chunk 282 optimal weight: 0.8980 chunk 218 optimal weight: 1.9990 chunk 325 optimal weight: 0.6980 chunk 216 optimal weight: 4.9990 chunk 385 optimal weight: 3.9990 chunk 241 optimal weight: 7.9990 chunk 235 optimal weight: 0.6980 chunk 177 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 33560 Z= 0.167 Angle : 0.354 4.118 45064 Z= 0.192 Chirality : 0.030 0.118 4840 Planarity : 0.002 0.027 5944 Dihedral : 3.233 12.013 4456 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer Outliers : 4.52 % 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: 5.18 (0.13), residues: 3976 helix: 4.19 (0.09), residues: 3216 sheet: None (None), residues: 0 loop : -0.49 (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 780 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 624 time to evaluate : 3.891 Fit side-chains revert: symmetry clash outliers start: 156 outliers final: 129 residues processed: 744 average time/residue: 1.5141 time to fit residues: 1337.9624 Evaluate side-chains 727 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 598 time to evaluate : 4.213 Switching outliers to nearest non-outliers outliers start: 129 outliers final: 102 residues processed: 27 average time/residue: 0.9526 time to fit residues: 38.6839 ------------------------------------------------------------------------------- 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: 0.8980 chunk 153 optimal weight: 2.9990 chunk 230 optimal weight: 4.9990 chunk 116 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 245 optimal weight: 0.8980 chunk 262 optimal weight: 7.9990 chunk 190 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 303 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.8393 moved from start: 0.1778 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= 0.150 Angle : 0.349 4.248 45064 Z= 0.190 Chirality : 0.030 0.118 4840 Planarity : 0.002 0.027 5944 Dihedral : 3.206 11.911 4456 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer Outliers : 3.83 % 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: 4.24 (0.09), residues: 3216 sheet: None (None), residues: 0 loop : -0.51 (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 746 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 614 time to evaluate : 3.948 Fit side-chains revert: symmetry clash outliers start: 132 outliers final: 109 residues processed: 731 average time/residue: 1.4529 time to fit residues: 1266.6062 Evaluate side-chains 697 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 588 time to evaluate : 3.823 Switching outliers to nearest non-outliers outliers start: 109 outliers final: 95 residues processed: 14 average time/residue: 1.3812 time to fit residues: 28.2417 ------------------------------------------------------------------------------- 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: 0.5980 chunk 369 optimal weight: 4.9990 chunk 336 optimal weight: 0.9980 chunk 359 optimal weight: 0.7980 chunk 216 optimal weight: 0.1980 chunk 156 optimal weight: 0.8980 chunk 282 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 chunk 324 optimal weight: 0.0010 chunk 339 optimal weight: 5.9990 chunk 358 optimal weight: 6.9990 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 147 ASN ** J 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 147 ASN L 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 33560 Z= 0.114 Angle : 0.336 7.086 45064 Z= 0.185 Chirality : 0.029 0.117 4840 Planarity : 0.002 0.027 5944 Dihedral : 3.137 11.980 4456 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer Outliers : 3.48 % 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: 5.36 (0.13), residues: 3976 helix: 4.33 (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 731 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 611 time to evaluate : 3.978 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 120 outliers final: 102 residues processed: 717 average time/residue: 1.5291 time to fit residues: 1299.7540 Evaluate side-chains 665 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 563 time to evaluate : 3.902 Switching outliers to nearest non-outliers outliers start: 102 outliers final: 91 residues processed: 12 average time/residue: 1.3764 time to fit residues: 24.9399 ------------------------------------------------------------------------------- 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: 0.7980 chunk 231 optimal weight: 0.9980 chunk 180 optimal weight: 1.9990 chunk 264 optimal weight: 0.7980 chunk 398 optimal weight: 1.9990 chunk 366 optimal weight: 3.9990 chunk 317 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 245 optimal weight: 0.9980 chunk 194 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 HIS F 50 HIS I 50 HIS I 147 ASN ** 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 U 50 HIS V 50 HIS V 70 GLN W 50 HIS Y 50 HIS Y 147 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1913 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= 0.153 Angle : 0.357 7.313 45064 Z= 0.194 Chirality : 0.030 0.115 4840 Planarity : 0.002 0.028 5944 Dihedral : 3.180 12.110 4456 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer Outliers : 2.99 % 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: 5.34 (0.13), residues: 3976 helix: 4.36 (0.09), residues: 3200 sheet: None (None), residues: 0 loop : -0.58 (0.20), residues: 776 ********************** 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 689 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 586 time to evaluate : 4.247 Fit side-chains revert: symmetry clash outliers start: 103 outliers final: 96 residues processed: 683 average time/residue: 1.4785 time to fit residues: 1202.0584 Evaluate side-chains 659 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 563 time to evaluate : 4.271 Switching outliers to nearest non-outliers outliers start: 96 outliers final: 91 residues processed: 6 average time/residue: 1.2396 time to fit residues: 14.9601 ------------------------------------------------------------------------------- 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: 5.9990 chunk 338 optimal weight: 0.9980 chunk 97 optimal weight: 6.9990 chunk 292 optimal weight: 0.1980 chunk 46 optimal weight: 3.9990 chunk 88 optimal weight: 0.0000 chunk 317 optimal weight: 5.9990 chunk 133 optimal weight: 0.0370 chunk 326 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 overall best weight: 1.0464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS B 50 HIS ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 HIS I 147 ASN ** J 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 147 ASN M 147 ASN P 50 HIS ** P 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 147 ASN S 147 ASN Y 147 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.101911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.090686 restraints weight = 41433.132| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 1.90 r_work: 0.2929 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2773 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2773 r_free = 0.2773 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2710 r_free = 0.2710 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2710 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.1893 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= 0.168 Angle : 0.362 6.665 45064 Z= 0.196 Chirality : 0.030 0.117 4840 Planarity : 0.003 0.039 5944 Dihedral : 3.193 12.034 4456 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer Outliers : 3.28 % 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: 5.28 (0.13), residues: 3976 helix: 4.32 (0.09), residues: 3200 sheet: None (None), residues: 0 loop : -0.61 (0.19), residues: 776 =============================================================================== Job complete usr+sys time: 16770.62 seconds wall clock time: 295 minutes 48.62 seconds (17748.62 seconds total)