Starting phenix.real_space_refine on Fri Mar 22 09:26:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zlg_11265/03_2024/6zlg_11265.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zlg_11265/03_2024/6zlg_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_11265/03_2024/6zlg_11265.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zlg_11265/03_2024/6zlg_11265.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zlg_11265/03_2024/6zlg_11265.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zlg_11265/03_2024/6zlg_11265.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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-dev-5265/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: 16.88, per 1000 atoms: 0.51 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: 12.81 Conformation dependent library (CDL) restraints added in 5.5 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: 2.38 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: 10.52 Time building geometry restraints manager: 13.81 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: 1.170 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: 0.030 Extract box with map and model: 5.480 Check model and map are aligned: 0.480 Set scattering table: 0.290 Process input model: 82.050 Find NCS groups from input model: 2.390 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.520 ------------------------------------------------------------------------------- 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 % Allowed : 18.91 % Favored : 76.94 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP M 90 HIS 0.008 0.001 HIS V 182 PHE 0.013 0.001 PHE L 129 TYR 0.009 0.001 TYR T 9 ARG 0.001 0.000 ARG N 26 *********************** 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 : 3.875 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7621 (mt-10) cc_final: 0.7350 (mt-10) REVERT: A 72 ASP cc_start: 0.8436 (m-30) cc_final: 0.8077 (m-30) REVERT: A 87 GLN cc_start: 0.9039 (mt0) cc_final: 0.8833 (mt0) REVERT: A 123 ASP cc_start: 0.8887 (t0) cc_final: 0.8610 (t0) REVERT: B 68 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7351 (mt-10) REVERT: B 72 ASP cc_start: 0.8219 (m-30) cc_final: 0.7984 (m-30) REVERT: B 97 MET cc_start: 0.7480 (tpp) cc_final: 0.7134 (tpp) REVERT: C 68 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7330 (mt-10) REVERT: C 72 ASP cc_start: 0.8396 (m-30) cc_final: 0.8019 (m-30) REVERT: C 123 ASP cc_start: 0.8897 (t0) cc_final: 0.8608 (t0) REVERT: C 138 GLU cc_start: 0.8368 (tp30) cc_final: 0.8140 (tp30) REVERT: D 68 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7353 (mt-10) REVERT: D 72 ASP cc_start: 0.8400 (m-30) cc_final: 0.8014 (m-30) REVERT: D 87 GLN cc_start: 0.9071 (mt0) cc_final: 0.8807 (mt0) REVERT: D 97 MET cc_start: 0.7555 (tpp) cc_final: 0.7281 (tpp) REVERT: E 68 GLU cc_start: 0.7625 (mt-10) cc_final: 0.7398 (mt-10) REVERT: E 72 ASP cc_start: 0.8375 (m-30) cc_final: 0.8043 (m-30) REVERT: E 87 GLN cc_start: 0.9057 (mt0) cc_final: 0.8821 (mt0) REVERT: E 123 ASP cc_start: 0.8975 (t0) cc_final: 0.8704 (t0) REVERT: F 68 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7402 (mt-10) REVERT: F 72 ASP cc_start: 0.8401 (m-30) cc_final: 0.8090 (m-30) REVERT: F 97 MET cc_start: 0.7520 (tpp) cc_final: 0.7317 (tpp) REVERT: F 123 ASP cc_start: 0.8890 (t0) cc_final: 0.8654 (t0) REVERT: I 68 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7214 (mt-10) REVERT: I 72 ASP cc_start: 0.8436 (m-30) cc_final: 0.8074 (m-30) REVERT: I 87 GLN cc_start: 0.9070 (mt0) cc_final: 0.8814 (mt0) REVERT: I 123 ASP cc_start: 0.8837 (t0) cc_final: 0.8618 (t0) REVERT: J 68 GLU cc_start: 0.7645 (mt-10) cc_final: 0.7304 (mt-10) REVERT: J 72 ASP cc_start: 0.8396 (m-30) cc_final: 0.8065 (m-30) REVERT: J 87 GLN cc_start: 0.9150 (mt0) cc_final: 0.8918 (mt0) REVERT: J 97 MET cc_start: 0.7528 (tpp) cc_final: 0.7232 (tpp) REVERT: K 68 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7382 (mt-10) REVERT: K 72 ASP cc_start: 0.8417 (m-30) cc_final: 0.8046 (m-30) REVERT: K 97 MET cc_start: 0.8760 (tpp) cc_final: 0.8024 (tpp) REVERT: K 123 ASP cc_start: 0.8893 (t0) cc_final: 0.8614 (t0) REVERT: L 68 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7195 (mt-10) REVERT: L 72 ASP cc_start: 0.8388 (m-30) cc_final: 0.7963 (m-30) REVERT: L 97 MET cc_start: 0.7488 (tpp) cc_final: 0.7260 (tpp) REVERT: M 68 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7334 (mt-10) REVERT: M 72 ASP cc_start: 0.8366 (m-30) cc_final: 0.8037 (m-30) REVERT: M 87 GLN cc_start: 0.9070 (mt0) cc_final: 0.8863 (mt0) REVERT: M 123 ASP cc_start: 0.8964 (t0) cc_final: 0.8742 (t0) REVERT: N 68 GLU cc_start: 0.7609 (mt-10) cc_final: 0.7353 (mt-10) REVERT: N 72 ASP cc_start: 0.8398 (m-30) cc_final: 0.8038 (m-30) REVERT: N 87 GLN cc_start: 0.9138 (mt0) cc_final: 0.8925 (mt0) REVERT: N 97 MET cc_start: 0.7456 (tpp) cc_final: 0.7159 (tpp) REVERT: N 123 ASP cc_start: 0.8889 (t0) cc_final: 0.8651 (t0) REVERT: O 61 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7539 (mm-30) REVERT: O 72 ASP cc_start: 0.8430 (m-30) cc_final: 0.8106 (m-30) REVERT: O 97 MET cc_start: 0.7585 (tpp) cc_final: 0.7233 (tpp) REVERT: O 169 SER cc_start: 0.8584 (p) cc_final: 0.8023 (p) REVERT: P 72 ASP cc_start: 0.8390 (m-30) cc_final: 0.8027 (m-30) REVERT: P 97 MET cc_start: 0.7501 (tpp) cc_final: 0.7163 (tpp) REVERT: Q 68 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7343 (mt-10) REVERT: Q 72 ASP cc_start: 0.8392 (m-30) cc_final: 0.7998 (m-30) REVERT: Q 97 MET cc_start: 0.8678 (tpp) cc_final: 0.8070 (tpp) REVERT: Q 123 ASP cc_start: 0.8879 (t0) cc_final: 0.8593 (t0) REVERT: R 72 ASP cc_start: 0.8394 (m-30) cc_final: 0.7996 (m-30) REVERT: R 87 GLN cc_start: 0.9128 (mt0) cc_final: 0.8878 (mt0) REVERT: R 97 MET cc_start: 0.7496 (tpp) cc_final: 0.7175 (tpp) REVERT: S 31 TYR cc_start: 0.9095 (m-80) cc_final: 0.8822 (m-10) REVERT: S 72 ASP cc_start: 0.8389 (m-30) cc_final: 0.8060 (m-30) REVERT: T 68 GLU cc_start: 0.7610 (mt-10) cc_final: 0.7349 (mt-10) REVERT: T 72 ASP cc_start: 0.8362 (m-30) cc_final: 0.8100 (m-30) REVERT: T 97 MET cc_start: 0.7509 (tpp) cc_final: 0.7186 (tpp) REVERT: T 123 ASP cc_start: 0.8966 (t0) cc_final: 0.8691 (t0) REVERT: T 181 LYS cc_start: 0.7508 (OUTLIER) cc_final: 0.7155 (mmmt) REVERT: U 72 ASP cc_start: 0.8417 (m-30) cc_final: 0.8087 (m-30) REVERT: U 87 GLN cc_start: 0.9153 (mt0) cc_final: 0.8899 (mt0) REVERT: U 123 ASP cc_start: 0.8929 (t0) cc_final: 0.8690 (t0) REVERT: V 68 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7254 (mt-10) REVERT: V 72 ASP cc_start: 0.8412 (m-30) cc_final: 0.8065 (m-30) REVERT: V 123 ASP cc_start: 0.8967 (t0) cc_final: 0.8716 (t0) REVERT: W 72 ASP cc_start: 0.8378 (m-30) cc_final: 0.7997 (m-30) REVERT: W 87 GLN cc_start: 0.9119 (mt0) cc_final: 0.8901 (mt0) REVERT: W 97 MET cc_start: 0.8748 (tpp) cc_final: 0.8016 (tpp) REVERT: W 123 ASP cc_start: 0.8938 (t0) cc_final: 0.8691 (t0) REVERT: X 68 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7170 (mt-10) REVERT: X 72 ASP cc_start: 0.8403 (m-30) cc_final: 0.8000 (m-30) REVERT: X 123 ASP cc_start: 0.8934 (t0) cc_final: 0.8676 (t0) REVERT: X 181 LYS cc_start: 0.7390 (OUTLIER) cc_final: 0.7109 (mmmt) REVERT: Y 72 ASP cc_start: 0.8365 (m-30) cc_final: 0.8038 (m-30) REVERT: Y 123 ASP cc_start: 0.8920 (t0) cc_final: 0.8654 (t0) REVERT: Y 138 GLU cc_start: 0.8117 (tp30) cc_final: 0.7677 (tp30) REVERT: Y 140 LYS cc_start: 0.8604 (mmtt) cc_final: 0.8267 (mmtp) REVERT: Z 72 ASP cc_start: 0.8383 (m-30) cc_final: 0.7966 (m-30) REVERT: Z 87 GLN cc_start: 0.9159 (mt0) cc_final: 0.8938 (mt0) REVERT: Z 97 MET cc_start: 0.7523 (tpp) cc_final: 0.7174 (tpp) REVERT: Z 123 ASP cc_start: 0.8910 (t0) cc_final: 0.8630 (t0) outliers start: 143 outliers final: 51 residues processed: 893 average time/residue: 1.4592 time to fit residues: 1559.1496 Evaluate side-chains 742 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 689 time to evaluate : 3.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 42 ASP Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 42 ASP Chi-restraints excluded: chain I residue 10 SER Chi-restraints excluded: chain J residue 10 SER Chi-restraints excluded: chain J residue 33 SER Chi-restraints excluded: chain J residue 42 ASP Chi-restraints excluded: chain J residue 86 SER Chi-restraints excluded: chain J residue 181 LYS Chi-restraints excluded: chain K residue 33 SER Chi-restraints excluded: chain K residue 42 ASP Chi-restraints excluded: chain L residue 42 ASP Chi-restraints excluded: chain L residue 46 GLU Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain N residue 42 ASP Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain O residue 42 ASP Chi-restraints excluded: chain O residue 86 SER Chi-restraints excluded: chain P residue 42 ASP Chi-restraints excluded: chain P residue 86 SER Chi-restraints excluded: chain P residue 181 LYS Chi-restraints excluded: chain Q residue 42 ASP Chi-restraints excluded: chain S residue 42 ASP Chi-restraints excluded: chain S residue 181 LYS Chi-restraints excluded: chain T residue 33 SER Chi-restraints excluded: chain T residue 42 ASP Chi-restraints excluded: chain T residue 126 LEU Chi-restraints excluded: chain T residue 181 LYS Chi-restraints excluded: chain U residue 42 ASP Chi-restraints excluded: chain U residue 181 LYS Chi-restraints excluded: chain U residue 182 HIS Chi-restraints excluded: chain V residue 86 SER Chi-restraints excluded: chain W residue 10 SER Chi-restraints excluded: chain W residue 33 SER Chi-restraints excluded: chain W residue 42 ASP Chi-restraints excluded: chain X residue 10 SER Chi-restraints excluded: chain X residue 33 SER Chi-restraints excluded: chain X residue 42 ASP Chi-restraints excluded: chain X residue 78 LEU Chi-restraints excluded: chain X residue 181 LYS Chi-restraints excluded: chain Y residue 33 SER Chi-restraints excluded: chain Y residue 46 GLU Chi-restraints excluded: chain Y residue 181 LYS Chi-restraints excluded: chain Z residue 10 SER Chi-restraints excluded: chain Z residue 33 SER Chi-restraints excluded: chain Z residue 86 SER 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: 6.9990 chunk 161 optimal weight: 0.9980 chunk 313 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 chunk 190 optimal weight: 0.8980 chunk 233 optimal weight: 0.8980 chunk 363 optimal weight: 5.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 GLN A 87 GLN A 133 HIS B 7 GLN B 133 HIS C 83 GLN C 133 HIS D 87 GLN D 133 HIS E 83 GLN E 87 GLN E 133 HIS F 133 HIS I 87 GLN I 133 HIS J 87 GLN J 133 HIS K 22 ASN K 83 GLN K 133 HIS L 133 HIS M 83 GLN M 87 GLN M 133 HIS N 87 GLN N 133 HIS N 182 HIS O 133 HIS P 133 HIS Q 133 HIS R 83 GLN R 87 GLN R 133 HIS S 22 ASN S 83 GLN S 133 HIS T 133 HIS U 22 ASN U 87 GLN U 133 HIS V 133 HIS W 87 GLN W 133 HIS W 182 HIS X 108 ASN X 133 HIS Y 83 GLN Y 133 HIS Z 87 GLN Z 133 HIS Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 33560 Z= 0.200 Angle : 0.375 4.067 45064 Z= 0.201 Chirality : 0.031 0.117 4840 Planarity : 0.003 0.027 5944 Dihedral : 5.239 56.691 4558 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 5.16 % Allowed : 19.72 % Favored : 75.12 % 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: 3.79 (0.13), residues: 3976 helix: 3.26 (0.09), residues: 3192 sheet: None (None), residues: 0 loop : -1.03 (0.19), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP P 90 HIS 0.007 0.000 HIS V 182 PHE 0.011 0.002 PHE L 129 TYR 0.007 0.001 TYR E 31 ARG 0.005 0.000 ARG U 76 *********************** 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 836 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 658 time to evaluate : 3.549 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 ASP cc_start: 0.8286 (m-30) cc_final: 0.7989 (m-30) REVERT: B 72 ASP cc_start: 0.8213 (m-30) cc_final: 0.7954 (m-30) REVERT: B 104 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7611 (mm-30) REVERT: C 68 GLU cc_start: 0.7554 (mt-10) cc_final: 0.7233 (mt-10) REVERT: C 72 ASP cc_start: 0.8310 (m-30) cc_final: 0.8006 (m-30) REVERT: C 121 ARG cc_start: 0.8337 (mmm160) cc_final: 0.8110 (mmp80) REVERT: C 128 ASP cc_start: 0.7597 (OUTLIER) cc_final: 0.7352 (t0) REVERT: D 72 ASP cc_start: 0.8300 (m-30) cc_final: 0.7955 (m-30) REVERT: E 68 GLU cc_start: 0.7542 (mt-10) cc_final: 0.7323 (mt-10) REVERT: E 72 ASP cc_start: 0.8286 (m-30) cc_final: 0.8067 (m-30) REVERT: E 128 ASP cc_start: 0.7611 (OUTLIER) cc_final: 0.7366 (t0) REVERT: E 140 LYS cc_start: 0.8620 (mmtt) cc_final: 0.8256 (mmtp) REVERT: F 72 ASP cc_start: 0.8362 (m-30) cc_final: 0.7954 (m-30) REVERT: F 128 ASP cc_start: 0.7621 (OUTLIER) cc_final: 0.7369 (t0) REVERT: F 140 LYS cc_start: 0.8614 (mmtt) cc_final: 0.8251 (mmtp) REVERT: I 72 ASP cc_start: 0.8268 (m-30) cc_final: 0.7971 (m-30) REVERT: I 87 GLN cc_start: 0.9013 (mt0) cc_final: 0.8770 (mt0) REVERT: I 138 GLU cc_start: 0.8267 (tp30) cc_final: 0.8051 (tp30) REVERT: I 140 LYS cc_start: 0.8639 (mmtt) cc_final: 0.8284 (mmtp) REVERT: I 181 LYS cc_start: 0.7519 (OUTLIER) cc_final: 0.7241 (tptp) REVERT: J 68 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7370 (mt-10) REVERT: J 72 ASP cc_start: 0.8286 (m-30) cc_final: 0.8063 (m-30) REVERT: J 128 ASP cc_start: 0.7594 (OUTLIER) cc_final: 0.7337 (t0) REVERT: J 138 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7572 (tp30) REVERT: K 68 GLU cc_start: 0.7549 (mt-10) cc_final: 0.7251 (mt-10) REVERT: K 72 ASP cc_start: 0.8321 (m-30) cc_final: 0.8060 (m-30) REVERT: L 72 ASP cc_start: 0.8272 (m-30) cc_final: 0.7992 (m-30) REVERT: M 72 ASP cc_start: 0.8284 (m-30) cc_final: 0.8073 (m-30) REVERT: N 72 ASP cc_start: 0.8285 (m-30) cc_final: 0.8021 (m-30) REVERT: N 140 LYS cc_start: 0.8582 (mmtt) cc_final: 0.8194 (mmtp) REVERT: O 72 ASP cc_start: 0.8260 (m-30) cc_final: 0.7980 (m-30) REVERT: O 169 SER cc_start: 0.8566 (p) cc_final: 0.8029 (p) REVERT: P 68 GLU cc_start: 0.7607 (mt-10) cc_final: 0.7405 (mt-10) REVERT: P 72 ASP cc_start: 0.8307 (m-30) cc_final: 0.8076 (m-30) REVERT: Q 68 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7292 (mt-10) REVERT: Q 72 ASP cc_start: 0.8333 (m-30) cc_final: 0.7931 (m-30) REVERT: Q 97 MET cc_start: 0.8633 (tpp) cc_final: 0.8293 (tpp) REVERT: Q 181 LYS cc_start: 0.7793 (OUTLIER) cc_final: 0.7515 (tptp) REVERT: R 72 ASP cc_start: 0.8314 (m-30) cc_final: 0.7999 (m-30) REVERT: S 72 ASP cc_start: 0.8298 (m-30) cc_final: 0.8066 (m-30) REVERT: T 72 ASP cc_start: 0.8279 (m-30) cc_final: 0.8035 (m-30) REVERT: T 128 ASP cc_start: 0.7614 (OUTLIER) cc_final: 0.7369 (t0) REVERT: T 140 LYS cc_start: 0.8597 (mmtt) cc_final: 0.8256 (mmtp) REVERT: T 181 LYS cc_start: 0.7672 (OUTLIER) cc_final: 0.7321 (mmmt) REVERT: U 72 ASP cc_start: 0.8282 (m-30) cc_final: 0.7975 (m-30) REVERT: U 181 LYS cc_start: 0.7587 (OUTLIER) cc_final: 0.7305 (tptp) REVERT: V 9 TYR cc_start: 0.9096 (OUTLIER) cc_final: 0.8303 (t80) REVERT: V 68 GLU cc_start: 0.7562 (mt-10) cc_final: 0.7336 (mt-10) REVERT: V 72 ASP cc_start: 0.8296 (m-30) cc_final: 0.8081 (m-30) REVERT: V 89 GLU cc_start: 0.7423 (mt-10) cc_final: 0.7091 (mt-10) REVERT: V 104 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7486 (mm-30) REVERT: V 181 LYS cc_start: 0.7701 (OUTLIER) cc_final: 0.7426 (tptp) REVERT: W 72 ASP cc_start: 0.8273 (m-30) cc_final: 0.7990 (m-30) REVERT: W 128 ASP cc_start: 0.7588 (OUTLIER) cc_final: 0.7340 (t0) REVERT: X 72 ASP cc_start: 0.8327 (m-30) cc_final: 0.7967 (m-30) REVERT: X 104 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7435 (mm-30) REVERT: X 181 LYS cc_start: 0.7350 (OUTLIER) cc_final: 0.7110 (mmmt) REVERT: Y 59 LYS cc_start: 0.8762 (mmtt) cc_final: 0.8516 (mmtp) REVERT: Y 72 ASP cc_start: 0.8228 (m-30) cc_final: 0.7935 (m-30) REVERT: Y 104 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7693 (tp30) REVERT: Z 68 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7341 (mt-10) REVERT: Z 72 ASP cc_start: 0.8288 (m-30) cc_final: 0.7948 (m-30) outliers start: 178 outliers final: 81 residues processed: 764 average time/residue: 1.5418 time to fit residues: 1385.6894 Evaluate side-chains 704 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 609 time to evaluate : 4.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain C residue 3 SER Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain D residue 42 ASP Chi-restraints excluded: chain E residue 3 SER Chi-restraints excluded: chain E residue 42 ASP Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 132 SER Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain I residue 42 ASP Chi-restraints excluded: chain I residue 132 SER Chi-restraints excluded: chain I residue 181 LYS Chi-restraints excluded: chain J residue 3 SER Chi-restraints excluded: chain J residue 128 ASP Chi-restraints excluded: chain J residue 132 SER Chi-restraints excluded: chain J residue 138 GLU Chi-restraints excluded: chain K residue 3 SER Chi-restraints excluded: chain K residue 10 SER Chi-restraints excluded: chain K residue 42 ASP Chi-restraints excluded: chain K residue 57 GLU Chi-restraints excluded: chain K residue 86 SER Chi-restraints excluded: chain L residue 3 SER Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 42 ASP Chi-restraints excluded: chain L residue 46 GLU Chi-restraints excluded: chain M residue 42 ASP Chi-restraints excluded: chain M residue 86 SER Chi-restraints excluded: chain M residue 132 SER Chi-restraints excluded: chain N residue 42 ASP Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 181 LYS Chi-restraints excluded: chain O residue 10 SER Chi-restraints excluded: chain O residue 42 ASP Chi-restraints excluded: chain O residue 126 LEU Chi-restraints excluded: chain P residue 3 SER Chi-restraints excluded: chain P residue 10 SER Chi-restraints excluded: chain P residue 33 SER Chi-restraints excluded: chain P residue 42 ASP Chi-restraints excluded: chain Q residue 3 SER Chi-restraints excluded: chain Q residue 10 SER Chi-restraints excluded: chain Q residue 42 ASP Chi-restraints excluded: chain Q residue 132 SER Chi-restraints excluded: chain Q residue 181 LYS Chi-restraints excluded: chain R residue 3 SER Chi-restraints excluded: chain R residue 10 SER Chi-restraints excluded: chain R residue 42 ASP Chi-restraints excluded: chain R residue 182 HIS Chi-restraints excluded: chain S residue 3 SER Chi-restraints excluded: chain S residue 10 SER Chi-restraints excluded: chain S residue 42 ASP Chi-restraints excluded: chain S residue 86 SER Chi-restraints excluded: chain S residue 132 SER Chi-restraints excluded: chain S residue 181 LYS Chi-restraints excluded: chain T residue 10 SER Chi-restraints excluded: chain T residue 42 ASP Chi-restraints excluded: chain T residue 128 ASP Chi-restraints excluded: chain T residue 181 LYS Chi-restraints excluded: chain U residue 10 SER Chi-restraints excluded: chain U residue 42 ASP Chi-restraints excluded: chain U residue 181 LYS Chi-restraints excluded: chain V residue 3 SER Chi-restraints excluded: chain V residue 9 TYR Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain V residue 33 SER Chi-restraints excluded: chain V residue 42 ASP Chi-restraints excluded: chain V residue 126 LEU Chi-restraints excluded: chain V residue 181 LYS Chi-restraints excluded: chain W residue 3 SER Chi-restraints excluded: chain W residue 42 ASP Chi-restraints excluded: chain W residue 86 SER Chi-restraints excluded: chain W residue 128 ASP Chi-restraints excluded: chain W residue 181 LYS Chi-restraints excluded: chain X residue 3 SER Chi-restraints excluded: chain X residue 42 ASP Chi-restraints excluded: chain X residue 88 ASP Chi-restraints excluded: chain X residue 181 LYS Chi-restraints excluded: chain Y residue 3 SER Chi-restraints excluded: chain Y residue 10 SER Chi-restraints excluded: chain Y residue 42 ASP Chi-restraints excluded: chain Y residue 46 GLU Chi-restraints excluded: chain Y residue 88 ASP Chi-restraints excluded: chain Y residue 181 LYS Chi-restraints excluded: chain Z residue 42 ASP Chi-restraints excluded: chain Z residue 119 SER Chi-restraints excluded: chain Z residue 126 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 201 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 302 optimal weight: 5.9990 chunk 247 optimal weight: 0.9990 chunk 100 optimal weight: 8.9990 chunk 363 optimal weight: 3.9990 chunk 393 optimal weight: 4.9990 chunk 324 optimal weight: 7.9990 chunk 360 optimal weight: 0.7980 chunk 124 optimal weight: 5.9990 chunk 291 optimal weight: 9.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 83 GLN V 182 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 33560 Z= 0.309 Angle : 0.411 4.068 45064 Z= 0.217 Chirality : 0.033 0.136 4840 Planarity : 0.003 0.047 5944 Dihedral : 4.931 55.146 4514 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 6.82 % Allowed : 17.92 % Favored : 75.26 % 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: 4.30 (0.13), residues: 3976 helix: 3.58 (0.09), residues: 3208 sheet: None (None), residues: 0 loop : -0.71 (0.20), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP P 90 HIS 0.006 0.001 HIS V 182 PHE 0.013 0.002 PHE P 38 TYR 0.010 0.001 TYR Y 31 ARG 0.005 0.000 ARG O 76 *********************** 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 881 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 235 poor density : 646 time to evaluate : 4.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ASP cc_start: 0.8262 (m-30) cc_final: 0.8000 (m-30) REVERT: A 128 ASP cc_start: 0.7625 (OUTLIER) cc_final: 0.7400 (t70) REVERT: C 68 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7348 (mt-10) REVERT: C 72 ASP cc_start: 0.8314 (m-30) cc_final: 0.7954 (m-30) REVERT: C 128 ASP cc_start: 0.7627 (OUTLIER) cc_final: 0.7390 (t0) REVERT: D 72 ASP cc_start: 0.8274 (m-30) cc_final: 0.7941 (m-30) REVERT: D 182 HIS cc_start: 0.6974 (OUTLIER) cc_final: 0.6530 (m90) REVERT: E 72 ASP cc_start: 0.8314 (m-30) cc_final: 0.8007 (m-30) REVERT: E 128 ASP cc_start: 0.7644 (OUTLIER) cc_final: 0.7404 (t0) REVERT: F 72 ASP cc_start: 0.8298 (m-30) cc_final: 0.7954 (m-30) REVERT: F 128 ASP cc_start: 0.7644 (OUTLIER) cc_final: 0.7399 (t0) REVERT: I 72 ASP cc_start: 0.8260 (m-30) cc_final: 0.7968 (m-30) REVERT: I 138 GLU cc_start: 0.8300 (tp30) cc_final: 0.8041 (tp30) REVERT: I 181 LYS cc_start: 0.7602 (OUTLIER) cc_final: 0.7281 (tptp) REVERT: J 72 ASP cc_start: 0.8331 (m-30) cc_final: 0.8040 (m-30) REVERT: J 128 ASP cc_start: 0.7632 (OUTLIER) cc_final: 0.7379 (t0) REVERT: K 72 ASP cc_start: 0.8342 (m-30) cc_final: 0.7999 (m-30) REVERT: L 72 ASP cc_start: 0.8268 (m-30) cc_final: 0.7945 (m-30) REVERT: M 68 GLU cc_start: 0.7590 (mt-10) cc_final: 0.7360 (mt-10) REVERT: M 72 ASP cc_start: 0.8327 (m-30) cc_final: 0.8014 (m-30) REVERT: N 72 ASP cc_start: 0.8299 (m-30) cc_final: 0.7942 (m-30) REVERT: N 128 ASP cc_start: 0.7635 (OUTLIER) cc_final: 0.7393 (t0) REVERT: O 68 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7363 (mt-10) REVERT: O 72 ASP cc_start: 0.8269 (m-30) cc_final: 0.7972 (m-30) REVERT: O 128 ASP cc_start: 0.7630 (OUTLIER) cc_final: 0.7392 (t0) REVERT: O 169 SER cc_start: 0.8599 (OUTLIER) cc_final: 0.8066 (p) REVERT: P 9 TYR cc_start: 0.9106 (OUTLIER) cc_final: 0.8340 (t80) REVERT: P 59 LYS cc_start: 0.8789 (mmtt) cc_final: 0.8549 (mmtm) REVERT: P 68 GLU cc_start: 0.7621 (mt-10) cc_final: 0.7380 (mt-10) REVERT: P 72 ASP cc_start: 0.8334 (m-30) cc_final: 0.8010 (m-30) REVERT: P 109 GLN cc_start: 0.8839 (tp40) cc_final: 0.8476 (mm-40) REVERT: P 138 GLU cc_start: 0.8545 (tp30) cc_final: 0.8241 (tp30) REVERT: Q 72 ASP cc_start: 0.8300 (m-30) cc_final: 0.7926 (m-30) REVERT: R 72 ASP cc_start: 0.8314 (m-30) cc_final: 0.8003 (m-30) REVERT: S 68 GLU cc_start: 0.7611 (mt-10) cc_final: 0.7372 (mt-10) REVERT: S 72 ASP cc_start: 0.8340 (m-30) cc_final: 0.8038 (m-30) REVERT: T 72 ASP cc_start: 0.8294 (m-30) cc_final: 0.8061 (m-30) REVERT: T 104 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7915 (mm-30) REVERT: T 128 ASP cc_start: 0.7651 (OUTLIER) cc_final: 0.7398 (t0) REVERT: U 72 ASP cc_start: 0.8287 (m-30) cc_final: 0.7974 (m-30) REVERT: V 9 TYR cc_start: 0.9111 (OUTLIER) cc_final: 0.8199 (t80) REVERT: V 72 ASP cc_start: 0.8328 (m-30) cc_final: 0.8022 (m-30) REVERT: V 128 ASP cc_start: 0.7640 (OUTLIER) cc_final: 0.7428 (t70) REVERT: W 68 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7372 (mt-10) REVERT: W 72 ASP cc_start: 0.8302 (m-30) cc_final: 0.7959 (m-30) REVERT: W 128 ASP cc_start: 0.7630 (OUTLIER) cc_final: 0.7383 (t0) REVERT: X 72 ASP cc_start: 0.8300 (m-30) cc_final: 0.7966 (m-30) REVERT: X 181 LYS cc_start: 0.7419 (OUTLIER) cc_final: 0.7171 (mmmt) REVERT: Y 68 GLU cc_start: 0.7584 (mt-10) cc_final: 0.7346 (mt-10) REVERT: Y 72 ASP cc_start: 0.8255 (m-30) cc_final: 0.7950 (m-30) REVERT: Z 72 ASP cc_start: 0.8270 (m-30) cc_final: 0.7942 (m-30) outliers start: 235 outliers final: 129 residues processed: 791 average time/residue: 1.5096 time to fit residues: 1407.9346 Evaluate side-chains 745 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 600 time to evaluate : 3.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain C residue 3 SER Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain D residue 42 ASP Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 182 HIS Chi-restraints excluded: chain E residue 3 SER Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 42 ASP Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 132 SER Chi-restraints excluded: chain F residue 42 ASP Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain F residue 132 SER Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 42 ASP Chi-restraints excluded: chain I residue 126 LEU Chi-restraints excluded: chain I residue 132 SER Chi-restraints excluded: chain I residue 181 LYS Chi-restraints excluded: chain J residue 3 SER Chi-restraints excluded: chain J residue 42 ASP Chi-restraints excluded: chain J residue 86 SER Chi-restraints excluded: chain J residue 128 ASP Chi-restraints excluded: chain J residue 132 SER Chi-restraints excluded: chain J residue 138 GLU Chi-restraints excluded: chain J residue 182 HIS Chi-restraints excluded: chain K residue 3 SER Chi-restraints excluded: chain K residue 10 SER Chi-restraints excluded: chain K residue 42 ASP Chi-restraints excluded: chain K residue 57 GLU Chi-restraints excluded: chain K residue 86 SER Chi-restraints excluded: chain K residue 132 SER Chi-restraints excluded: chain L residue 3 SER Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 42 ASP Chi-restraints excluded: chain L residue 46 GLU Chi-restraints excluded: chain L residue 132 SER Chi-restraints excluded: chain M residue 3 SER Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 42 ASP Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 86 SER Chi-restraints excluded: chain M residue 132 SER Chi-restraints excluded: chain M residue 138 GLU Chi-restraints excluded: chain N residue 10 SER Chi-restraints excluded: chain N residue 42 ASP Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 86 SER Chi-restraints excluded: chain N residue 128 ASP Chi-restraints excluded: chain N residue 132 SER Chi-restraints excluded: chain N residue 181 LYS Chi-restraints excluded: chain O residue 10 SER Chi-restraints excluded: chain O residue 42 ASP Chi-restraints excluded: chain O residue 86 SER Chi-restraints excluded: chain O residue 126 LEU Chi-restraints excluded: chain O residue 128 ASP Chi-restraints excluded: chain O residue 132 SER Chi-restraints excluded: chain O residue 138 GLU Chi-restraints excluded: chain O residue 169 SER Chi-restraints excluded: chain P residue 3 SER Chi-restraints excluded: chain P residue 9 TYR Chi-restraints excluded: chain P residue 10 SER Chi-restraints excluded: chain P residue 33 SER Chi-restraints excluded: chain P residue 42 ASP Chi-restraints excluded: chain P residue 86 SER Chi-restraints excluded: chain P residue 126 LEU Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain P residue 181 LYS Chi-restraints excluded: chain Q residue 3 SER Chi-restraints excluded: chain Q residue 10 SER Chi-restraints excluded: chain Q residue 42 ASP Chi-restraints excluded: chain Q residue 88 ASP Chi-restraints excluded: chain Q residue 132 SER Chi-restraints excluded: chain R residue 3 SER Chi-restraints excluded: chain R residue 10 SER Chi-restraints excluded: chain R residue 42 ASP Chi-restraints excluded: chain R residue 86 SER Chi-restraints excluded: chain R residue 132 SER Chi-restraints excluded: chain S residue 3 SER Chi-restraints excluded: chain S residue 10 SER Chi-restraints excluded: chain S residue 33 SER Chi-restraints excluded: chain S residue 42 ASP Chi-restraints excluded: chain S residue 86 SER Chi-restraints excluded: chain S residue 132 SER Chi-restraints excluded: chain S residue 181 LYS Chi-restraints excluded: chain T residue 10 SER Chi-restraints excluded: chain T residue 42 ASP Chi-restraints excluded: chain T residue 57 GLU Chi-restraints excluded: chain T residue 128 ASP Chi-restraints excluded: chain T residue 132 SER Chi-restraints excluded: chain U residue 10 SER Chi-restraints excluded: chain U residue 42 ASP Chi-restraints excluded: chain U residue 132 SER Chi-restraints excluded: chain U residue 181 LYS Chi-restraints excluded: chain V residue 3 SER Chi-restraints excluded: chain V residue 9 TYR Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain V residue 33 SER Chi-restraints excluded: chain V residue 42 ASP Chi-restraints excluded: chain V residue 86 SER Chi-restraints excluded: chain V residue 126 LEU Chi-restraints excluded: chain V residue 128 ASP Chi-restraints excluded: chain W residue 3 SER Chi-restraints excluded: chain W residue 42 ASP Chi-restraints excluded: chain W residue 86 SER Chi-restraints excluded: chain W residue 128 ASP Chi-restraints excluded: chain W residue 181 LYS Chi-restraints excluded: chain X residue 3 SER Chi-restraints excluded: chain X residue 42 ASP Chi-restraints excluded: chain X residue 78 LEU Chi-restraints excluded: chain X residue 88 ASP Chi-restraints excluded: chain X residue 132 SER Chi-restraints excluded: chain X residue 181 LYS Chi-restraints excluded: chain Y residue 3 SER Chi-restraints excluded: chain Y residue 10 SER Chi-restraints excluded: chain Y residue 42 ASP Chi-restraints excluded: chain Y residue 46 GLU Chi-restraints excluded: chain Y residue 88 ASP Chi-restraints excluded: chain Y residue 132 SER Chi-restraints excluded: chain Y residue 181 LYS Chi-restraints excluded: chain Z residue 42 ASP Chi-restraints excluded: chain Z residue 86 SER Chi-restraints excluded: chain Z residue 119 SER Chi-restraints excluded: chain Z residue 126 LEU Chi-restraints excluded: chain Z residue 132 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 359 optimal weight: 0.8980 chunk 273 optimal weight: 3.9990 chunk 188 optimal weight: 5.9990 chunk 40 optimal weight: 7.9990 chunk 173 optimal weight: 3.9990 chunk 244 optimal weight: 2.9990 chunk 365 optimal weight: 4.9990 chunk 386 optimal weight: 0.8980 chunk 190 optimal weight: 0.8980 chunk 346 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 87 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 33560 Z= 0.240 Angle : 0.383 4.070 45064 Z= 0.204 Chirality : 0.032 0.126 4840 Planarity : 0.003 0.033 5944 Dihedral : 4.711 55.469 4510 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 5.97 % Allowed : 18.53 % Favored : 75.49 % 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: 4.64 (0.13), residues: 3976 helix: 3.79 (0.09), residues: 3216 sheet: None (None), residues: 0 loop : -0.53 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP V 90 HIS 0.004 0.001 HIS K 182 PHE 0.011 0.002 PHE P 38 TYR 0.007 0.001 TYR V 31 ARG 0.006 0.000 ARG O 76 *********************** 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 839 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 633 time to evaluate : 4.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ASP cc_start: 0.8230 (m-30) cc_final: 0.7958 (m-30) REVERT: A 128 ASP cc_start: 0.7622 (OUTLIER) cc_final: 0.7391 (t70) REVERT: B 68 GLU cc_start: 0.7508 (mt-10) cc_final: 0.7284 (mt-10) REVERT: C 68 GLU cc_start: 0.7554 (mt-10) cc_final: 0.7243 (mt-10) REVERT: C 72 ASP cc_start: 0.8260 (m-30) cc_final: 0.7923 (m-30) REVERT: C 128 ASP cc_start: 0.7617 (OUTLIER) cc_final: 0.7378 (t0) REVERT: D 72 ASP cc_start: 0.8229 (m-30) cc_final: 0.7908 (m-30) REVERT: D 182 HIS cc_start: 0.6949 (OUTLIER) cc_final: 0.6444 (m90) REVERT: E 68 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7370 (mt-10) REVERT: E 72 ASP cc_start: 0.8289 (m-30) cc_final: 0.7976 (m-30) REVERT: E 128 ASP cc_start: 0.7632 (OUTLIER) cc_final: 0.7421 (t70) REVERT: F 72 ASP cc_start: 0.8242 (m-30) cc_final: 0.7906 (m-30) REVERT: F 104 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7898 (mm-30) REVERT: F 128 ASP cc_start: 0.7637 (OUTLIER) cc_final: 0.7387 (t0) REVERT: I 72 ASP cc_start: 0.8208 (m-30) cc_final: 0.7918 (m-30) REVERT: I 138 GLU cc_start: 0.8310 (tp30) cc_final: 0.8054 (tp30) REVERT: I 181 LYS cc_start: 0.7464 (OUTLIER) cc_final: 0.7131 (tptp) REVERT: J 72 ASP cc_start: 0.8301 (m-30) cc_final: 0.7991 (m-30) REVERT: J 128 ASP cc_start: 0.7627 (OUTLIER) cc_final: 0.7402 (t70) REVERT: K 68 GLU cc_start: 0.7573 (mt-10) cc_final: 0.7353 (mt-10) REVERT: K 72 ASP cc_start: 0.8292 (m-30) cc_final: 0.7963 (m-30) REVERT: L 72 ASP cc_start: 0.8230 (m-30) cc_final: 0.7912 (m-30) REVERT: M 68 GLU cc_start: 0.7572 (mt-10) cc_final: 0.7345 (mt-10) REVERT: M 72 ASP cc_start: 0.8293 (m-30) cc_final: 0.7983 (m-30) REVERT: N 72 ASP cc_start: 0.8242 (m-30) cc_final: 0.7914 (m-30) REVERT: N 128 ASP cc_start: 0.7629 (OUTLIER) cc_final: 0.7385 (t70) REVERT: N 181 LYS cc_start: 0.7509 (OUTLIER) cc_final: 0.7281 (mmmt) REVERT: O 72 ASP cc_start: 0.8237 (m-30) cc_final: 0.7930 (m-30) REVERT: O 128 ASP cc_start: 0.7704 (OUTLIER) cc_final: 0.7484 (t0) REVERT: O 169 SER cc_start: 0.8605 (p) cc_final: 0.8072 (p) REVERT: P 9 TYR cc_start: 0.9096 (OUTLIER) cc_final: 0.8326 (t80) REVERT: P 68 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7360 (mt-10) REVERT: P 72 ASP cc_start: 0.8315 (m-30) cc_final: 0.7994 (m-30) REVERT: P 138 GLU cc_start: 0.8452 (tp30) cc_final: 0.8232 (tp30) REVERT: Q 72 ASP cc_start: 0.8251 (m-30) cc_final: 0.7901 (m-30) REVERT: R 72 ASP cc_start: 0.8260 (m-30) cc_final: 0.7909 (m-30) REVERT: R 181 LYS cc_start: 0.7583 (OUTLIER) cc_final: 0.7286 (mmmt) REVERT: S 68 GLU cc_start: 0.7576 (mt-10) cc_final: 0.7346 (mt-10) REVERT: S 72 ASP cc_start: 0.8319 (m-30) cc_final: 0.8036 (m-30) REVERT: T 72 ASP cc_start: 0.8264 (m-30) cc_final: 0.8031 (m-30) REVERT: T 104 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7952 (mm-30) REVERT: T 128 ASP cc_start: 0.7635 (OUTLIER) cc_final: 0.7385 (t0) REVERT: U 68 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7312 (mt-10) REVERT: U 72 ASP cc_start: 0.8243 (m-30) cc_final: 0.7916 (m-30) REVERT: V 9 TYR cc_start: 0.9084 (OUTLIER) cc_final: 0.8264 (t80) REVERT: V 72 ASP cc_start: 0.8293 (m-30) cc_final: 0.8004 (m-30) REVERT: V 97 MET cc_start: 0.7478 (tpp) cc_final: 0.7255 (tpp) REVERT: V 128 ASP cc_start: 0.7629 (OUTLIER) cc_final: 0.7409 (t70) REVERT: W 72 ASP cc_start: 0.8241 (m-30) cc_final: 0.7913 (m-30) REVERT: W 128 ASP cc_start: 0.7625 (OUTLIER) cc_final: 0.7370 (t0) REVERT: X 72 ASP cc_start: 0.8262 (m-30) cc_final: 0.7927 (m-30) REVERT: X 181 LYS cc_start: 0.7376 (OUTLIER) cc_final: 0.7030 (mmmt) REVERT: Y 9 TYR cc_start: 0.9097 (OUTLIER) cc_final: 0.8317 (t80) REVERT: Y 72 ASP cc_start: 0.8205 (m-30) cc_final: 0.7927 (m-30) REVERT: Z 61 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7854 (mm-30) REVERT: Z 68 GLU cc_start: 0.7576 (mt-10) cc_final: 0.7369 (mt-10) REVERT: Z 72 ASP cc_start: 0.8219 (m-30) cc_final: 0.7887 (m-30) outliers start: 206 outliers final: 123 residues processed: 759 average time/residue: 1.5728 time to fit residues: 1408.1286 Evaluate side-chains 735 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 594 time to evaluate : 3.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain C residue 3 SER Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain D residue 42 ASP Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 182 HIS Chi-restraints excluded: chain E residue 3 SER Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 42 ASP Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 132 SER Chi-restraints excluded: chain F residue 42 ASP Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain F residue 132 SER Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 42 ASP Chi-restraints excluded: chain I residue 126 LEU Chi-restraints excluded: chain I residue 181 LYS Chi-restraints excluded: chain J residue 3 SER Chi-restraints excluded: chain J residue 42 ASP Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain J residue 86 SER Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 128 ASP Chi-restraints excluded: chain J residue 132 SER Chi-restraints excluded: chain J residue 138 GLU Chi-restraints excluded: chain J residue 182 HIS Chi-restraints excluded: chain K residue 3 SER Chi-restraints excluded: chain K residue 10 SER Chi-restraints excluded: chain K residue 42 ASP Chi-restraints excluded: chain K residue 57 GLU Chi-restraints excluded: chain K residue 86 SER Chi-restraints excluded: chain L residue 3 SER Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 42 ASP Chi-restraints excluded: chain L residue 126 LEU Chi-restraints excluded: chain M residue 3 SER Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 42 ASP Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 86 SER Chi-restraints excluded: chain M residue 132 SER Chi-restraints excluded: chain N residue 10 SER Chi-restraints excluded: chain N residue 42 ASP Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 57 GLU Chi-restraints excluded: chain N residue 86 SER Chi-restraints excluded: chain N residue 128 ASP Chi-restraints excluded: chain N residue 132 SER Chi-restraints excluded: chain N residue 181 LYS Chi-restraints excluded: chain O residue 10 SER Chi-restraints excluded: chain O residue 42 ASP Chi-restraints excluded: chain O residue 57 GLU Chi-restraints excluded: chain O residue 86 SER Chi-restraints excluded: chain O residue 126 LEU Chi-restraints excluded: chain O residue 128 ASP Chi-restraints excluded: chain O residue 132 SER Chi-restraints excluded: chain O residue 138 GLU Chi-restraints excluded: chain P residue 3 SER Chi-restraints excluded: chain P residue 9 TYR Chi-restraints excluded: chain P residue 10 SER Chi-restraints excluded: chain P residue 33 SER Chi-restraints excluded: chain P residue 42 ASP Chi-restraints excluded: chain P residue 86 SER Chi-restraints excluded: chain P residue 126 LEU Chi-restraints excluded: chain P residue 181 LYS Chi-restraints excluded: chain Q residue 3 SER Chi-restraints excluded: chain Q residue 10 SER Chi-restraints excluded: chain Q residue 42 ASP Chi-restraints excluded: chain Q residue 88 ASP Chi-restraints excluded: chain R residue 3 SER Chi-restraints excluded: chain R residue 10 SER Chi-restraints excluded: chain R residue 42 ASP Chi-restraints excluded: chain R residue 86 SER Chi-restraints excluded: chain R residue 126 LEU Chi-restraints excluded: chain R residue 181 LYS Chi-restraints excluded: chain S residue 3 SER Chi-restraints excluded: chain S residue 10 SER Chi-restraints excluded: chain S residue 33 SER Chi-restraints excluded: chain S residue 42 ASP Chi-restraints excluded: chain S residue 86 SER Chi-restraints excluded: chain S residue 181 LYS Chi-restraints excluded: chain T residue 10 SER Chi-restraints excluded: chain T residue 42 ASP Chi-restraints excluded: chain T residue 57 GLU Chi-restraints excluded: chain T residue 128 ASP Chi-restraints excluded: chain T residue 181 LYS Chi-restraints excluded: chain U residue 10 SER Chi-restraints excluded: chain U residue 42 ASP Chi-restraints excluded: chain U residue 132 SER Chi-restraints excluded: chain V residue 3 SER Chi-restraints excluded: chain V residue 9 TYR Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain V residue 33 SER Chi-restraints excluded: chain V residue 42 ASP Chi-restraints excluded: chain V residue 126 LEU Chi-restraints excluded: chain V residue 128 ASP Chi-restraints excluded: chain W residue 3 SER Chi-restraints excluded: chain W residue 42 ASP Chi-restraints excluded: chain W residue 86 SER Chi-restraints excluded: chain W residue 128 ASP Chi-restraints excluded: chain W residue 181 LYS Chi-restraints excluded: chain X residue 3 SER Chi-restraints excluded: chain X residue 42 ASP Chi-restraints excluded: chain X residue 78 LEU Chi-restraints excluded: chain X residue 88 ASP Chi-restraints excluded: chain X residue 126 LEU Chi-restraints excluded: chain X residue 132 SER Chi-restraints excluded: chain X residue 181 LYS Chi-restraints excluded: chain Y residue 3 SER Chi-restraints excluded: chain Y residue 9 TYR Chi-restraints excluded: chain Y residue 10 SER Chi-restraints excluded: chain Y residue 42 ASP Chi-restraints excluded: chain Y residue 46 GLU Chi-restraints excluded: chain Y residue 88 ASP Chi-restraints excluded: chain Y residue 132 SER Chi-restraints excluded: chain Y residue 181 LYS Chi-restraints excluded: chain Z residue 42 ASP Chi-restraints excluded: chain Z residue 86 SER Chi-restraints excluded: chain Z residue 119 SER Chi-restraints excluded: chain Z residue 126 LEU 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: 0.9990 chunk 5 optimal weight: 5.9990 chunk 287 optimal weight: 4.9990 chunk 159 optimal weight: 4.9990 chunk 329 optimal weight: 0.8980 chunk 267 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 197 optimal weight: 5.9990 chunk 347 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 182 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 33560 Z= 0.154 Angle : 0.351 4.400 45064 Z= 0.190 Chirality : 0.030 0.118 4840 Planarity : 0.002 0.031 5944 Dihedral : 4.102 54.239 4500 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 4.06 % Allowed : 21.55 % Favored : 74.39 % 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: 5.00 (0.13), residues: 3976 helix: 4.05 (0.09), residues: 3216 sheet: None (None), residues: 0 loop : -0.45 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP P 90 HIS 0.004 0.000 HIS K 182 PHE 0.009 0.001 PHE L 129 TYR 0.007 0.001 TYR R 31 ARG 0.006 0.000 ARG O 76 *********************** 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 778 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 638 time to evaluate : 3.954 Fit side-chains revert: symmetry clash REVERT: A 72 ASP cc_start: 0.8134 (m-30) cc_final: 0.7897 (m-30) REVERT: A 128 ASP cc_start: 0.7691 (OUTLIER) cc_final: 0.7463 (t70) REVERT: B 70 GLN cc_start: 0.9085 (OUTLIER) cc_final: 0.7902 (tt0) REVERT: C 72 ASP cc_start: 0.8187 (m-30) cc_final: 0.7875 (m-30) REVERT: D 72 ASP cc_start: 0.8190 (m-30) cc_final: 0.7897 (m-30) REVERT: E 72 ASP cc_start: 0.8233 (m-30) cc_final: 0.7930 (m-30) REVERT: F 68 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7308 (mt-10) REVERT: F 72 ASP cc_start: 0.8213 (m-30) cc_final: 0.7896 (m-30) REVERT: F 104 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7957 (mm-30) REVERT: I 72 ASP cc_start: 0.8160 (m-30) cc_final: 0.7960 (m-30) REVERT: I 138 GLU cc_start: 0.8317 (tp30) cc_final: 0.8020 (tp30) REVERT: J 9 TYR cc_start: 0.9112 (OUTLIER) cc_final: 0.8433 (t80) REVERT: J 72 ASP cc_start: 0.8253 (m-30) cc_final: 0.7979 (m-30) REVERT: J 128 ASP cc_start: 0.7597 (OUTLIER) cc_final: 0.7390 (t70) REVERT: K 72 ASP cc_start: 0.8210 (m-30) cc_final: 0.7935 (m-30) REVERT: L 72 ASP cc_start: 0.8183 (m-30) cc_final: 0.7912 (m-30) REVERT: M 72 ASP cc_start: 0.8236 (m-30) cc_final: 0.7933 (m-30) REVERT: N 68 GLU cc_start: 0.7511 (mt-10) cc_final: 0.7296 (mt-10) REVERT: N 72 ASP cc_start: 0.8212 (m-30) cc_final: 0.7872 (m-30) REVERT: N 104 GLU cc_start: 0.7912 (tp30) cc_final: 0.7712 (tp30) REVERT: N 128 ASP cc_start: 0.7624 (OUTLIER) cc_final: 0.7377 (t70) REVERT: N 181 LYS cc_start: 0.7517 (OUTLIER) cc_final: 0.7282 (mmmt) REVERT: O 169 SER cc_start: 0.8557 (OUTLIER) cc_final: 0.8040 (p) REVERT: P 9 TYR cc_start: 0.9090 (OUTLIER) cc_final: 0.8413 (t80) REVERT: P 72 ASP cc_start: 0.8253 (m-30) cc_final: 0.7932 (m-30) REVERT: Q 72 ASP cc_start: 0.8236 (m-30) cc_final: 0.7887 (m-30) REVERT: R 59 LYS cc_start: 0.8747 (mmtt) cc_final: 0.8497 (mmtm) REVERT: R 72 ASP cc_start: 0.8197 (m-30) cc_final: 0.7943 (m-30) REVERT: S 72 ASP cc_start: 0.8248 (m-30) cc_final: 0.7979 (m-30) REVERT: S 181 LYS cc_start: 0.7552 (OUTLIER) cc_final: 0.7235 (mmmt) REVERT: T 72 ASP cc_start: 0.8199 (m-30) cc_final: 0.7943 (m-30) REVERT: T 128 ASP cc_start: 0.7606 (OUTLIER) cc_final: 0.7351 (t0) REVERT: U 72 ASP cc_start: 0.8208 (m-30) cc_final: 0.7996 (m-30) REVERT: V 9 TYR cc_start: 0.9109 (OUTLIER) cc_final: 0.8378 (t80) REVERT: V 40 ARG cc_start: 0.6976 (mtp85) cc_final: 0.6738 (mtp85) REVERT: V 72 ASP cc_start: 0.8237 (m-30) cc_final: 0.7949 (m-30) REVERT: V 89 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7427 (mm-30) REVERT: W 68 GLU cc_start: 0.7530 (mt-10) cc_final: 0.7292 (mt-10) REVERT: W 72 ASP cc_start: 0.8207 (m-30) cc_final: 0.7919 (m-30) REVERT: W 128 ASP cc_start: 0.7603 (OUTLIER) cc_final: 0.7364 (t70) REVERT: X 72 ASP cc_start: 0.8208 (m-30) cc_final: 0.7876 (m-30) REVERT: X 181 LYS cc_start: 0.7346 (OUTLIER) cc_final: 0.7043 (mmmt) REVERT: Y 9 TYR cc_start: 0.9094 (OUTLIER) cc_final: 0.8382 (t80) REVERT: Y 72 ASP cc_start: 0.8152 (m-30) cc_final: 0.7899 (m-30) REVERT: Y 89 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7414 (mt-10) REVERT: Y 181 LYS cc_start: 0.7569 (OUTLIER) cc_final: 0.7215 (mmmt) REVERT: Z 72 ASP cc_start: 0.8205 (m-30) cc_final: 0.7942 (m-30) outliers start: 140 outliers final: 89 residues processed: 729 average time/residue: 1.5242 time to fit residues: 1308.5076 Evaluate side-chains 699 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 593 time to evaluate : 3.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain B residue 70 GLN Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain C residue 3 SER Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain D residue 42 ASP Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain E residue 3 SER Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 42 ASP Chi-restraints excluded: chain F residue 42 ASP Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 42 ASP Chi-restraints excluded: chain I residue 126 LEU Chi-restraints excluded: chain J residue 3 SER Chi-restraints excluded: chain J residue 9 TYR Chi-restraints excluded: chain J residue 42 ASP Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 128 ASP Chi-restraints excluded: chain K residue 3 SER Chi-restraints excluded: chain K residue 10 SER Chi-restraints excluded: chain K residue 42 ASP Chi-restraints excluded: chain K residue 86 SER Chi-restraints excluded: chain K residue 181 LYS Chi-restraints excluded: chain L residue 3 SER Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 42 ASP Chi-restraints excluded: chain L residue 126 LEU Chi-restraints excluded: chain M residue 3 SER Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 42 ASP Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 132 SER Chi-restraints excluded: chain N residue 10 SER Chi-restraints excluded: chain N residue 126 LEU Chi-restraints excluded: chain N residue 128 ASP Chi-restraints excluded: chain N residue 132 SER Chi-restraints excluded: chain N residue 181 LYS Chi-restraints excluded: chain O residue 10 SER Chi-restraints excluded: chain O residue 33 SER Chi-restraints excluded: chain O residue 42 ASP Chi-restraints excluded: chain O residue 126 LEU Chi-restraints excluded: chain O residue 138 GLU Chi-restraints excluded: chain O residue 169 SER Chi-restraints excluded: chain P residue 3 SER Chi-restraints excluded: chain P residue 9 TYR Chi-restraints excluded: chain P residue 33 SER Chi-restraints excluded: chain P residue 57 GLU Chi-restraints excluded: chain P residue 126 LEU Chi-restraints excluded: chain P residue 181 LYS Chi-restraints excluded: chain Q residue 3 SER Chi-restraints excluded: chain Q residue 10 SER Chi-restraints excluded: chain Q residue 33 SER Chi-restraints excluded: chain Q residue 42 ASP Chi-restraints excluded: chain Q residue 169 SER Chi-restraints excluded: chain R residue 3 SER Chi-restraints excluded: chain R residue 10 SER Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 42 ASP Chi-restraints excluded: chain R residue 57 GLU Chi-restraints excluded: chain R residue 126 LEU Chi-restraints excluded: chain R residue 132 SER Chi-restraints excluded: chain S residue 3 SER Chi-restraints excluded: chain S residue 10 SER Chi-restraints excluded: chain S residue 33 SER Chi-restraints excluded: chain S residue 42 ASP Chi-restraints excluded: chain S residue 181 LYS Chi-restraints excluded: chain T residue 128 ASP Chi-restraints excluded: chain U residue 10 SER Chi-restraints excluded: chain U residue 42 ASP Chi-restraints excluded: chain U residue 126 LEU Chi-restraints excluded: chain V residue 3 SER Chi-restraints excluded: chain V residue 9 TYR Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain V residue 42 ASP Chi-restraints excluded: chain V residue 86 SER Chi-restraints excluded: chain V residue 89 GLU Chi-restraints excluded: chain V residue 126 LEU Chi-restraints excluded: chain W residue 3 SER Chi-restraints excluded: chain W residue 42 ASP Chi-restraints excluded: chain W residue 57 GLU Chi-restraints excluded: chain W residue 126 LEU Chi-restraints excluded: chain W residue 128 ASP Chi-restraints excluded: chain W residue 181 LYS Chi-restraints excluded: chain X residue 3 SER Chi-restraints excluded: chain X residue 57 GLU Chi-restraints excluded: chain X residue 126 LEU Chi-restraints excluded: chain X residue 132 SER Chi-restraints excluded: chain X residue 181 LYS Chi-restraints excluded: chain Y residue 3 SER Chi-restraints excluded: chain Y residue 9 TYR Chi-restraints excluded: chain Y residue 10 SER Chi-restraints excluded: chain Y residue 42 ASP Chi-restraints excluded: chain Y residue 57 GLU Chi-restraints excluded: chain Y residue 89 GLU Chi-restraints excluded: chain Y residue 181 LYS Chi-restraints excluded: chain Z residue 42 ASP Chi-restraints excluded: chain Z residue 119 SER Chi-restraints excluded: chain Z residue 126 LEU 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: 0.9980 chunk 76 optimal weight: 1.9990 chunk 227 optimal weight: 0.6980 chunk 95 optimal weight: 5.9990 chunk 387 optimal weight: 0.9980 chunk 321 optimal weight: 0.8980 chunk 179 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 128 optimal weight: 0.7980 chunk 203 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1631 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= 0.148 Angle : 0.347 4.292 45064 Z= 0.188 Chirality : 0.030 0.118 4840 Planarity : 0.002 0.028 5944 Dihedral : 3.753 54.629 4484 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 4.64 % Allowed : 21.64 % Favored : 73.72 % 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: 5.19 (0.13), residues: 3976 helix: 4.19 (0.09), residues: 3216 sheet: None (None), residues: 0 loop : -0.40 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP J 90 HIS 0.001 0.000 HIS Z 182 PHE 0.009 0.001 PHE L 129 TYR 0.008 0.001 TYR R 31 ARG 0.007 0.000 ARG O 76 *********************** 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 797 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 637 time to evaluate : 3.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ASP cc_start: 0.8095 (m-30) cc_final: 0.7858 (m-30) REVERT: A 128 ASP cc_start: 0.7687 (OUTLIER) cc_final: 0.7459 (t70) REVERT: B 70 GLN cc_start: 0.9070 (OUTLIER) cc_final: 0.7926 (tt0) REVERT: C 72 ASP cc_start: 0.8140 (m-30) cc_final: 0.7807 (m-30) REVERT: D 72 ASP cc_start: 0.8185 (m-30) cc_final: 0.7882 (m-30) REVERT: E 68 GLU cc_start: 0.7595 (mt-10) cc_final: 0.7380 (mt-10) REVERT: E 72 ASP cc_start: 0.8225 (m-30) cc_final: 0.7942 (m-30) REVERT: F 72 ASP cc_start: 0.8162 (m-30) cc_final: 0.7933 (m-30) REVERT: F 104 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7778 (mm-30) REVERT: I 72 ASP cc_start: 0.8078 (m-30) cc_final: 0.7823 (m-30) REVERT: J 9 TYR cc_start: 0.9113 (OUTLIER) cc_final: 0.8312 (t80) REVERT: J 70 GLN cc_start: 0.9118 (OUTLIER) cc_final: 0.7459 (tp40) REVERT: J 72 ASP cc_start: 0.8241 (m-30) cc_final: 0.7951 (m-30) REVERT: J 128 ASP cc_start: 0.7599 (OUTLIER) cc_final: 0.7355 (t0) REVERT: K 181 LYS cc_start: 0.7536 (OUTLIER) cc_final: 0.7225 (mmmt) REVERT: L 72 ASP cc_start: 0.8168 (m-30) cc_final: 0.7895 (m-30) REVERT: M 72 ASP cc_start: 0.8252 (m-30) cc_final: 0.7942 (m-30) REVERT: M 181 LYS cc_start: 0.7317 (OUTLIER) cc_final: 0.7043 (mmmt) REVERT: N 72 ASP cc_start: 0.8160 (m-30) cc_final: 0.7906 (m-30) REVERT: N 104 GLU cc_start: 0.7924 (tp30) cc_final: 0.7718 (tp30) REVERT: N 128 ASP cc_start: 0.7637 (OUTLIER) cc_final: 0.7372 (t70) REVERT: N 181 LYS cc_start: 0.7554 (OUTLIER) cc_final: 0.7245 (mmmt) REVERT: O 169 SER cc_start: 0.8544 (OUTLIER) cc_final: 0.8022 (p) REVERT: P 9 TYR cc_start: 0.9111 (OUTLIER) cc_final: 0.8502 (t80) REVERT: P 72 ASP cc_start: 0.8238 (m-30) cc_final: 0.7991 (m-30) REVERT: P 138 GLU cc_start: 0.8571 (tp30) cc_final: 0.8369 (tp30) REVERT: Q 72 ASP cc_start: 0.8202 (m-30) cc_final: 0.7893 (m-30) REVERT: R 59 LYS cc_start: 0.8719 (mmtt) cc_final: 0.8489 (mmtm) REVERT: R 72 ASP cc_start: 0.8191 (m-30) cc_final: 0.7912 (m-30) REVERT: R 181 LYS cc_start: 0.7542 (OUTLIER) cc_final: 0.7302 (mmmt) REVERT: S 72 ASP cc_start: 0.8224 (m-30) cc_final: 0.7951 (m-30) REVERT: S 181 LYS cc_start: 0.7591 (OUTLIER) cc_final: 0.7303 (mmmt) REVERT: T 128 ASP cc_start: 0.7602 (OUTLIER) cc_final: 0.7340 (t0) REVERT: V 9 TYR cc_start: 0.9116 (OUTLIER) cc_final: 0.8356 (t80) REVERT: V 72 ASP cc_start: 0.8225 (m-30) cc_final: 0.7958 (m-30) REVERT: W 72 ASP cc_start: 0.8176 (m-30) cc_final: 0.7929 (m-30) REVERT: W 128 ASP cc_start: 0.7603 (OUTLIER) cc_final: 0.7347 (t0) REVERT: X 72 ASP cc_start: 0.8213 (m-30) cc_final: 0.7875 (m-30) REVERT: X 181 LYS cc_start: 0.7396 (OUTLIER) cc_final: 0.7137 (mmmt) REVERT: Y 9 TYR cc_start: 0.9088 (OUTLIER) cc_final: 0.8462 (t80) REVERT: Y 72 ASP cc_start: 0.8125 (m-30) cc_final: 0.7833 (m-30) REVERT: Y 89 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7387 (mt-10) REVERT: Y 181 LYS cc_start: 0.7500 (OUTLIER) cc_final: 0.7212 (tptp) REVERT: Z 72 ASP cc_start: 0.8170 (m-30) cc_final: 0.7862 (m-30) outliers start: 160 outliers final: 110 residues processed: 743 average time/residue: 1.4631 time to fit residues: 1286.8321 Evaluate side-chains 736 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 606 time to evaluate : 3.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain B residue 70 GLN Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain C residue 3 SER Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 42 ASP Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 33 SER Chi-restraints excluded: chain F residue 42 ASP Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 132 SER Chi-restraints excluded: chain I residue 42 ASP Chi-restraints excluded: chain I residue 126 LEU Chi-restraints excluded: chain J residue 3 SER Chi-restraints excluded: chain J residue 9 TYR Chi-restraints excluded: chain J residue 42 ASP Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain J residue 70 GLN Chi-restraints excluded: chain J residue 86 SER Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 128 ASP Chi-restraints excluded: chain J residue 182 HIS Chi-restraints excluded: chain K residue 3 SER Chi-restraints excluded: chain K residue 10 SER Chi-restraints excluded: chain K residue 86 SER Chi-restraints excluded: chain K residue 181 LYS Chi-restraints excluded: chain L residue 3 SER Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 126 LEU Chi-restraints excluded: chain M residue 3 SER Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 42 ASP Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 86 SER Chi-restraints excluded: chain M residue 119 SER Chi-restraints excluded: chain M residue 181 LYS Chi-restraints excluded: chain N residue 10 SER Chi-restraints excluded: chain N residue 86 SER Chi-restraints excluded: chain N residue 126 LEU Chi-restraints excluded: chain N residue 128 ASP Chi-restraints excluded: chain N residue 181 LYS Chi-restraints excluded: chain O residue 10 SER Chi-restraints excluded: chain O residue 33 SER Chi-restraints excluded: chain O residue 57 GLU Chi-restraints excluded: chain O residue 86 SER Chi-restraints excluded: chain O residue 126 LEU Chi-restraints excluded: chain O residue 138 GLU Chi-restraints excluded: chain O residue 169 SER Chi-restraints excluded: chain P residue 3 SER Chi-restraints excluded: chain P residue 9 TYR Chi-restraints excluded: chain P residue 10 SER Chi-restraints excluded: chain P residue 33 SER Chi-restraints excluded: chain P residue 86 SER Chi-restraints excluded: chain P residue 119 SER Chi-restraints excluded: chain P residue 126 LEU Chi-restraints excluded: chain P residue 181 LYS Chi-restraints excluded: chain Q residue 3 SER Chi-restraints excluded: chain Q residue 10 SER Chi-restraints excluded: chain Q residue 33 SER Chi-restraints excluded: chain Q residue 169 SER Chi-restraints excluded: chain R residue 3 SER Chi-restraints excluded: chain R residue 10 SER Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 42 ASP Chi-restraints excluded: chain R residue 86 SER Chi-restraints excluded: chain R residue 119 SER Chi-restraints excluded: chain R residue 126 LEU Chi-restraints excluded: chain R residue 181 LYS Chi-restraints excluded: chain S residue 3 SER Chi-restraints excluded: chain S residue 10 SER Chi-restraints excluded: chain S residue 33 SER Chi-restraints excluded: chain S residue 86 SER Chi-restraints excluded: chain S residue 181 LYS Chi-restraints excluded: chain T residue 10 SER Chi-restraints excluded: chain T residue 119 SER Chi-restraints excluded: chain T residue 128 ASP Chi-restraints excluded: chain U residue 10 SER Chi-restraints excluded: chain U residue 119 SER Chi-restraints excluded: chain U residue 126 LEU Chi-restraints excluded: chain U residue 181 LYS Chi-restraints excluded: chain V residue 3 SER Chi-restraints excluded: chain V residue 9 TYR Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain V residue 33 SER Chi-restraints excluded: chain V residue 42 ASP Chi-restraints excluded: chain V residue 57 GLU Chi-restraints excluded: chain V residue 86 SER Chi-restraints excluded: chain V residue 126 LEU Chi-restraints excluded: chain W residue 3 SER Chi-restraints excluded: chain W residue 57 GLU Chi-restraints excluded: chain W residue 86 SER Chi-restraints excluded: chain W residue 126 LEU Chi-restraints excluded: chain W residue 128 ASP Chi-restraints excluded: chain W residue 181 LYS Chi-restraints excluded: chain X residue 3 SER Chi-restraints excluded: chain X residue 42 ASP Chi-restraints excluded: chain X residue 78 LEU Chi-restraints excluded: chain X residue 119 SER Chi-restraints excluded: chain X residue 126 LEU Chi-restraints excluded: chain X residue 132 SER Chi-restraints excluded: chain X residue 181 LYS Chi-restraints excluded: chain Y residue 3 SER Chi-restraints excluded: chain Y residue 9 TYR Chi-restraints excluded: chain Y residue 10 SER Chi-restraints excluded: chain Y residue 42 ASP Chi-restraints excluded: chain Y residue 89 GLU Chi-restraints excluded: chain Y residue 119 SER Chi-restraints excluded: chain Y residue 181 LYS Chi-restraints excluded: chain Z residue 42 ASP Chi-restraints excluded: chain Z residue 57 GLU Chi-restraints excluded: chain Z residue 86 SER Chi-restraints excluded: chain Z residue 126 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 373 optimal weight: 6.9990 chunk 43 optimal weight: 0.6980 chunk 220 optimal weight: 4.9990 chunk 282 optimal weight: 4.9990 chunk 218 optimal weight: 2.9990 chunk 325 optimal weight: 0.9980 chunk 216 optimal weight: 7.9990 chunk 385 optimal weight: 1.9990 chunk 241 optimal weight: 4.9990 chunk 235 optimal weight: 0.7980 chunk 177 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 147 ASN ** K 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 147 ASN P 147 ASN ** W 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1656 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= 0.169 Angle : 0.354 4.414 45064 Z= 0.191 Chirality : 0.030 0.118 4840 Planarity : 0.002 0.027 5944 Dihedral : 3.674 55.290 4468 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 4.81 % Allowed : 21.75 % Favored : 73.43 % 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: 4.22 (0.08), residues: 3216 sheet: None (None), residues: 0 loop : -0.39 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 90 HIS 0.002 0.000 HIS Y 182 PHE 0.009 0.001 PHE L 129 TYR 0.008 0.001 TYR R 31 ARG 0.004 0.000 ARG U 121 *********************** 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 801 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 635 time to evaluate : 3.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ASP cc_start: 0.8081 (m-30) cc_final: 0.7813 (m-30) REVERT: A 128 ASP cc_start: 0.7694 (OUTLIER) cc_final: 0.7460 (t70) REVERT: B 70 GLN cc_start: 0.9059 (OUTLIER) cc_final: 0.7901 (tt0) REVERT: C 68 GLU cc_start: 0.7567 (mt-10) cc_final: 0.7298 (mt-10) REVERT: C 72 ASP cc_start: 0.8135 (m-30) cc_final: 0.7810 (m-30) REVERT: D 72 ASP cc_start: 0.8164 (m-30) cc_final: 0.7893 (m-30) REVERT: E 72 ASP cc_start: 0.8211 (m-30) cc_final: 0.7946 (m-30) REVERT: F 72 ASP cc_start: 0.8166 (m-30) cc_final: 0.7894 (m-30) REVERT: F 104 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7696 (mm-30) REVERT: I 72 ASP cc_start: 0.8088 (m-30) cc_final: 0.7833 (m-30) REVERT: I 128 ASP cc_start: 0.7594 (OUTLIER) cc_final: 0.7351 (t70) REVERT: J 70 GLN cc_start: 0.9111 (OUTLIER) cc_final: 0.7567 (tp40) REVERT: J 72 ASP cc_start: 0.8239 (m-30) cc_final: 0.7978 (m-30) REVERT: J 128 ASP cc_start: 0.7603 (OUTLIER) cc_final: 0.7364 (t0) REVERT: J 138 GLU cc_start: 0.8508 (tp30) cc_final: 0.8300 (tp30) REVERT: K 181 LYS cc_start: 0.7528 (OUTLIER) cc_final: 0.7233 (mmmt) REVERT: L 72 ASP cc_start: 0.8173 (m-30) cc_final: 0.7881 (m-30) REVERT: M 72 ASP cc_start: 0.8225 (m-30) cc_final: 0.7929 (m-30) REVERT: M 181 LYS cc_start: 0.7309 (OUTLIER) cc_final: 0.7037 (mmmt) REVERT: N 72 ASP cc_start: 0.8156 (m-30) cc_final: 0.7824 (m-30) REVERT: N 128 ASP cc_start: 0.7636 (OUTLIER) cc_final: 0.7373 (t70) REVERT: N 181 LYS cc_start: 0.7377 (OUTLIER) cc_final: 0.7082 (mmmt) REVERT: O 169 SER cc_start: 0.8547 (OUTLIER) cc_final: 0.8028 (p) REVERT: P 9 TYR cc_start: 0.9107 (OUTLIER) cc_final: 0.8603 (t80) REVERT: P 70 GLN cc_start: 0.9082 (OUTLIER) cc_final: 0.7792 (tt0) REVERT: P 72 ASP cc_start: 0.8263 (m-30) cc_final: 0.7954 (m-30) REVERT: Q 72 ASP cc_start: 0.8189 (m-30) cc_final: 0.7846 (m-30) REVERT: R 72 ASP cc_start: 0.8161 (m-30) cc_final: 0.7872 (m-30) REVERT: R 181 LYS cc_start: 0.7550 (OUTLIER) cc_final: 0.7308 (mmmt) REVERT: S 72 ASP cc_start: 0.8257 (m-30) cc_final: 0.7989 (m-30) REVERT: S 181 LYS cc_start: 0.7580 (OUTLIER) cc_final: 0.7320 (mmmt) REVERT: T 128 ASP cc_start: 0.7604 (OUTLIER) cc_final: 0.7345 (t0) REVERT: U 68 GLU cc_start: 0.7539 (mt-10) cc_final: 0.7179 (mt-10) REVERT: V 9 TYR cc_start: 0.9122 (OUTLIER) cc_final: 0.8434 (t80) REVERT: V 70 GLN cc_start: 0.9117 (OUTLIER) cc_final: 0.7869 (tt0) REVERT: V 72 ASP cc_start: 0.8243 (m-30) cc_final: 0.7968 (m-30) REVERT: W 72 ASP cc_start: 0.8205 (m-30) cc_final: 0.7926 (m-30) REVERT: X 72 ASP cc_start: 0.8196 (m-30) cc_final: 0.7853 (m-30) REVERT: X 181 LYS cc_start: 0.7414 (OUTLIER) cc_final: 0.7184 (mmmt) REVERT: Y 9 TYR cc_start: 0.9093 (OUTLIER) cc_final: 0.8479 (t80) REVERT: Y 72 ASP cc_start: 0.8114 (m-30) cc_final: 0.7859 (m-30) REVERT: Y 89 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7389 (mt-10) REVERT: Y 181 LYS cc_start: 0.7506 (OUTLIER) cc_final: 0.7274 (tptp) REVERT: Z 72 ASP cc_start: 0.8183 (m-30) cc_final: 0.7886 (m-30) outliers start: 166 outliers final: 125 residues processed: 736 average time/residue: 1.4525 time to fit residues: 1265.7851 Evaluate side-chains 759 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 613 time to evaluate : 3.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 70 GLN Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain C residue 3 SER Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 42 ASP Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 33 SER Chi-restraints excluded: chain F residue 42 ASP Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 132 SER Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 42 ASP Chi-restraints excluded: chain I residue 126 LEU Chi-restraints excluded: chain I residue 128 ASP Chi-restraints excluded: chain J residue 3 SER Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain J residue 70 GLN Chi-restraints excluded: chain J residue 86 SER Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 128 ASP Chi-restraints excluded: chain J residue 181 LYS Chi-restraints excluded: chain J residue 182 HIS Chi-restraints excluded: chain K residue 3 SER Chi-restraints excluded: chain K residue 10 SER Chi-restraints excluded: chain K residue 57 GLU Chi-restraints excluded: chain K residue 86 SER Chi-restraints excluded: chain K residue 119 SER Chi-restraints excluded: chain K residue 181 LYS Chi-restraints excluded: chain L residue 3 SER Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 119 SER Chi-restraints excluded: chain L residue 126 LEU Chi-restraints excluded: chain M residue 3 SER Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 42 ASP Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 86 SER Chi-restraints excluded: chain M residue 181 LYS Chi-restraints excluded: chain N residue 10 SER Chi-restraints excluded: chain N residue 86 SER Chi-restraints excluded: chain N residue 126 LEU Chi-restraints excluded: chain N residue 128 ASP Chi-restraints excluded: chain N residue 181 LYS Chi-restraints excluded: chain O residue 10 SER Chi-restraints excluded: chain O residue 33 SER Chi-restraints excluded: chain O residue 57 GLU Chi-restraints excluded: chain O residue 86 SER Chi-restraints excluded: chain O residue 126 LEU Chi-restraints excluded: chain O residue 138 GLU Chi-restraints excluded: chain O residue 169 SER Chi-restraints excluded: chain P residue 3 SER Chi-restraints excluded: chain P residue 9 TYR Chi-restraints excluded: chain P residue 10 SER Chi-restraints excluded: chain P residue 33 SER Chi-restraints excluded: chain P residue 42 ASP Chi-restraints excluded: chain P residue 57 GLU Chi-restraints excluded: chain P residue 70 GLN Chi-restraints excluded: chain P residue 86 SER Chi-restraints excluded: chain P residue 119 SER Chi-restraints excluded: chain P residue 126 LEU Chi-restraints excluded: chain P residue 181 LYS Chi-restraints excluded: chain Q residue 3 SER Chi-restraints excluded: chain Q residue 10 SER Chi-restraints excluded: chain Q residue 33 SER Chi-restraints excluded: chain Q residue 119 SER Chi-restraints excluded: chain Q residue 169 SER Chi-restraints excluded: chain R residue 3 SER Chi-restraints excluded: chain R residue 10 SER Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 42 ASP Chi-restraints excluded: chain R residue 86 SER Chi-restraints excluded: chain R residue 119 SER Chi-restraints excluded: chain R residue 126 LEU Chi-restraints excluded: chain R residue 181 LYS Chi-restraints excluded: chain S residue 3 SER Chi-restraints excluded: chain S residue 10 SER Chi-restraints excluded: chain S residue 33 SER Chi-restraints excluded: chain S residue 86 SER Chi-restraints excluded: chain S residue 119 SER Chi-restraints excluded: chain S residue 181 LYS Chi-restraints excluded: chain T residue 10 SER Chi-restraints excluded: chain T residue 119 SER Chi-restraints excluded: chain T residue 128 ASP Chi-restraints excluded: chain U residue 10 SER Chi-restraints excluded: chain U residue 42 ASP Chi-restraints excluded: chain U residue 119 SER Chi-restraints excluded: chain U residue 126 LEU Chi-restraints excluded: chain U residue 181 LYS Chi-restraints excluded: chain V residue 3 SER Chi-restraints excluded: chain V residue 9 TYR Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain V residue 42 ASP Chi-restraints excluded: chain V residue 57 GLU Chi-restraints excluded: chain V residue 70 GLN Chi-restraints excluded: chain V residue 86 SER Chi-restraints excluded: chain V residue 126 LEU Chi-restraints excluded: chain W residue 3 SER Chi-restraints excluded: chain W residue 57 GLU Chi-restraints excluded: chain W residue 86 SER Chi-restraints excluded: chain W residue 119 SER Chi-restraints excluded: chain W residue 126 LEU Chi-restraints excluded: chain W residue 138 GLU Chi-restraints excluded: chain W residue 181 LYS Chi-restraints excluded: chain X residue 3 SER Chi-restraints excluded: chain X residue 42 ASP Chi-restraints excluded: chain X residue 57 GLU Chi-restraints excluded: chain X residue 78 LEU Chi-restraints excluded: chain X residue 88 ASP Chi-restraints excluded: chain X residue 119 SER Chi-restraints excluded: chain X residue 126 LEU Chi-restraints excluded: chain X residue 181 LYS Chi-restraints excluded: chain Y residue 3 SER Chi-restraints excluded: chain Y residue 9 TYR Chi-restraints excluded: chain Y residue 10 SER Chi-restraints excluded: chain Y residue 42 ASP Chi-restraints excluded: chain Y residue 88 ASP Chi-restraints excluded: chain Y residue 89 GLU Chi-restraints excluded: chain Y residue 181 LYS Chi-restraints excluded: chain Z residue 42 ASP Chi-restraints excluded: chain Z residue 57 GLU Chi-restraints excluded: chain Z residue 86 SER Chi-restraints excluded: chain Z residue 126 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 238 optimal weight: 0.7980 chunk 153 optimal weight: 2.9990 chunk 230 optimal weight: 1.9990 chunk 116 optimal weight: 0.0170 chunk 75 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 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: 4.9990 overall best weight: 0.9220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 147 ASN ** K 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 147 ASN ** O 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 147 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 33560 Z= 0.153 Angle : 0.349 4.247 45064 Z= 0.189 Chirality : 0.030 0.118 4840 Planarity : 0.002 0.032 5944 Dihedral : 3.665 58.587 4468 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 4.99 % Allowed : 21.87 % Favored : 73.14 % 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: 5.30 (0.13), residues: 3976 helix: 4.27 (0.09), residues: 3216 sheet: None (None), residues: 0 loop : -0.40 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 90 HIS 0.002 0.000 HIS C 50 PHE 0.009 0.001 PHE L 129 TYR 0.010 0.001 TYR A 31 ARG 0.009 0.000 ARG U 76 *********************** 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 808 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 636 time to evaluate : 3.970 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 ASP cc_start: 0.8087 (m-30) cc_final: 0.7832 (m-30) REVERT: B 40 ARG cc_start: 0.6989 (mtp85) cc_final: 0.6701 (mtp85) REVERT: B 70 GLN cc_start: 0.9058 (OUTLIER) cc_final: 0.7723 (tp-100) REVERT: C 72 ASP cc_start: 0.8123 (m-30) cc_final: 0.7807 (m-30) REVERT: D 72 ASP cc_start: 0.8203 (m-30) cc_final: 0.7872 (m-30) REVERT: E 72 ASP cc_start: 0.8200 (m-30) cc_final: 0.7921 (m-30) REVERT: F 72 ASP cc_start: 0.8174 (m-30) cc_final: 0.7871 (m-30) REVERT: F 104 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7686 (mm-30) REVERT: I 72 ASP cc_start: 0.8097 (m-30) cc_final: 0.7878 (m-30) REVERT: I 128 ASP cc_start: 0.7594 (OUTLIER) cc_final: 0.7343 (t70) REVERT: I 138 GLU cc_start: 0.8546 (tp30) cc_final: 0.8323 (tp30) REVERT: J 9 TYR cc_start: 0.9110 (OUTLIER) cc_final: 0.8313 (t80) REVERT: J 70 GLN cc_start: 0.9112 (OUTLIER) cc_final: 0.7414 (tp40) REVERT: J 72 ASP cc_start: 0.8227 (m-30) cc_final: 0.7972 (m-30) REVERT: J 128 ASP cc_start: 0.7605 (OUTLIER) cc_final: 0.7344 (t0) REVERT: J 138 GLU cc_start: 0.8455 (tp30) cc_final: 0.8236 (tp30) REVERT: K 181 LYS cc_start: 0.7516 (OUTLIER) cc_final: 0.7226 (mmmt) REVERT: L 72 ASP cc_start: 0.8159 (m-30) cc_final: 0.7824 (m-30) REVERT: M 72 ASP cc_start: 0.8220 (m-30) cc_final: 0.7933 (m-30) REVERT: M 181 LYS cc_start: 0.7337 (OUTLIER) cc_final: 0.7059 (mmmt) REVERT: N 72 ASP cc_start: 0.8183 (m-30) cc_final: 0.7874 (m-30) REVERT: N 128 ASP cc_start: 0.7639 (OUTLIER) cc_final: 0.7368 (t70) REVERT: N 181 LYS cc_start: 0.7418 (OUTLIER) cc_final: 0.7147 (mmmt) REVERT: O 169 SER cc_start: 0.8538 (OUTLIER) cc_final: 0.8020 (p) REVERT: P 9 TYR cc_start: 0.9109 (OUTLIER) cc_final: 0.8589 (t80) REVERT: P 70 GLN cc_start: 0.9086 (OUTLIER) cc_final: 0.7786 (tt0) REVERT: P 72 ASP cc_start: 0.8250 (m-30) cc_final: 0.7956 (m-30) REVERT: P 119 SER cc_start: 0.9137 (OUTLIER) cc_final: 0.8914 (m) REVERT: Q 72 ASP cc_start: 0.8176 (m-30) cc_final: 0.7873 (m-30) REVERT: R 72 ASP cc_start: 0.8199 (m-30) cc_final: 0.7916 (m-30) REVERT: R 181 LYS cc_start: 0.7518 (OUTLIER) cc_final: 0.7279 (mmmt) REVERT: S 72 ASP cc_start: 0.8245 (m-30) cc_final: 0.7969 (m-30) REVERT: T 119 SER cc_start: 0.9178 (OUTLIER) cc_final: 0.8974 (m) REVERT: T 128 ASP cc_start: 0.7599 (OUTLIER) cc_final: 0.7338 (t0) REVERT: U 181 LYS cc_start: 0.7597 (OUTLIER) cc_final: 0.7364 (mmmt) REVERT: V 9 TYR cc_start: 0.9116 (OUTLIER) cc_final: 0.8429 (t80) REVERT: V 70 GLN cc_start: 0.9117 (OUTLIER) cc_final: 0.7869 (tt0) REVERT: V 72 ASP cc_start: 0.8232 (m-30) cc_final: 0.7959 (m-30) REVERT: W 72 ASP cc_start: 0.8213 (m-30) cc_final: 0.7924 (m-30) REVERT: X 72 ASP cc_start: 0.8180 (m-30) cc_final: 0.7876 (m-30) REVERT: Y 9 TYR cc_start: 0.9091 (OUTLIER) cc_final: 0.8470 (t80) REVERT: Y 72 ASP cc_start: 0.8124 (m-30) cc_final: 0.7832 (m-30) REVERT: Y 89 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7394 (mt-10) REVERT: Z 72 ASP cc_start: 0.8168 (m-30) cc_final: 0.7906 (m-30) outliers start: 172 outliers final: 126 residues processed: 739 average time/residue: 1.4970 time to fit residues: 1308.7657 Evaluate side-chains 746 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 599 time to evaluate : 3.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 70 GLN Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain C residue 3 SER Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 42 ASP Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 33 SER Chi-restraints excluded: chain F residue 42 ASP Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 132 SER Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 42 ASP Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 126 LEU Chi-restraints excluded: chain I residue 128 ASP Chi-restraints excluded: chain J residue 3 SER Chi-restraints excluded: chain J residue 9 TYR Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain J residue 70 GLN Chi-restraints excluded: chain J residue 86 SER Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 128 ASP Chi-restraints excluded: chain J residue 181 LYS Chi-restraints excluded: chain J residue 182 HIS Chi-restraints excluded: chain K residue 3 SER Chi-restraints excluded: chain K residue 10 SER Chi-restraints excluded: chain K residue 57 GLU Chi-restraints excluded: chain K residue 86 SER Chi-restraints excluded: chain K residue 119 SER Chi-restraints excluded: chain K residue 181 LYS Chi-restraints excluded: chain L residue 3 SER Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 33 SER Chi-restraints excluded: chain L residue 42 ASP Chi-restraints excluded: chain L residue 126 LEU Chi-restraints excluded: chain M residue 3 SER Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 42 ASP Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 86 SER Chi-restraints excluded: chain M residue 181 LYS Chi-restraints excluded: chain N residue 10 SER Chi-restraints excluded: chain N residue 33 SER Chi-restraints excluded: chain N residue 42 ASP Chi-restraints excluded: chain N residue 57 GLU Chi-restraints excluded: chain N residue 86 SER Chi-restraints excluded: chain N residue 126 LEU Chi-restraints excluded: chain N residue 128 ASP Chi-restraints excluded: chain N residue 181 LYS Chi-restraints excluded: chain O residue 10 SER Chi-restraints excluded: chain O residue 33 SER Chi-restraints excluded: chain O residue 57 GLU Chi-restraints excluded: chain O residue 86 SER Chi-restraints excluded: chain O residue 126 LEU Chi-restraints excluded: chain O residue 138 GLU Chi-restraints excluded: chain O residue 169 SER Chi-restraints excluded: chain P residue 3 SER Chi-restraints excluded: chain P residue 9 TYR Chi-restraints excluded: chain P residue 10 SER Chi-restraints excluded: chain P residue 33 SER Chi-restraints excluded: chain P residue 42 ASP Chi-restraints excluded: chain P residue 70 GLN Chi-restraints excluded: chain P residue 86 SER Chi-restraints excluded: chain P residue 119 SER Chi-restraints excluded: chain P residue 126 LEU Chi-restraints excluded: chain P residue 181 LYS Chi-restraints excluded: chain Q residue 3 SER Chi-restraints excluded: chain Q residue 10 SER Chi-restraints excluded: chain Q residue 33 SER Chi-restraints excluded: chain Q residue 119 SER Chi-restraints excluded: chain Q residue 126 LEU Chi-restraints excluded: chain Q residue 169 SER Chi-restraints excluded: chain R residue 3 SER Chi-restraints excluded: chain R residue 10 SER Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 42 ASP Chi-restraints excluded: chain R residue 57 GLU Chi-restraints excluded: chain R residue 86 SER Chi-restraints excluded: chain R residue 126 LEU Chi-restraints excluded: chain R residue 181 LYS Chi-restraints excluded: chain S residue 3 SER Chi-restraints excluded: chain S residue 10 SER Chi-restraints excluded: chain S residue 33 SER Chi-restraints excluded: chain S residue 42 ASP Chi-restraints excluded: chain S residue 57 GLU Chi-restraints excluded: chain S residue 86 SER Chi-restraints excluded: chain S residue 119 SER Chi-restraints excluded: chain T residue 10 SER Chi-restraints excluded: chain T residue 119 SER Chi-restraints excluded: chain T residue 128 ASP Chi-restraints excluded: chain U residue 10 SER Chi-restraints excluded: chain U residue 42 ASP Chi-restraints excluded: chain U residue 126 LEU Chi-restraints excluded: chain U residue 181 LYS Chi-restraints excluded: chain V residue 3 SER Chi-restraints excluded: chain V residue 9 TYR Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain V residue 33 SER Chi-restraints excluded: chain V residue 57 GLU Chi-restraints excluded: chain V residue 70 GLN Chi-restraints excluded: chain V residue 86 SER Chi-restraints excluded: chain V residue 119 SER Chi-restraints excluded: chain V residue 126 LEU Chi-restraints excluded: chain W residue 3 SER Chi-restraints excluded: chain W residue 57 GLU Chi-restraints excluded: chain W residue 86 SER Chi-restraints excluded: chain W residue 119 SER Chi-restraints excluded: chain W residue 126 LEU Chi-restraints excluded: chain W residue 181 LYS Chi-restraints excluded: chain X residue 3 SER Chi-restraints excluded: chain X residue 42 ASP Chi-restraints excluded: chain X residue 57 GLU Chi-restraints excluded: chain X residue 78 LEU Chi-restraints excluded: chain X residue 119 SER Chi-restraints excluded: chain X residue 126 LEU Chi-restraints excluded: chain Y residue 3 SER Chi-restraints excluded: chain Y residue 9 TYR Chi-restraints excluded: chain Y residue 10 SER Chi-restraints excluded: chain Y residue 42 ASP Chi-restraints excluded: chain Y residue 88 ASP Chi-restraints excluded: chain Y residue 89 GLU Chi-restraints excluded: chain Z residue 42 ASP Chi-restraints excluded: chain Z residue 57 GLU Chi-restraints excluded: chain Z residue 86 SER Chi-restraints excluded: chain Z residue 126 LEU 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: 0.5980 chunk 359 optimal weight: 0.7980 chunk 216 optimal weight: 6.9990 chunk 156 optimal weight: 0.7980 chunk 282 optimal weight: 6.9990 chunk 110 optimal weight: 0.9990 chunk 324 optimal weight: 2.9990 chunk 339 optimal weight: 5.9990 chunk 358 optimal weight: 7.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN C 50 HIS I 147 ASN J 147 ASN ** K 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 147 ASN O 147 ASN P 147 ASN S 147 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 33560 Z= 0.166 Angle : 0.355 4.154 45064 Z= 0.193 Chirality : 0.030 0.118 4840 Planarity : 0.002 0.027 5944 Dihedral : 3.244 12.132 4456 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 4.70 % Allowed : 22.24 % Favored : 73.06 % 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: 4.25 (0.09), residues: 3216 sheet: None (None), residues: 0 loop : -0.43 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP W 90 HIS 0.002 0.001 HIS C 50 PHE 0.009 0.001 PHE P 38 TYR 0.012 0.001 TYR A 31 ARG 0.005 0.000 ARG U 76 *********************** 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 784 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 622 time to evaluate : 4.191 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 ASP cc_start: 0.8096 (m-30) cc_final: 0.7841 (m-30) REVERT: B 70 GLN cc_start: 0.9052 (OUTLIER) cc_final: 0.7728 (tp-100) REVERT: C 72 ASP cc_start: 0.8137 (m-30) cc_final: 0.7825 (m-30) REVERT: D 72 ASP cc_start: 0.8162 (m-30) cc_final: 0.7869 (m-30) REVERT: E 72 ASP cc_start: 0.8212 (m-30) cc_final: 0.7956 (m-30) REVERT: F 72 ASP cc_start: 0.8177 (m-30) cc_final: 0.7874 (m-30) REVERT: F 104 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7693 (mm-30) REVERT: I 72 ASP cc_start: 0.8077 (m-30) cc_final: 0.7873 (m-30) REVERT: I 128 ASP cc_start: 0.7594 (OUTLIER) cc_final: 0.7353 (t70) REVERT: J 70 GLN cc_start: 0.9110 (OUTLIER) cc_final: 0.7535 (tp40) REVERT: J 72 ASP cc_start: 0.8240 (m-30) cc_final: 0.7963 (m-30) REVERT: J 128 ASP cc_start: 0.7599 (OUTLIER) cc_final: 0.7350 (t0) REVERT: K 181 LYS cc_start: 0.7521 (OUTLIER) cc_final: 0.7241 (mmmt) REVERT: L 72 ASP cc_start: 0.8168 (m-30) cc_final: 0.7876 (m-30) REVERT: M 72 ASP cc_start: 0.8230 (m-30) cc_final: 0.7939 (m-30) REVERT: M 181 LYS cc_start: 0.7332 (OUTLIER) cc_final: 0.7052 (mmmt) REVERT: N 72 ASP cc_start: 0.8191 (m-30) cc_final: 0.7876 (m-30) REVERT: N 181 LYS cc_start: 0.7457 (OUTLIER) cc_final: 0.7174 (mmmt) REVERT: O 9 TYR cc_start: 0.9109 (OUTLIER) cc_final: 0.8447 (t80) REVERT: O 169 SER cc_start: 0.8537 (OUTLIER) cc_final: 0.8018 (p) REVERT: P 9 TYR cc_start: 0.9112 (OUTLIER) cc_final: 0.8602 (t80) REVERT: P 70 GLN cc_start: 0.9083 (OUTLIER) cc_final: 0.7796 (tt0) REVERT: P 72 ASP cc_start: 0.8262 (m-30) cc_final: 0.7961 (m-30) REVERT: P 119 SER cc_start: 0.9130 (OUTLIER) cc_final: 0.8921 (m) REVERT: Q 72 ASP cc_start: 0.8183 (m-30) cc_final: 0.7869 (m-30) REVERT: R 72 ASP cc_start: 0.8184 (m-30) cc_final: 0.7918 (m-30) REVERT: R 181 LYS cc_start: 0.7529 (OUTLIER) cc_final: 0.7288 (mmmt) REVERT: S 72 ASP cc_start: 0.8257 (m-30) cc_final: 0.7975 (m-30) REVERT: T 119 SER cc_start: 0.9179 (OUTLIER) cc_final: 0.8974 (m) REVERT: T 128 ASP cc_start: 0.7601 (OUTLIER) cc_final: 0.7339 (t0) REVERT: U 181 LYS cc_start: 0.7581 (OUTLIER) cc_final: 0.7356 (mmmt) REVERT: V 9 TYR cc_start: 0.9121 (OUTLIER) cc_final: 0.8428 (t80) REVERT: V 70 GLN cc_start: 0.9115 (OUTLIER) cc_final: 0.7863 (tt0) REVERT: V 72 ASP cc_start: 0.8242 (m-30) cc_final: 0.7962 (m-30) REVERT: W 72 ASP cc_start: 0.8191 (m-30) cc_final: 0.7943 (m-30) REVERT: W 128 ASP cc_start: 0.7641 (OUTLIER) cc_final: 0.7368 (t0) REVERT: X 72 ASP cc_start: 0.8194 (m-30) cc_final: 0.7887 (m-30) REVERT: Y 9 TYR cc_start: 0.9093 (OUTLIER) cc_final: 0.8477 (t80) REVERT: Y 72 ASP cc_start: 0.8103 (m-30) cc_final: 0.7829 (m-30) REVERT: Y 89 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7395 (mt-10) REVERT: Z 72 ASP cc_start: 0.8180 (m-30) cc_final: 0.7862 (m-30) outliers start: 162 outliers final: 122 residues processed: 716 average time/residue: 1.4374 time to fit residues: 1222.8889 Evaluate side-chains 742 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 599 time to evaluate : 3.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 70 GLN Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain C residue 3 SER Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 42 ASP Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 33 SER Chi-restraints excluded: chain F residue 42 ASP Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 132 SER Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 42 ASP Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 126 LEU Chi-restraints excluded: chain I residue 128 ASP Chi-restraints excluded: chain J residue 3 SER Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain J residue 70 GLN Chi-restraints excluded: chain J residue 86 SER Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 128 ASP Chi-restraints excluded: chain J residue 181 LYS Chi-restraints excluded: chain J residue 182 HIS Chi-restraints excluded: chain K residue 3 SER Chi-restraints excluded: chain K residue 10 SER Chi-restraints excluded: chain K residue 57 GLU Chi-restraints excluded: chain K residue 86 SER Chi-restraints excluded: chain K residue 119 SER Chi-restraints excluded: chain K residue 181 LYS Chi-restraints excluded: chain L residue 3 SER Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 33 SER Chi-restraints excluded: chain L residue 42 ASP Chi-restraints excluded: chain L residue 126 LEU Chi-restraints excluded: chain M residue 3 SER Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 42 ASP Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 86 SER Chi-restraints excluded: chain M residue 181 LYS Chi-restraints excluded: chain N residue 10 SER Chi-restraints excluded: chain N residue 42 ASP Chi-restraints excluded: chain N residue 57 GLU Chi-restraints excluded: chain N residue 86 SER Chi-restraints excluded: chain N residue 126 LEU Chi-restraints excluded: chain N residue 181 LYS Chi-restraints excluded: chain O residue 9 TYR Chi-restraints excluded: chain O residue 10 SER Chi-restraints excluded: chain O residue 33 SER Chi-restraints excluded: chain O residue 57 GLU Chi-restraints excluded: chain O residue 86 SER Chi-restraints excluded: chain O residue 126 LEU Chi-restraints excluded: chain O residue 138 GLU Chi-restraints excluded: chain O residue 169 SER Chi-restraints excluded: chain P residue 3 SER Chi-restraints excluded: chain P residue 9 TYR Chi-restraints excluded: chain P residue 10 SER Chi-restraints excluded: chain P residue 33 SER Chi-restraints excluded: chain P residue 42 ASP Chi-restraints excluded: chain P residue 57 GLU Chi-restraints excluded: chain P residue 70 GLN Chi-restraints excluded: chain P residue 86 SER Chi-restraints excluded: chain P residue 119 SER Chi-restraints excluded: chain P residue 126 LEU Chi-restraints excluded: chain P residue 181 LYS Chi-restraints excluded: chain Q residue 3 SER Chi-restraints excluded: chain Q residue 10 SER Chi-restraints excluded: chain Q residue 33 SER Chi-restraints excluded: chain Q residue 119 SER Chi-restraints excluded: chain Q residue 126 LEU Chi-restraints excluded: chain Q residue 169 SER Chi-restraints excluded: chain R residue 3 SER Chi-restraints excluded: chain R residue 10 SER Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 42 ASP Chi-restraints excluded: chain R residue 86 SER Chi-restraints excluded: chain R residue 126 LEU Chi-restraints excluded: chain R residue 181 LYS Chi-restraints excluded: chain S residue 3 SER Chi-restraints excluded: chain S residue 10 SER Chi-restraints excluded: chain S residue 33 SER Chi-restraints excluded: chain S residue 42 ASP Chi-restraints excluded: chain S residue 57 GLU Chi-restraints excluded: chain S residue 86 SER Chi-restraints excluded: chain T residue 10 SER Chi-restraints excluded: chain T residue 119 SER Chi-restraints excluded: chain T residue 128 ASP Chi-restraints excluded: chain U residue 10 SER Chi-restraints excluded: chain U residue 42 ASP Chi-restraints excluded: chain U residue 126 LEU Chi-restraints excluded: chain U residue 181 LYS Chi-restraints excluded: chain V residue 9 TYR Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain V residue 33 SER Chi-restraints excluded: chain V residue 70 GLN Chi-restraints excluded: chain V residue 86 SER Chi-restraints excluded: chain V residue 126 LEU Chi-restraints excluded: chain W residue 3 SER Chi-restraints excluded: chain W residue 42 ASP Chi-restraints excluded: chain W residue 57 GLU Chi-restraints excluded: chain W residue 86 SER Chi-restraints excluded: chain W residue 126 LEU Chi-restraints excluded: chain W residue 128 ASP Chi-restraints excluded: chain W residue 181 LYS Chi-restraints excluded: chain X residue 3 SER Chi-restraints excluded: chain X residue 42 ASP Chi-restraints excluded: chain X residue 57 GLU Chi-restraints excluded: chain X residue 78 LEU Chi-restraints excluded: chain X residue 88 ASP Chi-restraints excluded: chain X residue 119 SER Chi-restraints excluded: chain X residue 126 LEU Chi-restraints excluded: chain Y residue 3 SER Chi-restraints excluded: chain Y residue 9 TYR Chi-restraints excluded: chain Y residue 10 SER Chi-restraints excluded: chain Y residue 42 ASP Chi-restraints excluded: chain Y residue 88 ASP Chi-restraints excluded: chain Y residue 89 GLU Chi-restraints excluded: chain Z residue 42 ASP Chi-restraints excluded: chain Z residue 57 GLU Chi-restraints excluded: chain Z residue 86 SER Chi-restraints excluded: chain Z residue 126 LEU 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: 4.9990 chunk 180 optimal weight: 0.6980 chunk 264 optimal weight: 0.9990 chunk 398 optimal weight: 0.7980 chunk 366 optimal weight: 3.9990 chunk 317 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 245 optimal weight: 0.9980 chunk 194 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN B 50 HIS E 50 HIS J 147 ASN ** K 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 147 ASN O 50 HIS ** O 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 50 HIS P 147 ASN S 147 ASN X 50 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1775 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= 0.153 Angle : 0.355 4.244 45064 Z= 0.194 Chirality : 0.030 0.118 4840 Planarity : 0.002 0.037 5944 Dihedral : 3.233 12.073 4456 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 4.29 % Allowed : 23.11 % Favored : 72.59 % 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: 5.30 (0.13), residues: 3976 helix: 4.27 (0.09), residues: 3216 sheet: None (None), residues: 0 loop : -0.43 (0.20), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP N 90 HIS 0.002 0.000 HIS X 50 PHE 0.009 0.001 PHE W 51 TYR 0.017 0.001 TYR A 31 ARG 0.008 0.000 ARG V 40 ********************** 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 759 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 611 time to evaluate : 3.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ASP cc_start: 0.8066 (m-30) cc_final: 0.7822 (m-30) REVERT: B 70 GLN cc_start: 0.9051 (OUTLIER) cc_final: 0.7726 (tp-100) REVERT: C 72 ASP cc_start: 0.8143 (m-30) cc_final: 0.7847 (m-30) REVERT: D 72 ASP cc_start: 0.8198 (m-30) cc_final: 0.7869 (m-30) REVERT: E 9 TYR cc_start: 0.9106 (OUTLIER) cc_final: 0.8481 (t80) REVERT: E 72 ASP cc_start: 0.8201 (m-30) cc_final: 0.7926 (m-30) REVERT: F 72 ASP cc_start: 0.8160 (m-30) cc_final: 0.7885 (m-30) REVERT: F 104 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7681 (mm-30) REVERT: I 72 ASP cc_start: 0.8074 (m-30) cc_final: 0.7816 (m-30) REVERT: I 128 ASP cc_start: 0.7595 (OUTLIER) cc_final: 0.7344 (t70) REVERT: J 9 TYR cc_start: 0.9109 (OUTLIER) cc_final: 0.8310 (t80) REVERT: J 70 GLN cc_start: 0.9110 (OUTLIER) cc_final: 0.7418 (tp40) REVERT: J 72 ASP cc_start: 0.8222 (m-30) cc_final: 0.7950 (m-30) REVERT: J 128 ASP cc_start: 0.7599 (OUTLIER) cc_final: 0.7346 (t0) REVERT: K 181 LYS cc_start: 0.7493 (OUTLIER) cc_final: 0.7209 (mmmt) REVERT: L 72 ASP cc_start: 0.8161 (m-30) cc_final: 0.7828 (m-30) REVERT: M 72 ASP cc_start: 0.8224 (m-30) cc_final: 0.7965 (m-30) REVERT: M 181 LYS cc_start: 0.7289 (OUTLIER) cc_final: 0.7045 (mmmt) REVERT: N 72 ASP cc_start: 0.8178 (m-30) cc_final: 0.7900 (m-30) REVERT: N 181 LYS cc_start: 0.7451 (OUTLIER) cc_final: 0.7185 (mmmt) REVERT: O 9 TYR cc_start: 0.9111 (OUTLIER) cc_final: 0.8444 (t80) REVERT: O 169 SER cc_start: 0.8528 (OUTLIER) cc_final: 0.8011 (p) REVERT: P 9 TYR cc_start: 0.9112 (OUTLIER) cc_final: 0.8593 (t80) REVERT: P 70 GLN cc_start: 0.9084 (OUTLIER) cc_final: 0.7785 (tt0) REVERT: P 72 ASP cc_start: 0.8253 (m-30) cc_final: 0.7934 (m-30) REVERT: Q 72 ASP cc_start: 0.8172 (m-30) cc_final: 0.7889 (m-30) REVERT: R 72 ASP cc_start: 0.8173 (m-30) cc_final: 0.7890 (m-30) REVERT: R 181 LYS cc_start: 0.7527 (OUTLIER) cc_final: 0.7290 (mmmt) REVERT: S 72 ASP cc_start: 0.8245 (m-30) cc_final: 0.7978 (m-30) REVERT: T 119 SER cc_start: 0.9170 (OUTLIER) cc_final: 0.8960 (m) REVERT: T 128 ASP cc_start: 0.7597 (OUTLIER) cc_final: 0.7338 (t0) REVERT: U 181 LYS cc_start: 0.7642 (OUTLIER) cc_final: 0.7392 (mmmt) REVERT: V 9 TYR cc_start: 0.9116 (OUTLIER) cc_final: 0.8527 (t80) REVERT: V 70 GLN cc_start: 0.9117 (OUTLIER) cc_final: 0.7868 (tt0) REVERT: V 72 ASP cc_start: 0.8230 (m-30) cc_final: 0.7936 (m-30) REVERT: W 72 ASP cc_start: 0.8210 (m-30) cc_final: 0.7944 (m-30) REVERT: W 128 ASP cc_start: 0.7634 (OUTLIER) cc_final: 0.7362 (t0) REVERT: X 72 ASP cc_start: 0.8170 (m-30) cc_final: 0.7871 (m-30) REVERT: X 89 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7363 (mt-10) REVERT: Y 9 TYR cc_start: 0.9091 (OUTLIER) cc_final: 0.8469 (t80) REVERT: Y 72 ASP cc_start: 0.8116 (m-30) cc_final: 0.7829 (m-30) REVERT: Y 89 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7406 (mt-10) REVERT: Z 72 ASP cc_start: 0.8169 (m-30) cc_final: 0.7886 (m-30) outliers start: 148 outliers final: 116 residues processed: 693 average time/residue: 1.4267 time to fit residues: 1177.1793 Evaluate side-chains 730 residues out of total 3448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 592 time to evaluate : 3.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 70 GLN Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain E residue 9 TYR Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 42 ASP Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 33 SER Chi-restraints excluded: chain F residue 42 ASP Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 42 ASP Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 126 LEU Chi-restraints excluded: chain I residue 128 ASP Chi-restraints excluded: chain J residue 3 SER Chi-restraints excluded: chain J residue 9 TYR Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain J residue 70 GLN Chi-restraints excluded: chain J residue 86 SER Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 128 ASP Chi-restraints excluded: chain J residue 181 LYS Chi-restraints excluded: chain J residue 182 HIS Chi-restraints excluded: chain K residue 3 SER Chi-restraints excluded: chain K residue 10 SER Chi-restraints excluded: chain K residue 57 GLU Chi-restraints excluded: chain K residue 86 SER Chi-restraints excluded: chain K residue 181 LYS Chi-restraints excluded: chain L residue 3 SER Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 33 SER Chi-restraints excluded: chain L residue 42 ASP Chi-restraints excluded: chain L residue 126 LEU Chi-restraints excluded: chain M residue 3 SER Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 42 ASP Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 86 SER Chi-restraints excluded: chain M residue 181 LYS Chi-restraints excluded: chain N residue 10 SER Chi-restraints excluded: chain N residue 33 SER Chi-restraints excluded: chain N residue 42 ASP Chi-restraints excluded: chain N residue 57 GLU Chi-restraints excluded: chain N residue 86 SER Chi-restraints excluded: chain N residue 126 LEU Chi-restraints excluded: chain N residue 181 LYS Chi-restraints excluded: chain O residue 9 TYR Chi-restraints excluded: chain O residue 10 SER Chi-restraints excluded: chain O residue 33 SER Chi-restraints excluded: chain O residue 57 GLU Chi-restraints excluded: chain O residue 86 SER Chi-restraints excluded: chain O residue 126 LEU Chi-restraints excluded: chain O residue 138 GLU Chi-restraints excluded: chain O residue 169 SER Chi-restraints excluded: chain P residue 3 SER Chi-restraints excluded: chain P residue 9 TYR Chi-restraints excluded: chain P residue 10 SER Chi-restraints excluded: chain P residue 33 SER Chi-restraints excluded: chain P residue 57 GLU Chi-restraints excluded: chain P residue 70 GLN Chi-restraints excluded: chain P residue 86 SER Chi-restraints excluded: chain P residue 126 LEU Chi-restraints excluded: chain P residue 181 LYS Chi-restraints excluded: chain Q residue 3 SER Chi-restraints excluded: chain Q residue 10 SER Chi-restraints excluded: chain Q residue 33 SER Chi-restraints excluded: chain Q residue 42 ASP Chi-restraints excluded: chain Q residue 126 LEU Chi-restraints excluded: chain Q residue 169 SER Chi-restraints excluded: chain R residue 3 SER Chi-restraints excluded: chain R residue 10 SER Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 42 ASP Chi-restraints excluded: chain R residue 57 GLU Chi-restraints excluded: chain R residue 86 SER Chi-restraints excluded: chain R residue 126 LEU Chi-restraints excluded: chain R residue 181 LYS Chi-restraints excluded: chain S residue 3 SER Chi-restraints excluded: chain S residue 10 SER Chi-restraints excluded: chain S residue 33 SER Chi-restraints excluded: chain S residue 42 ASP Chi-restraints excluded: chain S residue 57 GLU Chi-restraints excluded: chain S residue 86 SER Chi-restraints excluded: chain T residue 10 SER Chi-restraints excluded: chain T residue 119 SER Chi-restraints excluded: chain T residue 128 ASP Chi-restraints excluded: chain U residue 10 SER Chi-restraints excluded: chain U residue 42 ASP Chi-restraints excluded: chain U residue 126 LEU Chi-restraints excluded: chain U residue 181 LYS Chi-restraints excluded: chain V residue 9 TYR Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain V residue 33 SER Chi-restraints excluded: chain V residue 70 GLN Chi-restraints excluded: chain V residue 86 SER Chi-restraints excluded: chain V residue 126 LEU Chi-restraints excluded: chain W residue 3 SER Chi-restraints excluded: chain W residue 42 ASP Chi-restraints excluded: chain W residue 57 GLU Chi-restraints excluded: chain W residue 86 SER Chi-restraints excluded: chain W residue 126 LEU Chi-restraints excluded: chain W residue 128 ASP Chi-restraints excluded: chain W residue 181 LYS Chi-restraints excluded: chain X residue 3 SER Chi-restraints excluded: chain X residue 42 ASP Chi-restraints excluded: chain X residue 57 GLU Chi-restraints excluded: chain X residue 78 LEU Chi-restraints excluded: chain X residue 88 ASP Chi-restraints excluded: chain X residue 126 LEU Chi-restraints excluded: chain Y residue 3 SER Chi-restraints excluded: chain Y residue 9 TYR Chi-restraints excluded: chain Y residue 10 SER Chi-restraints excluded: chain Y residue 42 ASP Chi-restraints excluded: chain Y residue 89 GLU Chi-restraints excluded: chain Z residue 42 ASP Chi-restraints excluded: chain Z residue 57 GLU Chi-restraints excluded: chain Z residue 86 SER Chi-restraints excluded: chain Z residue 126 LEU 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: 0.6980 chunk 97 optimal weight: 6.9990 chunk 292 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 88 optimal weight: 0.0030 chunk 317 optimal weight: 5.9990 chunk 133 optimal weight: 0.6980 chunk 326 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 58 optimal weight: 0.1980 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS I 147 ASN J 147 ASN K 50 HIS L 50 HIS M 50 HIS M 147 ASN ** O 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 147 ASN Q 50 HIS S 147 ASN T 50 HIS U 50 HIS Y 147 ASN Z 50 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.104548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.093389 restraints weight = 41204.896| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 1.90 r_work: 0.2849 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2688 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2688 r_free = 0.2688 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2626 r_free = 0.2626 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2626 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 33560 Z= 0.113 Angle : 0.338 4.543 45064 Z= 0.186 Chirality : 0.029 0.118 4840 Planarity : 0.002 0.027 5944 Dihedral : 3.155 11.979 4456 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 3.10 % Allowed : 24.51 % Favored : 72.39 % 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: 5.38 (0.13), residues: 3976 helix: 4.34 (0.09), residues: 3216 sheet: None (None), residues: 0 loop : -0.44 (0.20), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 90 HIS 0.003 0.000 HIS L 50 PHE 0.009 0.001 PHE L 51 TYR 0.014 0.001 TYR I 31 ARG 0.007 0.000 ARG J 40 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16528.27 seconds wall clock time: 290 minutes 36.28 seconds (17436.28 seconds total)