Starting phenix.real_space_refine on Tue Feb 13 11:04:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfq_34724/02_2024/8hfq_34724_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfq_34724/02_2024/8hfq_34724.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfq_34724/02_2024/8hfq_34724.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfq_34724/02_2024/8hfq_34724.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfq_34724/02_2024/8hfq_34724_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfq_34724/02_2024/8hfq_34724_updated.pdb" } resolution = 2.64 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= 0.005 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 195 5.16 5 C 34029 2.51 5 N 9412 2.21 5 O 10557 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 23": "OE1" <-> "OE2" Residue "A ASP 77": "OD1" <-> "OD2" Residue "A TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 13": "OD1" <-> "OD2" Residue "B ASP 101": "OD1" <-> "OD2" Residue "B ASP 107": "OD1" <-> "OD2" Residue "B ASP 152": "OD1" <-> "OD2" Residue "C PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 77": "OD1" <-> "OD2" Residue "C TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 123": "OD1" <-> "OD2" Residue "C GLU 131": "OE1" <-> "OE2" Residue "D ASP 3": "OD1" <-> "OD2" Residue "E ASP 13": "OD1" <-> "OD2" Residue "E GLU 23": "OE1" <-> "OE2" Residue "E ASP 82": "OD1" <-> "OD2" Residue "E ASP 108": "OD1" <-> "OD2" Residue "E TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 123": "OD1" <-> "OD2" Residue "E TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 13": "OD1" <-> "OD2" Residue "F ASP 165": "OD1" <-> "OD2" Residue "G ASP 46": "OD1" <-> "OD2" Residue "G ASP 116": "OD1" <-> "OD2" Residue "G TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 77": "NH1" <-> "NH2" Residue "H ASP 107": "OD1" <-> "OD2" Residue "I ASP 46": "OD1" <-> "OD2" Residue "I TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 77": "OD1" <-> "OD2" Residue "I TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 117": "OE1" <-> "OE2" Residue "I TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 145": "OD1" <-> "OD2" Residue "I ASP 165": "OD1" <-> "OD2" Residue "J PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 106": "OE1" <-> "OE2" Residue "J ASP 107": "OD1" <-> "OD2" Residue "J ASP 165": "OD1" <-> "OD2" Residue "K TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 82": "OD1" <-> "OD2" Residue "K TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 117": "OE1" <-> "OE2" Residue "K PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 123": "OD1" <-> "OD2" Residue "K ASP 148": "OD1" <-> "OD2" Residue "K ASP 165": "OD1" <-> "OD2" Residue "L ASP 13": "OD1" <-> "OD2" Residue "L ASP 107": "OD1" <-> "OD2" Residue "L ASP 152": "OD1" <-> "OD2" Residue "M ASP 108": "OD1" <-> "OD2" Residue "M ASP 116": "OD1" <-> "OD2" Residue "M ASP 123": "OD1" <-> "OD2" Residue "N ASP 152": "OD1" <-> "OD2" Residue "N GLU 159": "OE1" <-> "OE2" Residue "O ASP 148": "OD1" <-> "OD2" Residue "P ASP 13": "OD1" <-> "OD2" Residue "P ASP 25": "OD1" <-> "OD2" Residue "P GLU 62": "OE1" <-> "OE2" Residue "P TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 107": "OD1" <-> "OD2" Residue "P GLU 115": "OE1" <-> "OE2" Residue "P GLU 136": "OE1" <-> "OE2" Residue "P ASP 140": "OD1" <-> "OD2" Residue "P ASP 144": "OD1" <-> "OD2" Residue "P GLU 159": "OE1" <-> "OE2" Residue "Q ASP 46": "OD1" <-> "OD2" Residue "Q TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 123": "OD1" <-> "OD2" Residue "Q ASP 165": "OD1" <-> "OD2" Residue "R TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 140": "OD1" <-> "OD2" Residue "S ASP 46": "OD1" <-> "OD2" Residue "T GLU 17": "OE1" <-> "OE2" Residue "T TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 77": "NH1" <-> "NH2" Residue "T GLU 115": "OE1" <-> "OE2" Residue "T GLU 159": "OE1" <-> "OE2" Residue "U ASP 13": "OD1" <-> "OD2" Residue "U ASP 148": "OD1" <-> "OD2" Residue "V ASP 3": "OD1" <-> "OD2" Residue "V ASP 39": "OD1" <-> "OD2" Residue "V GLU 87": "OE1" <-> "OE2" Residue "V ASP 101": "OD1" <-> "OD2" Residue "V ASP 107": "OD1" <-> "OD2" Residue "W ASP 46": "OD1" <-> "OD2" Residue "W ASP 116": "OD1" <-> "OD2" Residue "W GLU 117": "OE1" <-> "OE2" Residue "W TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 3": "OD1" <-> "OD2" Residue "X GLU 87": "OE1" <-> "OE2" Residue "Z ASP 3": "OD1" <-> "OD2" Residue "Z GLU 17": "OE1" <-> "OE2" Residue "Z GLU 106": "OE1" <-> "OE2" Residue "Z ASP 152": "OD1" <-> "OD2" Residue "a PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 82": "OD1" <-> "OD2" Residue "a GLU 117": "OE1" <-> "OE2" Residue "a ASP 123": "OD1" <-> "OD2" Residue "b TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 87": "OE1" <-> "OE2" Residue "b GLU 115": "OE1" <-> "OE2" Residue "b ASP 165": "OD1" <-> "OD2" Residue "c ASP 116": "OD1" <-> "OD2" Residue "c ASP 123": "OD1" <-> "OD2" Residue "c ASP 148": "OD1" <-> "OD2" Residue "c TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 87": "OE1" <-> "OE2" Residue "d TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 107": "OD1" <-> "OD2" Residue "d GLU 115": "OE1" <-> "OE2" Residue "d ASP 144": "OD1" <-> "OD2" Residue "d ASP 165": "OD1" <-> "OD2" Residue "e ASP 77": "OD1" <-> "OD2" Residue "e ASP 108": "OD1" <-> "OD2" Residue "e ASP 123": "OD1" <-> "OD2" Residue "e TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 165": "OD1" <-> "OD2" Residue "f TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 101": "OD1" <-> "OD2" Residue "f ASP 144": "OD1" <-> "OD2" Residue "f ASP 165": "OD1" <-> "OD2" Residue "h ASP 3": "OD1" <-> "OD2" Residue "h GLU 33": "OE1" <-> "OE2" Residue "i ASP 77": "OD1" <-> "OD2" Residue "i GLU 117": "OE1" <-> "OE2" Residue "i GLU 131": "OE1" <-> "OE2" Residue "i GLU 159": "OE1" <-> "OE2" Residue "j ASP 13": "OD1" <-> "OD2" Residue "j TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 87": "OE1" <-> "OE2" Residue "j ASP 101": "OD1" <-> "OD2" Residue "j GLU 106": "OE1" <-> "OE2" Residue "j ASP 144": "OD1" <-> "OD2" Residue "k ARG 19": "NH1" <-> "NH2" Residue "k ASP 131": "OD1" <-> "OD2" Residue "k TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ASP 178": "OD1" <-> "OD2" Residue "k GLU 183": "OE1" <-> "OE2" Residue "k TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 242": "OE1" <-> "OE2" Residue "k ARG 256": "NH1" <-> "NH2" Residue "l ARG 26": "NH1" <-> "NH2" Residue "l ASP 47": "OD1" <-> "OD2" Residue "l ARG 70": "NH1" <-> "NH2" Residue "l GLU 80": "OE1" <-> "OE2" Residue "l GLU 97": "OE1" <-> "OE2" Residue "l ASP 110": "OD1" <-> "OD2" Residue "l ASP 179": "OD1" <-> "OD2" Residue "l TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 245": "OE1" <-> "OE2" Residue "m GLU 24": "OE1" <-> "OE2" Residue "m ASP 38": "OD1" <-> "OD2" Residue "m PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 181": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 54193 Number of models: 1 Model: "" Number of chains: 76 Chain: "A" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1240 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "B" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1270 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "C" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1240 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "D" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1270 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "E" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1240 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "F" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1270 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "G" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1240 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "H" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1270 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "I" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1240 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "J" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1270 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "K" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1240 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "L" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1270 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "M" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1240 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "N" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1270 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "O" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1240 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "P" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1270 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "Q" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1240 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "R" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1270 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "S" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1240 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "T" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1270 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "U" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1240 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "V" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1270 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "W" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1240 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "X" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1270 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "Y" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1240 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "Z" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1270 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "a" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1240 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "b" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1270 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "c" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1240 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "d" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1270 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "e" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1240 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "f" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1270 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "g" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1240 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "h" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1270 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "i" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1240 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "j" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1270 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "k" Number of atoms: 2282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2282 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 13, 'TRANS': 275} Chain: "l" Number of atoms: 2164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2164 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 6, 'TRANS': 265} Chain: "m" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 626 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 5, 'TRANS': 75} Chain: "n" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1619 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 8, 'TRANS': 188} Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "a" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "c" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "e" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "g" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "h" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "i" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "j" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 21.27, per 1000 atoms: 0.39 Number of scatterers: 54193 At special positions: 0 Unit cell: (171.2, 180.83, 182.97, 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 195 16.00 O 10557 8.00 N 9412 7.00 C 34029 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=66, symmetry=0 Number of additional bonds: simple=66, symmetry=0 Coordination: Other bonds: Time building additional restraints: 18.59 Conformation dependent library (CDL) restraints added in 7.5 seconds 13542 Ramachandran restraints generated. 6771 Oldfield, 0 Emsley, 6771 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12612 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 357 helices and 3 sheets defined 71.2% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.40 Creating SS restraints... Processing helix chain 'A' and resid 4 through 14 Processing helix chain 'A' and resid 21 through 46 removed outlier: 4.157A pdb=" N ASN A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ALA A 36 " --> pdb=" O ARG A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 62 Processing helix chain 'A' and resid 64 through 67 Processing helix chain 'A' and resid 78 through 101 Processing helix chain 'A' and resid 105 through 110 Processing helix chain 'A' and resid 115 through 121 Processing helix chain 'A' and resid 126 through 139 Processing helix chain 'A' and resid 145 through 171 removed outlier: 3.847A pdb=" N TYR A 163 " --> pdb=" O GLU A 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 15 removed outlier: 4.157A pdb=" N VAL B 8 " --> pdb=" O VAL B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 46 removed outlier: 4.414A pdb=" N ASN B 35 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N LYS B 36 " --> pdb=" O ALA B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 62 Processing helix chain 'B' and resid 76 through 99 Processing helix chain 'B' and resid 103 through 108 Processing helix chain 'B' and resid 113 through 120 Processing helix chain 'B' and resid 124 through 142 Processing helix chain 'B' and resid 154 through 171 removed outlier: 3.775A pdb=" N VAL B 171 " --> pdb=" O ALA B 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 14 Processing helix chain 'C' and resid 21 through 46 removed outlier: 4.099A pdb=" N ASN C 35 " --> pdb=" O LEU C 31 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N ALA C 36 " --> pdb=" O ARG C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 62 Processing helix chain 'C' and resid 64 through 66 No H-bonds generated for 'chain 'C' and resid 64 through 66' Processing helix chain 'C' and resid 78 through 101 Processing helix chain 'C' and resid 105 through 110 Processing helix chain 'C' and resid 115 through 121 Processing helix chain 'C' and resid 126 through 139 Processing helix chain 'C' and resid 145 through 171 removed outlier: 3.716A pdb=" N TYR C 163 " --> pdb=" O GLU C 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 15 removed outlier: 4.019A pdb=" N VAL D 8 " --> pdb=" O VAL D 4 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 46 removed outlier: 4.447A pdb=" N ASN D 35 " --> pdb=" O VAL D 31 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N LYS D 36 " --> pdb=" O ALA D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 62 Processing helix chain 'D' and resid 76 through 99 Processing helix chain 'D' and resid 103 through 108 Processing helix chain 'D' and resid 113 through 120 Processing helix chain 'D' and resid 124 through 142 Processing helix chain 'D' and resid 154 through 169 Processing helix chain 'E' and resid 4 through 14 Processing helix chain 'E' and resid 21 through 46 removed outlier: 4.412A pdb=" N ASN E 35 " --> pdb=" O LEU E 31 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ALA E 36 " --> pdb=" O ARG E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 62 Processing helix chain 'E' and resid 64 through 68 Processing helix chain 'E' and resid 78 through 101 Processing helix chain 'E' and resid 105 through 110 Processing helix chain 'E' and resid 115 through 121 Processing helix chain 'E' and resid 126 through 138 Processing helix chain 'E' and resid 145 through 171 removed outlier: 3.562A pdb=" N TYR E 163 " --> pdb=" O GLU E 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 15 removed outlier: 4.082A pdb=" N VAL F 8 " --> pdb=" O VAL F 4 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 46 removed outlier: 4.455A pdb=" N ASN F 35 " --> pdb=" O VAL F 31 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N LYS F 36 " --> pdb=" O ALA F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 62 Processing helix chain 'F' and resid 76 through 99 Processing helix chain 'F' and resid 103 through 108 Processing helix chain 'F' and resid 113 through 119 Processing helix chain 'F' and resid 124 through 142 Processing helix chain 'F' and resid 154 through 169 Processing helix chain 'G' and resid 4 through 14 Processing helix chain 'G' and resid 21 through 46 removed outlier: 4.353A pdb=" N ASN G 35 " --> pdb=" O LEU G 31 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ALA G 36 " --> pdb=" O ARG G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 62 Processing helix chain 'G' and resid 64 through 67 Processing helix chain 'G' and resid 78 through 101 Processing helix chain 'G' and resid 105 through 110 Processing helix chain 'G' and resid 115 through 121 Processing helix chain 'G' and resid 126 through 139 Processing helix chain 'G' and resid 145 through 171 removed outlier: 3.814A pdb=" N TYR G 163 " --> pdb=" O GLU G 159 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 15 removed outlier: 3.885A pdb=" N VAL H 8 " --> pdb=" O VAL H 4 " (cutoff:3.500A) Processing helix chain 'H' and resid 21 through 46 removed outlier: 4.432A pdb=" N ASN H 35 " --> pdb=" O VAL H 31 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N LYS H 36 " --> pdb=" O ALA H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 62 Processing helix chain 'H' and resid 76 through 99 Processing helix chain 'H' and resid 103 through 108 Processing helix chain 'H' and resid 113 through 119 Processing helix chain 'H' and resid 124 through 142 Processing helix chain 'H' and resid 154 through 169 Processing helix chain 'I' and resid 4 through 14 Processing helix chain 'I' and resid 21 through 46 removed outlier: 3.976A pdb=" N ASN I 35 " --> pdb=" O LEU I 31 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N ALA I 36 " --> pdb=" O ARG I 32 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 62 Processing helix chain 'I' and resid 64 through 66 No H-bonds generated for 'chain 'I' and resid 64 through 66' Processing helix chain 'I' and resid 78 through 101 Processing helix chain 'I' and resid 105 through 110 Processing helix chain 'I' and resid 115 through 121 Processing helix chain 'I' and resid 126 through 139 Processing helix chain 'I' and resid 145 through 171 Processing helix chain 'J' and resid 4 through 14 removed outlier: 4.208A pdb=" N VAL J 8 " --> pdb=" O VAL J 4 " (cutoff:3.500A) Processing helix chain 'J' and resid 21 through 46 removed outlier: 4.432A pdb=" N ASN J 35 " --> pdb=" O VAL J 31 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N LYS J 36 " --> pdb=" O ALA J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 48 through 62 Processing helix chain 'J' and resid 76 through 99 Processing helix chain 'J' and resid 103 through 108 Processing helix chain 'J' and resid 113 through 119 Processing helix chain 'J' and resid 124 through 142 Processing helix chain 'J' and resid 154 through 169 Processing helix chain 'K' and resid 4 through 14 Processing helix chain 'K' and resid 21 through 46 removed outlier: 4.402A pdb=" N ASN K 35 " --> pdb=" O LEU K 31 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ALA K 36 " --> pdb=" O ARG K 32 " (cutoff:3.500A) Processing helix chain 'K' and resid 48 through 62 Processing helix chain 'K' and resid 64 through 68 removed outlier: 3.809A pdb=" N GLN K 68 " --> pdb=" O TYR K 65 " (cutoff:3.500A) Processing helix chain 'K' and resid 78 through 101 Processing helix chain 'K' and resid 105 through 110 Processing helix chain 'K' and resid 115 through 121 Processing helix chain 'K' and resid 126 through 139 Processing helix chain 'K' and resid 144 through 171 removed outlier: 3.637A pdb=" N ASP K 148 " --> pdb=" O ASP K 145 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU K 159 " --> pdb=" O ALA K 146 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN K 161 " --> pdb=" O ASP K 148 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU K 164 " --> pdb=" O ASN K 161 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASP K 165 " --> pdb=" O SER K 162 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN K 169 " --> pdb=" O TYR K 166 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA K 170 " --> pdb=" O ALA K 167 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 15 removed outlier: 4.331A pdb=" N VAL L 8 " --> pdb=" O VAL L 4 " (cutoff:3.500A) Processing helix chain 'L' and resid 21 through 46 removed outlier: 4.335A pdb=" N ASN L 35 " --> pdb=" O VAL L 31 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N LYS L 36 " --> pdb=" O ALA L 32 " (cutoff:3.500A) Processing helix chain 'L' and resid 48 through 62 Processing helix chain 'L' and resid 64 through 67 No H-bonds generated for 'chain 'L' and resid 64 through 67' Processing helix chain 'L' and resid 76 through 99 Processing helix chain 'L' and resid 103 through 108 Processing helix chain 'L' and resid 113 through 120 Processing helix chain 'L' and resid 124 through 142 Processing helix chain 'L' and resid 154 through 169 Processing helix chain 'M' and resid 4 through 14 Processing helix chain 'M' and resid 21 through 46 removed outlier: 4.331A pdb=" N ASN M 35 " --> pdb=" O LEU M 31 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N ALA M 36 " --> pdb=" O ARG M 32 " (cutoff:3.500A) Processing helix chain 'M' and resid 48 through 62 Processing helix chain 'M' and resid 64 through 68 removed outlier: 3.736A pdb=" N GLN M 68 " --> pdb=" O TYR M 65 " (cutoff:3.500A) Processing helix chain 'M' and resid 78 through 101 Processing helix chain 'M' and resid 105 through 110 Processing helix chain 'M' and resid 115 through 121 Processing helix chain 'M' and resid 126 through 139 Processing helix chain 'M' and resid 145 through 170 removed outlier: 4.095A pdb=" N TYR M 163 " --> pdb=" O GLU M 159 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 15 removed outlier: 4.141A pdb=" N VAL N 8 " --> pdb=" O VAL N 4 " (cutoff:3.500A) Processing helix chain 'N' and resid 21 through 32 Processing helix chain 'N' and resid 34 through 46 Processing helix chain 'N' and resid 48 through 62 Processing helix chain 'N' and resid 76 through 99 Processing helix chain 'N' and resid 103 through 108 Processing helix chain 'N' and resid 113 through 120 Processing helix chain 'N' and resid 124 through 142 Processing helix chain 'N' and resid 154 through 168 Processing helix chain 'O' and resid 4 through 14 Processing helix chain 'O' and resid 21 through 46 removed outlier: 4.268A pdb=" N ASN O 35 " --> pdb=" O LEU O 31 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N ALA O 36 " --> pdb=" O ARG O 32 " (cutoff:3.500A) Processing helix chain 'O' and resid 48 through 62 Processing helix chain 'O' and resid 64 through 68 removed outlier: 3.802A pdb=" N GLN O 68 " --> pdb=" O TYR O 65 " (cutoff:3.500A) Processing helix chain 'O' and resid 78 through 101 Processing helix chain 'O' and resid 105 through 110 Processing helix chain 'O' and resid 115 through 121 Processing helix chain 'O' and resid 126 through 139 Processing helix chain 'O' and resid 145 through 171 Processing helix chain 'P' and resid 4 through 14 removed outlier: 4.029A pdb=" N VAL P 8 " --> pdb=" O VAL P 4 " (cutoff:3.500A) Processing helix chain 'P' and resid 21 through 32 Processing helix chain 'P' and resid 34 through 46 Processing helix chain 'P' and resid 48 through 62 Processing helix chain 'P' and resid 76 through 99 Processing helix chain 'P' and resid 103 through 108 Processing helix chain 'P' and resid 113 through 120 Processing helix chain 'P' and resid 124 through 142 Processing helix chain 'P' and resid 154 through 169 Processing helix chain 'Q' and resid 4 through 14 Processing helix chain 'Q' and resid 21 through 46 removed outlier: 4.169A pdb=" N ASN Q 35 " --> pdb=" O LEU Q 31 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ALA Q 36 " --> pdb=" O ARG Q 32 " (cutoff:3.500A) Processing helix chain 'Q' and resid 48 through 62 Processing helix chain 'Q' and resid 64 through 67 Processing helix chain 'Q' and resid 78 through 101 Processing helix chain 'Q' and resid 105 through 110 Processing helix chain 'Q' and resid 115 through 121 Processing helix chain 'Q' and resid 126 through 139 Processing helix chain 'Q' and resid 145 through 171 removed outlier: 3.587A pdb=" N TYR Q 163 " --> pdb=" O GLU Q 159 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 15 removed outlier: 3.910A pdb=" N VAL R 8 " --> pdb=" O VAL R 4 " (cutoff:3.500A) Processing helix chain 'R' and resid 21 through 46 removed outlier: 4.357A pdb=" N ASN R 35 " --> pdb=" O VAL R 31 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N LYS R 36 " --> pdb=" O ALA R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 62 Processing helix chain 'R' and resid 64 through 66 No H-bonds generated for 'chain 'R' and resid 64 through 66' Processing helix chain 'R' and resid 76 through 99 Processing helix chain 'R' and resid 102 through 108 removed outlier: 3.692A pdb=" N GLU R 106 " --> pdb=" O SER R 103 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP R 107 " --> pdb=" O VAL R 104 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG R 108 " --> pdb=" O LEU R 105 " (cutoff:3.500A) Processing helix chain 'R' and resid 113 through 119 Processing helix chain 'R' and resid 124 through 142 Processing helix chain 'R' and resid 154 through 169 Processing helix chain 'S' and resid 4 through 14 Processing helix chain 'S' and resid 21 through 46 removed outlier: 4.225A pdb=" N ASN S 35 " --> pdb=" O LEU S 31 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ALA S 36 " --> pdb=" O ARG S 32 " (cutoff:3.500A) Processing helix chain 'S' and resid 48 through 62 Processing helix chain 'S' and resid 64 through 68 Processing helix chain 'S' and resid 78 through 101 Processing helix chain 'S' and resid 105 through 110 Processing helix chain 'S' and resid 115 through 121 Processing helix chain 'S' and resid 126 through 139 Processing helix chain 'S' and resid 145 through 171 removed outlier: 3.624A pdb=" N GLU S 159 " --> pdb=" O ASP S 145 " (cutoff:3.500A) Processing helix chain 'T' and resid 4 through 15 removed outlier: 4.010A pdb=" N VAL T 8 " --> pdb=" O VAL T 4 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG T 15 " --> pdb=" O GLN T 11 " (cutoff:3.500A) Processing helix chain 'T' and resid 21 through 46 removed outlier: 4.436A pdb=" N ASN T 35 " --> pdb=" O VAL T 31 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N LYS T 36 " --> pdb=" O ALA T 32 " (cutoff:3.500A) Processing helix chain 'T' and resid 48 through 62 Processing helix chain 'T' and resid 76 through 99 Processing helix chain 'T' and resid 103 through 108 Processing helix chain 'T' and resid 113 through 120 Processing helix chain 'T' and resid 124 through 142 Processing helix chain 'T' and resid 154 through 169 Processing helix chain 'U' and resid 4 through 14 Processing helix chain 'U' and resid 21 through 46 removed outlier: 4.294A pdb=" N ASN U 35 " --> pdb=" O LEU U 31 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ALA U 36 " --> pdb=" O ARG U 32 " (cutoff:3.500A) Processing helix chain 'U' and resid 48 through 62 Processing helix chain 'U' and resid 64 through 66 No H-bonds generated for 'chain 'U' and resid 64 through 66' Processing helix chain 'U' and resid 78 through 101 Processing helix chain 'U' and resid 105 through 110 Processing helix chain 'U' and resid 115 through 121 Processing helix chain 'U' and resid 126 through 139 Processing helix chain 'U' and resid 145 through 171 removed outlier: 3.656A pdb=" N TYR U 163 " --> pdb=" O GLU U 159 " (cutoff:3.500A) Processing helix chain 'V' and resid 4 through 15 removed outlier: 4.034A pdb=" N VAL V 8 " --> pdb=" O VAL V 4 " (cutoff:3.500A) Processing helix chain 'V' and resid 21 through 46 removed outlier: 4.379A pdb=" N ASN V 35 " --> pdb=" O VAL V 31 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N LYS V 36 " --> pdb=" O ALA V 32 " (cutoff:3.500A) Processing helix chain 'V' and resid 48 through 62 Processing helix chain 'V' and resid 76 through 99 Processing helix chain 'V' and resid 103 through 108 Processing helix chain 'V' and resid 113 through 119 Processing helix chain 'V' and resid 124 through 142 Processing helix chain 'V' and resid 154 through 169 Processing helix chain 'W' and resid 4 through 14 Processing helix chain 'W' and resid 21 through 46 removed outlier: 4.233A pdb=" N ASN W 35 " --> pdb=" O LEU W 31 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ALA W 36 " --> pdb=" O ARG W 32 " (cutoff:3.500A) Processing helix chain 'W' and resid 48 through 62 Processing helix chain 'W' and resid 64 through 68 removed outlier: 3.640A pdb=" N GLN W 68 " --> pdb=" O TYR W 65 " (cutoff:3.500A) Processing helix chain 'W' and resid 78 through 101 Processing helix chain 'W' and resid 105 through 110 Processing helix chain 'W' and resid 115 through 121 Processing helix chain 'W' and resid 126 through 139 Processing helix chain 'W' and resid 145 through 171 removed outlier: 3.624A pdb=" N GLU W 159 " --> pdb=" O ASP W 145 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N TYR W 163 " --> pdb=" O GLU W 159 " (cutoff:3.500A) Processing helix chain 'X' and resid 4 through 15 removed outlier: 3.831A pdb=" N VAL X 8 " --> pdb=" O VAL X 4 " (cutoff:3.500A) Processing helix chain 'X' and resid 21 through 46 removed outlier: 4.480A pdb=" N ASN X 35 " --> pdb=" O VAL X 31 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N LYS X 36 " --> pdb=" O ALA X 32 " (cutoff:3.500A) Processing helix chain 'X' and resid 48 through 62 Processing helix chain 'X' and resid 64 through 66 No H-bonds generated for 'chain 'X' and resid 64 through 66' Processing helix chain 'X' and resid 76 through 99 Processing helix chain 'X' and resid 103 through 108 Processing helix chain 'X' and resid 113 through 120 Processing helix chain 'X' and resid 124 through 142 Processing helix chain 'X' and resid 154 through 169 Processing helix chain 'Y' and resid 4 through 14 Processing helix chain 'Y' and resid 21 through 46 removed outlier: 4.347A pdb=" N ASN Y 35 " --> pdb=" O LEU Y 31 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N ALA Y 36 " --> pdb=" O ARG Y 32 " (cutoff:3.500A) Processing helix chain 'Y' and resid 48 through 62 Processing helix chain 'Y' and resid 64 through 68 Processing helix chain 'Y' and resid 78 through 101 Processing helix chain 'Y' and resid 105 through 110 Processing helix chain 'Y' and resid 115 through 121 Processing helix chain 'Y' and resid 126 through 139 Processing helix chain 'Y' and resid 145 through 170 removed outlier: 3.547A pdb=" N SER Y 162 " --> pdb=" O ASP Y 148 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR Y 163 " --> pdb=" O GLU Y 159 " (cutoff:3.500A) Processing helix chain 'Z' and resid 4 through 15 removed outlier: 4.157A pdb=" N VAL Z 8 " --> pdb=" O VAL Z 4 " (cutoff:3.500A) Processing helix chain 'Z' and resid 21 through 46 removed outlier: 4.377A pdb=" N ASN Z 35 " --> pdb=" O VAL Z 31 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N LYS Z 36 " --> pdb=" O ALA Z 32 " (cutoff:3.500A) Processing helix chain 'Z' and resid 48 through 62 Processing helix chain 'Z' and resid 76 through 99 Processing helix chain 'Z' and resid 103 through 107 Processing helix chain 'Z' and resid 113 through 119 Processing helix chain 'Z' and resid 124 through 142 Processing helix chain 'Z' and resid 154 through 171 removed outlier: 3.781A pdb=" N VAL Z 171 " --> pdb=" O ALA Z 167 " (cutoff:3.500A) Processing helix chain 'a' and resid 4 through 14 Processing helix chain 'a' and resid 21 through 46 removed outlier: 4.233A pdb=" N ASN a 35 " --> pdb=" O LEU a 31 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N ALA a 36 " --> pdb=" O ARG a 32 " (cutoff:3.500A) Processing helix chain 'a' and resid 48 through 62 Processing helix chain 'a' and resid 64 through 68 removed outlier: 3.848A pdb=" N GLN a 68 " --> pdb=" O TYR a 65 " (cutoff:3.500A) Processing helix chain 'a' and resid 78 through 101 Processing helix chain 'a' and resid 105 through 110 Processing helix chain 'a' and resid 115 through 121 Processing helix chain 'a' and resid 126 through 139 Processing helix chain 'a' and resid 145 through 171 Processing helix chain 'b' and resid 4 through 15 removed outlier: 3.899A pdb=" N VAL b 8 " --> pdb=" O VAL b 4 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG b 15 " --> pdb=" O GLN b 11 " (cutoff:3.500A) Processing helix chain 'b' and resid 21 through 46 removed outlier: 4.371A pdb=" N ASN b 35 " --> pdb=" O VAL b 31 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N LYS b 36 " --> pdb=" O ALA b 32 " (cutoff:3.500A) Processing helix chain 'b' and resid 48 through 62 Processing helix chain 'b' and resid 64 through 66 No H-bonds generated for 'chain 'b' and resid 64 through 66' Processing helix chain 'b' and resid 76 through 99 Processing helix chain 'b' and resid 103 through 108 Processing helix chain 'b' and resid 113 through 120 Processing helix chain 'b' and resid 124 through 142 Processing helix chain 'b' and resid 154 through 169 Processing helix chain 'c' and resid 4 through 14 Processing helix chain 'c' and resid 21 through 46 removed outlier: 4.074A pdb=" N ASN c 35 " --> pdb=" O LEU c 31 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ALA c 36 " --> pdb=" O ARG c 32 " (cutoff:3.500A) Processing helix chain 'c' and resid 48 through 62 Processing helix chain 'c' and resid 64 through 68 Processing helix chain 'c' and resid 78 through 101 Processing helix chain 'c' and resid 105 through 110 Processing helix chain 'c' and resid 115 through 121 Processing helix chain 'c' and resid 126 through 139 Processing helix chain 'c' and resid 145 through 171 removed outlier: 3.707A pdb=" N TYR c 163 " --> pdb=" O GLU c 159 " (cutoff:3.500A) Processing helix chain 'd' and resid 4 through 15 removed outlier: 3.994A pdb=" N VAL d 8 " --> pdb=" O VAL d 4 " (cutoff:3.500A) Processing helix chain 'd' and resid 21 through 46 removed outlier: 4.303A pdb=" N ASN d 35 " --> pdb=" O VAL d 31 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N LYS d 36 " --> pdb=" O ALA d 32 " (cutoff:3.500A) Processing helix chain 'd' and resid 48 through 62 Processing helix chain 'd' and resid 64 through 67 No H-bonds generated for 'chain 'd' and resid 64 through 67' Processing helix chain 'd' and resid 76 through 99 Processing helix chain 'd' and resid 103 through 108 Processing helix chain 'd' and resid 113 through 120 Processing helix chain 'd' and resid 124 through 142 Processing helix chain 'd' and resid 154 through 169 Processing helix chain 'e' and resid 4 through 15 Processing helix chain 'e' and resid 21 through 46 removed outlier: 4.424A pdb=" N ASN e 35 " --> pdb=" O LEU e 31 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N ALA e 36 " --> pdb=" O ARG e 32 " (cutoff:3.500A) Processing helix chain 'e' and resid 48 through 62 Processing helix chain 'e' and resid 64 through 66 No H-bonds generated for 'chain 'e' and resid 64 through 66' Processing helix chain 'e' and resid 78 through 101 Processing helix chain 'e' and resid 105 through 110 Processing helix chain 'e' and resid 115 through 121 Processing helix chain 'e' and resid 126 through 139 Processing helix chain 'e' and resid 145 through 171 Processing helix chain 'f' and resid 4 through 15 removed outlier: 4.085A pdb=" N VAL f 8 " --> pdb=" O VAL f 4 " (cutoff:3.500A) Processing helix chain 'f' and resid 21 through 46 removed outlier: 4.325A pdb=" N ASN f 35 " --> pdb=" O VAL f 31 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N LYS f 36 " --> pdb=" O ALA f 32 " (cutoff:3.500A) Processing helix chain 'f' and resid 48 through 62 Processing helix chain 'f' and resid 64 through 66 No H-bonds generated for 'chain 'f' and resid 64 through 66' Processing helix chain 'f' and resid 76 through 99 Processing helix chain 'f' and resid 103 through 108 Processing helix chain 'f' and resid 113 through 120 Processing helix chain 'f' and resid 124 through 142 Processing helix chain 'f' and resid 154 through 169 Processing helix chain 'g' and resid 4 through 14 Processing helix chain 'g' and resid 21 through 46 removed outlier: 4.106A pdb=" N ASN g 35 " --> pdb=" O LEU g 31 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N ALA g 36 " --> pdb=" O ARG g 32 " (cutoff:3.500A) Processing helix chain 'g' and resid 48 through 62 Processing helix chain 'g' and resid 64 through 68 removed outlier: 3.793A pdb=" N GLN g 68 " --> pdb=" O TYR g 65 " (cutoff:3.500A) Processing helix chain 'g' and resid 78 through 101 Processing helix chain 'g' and resid 105 through 110 Processing helix chain 'g' and resid 115 through 121 Processing helix chain 'g' and resid 126 through 139 Processing helix chain 'g' and resid 145 through 171 removed outlier: 3.526A pdb=" N GLU g 159 " --> pdb=" O ASP g 145 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR g 163 " --> pdb=" O GLU g 159 " (cutoff:3.500A) Processing helix chain 'h' and resid 6 through 15 Processing helix chain 'h' and resid 21 through 32 Processing helix chain 'h' and resid 34 through 46 Processing helix chain 'h' and resid 48 through 62 Processing helix chain 'h' and resid 76 through 99 Processing helix chain 'h' and resid 103 through 108 Processing helix chain 'h' and resid 113 through 120 Processing helix chain 'h' and resid 124 through 142 Processing helix chain 'h' and resid 154 through 171 removed outlier: 3.746A pdb=" N VAL h 171 " --> pdb=" O ALA h 167 " (cutoff:3.500A) Processing helix chain 'i' and resid 4 through 15 Processing helix chain 'i' and resid 21 through 46 removed outlier: 4.288A pdb=" N ASN i 35 " --> pdb=" O LEU i 31 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ALA i 36 " --> pdb=" O ARG i 32 " (cutoff:3.500A) Processing helix chain 'i' and resid 48 through 62 Processing helix chain 'i' and resid 64 through 68 removed outlier: 3.793A pdb=" N GLN i 68 " --> pdb=" O TYR i 65 " (cutoff:3.500A) Processing helix chain 'i' and resid 78 through 101 Processing helix chain 'i' and resid 105 through 110 Processing helix chain 'i' and resid 115 through 121 Processing helix chain 'i' and resid 126 through 139 Processing helix chain 'i' and resid 145 through 171 Processing helix chain 'j' and resid 4 through 15 removed outlier: 4.174A pdb=" N VAL j 8 " --> pdb=" O VAL j 4 " (cutoff:3.500A) Processing helix chain 'j' and resid 21 through 32 Processing helix chain 'j' and resid 34 through 46 Processing helix chain 'j' and resid 48 through 62 Processing helix chain 'j' and resid 76 through 99 Processing helix chain 'j' and resid 103 through 108 Processing helix chain 'j' and resid 113 through 120 Processing helix chain 'j' and resid 124 through 142 Processing helix chain 'j' and resid 154 through 169 Processing helix chain 'k' and resid 7 through 10 No H-bonds generated for 'chain 'k' and resid 7 through 10' Processing helix chain 'k' and resid 13 through 16 No H-bonds generated for 'chain 'k' and resid 13 through 16' Processing helix chain 'k' and resid 29 through 42 Processing helix chain 'k' and resid 51 through 53 No H-bonds generated for 'chain 'k' and resid 51 through 53' Processing helix chain 'k' and resid 56 through 63 Processing helix chain 'k' and resid 69 through 78 Processing helix chain 'k' and resid 80 through 86 Processing helix chain 'k' and resid 92 through 103 Processing helix chain 'k' and resid 111 through 134 removed outlier: 7.962A pdb=" N PHE k 126 " --> pdb=" O GLU k 122 " (cutoff:3.500A) removed outlier: 9.846A pdb=" N ASP k 127 " --> pdb=" O ASN k 123 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ALA k 128 " --> pdb=" O GLN k 124 " (cutoff:3.500A) Processing helix chain 'k' and resid 137 through 142 Processing helix chain 'k' and resid 161 through 170 removed outlier: 3.808A pdb=" N THR k 165 " --> pdb=" O THR k 161 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE k 168 " --> pdb=" O PHE k 164 " (cutoff:3.500A) Processing helix chain 'k' and resid 190 through 194 Processing helix chain 'k' and resid 228 through 232 Proline residue: k 231 - end of helix No H-bonds generated for 'chain 'k' and resid 228 through 232' Processing helix chain 'k' and resid 268 through 278 Processing helix chain 'l' and resid 4 through 10 removed outlier: 3.572A pdb=" N ARG l 9 " --> pdb=" O VAL l 5 " (cutoff:3.500A) Processing helix chain 'l' and resid 13 through 16 No H-bonds generated for 'chain 'l' and resid 13 through 16' Processing helix chain 'l' and resid 29 through 42 Processing helix chain 'l' and resid 51 through 53 No H-bonds generated for 'chain 'l' and resid 51 through 53' Processing helix chain 'l' and resid 56 through 63 Processing helix chain 'l' and resid 69 through 77 Processing helix chain 'l' and resid 80 through 86 Processing helix chain 'l' and resid 92 through 103 Processing helix chain 'l' and resid 111 through 134 removed outlier: 8.179A pdb=" N TYR l 126 " --> pdb=" O HIS l 122 " (cutoff:3.500A) removed outlier: 9.477A pdb=" N GLU l 127 " --> pdb=" O GLN l 123 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA l 128 " --> pdb=" O GLY l 124 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR l 133 " --> pdb=" O GLU l 129 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE l 134 " --> pdb=" O ILE l 130 " (cutoff:3.500A) Processing helix chain 'l' and resid 137 through 142 Processing helix chain 'l' and resid 162 through 171 removed outlier: 3.822A pdb=" N SER l 166 " --> pdb=" O THR l 162 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N PHE l 169 " --> pdb=" O PHE l 165 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLN l 170 " --> pdb=" O SER l 166 " (cutoff:3.500A) Processing helix chain 'l' and resid 191 through 194 No H-bonds generated for 'chain 'l' and resid 191 through 194' Processing helix chain 'l' and resid 205 through 208 Processing helix chain 'l' and resid 253 through 262 Processing helix chain 'm' and resid 16 through 18 No H-bonds generated for 'chain 'm' and resid 16 through 18' Processing helix chain 'm' and resid 56 through 65 Processing helix chain 'm' and resid 82 through 84 No H-bonds generated for 'chain 'm' and resid 82 through 84' Processing helix chain 'n' and resid 14 through 16 No H-bonds generated for 'chain 'n' and resid 14 through 16' Processing helix chain 'n' and resid 39 through 53 Processing helix chain 'n' and resid 66 through 73 Processing helix chain 'n' and resid 79 through 87 Processing helix chain 'n' and resid 90 through 95 Processing helix chain 'n' and resid 102 through 113 Processing helix chain 'n' and resid 121 through 145 removed outlier: 3.661A pdb=" N ILE n 129 " --> pdb=" O ILE n 125 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL n 130 " --> pdb=" O ALA n 126 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N LEU n 136 " --> pdb=" O ALA n 132 " (cutoff:3.500A) Proline residue: n 137 - end of helix Processing helix chain 'n' and resid 147 through 153 Processing helix chain 'n' and resid 176 through 178 No H-bonds generated for 'chain 'n' and resid 176 through 178' Processing helix chain 'n' and resid 184 through 193 Processing sheet with id= A, first strand: chain 'k' and resid 259 through 264 removed outlier: 3.725A pdb=" N SER k 284 " --> pdb=" O GLU k 242 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N THR k 244 " --> pdb=" O VAL k 282 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N VAL k 282 " --> pdb=" O THR k 244 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'l' and resid 243 through 249 removed outlier: 4.060A pdb=" N MET l 222 " --> pdb=" O ALA l 273 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE l 228 " --> pdb=" O VAL l 267 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N VAL l 267 " --> pdb=" O ILE l 228 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'm' and resid 47 through 52 removed outlier: 3.606A pdb=" N SER m 72 " --> pdb=" O GLU m 24 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE m 26 " --> pdb=" O ILE m 70 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N ILE m 70 " --> pdb=" O ILE m 26 " (cutoff:3.500A) 3370 hydrogen bonds defined for protein. 10020 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: 15.15 Time building geometry restraints manager: 19.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 9338 1.31 - 1.43: 14377 1.43 - 1.56: 31007 1.56 - 1.69: 86 1.69 - 1.82: 300 Bond restraints: 55108 Sorted by residual: bond pdb=" C3C CYC j 201 " pdb=" C4C CYC j 201 " ideal model delta sigma weight residual 1.514 1.719 -0.205 2.00e-02 2.50e+03 1.05e+02 bond pdb=" C4C CYC B 201 " pdb=" NC CYC B 201 " ideal model delta sigma weight residual 1.377 1.211 0.166 2.00e-02 2.50e+03 6.88e+01 bond pdb=" NB CYC B 201 " pdb=" C4B CYC B 201 " ideal model delta sigma weight residual 1.369 1.534 -0.165 2.00e-02 2.50e+03 6.83e+01 bond pdb=" NB CYC L 201 " pdb=" C4B CYC L 201 " ideal model delta sigma weight residual 1.369 1.533 -0.164 2.00e-02 2.50e+03 6.71e+01 bond pdb=" NB CYC H 201 " pdb=" C4B CYC H 201 " ideal model delta sigma weight residual 1.369 1.533 -0.164 2.00e-02 2.50e+03 6.69e+01 ... (remaining 55103 not shown) Histogram of bond angle deviations from ideal: 93.03 - 101.81: 180 101.81 - 110.59: 14633 110.59 - 119.37: 30880 119.37 - 128.16: 28680 128.16 - 136.94: 586 Bond angle restraints: 74959 Sorted by residual: angle pdb=" N GLU k 183 " pdb=" CA GLU k 183 " pdb=" C GLU k 183 " ideal model delta sigma weight residual 108.67 95.64 13.03 1.55e+00 4.16e-01 7.07e+01 angle pdb=" C MET n 179 " pdb=" N PRO n 180 " pdb=" CA PRO n 180 " ideal model delta sigma weight residual 120.31 127.80 -7.49 9.80e-01 1.04e+00 5.84e+01 angle pdb=" N GLN l 160 " pdb=" CA GLN l 160 " pdb=" C GLN l 160 " ideal model delta sigma weight residual 110.50 120.48 -9.98 1.41e+00 5.03e-01 5.01e+01 angle pdb=" N TYR B 74 " pdb=" CA TYR B 74 " pdb=" CB TYR B 74 " ideal model delta sigma weight residual 110.35 118.07 -7.72 1.12e+00 7.97e-01 4.75e+01 angle pdb=" N PRO L 145 " pdb=" CD PRO L 145 " pdb=" CG PRO L 145 " ideal model delta sigma weight residual 103.20 94.01 9.19 1.50e+00 4.44e-01 3.75e+01 ... (remaining 74954 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 30837 17.88 - 35.77: 2469 35.77 - 53.65: 531 53.65 - 71.54: 144 71.54 - 89.42: 69 Dihedral angle restraints: 34050 sinusoidal: 14297 harmonic: 19753 Sorted by residual: dihedral pdb=" CD ARG T 78 " pdb=" NE ARG T 78 " pdb=" CZ ARG T 78 " pdb=" NH1 ARG T 78 " ideal model delta sinusoidal sigma weight residual 0.00 -47.55 47.55 1 1.00e+01 1.00e-02 3.12e+01 dihedral pdb=" CD ARG T 77 " pdb=" NE ARG T 77 " pdb=" CZ ARG T 77 " pdb=" NH1 ARG T 77 " ideal model delta sinusoidal sigma weight residual 0.00 -44.34 44.34 1 1.00e+01 1.00e-02 2.73e+01 dihedral pdb=" CA MET C 1 " pdb=" C MET C 1 " pdb=" N LYS C 2 " pdb=" CA LYS C 2 " ideal model delta harmonic sigma weight residual -180.00 -154.28 -25.72 0 5.00e+00 4.00e-02 2.65e+01 ... (remaining 34047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 7644 0.100 - 0.201: 444 0.201 - 0.301: 55 0.301 - 0.401: 34 0.401 - 0.501: 21 Chirality restraints: 8198 Sorted by residual: chirality pdb=" CB THR B 75 " pdb=" CA THR B 75 " pdb=" OG1 THR B 75 " pdb=" CG2 THR B 75 " both_signs ideal model delta sigma weight residual False 2.55 2.05 0.50 2.00e-01 2.50e+01 6.29e+00 chirality pdb=" C2C CYC d 202 " pdb=" C1C CYC d 202 " pdb=" C3C CYC d 202 " pdb=" CMC CYC d 202 " both_signs ideal model delta sigma weight residual False -2.52 -2.97 0.44 2.00e-01 2.50e+01 4.89e+00 chirality pdb=" C2C CYC f 202 " pdb=" C1C CYC f 202 " pdb=" C3C CYC f 202 " pdb=" CMC CYC f 202 " both_signs ideal model delta sigma weight residual False -2.52 -2.97 0.44 2.00e-01 2.50e+01 4.88e+00 ... (remaining 8195 not shown) Planarity restraints: 9826 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG T 78 " 0.805 9.50e-02 1.11e+02 3.61e-01 7.92e+01 pdb=" NE ARG T 78 " -0.049 2.00e-02 2.50e+03 pdb=" CZ ARG T 78 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG T 78 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG T 78 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG T 77 " 0.775 9.50e-02 1.11e+02 3.48e-01 7.35e+01 pdb=" NE ARG T 77 " -0.046 2.00e-02 2.50e+03 pdb=" CZ ARG T 77 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG T 77 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG T 77 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG U 32 " 0.544 9.50e-02 1.11e+02 2.45e-01 4.11e+01 pdb=" NE ARG U 32 " -0.019 2.00e-02 2.50e+03 pdb=" CZ ARG U 32 " -0.044 2.00e-02 2.50e+03 pdb=" NH1 ARG U 32 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG U 32 " 0.031 2.00e-02 2.50e+03 ... (remaining 9823 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 530 2.52 - 3.11: 40281 3.11 - 3.71: 97271 3.71 - 4.30: 140509 4.30 - 4.90: 224680 Nonbonded interactions: 503271 Sorted by model distance: nonbonded pdb=" OE1 GLU l 141 " pdb=" NH2 ARG l 158 " model vdw 1.919 2.520 nonbonded pdb=" NH1 ARG m 61 " pdb=" CBB CYC h 201 " model vdw 1.951 3.540 nonbonded pdb=" NE ARG l 180 " pdb=" O2D CYC Z 201 " model vdw 2.028 2.496 nonbonded pdb=" O ALA l 77 " pdb=" OH TYR l 126 " model vdw 2.030 2.440 nonbonded pdb=" OD1 ASP l 33 " pdb=" NH2 ARG l 63 " model vdw 2.057 2.520 ... (remaining 503266 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 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' selection = chain 'Y' selection = chain 'a' selection = chain 'c' selection = chain 'e' selection = chain 'g' selection = chain 'i' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'X' selection = chain 'Z' selection = chain 'b' selection = chain 'd' selection = chain 'f' selection = chain 'h' selection = chain 'j' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.560 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: 0.050 Extract box with map and model: 11.160 Check model and map are aligned: 0.630 Set scattering table: 0.390 Process input model: 110.330 Find NCS groups from input model: 3.150 Set up NCS constraints: 0.870 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:9.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 138.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.205 55108 Z= 0.828 Angle : 1.310 13.033 74959 Z= 0.602 Chirality : 0.062 0.501 8198 Planarity : 0.010 0.361 9826 Dihedral : 14.441 89.419 21438 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.65 % Favored : 98.24 % Rotamer: Outliers : 0.45 % Allowed : 0.66 % Favored : 98.88 % Cbeta Deviations : 0.02 % 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: -0.95 (0.09), residues: 6771 helix: -0.33 (0.06), residues: 5087 sheet: 0.28 (0.62), residues: 48 loop : -1.15 (0.14), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP U 128 HIS 0.014 0.002 HIS G 140 PHE 0.033 0.002 PHE Q 28 TYR 0.030 0.002 TYR n 103 ARG 0.038 0.001 ARG U 32 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13542 Ramachandran restraints generated. 6771 Oldfield, 0 Emsley, 6771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13542 Ramachandran restraints generated. 6771 Oldfield, 0 Emsley, 6771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1521 residues out of total 5289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 1497 time to evaluate : 4.680 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 GLN cc_start: 0.7298 (mt0) cc_final: 0.7082 (mt0) REVERT: A 42 LYS cc_start: 0.8191 (tmtt) cc_final: 0.7837 (tmtp) REVERT: A 116 ASP cc_start: 0.7125 (m-30) cc_final: 0.6843 (m-30) REVERT: A 134 LYS cc_start: 0.8025 (mmtp) cc_final: 0.7800 (tppp) REVERT: A 139 ASN cc_start: 0.8101 (m110) cc_final: 0.7891 (m110) REVERT: B 1 MET cc_start: 0.7740 (ptp) cc_final: 0.7476 (ptp) REVERT: B 36 LYS cc_start: 0.8236 (mttm) cc_final: 0.7819 (mtpt) REVERT: C 35 ASN cc_start: 0.8352 (m-40) cc_final: 0.8094 (m110) REVERT: C 131 GLU cc_start: 0.7819 (tp30) cc_final: 0.7416 (tp30) REVERT: D 23 GLN cc_start: 0.7207 (tt0) cc_final: 0.6765 (tt0) REVERT: D 25 ASP cc_start: 0.7379 (m-30) cc_final: 0.6832 (m-30) REVERT: D 92 TYR cc_start: 0.8881 (m-80) cc_final: 0.8634 (m-80) REVERT: D 132 GLN cc_start: 0.7269 (mm-40) cc_final: 0.7049 (mm-40) REVERT: D 148 ILE cc_start: 0.7483 (tt) cc_final: 0.7242 (tt) REVERT: D 166 ARG cc_start: 0.7638 (ptm160) cc_final: 0.7212 (ptp-170) REVERT: E 17 ARG cc_start: 0.7193 (ptt90) cc_final: 0.6958 (ptm-80) REVERT: E 42 LYS cc_start: 0.7525 (tptt) cc_final: 0.7267 (tptm) REVERT: E 120 ARG cc_start: 0.7269 (ttm110) cc_final: 0.6979 (ttm-80) REVERT: E 165 ASP cc_start: 0.7539 (m-30) cc_final: 0.7103 (m-30) REVERT: G 131 GLU cc_start: 0.7804 (tp30) cc_final: 0.7514 (tp30) REVERT: G 169 ASN cc_start: 0.8426 (m-40) cc_final: 0.7888 (m-40) REVERT: H 107 ASP cc_start: 0.8025 (m-30) cc_final: 0.7713 (m-30) REVERT: H 114 ARG cc_start: 0.7585 (ttm110) cc_final: 0.6997 (ttp-170) REVERT: H 134 MET cc_start: 0.8563 (mtm) cc_final: 0.8345 (mtp) REVERT: I 11 THR cc_start: 0.8267 (m) cc_final: 0.7984 (m) REVERT: I 20 SER cc_start: 0.8319 (p) cc_final: 0.8021 (p) REVERT: I 42 LYS cc_start: 0.7428 (ttmm) cc_final: 0.7079 (ttpt) REVERT: I 47 ASN cc_start: 0.7739 (t0) cc_final: 0.7328 (t0) REVERT: I 49 GLN cc_start: 0.6981 (tp-100) cc_final: 0.6605 (pm20) REVERT: I 50 SER cc_start: 0.8375 (t) cc_final: 0.7980 (p) REVERT: I 109 GLU cc_start: 0.6377 (mm-30) cc_final: 0.6087 (mm-30) REVERT: I 143 SER cc_start: 0.6175 (p) cc_final: 0.5968 (m) REVERT: J 33 GLU cc_start: 0.7112 (mm-30) cc_final: 0.6886 (mm-30) REVERT: J 115 GLU cc_start: 0.7723 (mp0) cc_final: 0.7406 (mp0) REVERT: K 53 ASN cc_start: 0.7214 (m-40) cc_final: 0.6847 (m110) REVERT: K 72 ASN cc_start: 0.7678 (m-40) cc_final: 0.7442 (m110) REVERT: K 117 GLU cc_start: 0.6859 (mp0) cc_final: 0.6608 (mp0) REVERT: L 3 ASP cc_start: 0.7756 (p0) cc_final: 0.7473 (p0) REVERT: M 49 GLN cc_start: 0.7862 (tp-100) cc_final: 0.7408 (pm20) REVERT: M 134 LYS cc_start: 0.8660 (mttm) cc_final: 0.8445 (mttp) REVERT: M 159 GLU cc_start: 0.6803 (tm-30) cc_final: 0.5752 (tm-30) REVERT: N 107 ASP cc_start: 0.7492 (m-30) cc_final: 0.7192 (m-30) REVERT: O 10 SER cc_start: 0.8399 (m) cc_final: 0.8180 (m) REVERT: O 42 LYS cc_start: 0.8048 (ttmm) cc_final: 0.7653 (ttmp) REVERT: Q 39 GLN cc_start: 0.7574 (tm-30) cc_final: 0.7178 (tm130) REVERT: Q 47 ASN cc_start: 0.7690 (t0) cc_final: 0.7279 (t0) REVERT: Q 148 ASP cc_start: 0.6947 (m-30) cc_final: 0.6662 (m-30) REVERT: R 1 MET cc_start: 0.7382 (ptp) cc_final: 0.6787 (ptp) REVERT: R 30 THR cc_start: 0.8417 (m) cc_final: 0.8175 (m) REVERT: S 35 ASN cc_start: 0.8513 (m-40) cc_final: 0.8261 (m-40) REVERT: T 146 ASN cc_start: 0.7211 (m-40) cc_final: 0.6982 (m-40) REVERT: U 116 ASP cc_start: 0.6970 (p0) cc_final: 0.6632 (p0) REVERT: U 143 SER cc_start: 0.8132 (p) cc_final: 0.7829 (p) REVERT: V 39 ASP cc_start: 0.7808 (m-30) cc_final: 0.7452 (m-30) REVERT: V 135 LYS cc_start: 0.8378 (tttt) cc_final: 0.8093 (ttmt) REVERT: V 152 ASP cc_start: 0.6404 (t0) cc_final: 0.6131 (t0) REVERT: W 143 SER cc_start: 0.7634 (p) cc_final: 0.7417 (p) REVERT: X 25 ASP cc_start: 0.6337 (m-30) cc_final: 0.6060 (m-30) REVERT: X 101 ASP cc_start: 0.7846 (t70) cc_final: 0.7632 (t70) REVERT: X 132 GLN cc_start: 0.7824 (mm110) cc_final: 0.7608 (mm-40) REVERT: Y 1 MET cc_start: 0.6608 (mtm) cc_final: 0.6120 (mtm) REVERT: Y 11 THR cc_start: 0.7872 (m) cc_final: 0.6860 (p) REVERT: Y 15 GLN cc_start: 0.7724 (mp10) cc_final: 0.7292 (mp10) REVERT: Y 20 SER cc_start: 0.7836 (p) cc_final: 0.7612 (p) REVERT: Z 101 ASP cc_start: 0.7434 (t0) cc_final: 0.7139 (t0) REVERT: Z 132 GLN cc_start: 0.7043 (mm-40) cc_final: 0.6442 (mt0) REVERT: a 15 GLN cc_start: 0.8129 (mt0) cc_final: 0.7904 (mt0) REVERT: a 65 TYR cc_start: 0.7757 (p90) cc_final: 0.7449 (p90) REVERT: a 67 THR cc_start: 0.7145 (m) cc_final: 0.6761 (p) REVERT: a 131 GLU cc_start: 0.7588 (tp30) cc_final: 0.7264 (tp30) REVERT: a 159 GLU cc_start: 0.7104 (tt0) cc_final: 0.6903 (tt0) REVERT: b 11 GLN cc_start: 0.7587 (mt0) cc_final: 0.6791 (mt0) REVERT: b 135 LYS cc_start: 0.8074 (ttpt) cc_final: 0.7829 (tttt) REVERT: c 49 GLN cc_start: 0.7389 (tp-100) cc_final: 0.7187 (pm20) REVERT: c 53 ASN cc_start: 0.8542 (m-40) cc_final: 0.8127 (m110) REVERT: c 68 GLN cc_start: 0.7290 (mt0) cc_final: 0.7053 (mt0) REVERT: c 162 SER cc_start: 0.7891 (m) cc_final: 0.7669 (t) REVERT: d 133 LYS cc_start: 0.8409 (mttm) cc_final: 0.8117 (mttm) REVERT: d 134 MET cc_start: 0.8743 (mtm) cc_final: 0.8466 (mtm) REVERT: d 159 GLU cc_start: 0.7821 (tt0) cc_final: 0.7469 (tt0) REVERT: e 42 LYS cc_start: 0.7432 (ttpt) cc_final: 0.7192 (tptm) REVERT: e 53 ASN cc_start: 0.7860 (m-40) cc_final: 0.7625 (m110) REVERT: e 120 ARG cc_start: 0.7483 (ttm110) cc_final: 0.7248 (ttp80) REVERT: e 123 ASP cc_start: 0.7485 (t0) cc_final: 0.7085 (t0) REVERT: e 161 ASN cc_start: 0.7285 (m-40) cc_final: 0.7049 (m-40) REVERT: f 22 SER cc_start: 0.7829 (p) cc_final: 0.7590 (p) REVERT: f 156 ILE cc_start: 0.8470 (tp) cc_final: 0.8270 (mp) REVERT: g 45 THR cc_start: 0.8095 (m) cc_final: 0.7837 (m) REVERT: h 87 GLU cc_start: 0.7355 (tt0) cc_final: 0.7117 (mt-10) REVERT: i 42 LYS cc_start: 0.7304 (tttm) cc_final: 0.6900 (tppt) REVERT: i 70 GLN cc_start: 0.7126 (mm-40) cc_final: 0.6841 (mm110) REVERT: i 139 ASN cc_start: 0.7868 (m110) cc_final: 0.7655 (m110) REVERT: i 148 ASP cc_start: 0.8063 (m-30) cc_final: 0.7819 (m-30) REVERT: j 10 SER cc_start: 0.7601 (p) cc_final: 0.7358 (t) REVERT: j 103 SER cc_start: 0.7761 (p) cc_final: 0.7412 (p) REVERT: j 107 ASP cc_start: 0.6758 (m-30) cc_final: 0.6460 (m-30) REVERT: l 5 VAL cc_start: 0.7750 (p) cc_final: 0.7522 (p) REVERT: m 66 MET cc_start: 0.7148 (mtm) cc_final: 0.6703 (mtm) REVERT: n 55 ASN cc_start: 0.7752 (m-40) cc_final: 0.7202 (t0) REVERT: n 134 LYS cc_start: 0.7538 (mttp) cc_final: 0.7106 (mttp) REVERT: n 142 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.6903 (tp30) outliers start: 24 outliers final: 3 residues processed: 1508 average time/residue: 1.5094 time to fit residues: 2810.3463 Evaluate side-chains 945 residues out of total 5289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 941 time to evaluate : 4.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain m residue 56 MET Chi-restraints excluded: chain n residue 142 GLU Chi-restraints excluded: chain n residue 170 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 676 random chunks: chunk 570 optimal weight: 0.9980 chunk 512 optimal weight: 2.9990 chunk 284 optimal weight: 0.9980 chunk 175 optimal weight: 5.9990 chunk 345 optimal weight: 0.5980 chunk 273 optimal weight: 0.6980 chunk 529 optimal weight: 0.6980 chunk 205 optimal weight: 0.9980 chunk 322 optimal weight: 2.9990 chunk 394 optimal weight: 1.9990 chunk 613 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN A 25 GLN A 140 HIS B 72 ASN ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 11 GLN D 72 ASN E 39 GLN E 47 ASN E 53 ASN E 70 GLN E 78 GLN F 23 GLN F 111 ASN F 132 GLN ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 ASN ** G 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 47 ASN K 15 GLN K 47 ASN ** K 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 169 ASN L 68 GLN M 15 GLN M 35 ASN N 23 GLN N 68 GLN N 132 GLN O 33 GLN O 72 ASN P 68 GLN P 132 GLN Q 35 ASN Q 139 ASN ** Q 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 65 GLN R 68 GLN S 57 GLN T 47 ASN T 72 ASN ** U 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 53 ASN U 78 GLN ** U 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 35 ASN V 111 ASN V 146 ASN W 33 GLN W 47 ASN ** W 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 39 GLN ** Y 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 25 GLN a 39 GLN a 53 ASN a 57 GLN a 61 ASN a 119 ASN a 169 ASN b 72 ASN e 15 GLN ** e 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 72 ASN e 140 HIS g 39 GLN g 57 GLN g 61 ASN g 140 HIS h 35 ASN h 63 GLN h 68 GLN h 72 ASN i 49 GLN i 140 HIS j 132 GLN k 102 HIS k 124 GLN k 270 GLN l 197 ASN l 259 GLN m 84 HIS n 57 GLN n 74 ASN n 75 GLN n 141 ASN n 186 HIS Total number of N/Q/H flips: 77 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 55108 Z= 0.195 Angle : 0.643 11.898 74959 Z= 0.299 Chirality : 0.037 0.236 8198 Planarity : 0.004 0.087 9826 Dihedral : 10.075 89.365 10022 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.09 % Favored : 98.86 % Rotamer: Outliers : 2.51 % Allowed : 10.46 % Favored : 87.03 % 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: 0.58 (0.09), residues: 6771 helix: 0.80 (0.07), residues: 5293 sheet: 0.52 (0.61), residues: 48 loop : -0.87 (0.15), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP l 146 HIS 0.009 0.002 HIS M 140 PHE 0.014 0.001 PHE G 28 TYR 0.024 0.001 TYR k 133 ARG 0.028 0.001 ARG E 17 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13542 Ramachandran restraints generated. 6771 Oldfield, 0 Emsley, 6771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13542 Ramachandran restraints generated. 6771 Oldfield, 0 Emsley, 6771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1179 residues out of total 5289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 1046 time to evaluate : 4.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LYS cc_start: 0.8206 (tmtt) cc_final: 0.7962 (tttp) REVERT: A 109 GLU cc_start: 0.7240 (mt-10) cc_final: 0.6912 (mt-10) REVERT: A 116 ASP cc_start: 0.7116 (m-30) cc_final: 0.6830 (m-30) REVERT: A 121 THR cc_start: 0.7890 (p) cc_final: 0.7624 (t) REVERT: A 134 LYS cc_start: 0.8008 (mmtp) cc_final: 0.7754 (tppp) REVERT: A 159 GLU cc_start: 0.7430 (tm-30) cc_final: 0.7043 (tt0) REVERT: B 135 LYS cc_start: 0.7867 (OUTLIER) cc_final: 0.7655 (ttpt) REVERT: C 33 GLN cc_start: 0.8336 (tp-100) cc_final: 0.8105 (tp-100) REVERT: C 46 ASP cc_start: 0.6851 (m-30) cc_final: 0.6519 (m-30) REVERT: D 15 ARG cc_start: 0.6641 (OUTLIER) cc_final: 0.5942 (ttm-80) REVERT: D 23 GLN cc_start: 0.7382 (tt0) cc_final: 0.7015 (tt0) REVERT: D 40 SER cc_start: 0.8695 (OUTLIER) cc_final: 0.8477 (p) REVERT: D 115 GLU cc_start: 0.6792 (mm-30) cc_final: 0.6579 (mm-30) REVERT: D 141 ILE cc_start: 0.8225 (pp) cc_final: 0.7964 (mt) REVERT: E 1 MET cc_start: 0.6385 (ttt) cc_final: 0.5390 (ttt) REVERT: E 120 ARG cc_start: 0.7067 (ttm110) cc_final: 0.6831 (ttm110) REVERT: G 39 GLN cc_start: 0.7559 (tp40) cc_final: 0.7355 (mm110) REVERT: G 131 GLU cc_start: 0.7918 (tp30) cc_final: 0.7584 (tp30) REVERT: G 169 ASN cc_start: 0.8353 (m-40) cc_final: 0.8078 (m110) REVERT: H 11 GLN cc_start: 0.7765 (OUTLIER) cc_final: 0.6462 (mt0) REVERT: H 107 ASP cc_start: 0.7878 (m-30) cc_final: 0.7669 (m-30) REVERT: I 42 LYS cc_start: 0.7413 (ttmm) cc_final: 0.7108 (ttpt) REVERT: I 47 ASN cc_start: 0.7679 (t0) cc_final: 0.7459 (t0) REVERT: I 49 GLN cc_start: 0.6992 (tp-100) cc_final: 0.6523 (pm20) REVERT: I 50 SER cc_start: 0.8382 (t) cc_final: 0.8007 (p) REVERT: I 143 SER cc_start: 0.6644 (p) cc_final: 0.6354 (m) REVERT: J 106 GLU cc_start: 0.6526 (OUTLIER) cc_final: 0.6102 (tm-30) REVERT: J 115 GLU cc_start: 0.7804 (mp0) cc_final: 0.7457 (mp0) REVERT: K 53 ASN cc_start: 0.7283 (m-40) cc_final: 0.6879 (m110) REVERT: K 117 GLU cc_start: 0.6933 (mp0) cc_final: 0.6644 (mp0) REVERT: L 165 ASP cc_start: 0.7475 (m-30) cc_final: 0.7257 (m-30) REVERT: M 49 GLN cc_start: 0.7961 (tp-100) cc_final: 0.7471 (pm20) REVERT: N 87 GLU cc_start: 0.7447 (tm-30) cc_final: 0.7245 (tm-30) REVERT: N 107 ASP cc_start: 0.7525 (m-30) cc_final: 0.7208 (m-30) REVERT: N 115 GLU cc_start: 0.7243 (mp0) cc_final: 0.6941 (mp0) REVERT: O 120 ARG cc_start: 0.7409 (ttm-80) cc_final: 0.7192 (ttm-80) REVERT: P 22 SER cc_start: 0.8409 (OUTLIER) cc_final: 0.8062 (t) REVERT: P 107 ASP cc_start: 0.7176 (m-30) cc_final: 0.6923 (m-30) REVERT: Q 39 GLN cc_start: 0.7716 (tm-30) cc_final: 0.7251 (tm-30) REVERT: Q 108 ASP cc_start: 0.8585 (m-30) cc_final: 0.8296 (m-30) REVERT: Q 148 ASP cc_start: 0.7406 (m-30) cc_final: 0.7130 (m-30) REVERT: R 1 MET cc_start: 0.7473 (ptp) cc_final: 0.6808 (ptp) REVERT: R 68 GLN cc_start: 0.7552 (mm-40) cc_final: 0.7333 (mp10) REVERT: R 166 ARG cc_start: 0.7321 (OUTLIER) cc_final: 0.6772 (ptp-170) REVERT: S 35 ASN cc_start: 0.8574 (m-40) cc_final: 0.8273 (m-40) REVERT: S 116 ASP cc_start: 0.7016 (OUTLIER) cc_final: 0.6792 (m-30) REVERT: T 15 ARG cc_start: 0.7743 (mtp85) cc_final: 0.7518 (mtm110) REVERT: T 135 LYS cc_start: 0.8168 (ttpt) cc_final: 0.7925 (ttpt) REVERT: V 79 MET cc_start: 0.7986 (OUTLIER) cc_final: 0.7479 (tmm) REVERT: V 152 ASP cc_start: 0.6682 (t0) cc_final: 0.6342 (t0) REVERT: X 25 ASP cc_start: 0.6512 (m-30) cc_final: 0.6224 (m-30) REVERT: X 33 GLU cc_start: 0.6957 (mm-30) cc_final: 0.6656 (mm-30) REVERT: X 132 GLN cc_start: 0.7678 (mm110) cc_final: 0.7407 (mm110) REVERT: Y 1 MET cc_start: 0.6760 (mtm) cc_final: 0.6264 (mtm) REVERT: Y 11 THR cc_start: 0.7975 (m) cc_final: 0.6978 (p) REVERT: Y 15 GLN cc_start: 0.7762 (mp10) cc_final: 0.7201 (mp10) REVERT: Y 68 GLN cc_start: 0.7632 (OUTLIER) cc_final: 0.6956 (mt0) REVERT: Y 117 GLU cc_start: 0.6946 (OUTLIER) cc_final: 0.6712 (tt0) REVERT: Z 114 ARG cc_start: 0.7547 (tpt-90) cc_final: 0.7328 (tpp-160) REVERT: a 65 TYR cc_start: 0.7950 (p90) cc_final: 0.7487 (p90) REVERT: a 67 THR cc_start: 0.7441 (m) cc_final: 0.7158 (p) REVERT: b 11 GLN cc_start: 0.7661 (mt0) cc_final: 0.7420 (mt0) REVERT: b 36 LYS cc_start: 0.8177 (OUTLIER) cc_final: 0.7703 (mtpt) REVERT: b 106 GLU cc_start: 0.6847 (mm-30) cc_final: 0.6105 (mm-30) REVERT: c 11 THR cc_start: 0.8387 (t) cc_final: 0.8071 (m) REVERT: c 49 GLN cc_start: 0.7512 (tp-100) cc_final: 0.7049 (pm20) REVERT: c 53 ASN cc_start: 0.8470 (m-40) cc_final: 0.8034 (m110) REVERT: c 68 GLN cc_start: 0.7351 (mt0) cc_final: 0.7095 (mt0) REVERT: d 133 LYS cc_start: 0.8401 (mttm) cc_final: 0.8118 (mttm) REVERT: d 134 MET cc_start: 0.8803 (mtm) cc_final: 0.8591 (mtm) REVERT: d 159 GLU cc_start: 0.7732 (tt0) cc_final: 0.7420 (tt0) REVERT: e 42 LYS cc_start: 0.7668 (ttpt) cc_final: 0.7307 (tptp) REVERT: e 53 ASN cc_start: 0.7996 (m-40) cc_final: 0.7711 (m110) REVERT: e 123 ASP cc_start: 0.7462 (t0) cc_final: 0.7060 (t0) REVERT: e 161 ASN cc_start: 0.7848 (m-40) cc_final: 0.7631 (m-40) REVERT: e 162 SER cc_start: 0.8266 (OUTLIER) cc_final: 0.8010 (p) REVERT: f 35 ASN cc_start: 0.7609 (OUTLIER) cc_final: 0.7309 (m-40) REVERT: f 87 GLU cc_start: 0.6965 (mt-10) cc_final: 0.6761 (tm-30) REVERT: g 131 GLU cc_start: 0.7080 (tp30) cc_final: 0.6712 (tp30) REVERT: h 11 GLN cc_start: 0.7878 (OUTLIER) cc_final: 0.7475 (mt0) REVERT: h 79 MET cc_start: 0.8809 (tpp) cc_final: 0.8376 (tpp) REVERT: i 42 LYS cc_start: 0.7341 (tttm) cc_final: 0.7083 (tppt) REVERT: i 70 GLN cc_start: 0.7092 (mm-40) cc_final: 0.6832 (mm110) REVERT: j 62 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.7018 (tt0) REVERT: j 106 GLU cc_start: 0.7159 (OUTLIER) cc_final: 0.5672 (pm20) REVERT: k 17 GLU cc_start: 0.6469 (OUTLIER) cc_final: 0.6132 (mp0) REVERT: l 41 ARG cc_start: 0.7732 (OUTLIER) cc_final: 0.7353 (ttt-90) REVERT: l 101 LYS cc_start: 0.8652 (tttt) cc_final: 0.8402 (tttp) REVERT: m 11 SER cc_start: 0.7026 (m) cc_final: 0.6814 (t) REVERT: m 19 ARG cc_start: 0.7561 (OUTLIER) cc_final: 0.6844 (tpm170) REVERT: m 30 GLN cc_start: 0.7121 (mm-40) cc_final: 0.6909 (mm-40) REVERT: m 66 MET cc_start: 0.7039 (mtm) cc_final: 0.6559 (mtm) REVERT: n 29 ARG cc_start: 0.7175 (ttm110) cc_final: 0.6457 (mtt90) REVERT: n 44 ASN cc_start: 0.6883 (t160) cc_final: 0.6633 (t0) REVERT: n 55 ASN cc_start: 0.7806 (m-40) cc_final: 0.7395 (t0) REVERT: n 134 LYS cc_start: 0.7502 (mttp) cc_final: 0.7095 (mttp) outliers start: 133 outliers final: 40 residues processed: 1113 average time/residue: 1.4717 time to fit residues: 2036.0778 Evaluate side-chains 1004 residues out of total 5289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 944 time to evaluate : 4.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 135 LYS Chi-restraints excluded: chain D residue 15 ARG Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 116 ASP Chi-restraints excluded: chain H residue 11 GLN Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 154 SER Chi-restraints excluded: chain I residue 112 ILE Chi-restraints excluded: chain I residue 125 SER Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 106 GLU Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain M residue 50 SER Chi-restraints excluded: chain P residue 22 SER Chi-restraints excluded: chain P residue 103 SER Chi-restraints excluded: chain P residue 154 SER Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 166 ARG Chi-restraints excluded: chain S residue 50 SER Chi-restraints excluded: chain S residue 116 ASP Chi-restraints excluded: chain T residue 149 THR Chi-restraints excluded: chain U residue 50 SER Chi-restraints excluded: chain U residue 162 SER Chi-restraints excluded: chain V residue 28 SER Chi-restraints excluded: chain V residue 79 MET Chi-restraints excluded: chain W residue 3 THR Chi-restraints excluded: chain W residue 50 SER Chi-restraints excluded: chain W residue 125 SER Chi-restraints excluded: chain Y residue 68 GLN Chi-restraints excluded: chain Y residue 117 GLU Chi-restraints excluded: chain a residue 164 LEU Chi-restraints excluded: chain b residue 36 LYS Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain e residue 116 ASP Chi-restraints excluded: chain e residue 162 SER Chi-restraints excluded: chain f residue 35 ASN Chi-restraints excluded: chain g residue 10 SER Chi-restraints excluded: chain g residue 50 SER Chi-restraints excluded: chain h residue 11 GLN Chi-restraints excluded: chain j residue 22 SER Chi-restraints excluded: chain j residue 30 THR Chi-restraints excluded: chain j residue 62 GLU Chi-restraints excluded: chain j residue 106 GLU Chi-restraints excluded: chain k residue 17 GLU Chi-restraints excluded: chain k residue 207 SER Chi-restraints excluded: chain l residue 41 ARG Chi-restraints excluded: chain l residue 206 SER Chi-restraints excluded: chain l residue 251 ASP Chi-restraints excluded: chain m residue 19 ARG Chi-restraints excluded: chain m residue 46 SER Chi-restraints excluded: chain m residue 71 VAL Chi-restraints excluded: chain n residue 37 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 676 random chunks: chunk 341 optimal weight: 0.7980 chunk 190 optimal weight: 5.9990 chunk 510 optimal weight: 1.9990 chunk 418 optimal weight: 0.0020 chunk 169 optimal weight: 8.9990 chunk 614 optimal weight: 0.9980 chunk 664 optimal weight: 0.9990 chunk 547 optimal weight: 0.6980 chunk 609 optimal weight: 2.9990 chunk 209 optimal weight: 3.9990 chunk 493 optimal weight: 0.9980 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 140 HIS C 35 ASN D 11 GLN E 15 GLN E 33 GLN E 39 GLN E 47 ASN E 139 ASN E 169 ASN ** F 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 132 GLN ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 ASN ** G 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 132 GLN K 15 GLN ** K 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 68 GLN M 35 ASN N 132 GLN Q 47 ASN Q 78 GLN Q 139 ASN Q 140 HIS R 132 GLN S 139 ASN T 47 ASN ** T 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 146 ASN U 15 GLN ** U 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 53 ASN ** U 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 111 ASN V 146 ASN ** W 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 39 GLN ** Y 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 11 GLN ** Z 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 15 GLN a 39 GLN a 61 ASN a 169 ASN b 72 ASN b 132 GLN ** c 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 15 GLN e 72 ASN e 139 ASN g 39 GLN h 11 GLN h 68 GLN i 39 GLN i 140 HIS j 132 GLN k 270 GLN n 141 ASN n 147 GLN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 55108 Z= 0.173 Angle : 0.576 12.221 74959 Z= 0.269 Chirality : 0.036 0.185 8198 Planarity : 0.004 0.072 9826 Dihedral : 10.146 88.521 10012 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.21 % Favored : 98.76 % Rotamer: Outliers : 2.70 % Allowed : 12.27 % Favored : 85.03 % 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: 1.59 (0.10), residues: 6771 helix: 1.53 (0.07), residues: 5185 sheet: 0.86 (0.62), residues: 48 loop : -0.45 (0.15), residues: 1538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP n 127 HIS 0.009 0.002 HIS M 140 PHE 0.013 0.001 PHE b 98 TYR 0.017 0.001 TYR B 74 ARG 0.007 0.000 ARG M 17 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13542 Ramachandran restraints generated. 6771 Oldfield, 0 Emsley, 6771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13542 Ramachandran restraints generated. 6771 Oldfield, 0 Emsley, 6771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1159 residues out of total 5289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 1016 time to evaluate : 4.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LYS cc_start: 0.8220 (tmtt) cc_final: 0.7987 (tttp) REVERT: A 116 ASP cc_start: 0.7197 (m-30) cc_final: 0.6933 (m-30) REVERT: A 134 LYS cc_start: 0.8065 (mmtp) cc_final: 0.7803 (tppp) REVERT: A 159 GLU cc_start: 0.7609 (tm-30) cc_final: 0.7279 (tt0) REVERT: B 133 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.8026 (mttm) REVERT: B 135 LYS cc_start: 0.7858 (ttpp) cc_final: 0.7607 (ttpt) REVERT: C 15 GLN cc_start: 0.7478 (mp10) cc_final: 0.7270 (mt0) REVERT: C 46 ASP cc_start: 0.6985 (m-30) cc_final: 0.6715 (m-30) REVERT: C 50 SER cc_start: 0.8236 (OUTLIER) cc_final: 0.7984 (p) REVERT: C 131 GLU cc_start: 0.7949 (tp30) cc_final: 0.7654 (tp30) REVERT: D 15 ARG cc_start: 0.6910 (OUTLIER) cc_final: 0.6154 (ttm-80) REVERT: D 23 GLN cc_start: 0.7516 (tt0) cc_final: 0.7173 (tt0) REVERT: D 141 ILE cc_start: 0.8207 (pp) cc_final: 0.7950 (mt) REVERT: E 31 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8110 (mt) REVERT: E 46 ASP cc_start: 0.7074 (p0) cc_final: 0.6867 (p0) REVERT: G 39 GLN cc_start: 0.7599 (tp40) cc_final: 0.7392 (mm110) REVERT: G 131 GLU cc_start: 0.7903 (tp30) cc_final: 0.7580 (tp30) REVERT: G 169 ASN cc_start: 0.8380 (m-40) cc_final: 0.8089 (m110) REVERT: H 11 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.6509 (mt0) REVERT: H 68 GLN cc_start: 0.7590 (OUTLIER) cc_final: 0.6357 (pp30) REVERT: I 49 GLN cc_start: 0.6993 (tp-100) cc_final: 0.6499 (pm20) REVERT: I 50 SER cc_start: 0.8432 (t) cc_final: 0.7999 (p) REVERT: I 109 GLU cc_start: 0.6499 (mm-30) cc_final: 0.6292 (mm-30) REVERT: I 143 SER cc_start: 0.7008 (p) cc_final: 0.6607 (m) REVERT: I 145 ASP cc_start: 0.7260 (m-30) cc_final: 0.7018 (m-30) REVERT: J 15 ARG cc_start: 0.7046 (mtm110) cc_final: 0.6771 (mtm110) REVERT: J 79 MET cc_start: 0.8603 (tpp) cc_final: 0.8292 (tpp) REVERT: J 115 GLU cc_start: 0.7851 (mp0) cc_final: 0.7487 (mp0) REVERT: K 53 ASN cc_start: 0.7253 (m-40) cc_final: 0.6862 (m110) REVERT: K 81 LYS cc_start: 0.8425 (mttm) cc_final: 0.8054 (mttt) REVERT: K 117 GLU cc_start: 0.6981 (mp0) cc_final: 0.6733 (mp0) REVERT: K 137 LYS cc_start: 0.8323 (OUTLIER) cc_final: 0.7996 (mtmm) REVERT: M 20 SER cc_start: 0.8643 (p) cc_final: 0.8417 (m) REVERT: M 49 GLN cc_start: 0.7966 (tp-100) cc_final: 0.7488 (pm20) REVERT: N 87 GLU cc_start: 0.7406 (tm-30) cc_final: 0.7187 (tm-30) REVERT: N 107 ASP cc_start: 0.7552 (m-30) cc_final: 0.7263 (m-30) REVERT: N 115 GLU cc_start: 0.7258 (mp0) cc_final: 0.6905 (mp0) REVERT: O 120 ARG cc_start: 0.7426 (ttm-80) cc_final: 0.7189 (ttm-80) REVERT: P 22 SER cc_start: 0.8467 (OUTLIER) cc_final: 0.8149 (t) REVERT: Q 108 ASP cc_start: 0.8604 (m-30) cc_final: 0.8274 (m-30) REVERT: Q 148 ASP cc_start: 0.7439 (m-30) cc_final: 0.7225 (m-30) REVERT: R 1 MET cc_start: 0.7698 (ptp) cc_final: 0.7063 (ptp) REVERT: S 35 ASN cc_start: 0.8535 (m-40) cc_final: 0.8289 (m-40) REVERT: T 135 LYS cc_start: 0.8305 (ttpt) cc_final: 0.8088 (ttpt) REVERT: U 39 GLN cc_start: 0.7428 (OUTLIER) cc_final: 0.7136 (tm130) REVERT: U 77 ASP cc_start: 0.7916 (OUTLIER) cc_final: 0.7584 (p0) REVERT: U 125 SER cc_start: 0.8706 (m) cc_final: 0.8438 (t) REVERT: V 79 MET cc_start: 0.7784 (OUTLIER) cc_final: 0.7577 (tmm) REVERT: V 152 ASP cc_start: 0.7043 (t0) cc_final: 0.6601 (t0) REVERT: W 78 GLN cc_start: 0.7887 (tp40) cc_final: 0.7243 (tp40) REVERT: X 25 ASP cc_start: 0.6557 (m-30) cc_final: 0.6280 (m-30) REVERT: X 68 GLN cc_start: 0.7913 (OUTLIER) cc_final: 0.7648 (tp-100) REVERT: X 132 GLN cc_start: 0.7677 (mm110) cc_final: 0.7400 (mm-40) REVERT: Y 1 MET cc_start: 0.6791 (mtm) cc_final: 0.6318 (mtm) REVERT: Y 11 THR cc_start: 0.8060 (m) cc_final: 0.7034 (p) REVERT: Y 15 GLN cc_start: 0.7880 (mp10) cc_final: 0.7432 (mp10) REVERT: Y 39 GLN cc_start: 0.7551 (OUTLIER) cc_final: 0.7244 (mt0) REVERT: Y 68 GLN cc_start: 0.7733 (OUTLIER) cc_final: 0.6979 (mt0) REVERT: Y 117 GLU cc_start: 0.6920 (OUTLIER) cc_final: 0.6695 (tt0) REVERT: Z 17 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.6838 (tm-30) REVERT: a 62 LYS cc_start: 0.7893 (ttmp) cc_final: 0.7641 (ttmm) REVERT: a 65 TYR cc_start: 0.7992 (p90) cc_final: 0.7542 (p90) REVERT: a 67 THR cc_start: 0.7566 (m) cc_final: 0.7200 (p) REVERT: b 106 GLU cc_start: 0.6912 (mm-30) cc_final: 0.6295 (mm-30) REVERT: c 11 THR cc_start: 0.8410 (t) cc_final: 0.8159 (m) REVERT: c 49 GLN cc_start: 0.7531 (tp-100) cc_final: 0.7066 (pm20) REVERT: c 53 ASN cc_start: 0.8501 (m-40) cc_final: 0.8079 (m110) REVERT: c 68 GLN cc_start: 0.7406 (mt0) cc_final: 0.7164 (mt0) REVERT: d 36 LYS cc_start: 0.8465 (mtmm) cc_final: 0.8256 (mtmp) REVERT: d 134 MET cc_start: 0.8803 (mtm) cc_final: 0.8354 (mtm) REVERT: d 136 GLU cc_start: 0.6963 (OUTLIER) cc_final: 0.6437 (pt0) REVERT: d 140 ASP cc_start: 0.6563 (OUTLIER) cc_final: 0.6193 (m-30) REVERT: d 159 GLU cc_start: 0.7732 (tt0) cc_final: 0.7436 (tt0) REVERT: e 42 LYS cc_start: 0.7727 (ttpt) cc_final: 0.7359 (tptp) REVERT: e 70 GLN cc_start: 0.6484 (mp10) cc_final: 0.6114 (mm110) REVERT: e 123 ASP cc_start: 0.7413 (t0) cc_final: 0.7018 (t0) REVERT: e 159 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.7194 (mt-10) REVERT: e 162 SER cc_start: 0.8278 (OUTLIER) cc_final: 0.8049 (p) REVERT: f 35 ASN cc_start: 0.7836 (OUTLIER) cc_final: 0.7593 (m-40) REVERT: g 131 GLU cc_start: 0.7121 (tp30) cc_final: 0.6802 (tp30) REVERT: g 147 ARG cc_start: 0.7250 (ttp-170) cc_final: 0.6976 (ttp80) REVERT: h 17 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7315 (pt0) REVERT: h 79 MET cc_start: 0.8836 (tpp) cc_final: 0.8340 (tpp) REVERT: i 1 MET cc_start: 0.6805 (mmt) cc_final: 0.6218 (mmt) REVERT: i 15 GLN cc_start: 0.7505 (mp10) cc_final: 0.7289 (mp10) REVERT: i 42 LYS cc_start: 0.7341 (tttm) cc_final: 0.7128 (tppt) REVERT: i 70 GLN cc_start: 0.7095 (mm-40) cc_final: 0.6870 (mm110) REVERT: j 15 ARG cc_start: 0.7084 (mtp-110) cc_final: 0.6773 (mtm-85) REVERT: j 62 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.7121 (tt0) REVERT: j 106 GLU cc_start: 0.7159 (OUTLIER) cc_final: 0.5695 (pm20) REVERT: k 17 GLU cc_start: 0.6507 (OUTLIER) cc_final: 0.6187 (mp0) REVERT: k 19 ARG cc_start: 0.7283 (OUTLIER) cc_final: 0.6890 (mmt90) REVERT: k 278 LEU cc_start: 0.7536 (OUTLIER) cc_final: 0.7270 (mp) REVERT: l 41 ARG cc_start: 0.7802 (OUTLIER) cc_final: 0.7448 (ttt-90) REVERT: l 101 LYS cc_start: 0.8632 (tttt) cc_final: 0.8374 (tttp) REVERT: m 11 SER cc_start: 0.7213 (m) cc_final: 0.6876 (t) REVERT: m 19 ARG cc_start: 0.7592 (OUTLIER) cc_final: 0.6913 (tpm170) REVERT: m 30 GLN cc_start: 0.7122 (mm-40) cc_final: 0.6892 (mm-40) REVERT: m 66 MET cc_start: 0.7002 (mtm) cc_final: 0.6528 (mtm) REVERT: n 55 ASN cc_start: 0.8006 (m-40) cc_final: 0.7532 (t0) REVERT: n 134 LYS cc_start: 0.7497 (mttp) cc_final: 0.7059 (mttp) REVERT: n 156 ASP cc_start: 0.7565 (OUTLIER) cc_final: 0.7225 (m-30) outliers start: 143 outliers final: 46 residues processed: 1082 average time/residue: 1.4891 time to fit residues: 1998.7522 Evaluate side-chains 1022 residues out of total 5289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 946 time to evaluate : 4.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain D residue 15 ARG Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 116 ASP Chi-restraints excluded: chain H residue 11 GLN Chi-restraints excluded: chain H residue 68 GLN Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain K residue 137 LYS Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 132 GLN Chi-restraints excluded: chain L residue 156 ILE Chi-restraints excluded: chain M residue 50 SER Chi-restraints excluded: chain M residue 70 GLN Chi-restraints excluded: chain P residue 22 SER Chi-restraints excluded: chain Q residue 10 SER Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 166 ARG Chi-restraints excluded: chain S residue 50 SER Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 39 GLN Chi-restraints excluded: chain U residue 50 SER Chi-restraints excluded: chain U residue 77 ASP Chi-restraints excluded: chain U residue 116 ASP Chi-restraints excluded: chain V residue 28 SER Chi-restraints excluded: chain V residue 79 MET Chi-restraints excluded: chain W residue 3 THR Chi-restraints excluded: chain W residue 50 SER Chi-restraints excluded: chain X residue 68 GLN Chi-restraints excluded: chain Y residue 39 GLN Chi-restraints excluded: chain Y residue 67 THR Chi-restraints excluded: chain Y residue 68 GLN Chi-restraints excluded: chain Y residue 117 GLU Chi-restraints excluded: chain Z residue 1 MET Chi-restraints excluded: chain Z residue 17 GLU Chi-restraints excluded: chain a residue 162 SER Chi-restraints excluded: chain a residue 164 LEU Chi-restraints excluded: chain c residue 7 GLU Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain d residue 136 GLU Chi-restraints excluded: chain d residue 140 ASP Chi-restraints excluded: chain e residue 20 SER Chi-restraints excluded: chain e residue 116 ASP Chi-restraints excluded: chain e residue 159 GLU Chi-restraints excluded: chain e residue 162 SER Chi-restraints excluded: chain f residue 33 GLU Chi-restraints excluded: chain f residue 35 ASN Chi-restraints excluded: chain f residue 115 GLU Chi-restraints excluded: chain g residue 10 SER Chi-restraints excluded: chain g residue 50 SER Chi-restraints excluded: chain g residue 143 SER Chi-restraints excluded: chain h residue 17 GLU Chi-restraints excluded: chain i residue 31 LEU Chi-restraints excluded: chain j residue 4 VAL Chi-restraints excluded: chain j residue 17 GLU Chi-restraints excluded: chain j residue 62 GLU Chi-restraints excluded: chain j residue 106 GLU Chi-restraints excluded: chain k residue 17 GLU Chi-restraints excluded: chain k residue 19 ARG Chi-restraints excluded: chain k residue 207 SER Chi-restraints excluded: chain k residue 278 LEU Chi-restraints excluded: chain l residue 41 ARG Chi-restraints excluded: chain l residue 206 SER Chi-restraints excluded: chain l residue 251 ASP Chi-restraints excluded: chain m residue 19 ARG Chi-restraints excluded: chain m residue 46 SER Chi-restraints excluded: chain n residue 37 LEU Chi-restraints excluded: chain n residue 156 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 676 random chunks: chunk 607 optimal weight: 1.9990 chunk 462 optimal weight: 6.9990 chunk 319 optimal weight: 3.9990 chunk 68 optimal weight: 8.9990 chunk 293 optimal weight: 2.9990 chunk 412 optimal weight: 1.9990 chunk 617 optimal weight: 1.9990 chunk 653 optimal weight: 6.9990 chunk 322 optimal weight: 5.9990 chunk 584 optimal weight: 10.0000 chunk 176 optimal weight: 0.6980 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 GLN D 11 GLN D 47 ASN D 111 ASN D 132 GLN E 33 GLN E 39 GLN ** F 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 132 GLN ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 ASN ** G 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 169 ASN H 47 ASN ** I 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 132 GLN K 15 GLN ** K 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 11 GLN L 68 GLN M 35 ASN M 78 GLN M 139 ASN N 132 GLN ** O 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 146 ASN Q 47 ASN Q 139 ASN R 42 ASN R 47 ASN ** S 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 47 ASN ** T 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 146 ASN U 15 GLN ** U 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 140 HIS V 47 ASN V 111 ASN V 146 ASN ** W 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 47 ASN ** X 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 11 GLN Z 35 ASN ** Z 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 61 ASN a 169 ASN b 132 GLN ** c 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 132 GLN ** d 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 15 GLN e 139 ASN g 39 GLN h 11 GLN h 68 GLN j 132 GLN ** k 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 270 GLN l 259 GLN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 55108 Z= 0.313 Angle : 0.657 12.363 74959 Z= 0.314 Chirality : 0.040 0.213 8198 Planarity : 0.005 0.052 9826 Dihedral : 10.446 89.399 10012 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.48 % Favored : 98.51 % Rotamer: Outliers : 3.25 % Allowed : 12.91 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 1.48 (0.10), residues: 6771 helix: 1.44 (0.07), residues: 5296 sheet: 0.78 (0.62), residues: 48 loop : -0.59 (0.16), residues: 1427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP i 128 HIS 0.009 0.003 HIS G 140 PHE 0.020 0.002 PHE O 122 TYR 0.023 0.002 TYR b 92 ARG 0.016 0.001 ARG H 77 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13542 Ramachandran restraints generated. 6771 Oldfield, 0 Emsley, 6771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13542 Ramachandran restraints generated. 6771 Oldfield, 0 Emsley, 6771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1159 residues out of total 5289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 987 time to evaluate : 4.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LYS cc_start: 0.8290 (tmtt) cc_final: 0.8060 (tttp) REVERT: A 116 ASP cc_start: 0.7291 (m-30) cc_final: 0.6987 (m-30) REVERT: B 135 LYS cc_start: 0.7917 (OUTLIER) cc_final: 0.7644 (ttpt) REVERT: B 136 GLU cc_start: 0.7411 (pp20) cc_final: 0.7195 (pp20) REVERT: C 46 ASP cc_start: 0.7006 (m-30) cc_final: 0.6534 (m-30) REVERT: D 15 ARG cc_start: 0.7383 (OUTLIER) cc_final: 0.6657 (ttm-80) REVERT: D 23 GLN cc_start: 0.7853 (tt0) cc_final: 0.7646 (tt0) REVERT: D 40 SER cc_start: 0.8733 (OUTLIER) cc_final: 0.8471 (p) REVERT: E 46 ASP cc_start: 0.7117 (p0) cc_final: 0.6891 (p0) REVERT: E 159 GLU cc_start: 0.7319 (tp30) cc_final: 0.7095 (tt0) REVERT: G 39 GLN cc_start: 0.7552 (tp40) cc_final: 0.7317 (mm110) REVERT: G 131 GLU cc_start: 0.7984 (tp30) cc_final: 0.7644 (tp30) REVERT: G 147 ARG cc_start: 0.8314 (ttp-110) cc_final: 0.8005 (tmm-80) REVERT: G 169 ASN cc_start: 0.8496 (m110) cc_final: 0.8251 (m110) REVERT: H 11 GLN cc_start: 0.8039 (OUTLIER) cc_final: 0.6821 (mt0) REVERT: H 149 THR cc_start: 0.8590 (OUTLIER) cc_final: 0.8387 (t) REVERT: I 1 MET cc_start: 0.6807 (OUTLIER) cc_final: 0.6603 (mpp) REVERT: I 15 GLN cc_start: 0.7836 (mt0) cc_final: 0.7580 (mt0) REVERT: I 49 GLN cc_start: 0.7051 (tp-100) cc_final: 0.6511 (pm20) REVERT: I 50 SER cc_start: 0.8386 (t) cc_final: 0.7881 (p) REVERT: I 109 GLU cc_start: 0.6824 (mm-30) cc_final: 0.6616 (mm-30) REVERT: I 143 SER cc_start: 0.7244 (p) cc_final: 0.6842 (m) REVERT: I 145 ASP cc_start: 0.7289 (m-30) cc_final: 0.7020 (m-30) REVERT: J 15 ARG cc_start: 0.7300 (mtm110) cc_final: 0.7100 (mtm110) REVERT: J 79 MET cc_start: 0.8631 (tpp) cc_final: 0.8384 (tpp) REVERT: J 115 GLU cc_start: 0.7883 (mp0) cc_final: 0.7531 (mp0) REVERT: K 67 THR cc_start: 0.8094 (m) cc_final: 0.7752 (p) REVERT: K 68 GLN cc_start: 0.6895 (mp10) cc_final: 0.6538 (mm110) REVERT: K 81 LYS cc_start: 0.8446 (mttm) cc_final: 0.8125 (mttt) REVERT: K 117 GLU cc_start: 0.6944 (mp0) cc_final: 0.6722 (mp0) REVERT: K 137 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.7933 (mtmm) REVERT: L 25 ASP cc_start: 0.7021 (m-30) cc_final: 0.6484 (m-30) REVERT: M 20 SER cc_start: 0.8787 (p) cc_final: 0.8516 (m) REVERT: M 49 GLN cc_start: 0.7996 (tp-100) cc_final: 0.7418 (pm20) REVERT: N 107 ASP cc_start: 0.7753 (m-30) cc_final: 0.7485 (m-30) REVERT: N 115 GLU cc_start: 0.7173 (mp0) cc_final: 0.6849 (mp0) REVERT: N 133 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8599 (mttm) REVERT: N 134 MET cc_start: 0.8837 (mtm) cc_final: 0.8350 (mtm) REVERT: P 22 SER cc_start: 0.8588 (OUTLIER) cc_final: 0.8344 (t) REVERT: Q 15 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.8082 (mt0) REVERT: Q 148 ASP cc_start: 0.7518 (m-30) cc_final: 0.7314 (m-30) REVERT: R 1 MET cc_start: 0.7916 (ptp) cc_final: 0.7452 (ptp) REVERT: R 68 GLN cc_start: 0.7314 (OUTLIER) cc_final: 0.6975 (mt0) REVERT: S 35 ASN cc_start: 0.8781 (m-40) cc_final: 0.8505 (m-40) REVERT: U 77 ASP cc_start: 0.7952 (OUTLIER) cc_final: 0.7611 (p0) REVERT: U 125 SER cc_start: 0.8767 (m) cc_final: 0.8551 (t) REVERT: V 152 ASP cc_start: 0.7412 (t0) cc_final: 0.6993 (t0) REVERT: W 49 GLN cc_start: 0.7451 (OUTLIER) cc_final: 0.7123 (tp-100) REVERT: X 25 ASP cc_start: 0.6897 (m-30) cc_final: 0.6642 (m-30) REVERT: X 68 GLN cc_start: 0.7879 (OUTLIER) cc_final: 0.7646 (tp-100) REVERT: X 132 GLN cc_start: 0.7785 (mm110) cc_final: 0.7514 (mm-40) REVERT: X 143 ASN cc_start: 0.7671 (m-40) cc_final: 0.7452 (m-40) REVERT: Y 39 GLN cc_start: 0.7448 (OUTLIER) cc_final: 0.7176 (mt0) REVERT: Y 68 GLN cc_start: 0.7783 (OUTLIER) cc_final: 0.7081 (mt0) REVERT: a 62 LYS cc_start: 0.7924 (ttmp) cc_final: 0.7654 (ttmm) REVERT: a 65 TYR cc_start: 0.8024 (p90) cc_final: 0.7579 (p90) REVERT: a 86 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.6863 (tmm-80) REVERT: a 109 GLU cc_start: 0.7453 (tm-30) cc_final: 0.6929 (tm-30) REVERT: a 159 GLU cc_start: 0.6913 (tt0) cc_final: 0.6613 (mt-10) REVERT: b 11 GLN cc_start: 0.7776 (mt0) cc_final: 0.7504 (mm-40) REVERT: b 36 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7791 (mtpt) REVERT: b 86 MET cc_start: 0.8177 (mmm) cc_final: 0.7875 (mtp) REVERT: b 106 GLU cc_start: 0.6823 (mm-30) cc_final: 0.6168 (mm-30) REVERT: c 11 THR cc_start: 0.8493 (t) cc_final: 0.8198 (m) REVERT: c 49 GLN cc_start: 0.7721 (tp-100) cc_final: 0.7073 (pm20) REVERT: c 53 ASN cc_start: 0.8365 (m-40) cc_final: 0.7963 (m110) REVERT: d 136 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.6714 (mt-10) REVERT: d 140 ASP cc_start: 0.6665 (OUTLIER) cc_final: 0.6330 (m-30) REVERT: d 159 GLU cc_start: 0.7805 (tt0) cc_final: 0.7539 (tt0) REVERT: e 42 LYS cc_start: 0.7829 (ttpt) cc_final: 0.7448 (tptp) REVERT: e 78 GLN cc_start: 0.7322 (tp40) cc_final: 0.7030 (tp-100) REVERT: e 123 ASP cc_start: 0.7404 (t0) cc_final: 0.7029 (t0) REVERT: e 162 SER cc_start: 0.8257 (OUTLIER) cc_final: 0.8019 (p) REVERT: f 62 GLU cc_start: 0.6133 (OUTLIER) cc_final: 0.5748 (pm20) REVERT: f 86 MET cc_start: 0.8260 (mtp) cc_final: 0.7953 (mtp) REVERT: g 23 GLU cc_start: 0.8113 (mp0) cc_final: 0.7897 (mp0) REVERT: g 131 GLU cc_start: 0.7186 (tp30) cc_final: 0.6865 (tp30) REVERT: h 79 MET cc_start: 0.8890 (tpp) cc_final: 0.8591 (tpp) REVERT: i 42 LYS cc_start: 0.7511 (tttm) cc_final: 0.7247 (tptt) REVERT: i 70 GLN cc_start: 0.7132 (mm-40) cc_final: 0.6904 (mm110) REVERT: j 15 ARG cc_start: 0.7278 (mtp180) cc_final: 0.7014 (mtm-85) REVERT: j 62 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.7072 (tt0) REVERT: j 79 MET cc_start: 0.8985 (tpp) cc_final: 0.7268 (tpp) REVERT: j 106 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.5897 (pm20) REVERT: k 17 GLU cc_start: 0.6822 (OUTLIER) cc_final: 0.6455 (mp0) REVERT: l 41 ARG cc_start: 0.7953 (OUTLIER) cc_final: 0.7632 (ttm-80) REVERT: l 206 SER cc_start: 0.7711 (OUTLIER) cc_final: 0.7496 (t) REVERT: m 11 SER cc_start: 0.7358 (m) cc_final: 0.7025 (t) REVERT: m 19 ARG cc_start: 0.7694 (OUTLIER) cc_final: 0.7019 (tpm170) REVERT: m 25 VAL cc_start: 0.8494 (m) cc_final: 0.8283 (t) REVERT: m 30 GLN cc_start: 0.7132 (mm-40) cc_final: 0.6857 (mm-40) REVERT: m 66 MET cc_start: 0.7006 (mtm) cc_final: 0.6515 (mtm) REVERT: m 69 LYS cc_start: 0.7784 (OUTLIER) cc_final: 0.6926 (tmtm) REVERT: n 55 ASN cc_start: 0.8100 (m-40) cc_final: 0.7605 (t0) REVERT: n 121 GLU cc_start: 0.6973 (OUTLIER) cc_final: 0.6685 (pt0) REVERT: n 134 LYS cc_start: 0.7675 (mttp) cc_final: 0.7290 (mttp) outliers start: 172 outliers final: 73 residues processed: 1069 average time/residue: 1.5241 time to fit residues: 2014.6610 Evaluate side-chains 1027 residues out of total 5289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 924 time to evaluate : 4.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 135 LYS Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain D residue 15 ARG Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain G residue 116 ASP Chi-restraints excluded: chain H residue 11 GLN Chi-restraints excluded: chain H residue 141 ILE Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 154 SER Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain K residue 137 LYS Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 132 GLN Chi-restraints excluded: chain L residue 156 ILE Chi-restraints excluded: chain M residue 50 SER Chi-restraints excluded: chain M residue 68 GLN Chi-restraints excluded: chain M residue 70 GLN Chi-restraints excluded: chain N residue 133 LYS Chi-restraints excluded: chain O residue 116 ASP Chi-restraints excluded: chain P residue 22 SER Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain P residue 103 SER Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain Q residue 10 SER Chi-restraints excluded: chain Q residue 15 GLN Chi-restraints excluded: chain Q residue 172 SER Chi-restraints excluded: chain R residue 68 GLN Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 166 ARG Chi-restraints excluded: chain S residue 32 ARG Chi-restraints excluded: chain S residue 50 SER Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 149 THR Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 50 SER Chi-restraints excluded: chain U residue 77 ASP Chi-restraints excluded: chain V residue 28 SER Chi-restraints excluded: chain V residue 62 GLU Chi-restraints excluded: chain W residue 3 THR Chi-restraints excluded: chain W residue 42 LYS Chi-restraints excluded: chain W residue 49 GLN Chi-restraints excluded: chain W residue 50 SER Chi-restraints excluded: chain W residue 125 SER Chi-restraints excluded: chain X residue 68 GLN Chi-restraints excluded: chain Y residue 2 LYS Chi-restraints excluded: chain Y residue 39 GLN Chi-restraints excluded: chain Y residue 67 THR Chi-restraints excluded: chain Y residue 68 GLN Chi-restraints excluded: chain a residue 86 ARG Chi-restraints excluded: chain a residue 162 SER Chi-restraints excluded: chain b residue 36 LYS Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain d residue 136 GLU Chi-restraints excluded: chain d residue 140 ASP Chi-restraints excluded: chain e residue 20 SER Chi-restraints excluded: chain e residue 116 ASP Chi-restraints excluded: chain e residue 159 GLU Chi-restraints excluded: chain e residue 162 SER Chi-restraints excluded: chain f residue 62 GLU Chi-restraints excluded: chain f residue 115 GLU Chi-restraints excluded: chain f residue 166 ARG Chi-restraints excluded: chain g residue 10 SER Chi-restraints excluded: chain g residue 50 SER Chi-restraints excluded: chain g residue 143 SER Chi-restraints excluded: chain g residue 145 ASP Chi-restraints excluded: chain h residue 17 GLU Chi-restraints excluded: chain i residue 31 LEU Chi-restraints excluded: chain j residue 4 VAL Chi-restraints excluded: chain j residue 17 GLU Chi-restraints excluded: chain j residue 22 SER Chi-restraints excluded: chain j residue 62 GLU Chi-restraints excluded: chain j residue 75 THR Chi-restraints excluded: chain j residue 106 GLU Chi-restraints excluded: chain j residue 149 THR Chi-restraints excluded: chain k residue 17 GLU Chi-restraints excluded: chain k residue 207 SER Chi-restraints excluded: chain l residue 41 ARG Chi-restraints excluded: chain l residue 198 THR Chi-restraints excluded: chain l residue 206 SER Chi-restraints excluded: chain l residue 251 ASP Chi-restraints excluded: chain m residue 19 ARG Chi-restraints excluded: chain m residue 41 ILE Chi-restraints excluded: chain m residue 46 SER Chi-restraints excluded: chain m residue 47 THR Chi-restraints excluded: chain m residue 69 LYS Chi-restraints excluded: chain n residue 44 ASN Chi-restraints excluded: chain n residue 61 GLN Chi-restraints excluded: chain n residue 121 GLU Chi-restraints excluded: chain n residue 170 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 676 random chunks: chunk 544 optimal weight: 0.6980 chunk 370 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 486 optimal weight: 0.8980 chunk 269 optimal weight: 1.9990 chunk 557 optimal weight: 0.5980 chunk 451 optimal weight: 0.0980 chunk 0 optimal weight: 6.9990 chunk 333 optimal weight: 0.9980 chunk 586 optimal weight: 0.6980 chunk 164 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 11 GLN D 111 ASN D 132 GLN E 33 GLN E 39 GLN E 139 ASN ** F 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 132 GLN ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 ASN ** G 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 169 ASN ** I 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 132 GLN K 15 GLN K 53 ASN L 11 GLN L 68 GLN L 132 GLN M 78 GLN M 139 ASN P 132 GLN Q 15 GLN Q 47 ASN Q 139 ASN ** S 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 63 GLN ** T 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 143 ASN T 146 ASN U 15 GLN ** U 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 111 ASN V 146 ASN ** W 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 39 GLN ** Y 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 11 GLN Z 72 ASN a 61 ASN ** c 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 15 GLN e 139 ASN g 39 GLN h 68 GLN j 132 GLN ** k 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 270 GLN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 55108 Z= 0.164 Angle : 0.557 12.985 74959 Z= 0.263 Chirality : 0.035 0.177 8198 Planarity : 0.003 0.050 9826 Dihedral : 10.384 89.958 10012 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.03 % Favored : 98.95 % Rotamer: Outliers : 2.72 % Allowed : 14.33 % Favored : 82.95 % 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: 1.86 (0.10), residues: 6771 helix: 1.73 (0.07), residues: 5289 sheet: 0.49 (0.61), residues: 45 loop : -0.50 (0.16), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP l 146 HIS 0.008 0.002 HIS M 140 PHE 0.011 0.001 PHE R 98 TYR 0.016 0.001 TYR L 74 ARG 0.011 0.000 ARG n 29 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13542 Ramachandran restraints generated. 6771 Oldfield, 0 Emsley, 6771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13542 Ramachandran restraints generated. 6771 Oldfield, 0 Emsley, 6771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1116 residues out of total 5289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 972 time to evaluate : 4.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LYS cc_start: 0.8268 (tmtt) cc_final: 0.8034 (tttp) REVERT: A 116 ASP cc_start: 0.7204 (m-30) cc_final: 0.6904 (m-30) REVERT: B 115 GLU cc_start: 0.8086 (mp0) cc_final: 0.7702 (mp0) REVERT: B 133 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.8113 (mttm) REVERT: B 135 LYS cc_start: 0.7948 (OUTLIER) cc_final: 0.7677 (ttpt) REVERT: C 50 SER cc_start: 0.8208 (p) cc_final: 0.7941 (p) REVERT: C 70 GLN cc_start: 0.7165 (OUTLIER) cc_final: 0.6084 (tp40) REVERT: C 131 GLU cc_start: 0.7914 (tp30) cc_final: 0.7687 (tp30) REVERT: D 15 ARG cc_start: 0.7352 (OUTLIER) cc_final: 0.6980 (ttm-80) REVERT: D 23 GLN cc_start: 0.7796 (tt0) cc_final: 0.7443 (tt0) REVERT: D 115 GLU cc_start: 0.6875 (mm-30) cc_final: 0.6485 (mm-30) REVERT: E 13 ASP cc_start: 0.7885 (t0) cc_final: 0.7653 (t70) REVERT: E 139 ASN cc_start: 0.8027 (OUTLIER) cc_final: 0.7708 (p0) REVERT: F 166 ARG cc_start: 0.7399 (ttm-80) cc_final: 0.6580 (tpp-160) REVERT: G 3 THR cc_start: 0.8364 (p) cc_final: 0.8070 (t) REVERT: G 131 GLU cc_start: 0.7955 (tp30) cc_final: 0.7616 (tp30) REVERT: G 147 ARG cc_start: 0.8278 (ttp-110) cc_final: 0.8039 (tmm-80) REVERT: G 169 ASN cc_start: 0.8543 (m-40) cc_final: 0.8235 (m110) REVERT: H 11 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.6644 (mt0) REVERT: H 62 GLU cc_start: 0.6972 (OUTLIER) cc_final: 0.6676 (pt0) REVERT: H 86 MET cc_start: 0.8177 (mtp) cc_final: 0.7463 (mtt) REVERT: I 49 GLN cc_start: 0.7074 (tp-100) cc_final: 0.6388 (pm20) REVERT: I 50 SER cc_start: 0.8422 (t) cc_final: 0.7927 (p) REVERT: I 109 GLU cc_start: 0.6802 (mm-30) cc_final: 0.6597 (mm-30) REVERT: I 143 SER cc_start: 0.7175 (p) cc_final: 0.6775 (m) REVERT: I 145 ASP cc_start: 0.7274 (m-30) cc_final: 0.7021 (m-30) REVERT: J 79 MET cc_start: 0.8634 (tpp) cc_final: 0.8431 (tpp) REVERT: J 115 GLU cc_start: 0.7859 (mp0) cc_final: 0.7527 (mp0) REVERT: K 67 THR cc_start: 0.8091 (m) cc_final: 0.7758 (p) REVERT: K 68 GLN cc_start: 0.6831 (mp10) cc_final: 0.6443 (mm110) REVERT: K 81 LYS cc_start: 0.8408 (mttm) cc_final: 0.8079 (mttt) REVERT: K 117 GLU cc_start: 0.6918 (mp0) cc_final: 0.6708 (mp0) REVERT: K 137 LYS cc_start: 0.8323 (OUTLIER) cc_final: 0.7970 (mtmm) REVERT: L 25 ASP cc_start: 0.6995 (m-30) cc_final: 0.6476 (m-30) REVERT: L 132 GLN cc_start: 0.7787 (OUTLIER) cc_final: 0.6331 (mp-120) REVERT: M 49 GLN cc_start: 0.7900 (tp-100) cc_final: 0.7416 (pm20) REVERT: M 68 GLN cc_start: 0.7728 (OUTLIER) cc_final: 0.7232 (pt0) REVERT: N 107 ASP cc_start: 0.7646 (m-30) cc_final: 0.7386 (m-30) REVERT: N 115 GLU cc_start: 0.7170 (mp0) cc_final: 0.6861 (mp0) REVERT: P 22 SER cc_start: 0.8550 (OUTLIER) cc_final: 0.8298 (t) REVERT: Q 108 ASP cc_start: 0.8486 (m-30) cc_final: 0.8276 (m-30) REVERT: Q 148 ASP cc_start: 0.7533 (m-30) cc_final: 0.7332 (m-30) REVERT: R 1 MET cc_start: 0.7892 (ptp) cc_final: 0.7344 (ptp) REVERT: S 35 ASN cc_start: 0.8744 (m-40) cc_final: 0.8498 (m-40) REVERT: T 8 VAL cc_start: 0.8577 (OUTLIER) cc_final: 0.8322 (m) REVERT: U 33 GLN cc_start: 0.8398 (tp40) cc_final: 0.7970 (tp40) REVERT: U 77 ASP cc_start: 0.7910 (OUTLIER) cc_final: 0.7576 (p0) REVERT: V 152 ASP cc_start: 0.7369 (t0) cc_final: 0.6916 (t0) REVERT: W 78 GLN cc_start: 0.7900 (tp40) cc_final: 0.7221 (tp40) REVERT: X 25 ASP cc_start: 0.6663 (m-30) cc_final: 0.6391 (m-30) REVERT: X 132 GLN cc_start: 0.7727 (mm110) cc_final: 0.7428 (mm-40) REVERT: Y 39 GLN cc_start: 0.7624 (OUTLIER) cc_final: 0.7319 (mt0) REVERT: Y 68 GLN cc_start: 0.7744 (OUTLIER) cc_final: 0.6999 (mt0) REVERT: Z 17 GLU cc_start: 0.7439 (pm20) cc_final: 0.6762 (tm-30) REVERT: Z 85 ASP cc_start: 0.8365 (m-30) cc_final: 0.8104 (m-30) REVERT: a 62 LYS cc_start: 0.7828 (ttmp) cc_final: 0.7532 (ttmm) REVERT: a 65 TYR cc_start: 0.8038 (p90) cc_final: 0.7602 (p90) REVERT: a 109 GLU cc_start: 0.7381 (tm-30) cc_final: 0.6828 (tm-30) REVERT: a 159 GLU cc_start: 0.6799 (tt0) cc_final: 0.6550 (tt0) REVERT: b 106 GLU cc_start: 0.6898 (mm-30) cc_final: 0.6264 (mm-30) REVERT: c 11 THR cc_start: 0.8427 (t) cc_final: 0.8183 (m) REVERT: c 49 GLN cc_start: 0.7716 (tp-100) cc_final: 0.7177 (pm20) REVERT: c 53 ASN cc_start: 0.8356 (m-40) cc_final: 0.7975 (m110) REVERT: d 134 MET cc_start: 0.8811 (mtm) cc_final: 0.8338 (mtm) REVERT: d 136 GLU cc_start: 0.6994 (OUTLIER) cc_final: 0.6647 (mt-10) REVERT: d 140 ASP cc_start: 0.6644 (OUTLIER) cc_final: 0.6262 (m-30) REVERT: d 159 GLU cc_start: 0.7783 (tt0) cc_final: 0.7559 (tt0) REVERT: e 42 LYS cc_start: 0.7852 (ttpt) cc_final: 0.7430 (tptp) REVERT: e 78 GLN cc_start: 0.7275 (tp40) cc_final: 0.6976 (tp-100) REVERT: e 123 ASP cc_start: 0.7390 (t0) cc_final: 0.7022 (t0) REVERT: f 17 GLU cc_start: 0.6929 (pt0) cc_final: 0.6728 (pt0) REVERT: f 86 MET cc_start: 0.8280 (mtp) cc_final: 0.7978 (mtp) REVERT: g 131 GLU cc_start: 0.7171 (tp30) cc_final: 0.6823 (tp30) REVERT: h 79 MET cc_start: 0.8881 (tpp) cc_final: 0.8489 (tpp) REVERT: i 42 LYS cc_start: 0.7511 (tttm) cc_final: 0.7230 (tptt) REVERT: i 70 GLN cc_start: 0.7071 (mm-40) cc_final: 0.6865 (mm110) REVERT: i 109 GLU cc_start: 0.7660 (mm-30) cc_final: 0.7443 (tp30) REVERT: j 62 GLU cc_start: 0.7190 (OUTLIER) cc_final: 0.6984 (tt0) REVERT: j 106 GLU cc_start: 0.7095 (OUTLIER) cc_final: 0.5734 (pm20) REVERT: k 17 GLU cc_start: 0.6618 (OUTLIER) cc_final: 0.6262 (mp0) REVERT: k 19 ARG cc_start: 0.7315 (OUTLIER) cc_final: 0.6942 (mmt90) REVERT: l 41 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.7581 (ttt-90) REVERT: l 206 SER cc_start: 0.7749 (OUTLIER) cc_final: 0.7412 (t) REVERT: m 11 SER cc_start: 0.7314 (m) cc_final: 0.6933 (t) REVERT: m 19 ARG cc_start: 0.7710 (OUTLIER) cc_final: 0.6919 (tpm170) REVERT: m 25 VAL cc_start: 0.8408 (m) cc_final: 0.8162 (t) REVERT: m 30 GLN cc_start: 0.7132 (mm-40) cc_final: 0.6900 (mm-40) REVERT: m 35 ASP cc_start: 0.6297 (m-30) cc_final: 0.6090 (m-30) REVERT: m 66 MET cc_start: 0.6942 (mtm) cc_final: 0.6462 (mtm) REVERT: n 55 ASN cc_start: 0.8049 (m-40) cc_final: 0.7618 (t0) REVERT: n 134 LYS cc_start: 0.7595 (mttp) cc_final: 0.7196 (mttp) outliers start: 144 outliers final: 49 residues processed: 1046 average time/residue: 1.5074 time to fit residues: 1953.8536 Evaluate side-chains 996 residues out of total 5289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 923 time to evaluate : 4.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 135 LYS Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain C residue 70 GLN Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain D residue 15 ARG Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 139 ASN Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain G residue 116 ASP Chi-restraints excluded: chain H residue 11 GLN Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 141 ILE Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain K residue 137 LYS Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 132 GLN Chi-restraints excluded: chain M residue 50 SER Chi-restraints excluded: chain M residue 68 GLN Chi-restraints excluded: chain M residue 70 GLN Chi-restraints excluded: chain O residue 116 ASP Chi-restraints excluded: chain P residue 22 SER Chi-restraints excluded: chain P residue 103 SER Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain P residue 154 SER Chi-restraints excluded: chain Q residue 10 SER Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 166 ARG Chi-restraints excluded: chain S residue 50 SER Chi-restraints excluded: chain T residue 8 VAL Chi-restraints excluded: chain T residue 149 THR Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 77 ASP Chi-restraints excluded: chain U residue 116 ASP Chi-restraints excluded: chain V residue 28 SER Chi-restraints excluded: chain W residue 3 THR Chi-restraints excluded: chain W residue 50 SER Chi-restraints excluded: chain W residue 125 SER Chi-restraints excluded: chain Y residue 2 LYS Chi-restraints excluded: chain Y residue 39 GLN Chi-restraints excluded: chain Y residue 67 THR Chi-restraints excluded: chain Y residue 68 GLN Chi-restraints excluded: chain a residue 162 SER Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain d residue 136 GLU Chi-restraints excluded: chain d residue 140 ASP Chi-restraints excluded: chain e residue 159 GLU Chi-restraints excluded: chain f residue 115 GLU Chi-restraints excluded: chain f residue 166 ARG Chi-restraints excluded: chain g residue 10 SER Chi-restraints excluded: chain g residue 50 SER Chi-restraints excluded: chain i residue 31 LEU Chi-restraints excluded: chain j residue 4 VAL Chi-restraints excluded: chain j residue 22 SER Chi-restraints excluded: chain j residue 62 GLU Chi-restraints excluded: chain j residue 75 THR Chi-restraints excluded: chain j residue 106 GLU Chi-restraints excluded: chain k residue 17 GLU Chi-restraints excluded: chain k residue 19 ARG Chi-restraints excluded: chain k residue 207 SER Chi-restraints excluded: chain l residue 41 ARG Chi-restraints excluded: chain l residue 206 SER Chi-restraints excluded: chain l residue 251 ASP Chi-restraints excluded: chain m residue 19 ARG Chi-restraints excluded: chain m residue 31 SER Chi-restraints excluded: chain m residue 41 ILE Chi-restraints excluded: chain m residue 46 SER Chi-restraints excluded: chain m residue 47 THR Chi-restraints excluded: chain m residue 64 THR Chi-restraints excluded: chain n residue 44 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 676 random chunks: chunk 219 optimal weight: 0.4980 chunk 588 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 chunk 383 optimal weight: 7.9990 chunk 161 optimal weight: 0.9990 chunk 654 optimal weight: 5.9990 chunk 542 optimal weight: 10.0000 chunk 302 optimal weight: 5.9990 chunk 54 optimal weight: 8.9990 chunk 216 optimal weight: 1.9990 chunk 343 optimal weight: 0.9980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 11 GLN D 111 ASN D 132 GLN E 33 GLN E 139 ASN ** F 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 132 GLN ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 ASN ** G 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 53 ASN ** I 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 132 GLN K 15 GLN K 53 ASN L 11 GLN L 68 GLN L 132 GLN M 78 GLN M 139 ASN O 33 GLN ** O 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 47 ASN Q 139 ASN ** S 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 146 ASN U 15 GLN ** U 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 111 ASN V 146 ASN ** W 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 11 GLN a 61 ASN b 132 GLN ** c 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 132 GLN e 15 GLN e 139 ASN e 161 ASN h 68 GLN j 132 GLN ** k 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 270 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 55108 Z= 0.236 Angle : 0.599 12.955 74959 Z= 0.284 Chirality : 0.038 0.224 8198 Planarity : 0.004 0.142 9826 Dihedral : 10.422 89.170 10012 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.68 % Allowed : 14.73 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 1.88 (0.10), residues: 6771 helix: 1.74 (0.07), residues: 5297 sheet: 0.60 (0.61), residues: 48 loop : -0.49 (0.16), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP l 146 HIS 0.009 0.002 HIS E 140 PHE 0.016 0.002 PHE b 98 TYR 0.024 0.001 TYR L 74 ARG 0.027 0.001 ARG m 61 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13542 Ramachandran restraints generated. 6771 Oldfield, 0 Emsley, 6771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13542 Ramachandran restraints generated. 6771 Oldfield, 0 Emsley, 6771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1090 residues out of total 5289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 948 time to evaluate : 4.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LYS cc_start: 0.8238 (tmtt) cc_final: 0.8037 (tttp) REVERT: A 116 ASP cc_start: 0.7324 (m-30) cc_final: 0.7014 (m-30) REVERT: B 115 GLU cc_start: 0.8086 (mp0) cc_final: 0.7747 (mp0) REVERT: B 135 LYS cc_start: 0.7964 (OUTLIER) cc_final: 0.7711 (ttpt) REVERT: C 13 ASP cc_start: 0.7558 (t0) cc_final: 0.7271 (t0) REVERT: C 46 ASP cc_start: 0.7000 (m-30) cc_final: 0.6511 (m-30) REVERT: C 50 SER cc_start: 0.8261 (OUTLIER) cc_final: 0.7964 (p) REVERT: C 70 GLN cc_start: 0.7216 (OUTLIER) cc_final: 0.6126 (tp40) REVERT: D 15 ARG cc_start: 0.7445 (OUTLIER) cc_final: 0.7098 (ttm-80) REVERT: D 23 GLN cc_start: 0.7893 (tt0) cc_final: 0.7679 (tt0) REVERT: D 115 GLU cc_start: 0.6976 (mm-30) cc_final: 0.6583 (mm-30) REVERT: F 25 ASP cc_start: 0.6425 (m-30) cc_final: 0.6206 (m-30) REVERT: F 166 ARG cc_start: 0.7393 (ttm-80) cc_final: 0.6644 (tpp-160) REVERT: G 3 THR cc_start: 0.8426 (p) cc_final: 0.8063 (t) REVERT: G 131 GLU cc_start: 0.7996 (tp30) cc_final: 0.7651 (tp30) REVERT: G 147 ARG cc_start: 0.8190 (ttp-110) cc_final: 0.7912 (tmm-80) REVERT: G 169 ASN cc_start: 0.8450 (m-40) cc_final: 0.8185 (m110) REVERT: H 11 GLN cc_start: 0.7999 (OUTLIER) cc_final: 0.6738 (mt0) REVERT: H 19 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.7754 (mp) REVERT: H 62 GLU cc_start: 0.7135 (OUTLIER) cc_final: 0.6863 (pt0) REVERT: H 86 MET cc_start: 0.8121 (mtp) cc_final: 0.7336 (mtt) REVERT: H 134 MET cc_start: 0.8672 (mtm) cc_final: 0.8247 (mtm) REVERT: I 49 GLN cc_start: 0.6889 (tp-100) cc_final: 0.6296 (pm20) REVERT: I 50 SER cc_start: 0.8426 (t) cc_final: 0.7917 (p) REVERT: I 143 SER cc_start: 0.7215 (p) cc_final: 0.6810 (m) REVERT: I 145 ASP cc_start: 0.7289 (m-30) cc_final: 0.7024 (m-30) REVERT: J 79 MET cc_start: 0.8630 (tpp) cc_final: 0.8419 (tpp) REVERT: J 115 GLU cc_start: 0.7882 (mp0) cc_final: 0.7528 (mp0) REVERT: K 67 THR cc_start: 0.8175 (m) cc_final: 0.7868 (p) REVERT: K 68 GLN cc_start: 0.6908 (mp10) cc_final: 0.6542 (mm110) REVERT: K 137 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.7958 (mtmm) REVERT: L 25 ASP cc_start: 0.7019 (m-30) cc_final: 0.6479 (m-30) REVERT: L 132 GLN cc_start: 0.7653 (OUTLIER) cc_final: 0.7338 (tp40) REVERT: M 49 GLN cc_start: 0.7923 (tp-100) cc_final: 0.7392 (pm20) REVERT: M 68 GLN cc_start: 0.7729 (OUTLIER) cc_final: 0.7334 (pt0) REVERT: N 107 ASP cc_start: 0.7729 (m-30) cc_final: 0.7397 (m-30) REVERT: N 115 GLU cc_start: 0.7173 (mp0) cc_final: 0.6877 (mp0) REVERT: P 22 SER cc_start: 0.8557 (OUTLIER) cc_final: 0.8344 (t) REVERT: Q 108 ASP cc_start: 0.8502 (m-30) cc_final: 0.8270 (m-30) REVERT: R 1 MET cc_start: 0.7864 (ptp) cc_final: 0.7320 (ptp) REVERT: S 35 ASN cc_start: 0.8771 (m-40) cc_final: 0.8506 (m-40) REVERT: S 116 ASP cc_start: 0.7226 (OUTLIER) cc_final: 0.6843 (m-30) REVERT: S 137 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.7765 (mttp) REVERT: T 8 VAL cc_start: 0.8614 (OUTLIER) cc_final: 0.8378 (m) REVERT: U 68 GLN cc_start: 0.7625 (OUTLIER) cc_final: 0.7100 (pm20) REVERT: U 77 ASP cc_start: 0.7935 (OUTLIER) cc_final: 0.7591 (p0) REVERT: V 152 ASP cc_start: 0.7482 (t0) cc_final: 0.7035 (t0) REVERT: W 49 GLN cc_start: 0.7390 (OUTLIER) cc_final: 0.7098 (tp-100) REVERT: W 78 GLN cc_start: 0.7955 (tp40) cc_final: 0.7272 (tp40) REVERT: X 25 ASP cc_start: 0.6893 (m-30) cc_final: 0.6643 (m-30) REVERT: X 86 MET cc_start: 0.7832 (mtm) cc_final: 0.7571 (mtp) REVERT: X 132 GLN cc_start: 0.7746 (mm110) cc_final: 0.7485 (mm-40) REVERT: Y 39 GLN cc_start: 0.7524 (OUTLIER) cc_final: 0.7136 (mt0) REVERT: Y 68 GLN cc_start: 0.7731 (OUTLIER) cc_final: 0.6984 (mt0) REVERT: a 65 TYR cc_start: 0.8047 (p90) cc_final: 0.7674 (p90) REVERT: a 109 GLU cc_start: 0.7474 (tm-30) cc_final: 0.6932 (tm-30) REVERT: a 159 GLU cc_start: 0.6838 (tt0) cc_final: 0.6570 (tt0) REVERT: b 106 GLU cc_start: 0.6861 (mm-30) cc_final: 0.6225 (mm-30) REVERT: c 11 THR cc_start: 0.8454 (t) cc_final: 0.8189 (m) REVERT: c 49 GLN cc_start: 0.7750 (tp-100) cc_final: 0.7176 (pm20) REVERT: c 53 ASN cc_start: 0.8352 (m-40) cc_final: 0.7952 (m110) REVERT: d 136 GLU cc_start: 0.7072 (OUTLIER) cc_final: 0.6726 (mt-10) REVERT: d 140 ASP cc_start: 0.6695 (OUTLIER) cc_final: 0.6312 (m-30) REVERT: d 159 GLU cc_start: 0.7794 (tt0) cc_final: 0.7536 (tt0) REVERT: e 42 LYS cc_start: 0.7849 (ttpt) cc_final: 0.7392 (tttm) REVERT: e 78 GLN cc_start: 0.7346 (tp40) cc_final: 0.7087 (tp-100) REVERT: e 123 ASP cc_start: 0.7389 (t0) cc_final: 0.7010 (t0) REVERT: f 86 MET cc_start: 0.8196 (mtp) cc_final: 0.7896 (mtp) REVERT: g 67 THR cc_start: 0.8733 (m) cc_final: 0.8519 (m) REVERT: g 117 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.6835 (mp0) REVERT: g 131 GLU cc_start: 0.7242 (tp30) cc_final: 0.6908 (tp30) REVERT: h 79 MET cc_start: 0.8912 (tpp) cc_final: 0.8549 (tpp) REVERT: i 15 GLN cc_start: 0.7594 (mp10) cc_final: 0.7353 (mp10) REVERT: i 42 LYS cc_start: 0.7581 (tttm) cc_final: 0.7337 (tptt) REVERT: i 70 GLN cc_start: 0.7110 (mm-40) cc_final: 0.6776 (mm110) REVERT: i 109 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7502 (tp30) REVERT: i 111 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8460 (tt) REVERT: j 25 ASP cc_start: 0.6582 (m-30) cc_final: 0.6271 (m-30) REVERT: j 62 GLU cc_start: 0.7295 (OUTLIER) cc_final: 0.7094 (tt0) REVERT: k 17 GLU cc_start: 0.6671 (OUTLIER) cc_final: 0.6286 (mp0) REVERT: k 19 ARG cc_start: 0.7343 (OUTLIER) cc_final: 0.6971 (mmt90) REVERT: l 41 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.7577 (ttt-90) REVERT: l 206 SER cc_start: 0.7778 (OUTLIER) cc_final: 0.7436 (t) REVERT: m 11 SER cc_start: 0.7349 (m) cc_final: 0.6975 (t) REVERT: m 19 ARG cc_start: 0.7715 (OUTLIER) cc_final: 0.6866 (tpm170) REVERT: m 25 VAL cc_start: 0.8447 (m) cc_final: 0.8242 (t) REVERT: m 30 GLN cc_start: 0.7072 (mm-40) cc_final: 0.6847 (mm-40) REVERT: m 66 MET cc_start: 0.6975 (mtm) cc_final: 0.6509 (mtm) REVERT: n 55 ASN cc_start: 0.8131 (m-40) cc_final: 0.7690 (t0) REVERT: n 134 LYS cc_start: 0.7611 (mttp) cc_final: 0.7214 (mttp) outliers start: 142 outliers final: 66 residues processed: 1015 average time/residue: 1.5161 time to fit residues: 1901.8940 Evaluate side-chains 1001 residues out of total 5289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 906 time to evaluate : 4.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 135 LYS Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 70 GLN Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain D residue 15 ARG Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 33 GLN Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain G residue 116 ASP Chi-restraints excluded: chain G residue 162 SER Chi-restraints excluded: chain H residue 11 GLN Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 141 ILE Chi-restraints excluded: chain H residue 154 SER Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain K residue 137 LYS Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 132 GLN Chi-restraints excluded: chain M residue 50 SER Chi-restraints excluded: chain M residue 68 GLN Chi-restraints excluded: chain M residue 70 GLN Chi-restraints excluded: chain P residue 22 SER Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain P residue 103 SER Chi-restraints excluded: chain Q residue 10 SER Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 166 ARG Chi-restraints excluded: chain S residue 32 ARG Chi-restraints excluded: chain S residue 50 SER Chi-restraints excluded: chain S residue 116 ASP Chi-restraints excluded: chain S residue 137 LYS Chi-restraints excluded: chain T residue 8 VAL Chi-restraints excluded: chain T residue 149 THR Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 68 GLN Chi-restraints excluded: chain U residue 77 ASP Chi-restraints excluded: chain U residue 116 ASP Chi-restraints excluded: chain V residue 28 SER Chi-restraints excluded: chain W residue 3 THR Chi-restraints excluded: chain W residue 49 GLN Chi-restraints excluded: chain W residue 50 SER Chi-restraints excluded: chain W residue 125 SER Chi-restraints excluded: chain Y residue 2 LYS Chi-restraints excluded: chain Y residue 39 GLN Chi-restraints excluded: chain Y residue 67 THR Chi-restraints excluded: chain Y residue 68 GLN Chi-restraints excluded: chain a residue 162 SER Chi-restraints excluded: chain b residue 67 ILE Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain d residue 136 GLU Chi-restraints excluded: chain d residue 140 ASP Chi-restraints excluded: chain e residue 20 SER Chi-restraints excluded: chain e residue 134 LYS Chi-restraints excluded: chain e residue 159 GLU Chi-restraints excluded: chain f residue 115 GLU Chi-restraints excluded: chain f residue 166 ARG Chi-restraints excluded: chain g residue 10 SER Chi-restraints excluded: chain g residue 50 SER Chi-restraints excluded: chain g residue 117 GLU Chi-restraints excluded: chain g residue 145 ASP Chi-restraints excluded: chain i residue 31 LEU Chi-restraints excluded: chain i residue 111 LEU Chi-restraints excluded: chain j residue 4 VAL Chi-restraints excluded: chain j residue 22 SER Chi-restraints excluded: chain j residue 62 GLU Chi-restraints excluded: chain j residue 75 THR Chi-restraints excluded: chain j residue 106 GLU Chi-restraints excluded: chain j residue 149 THR Chi-restraints excluded: chain j residue 165 ASP Chi-restraints excluded: chain k residue 17 GLU Chi-restraints excluded: chain k residue 19 ARG Chi-restraints excluded: chain k residue 207 SER Chi-restraints excluded: chain l residue 41 ARG Chi-restraints excluded: chain l residue 141 GLU Chi-restraints excluded: chain l residue 198 THR Chi-restraints excluded: chain l residue 206 SER Chi-restraints excluded: chain l residue 251 ASP Chi-restraints excluded: chain m residue 19 ARG Chi-restraints excluded: chain m residue 31 SER Chi-restraints excluded: chain m residue 41 ILE Chi-restraints excluded: chain m residue 46 SER Chi-restraints excluded: chain m residue 47 THR Chi-restraints excluded: chain m residue 56 MET Chi-restraints excluded: chain m residue 64 THR Chi-restraints excluded: chain n residue 44 ASN Chi-restraints excluded: chain n residue 170 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 676 random chunks: chunk 630 optimal weight: 3.9990 chunk 73 optimal weight: 0.3980 chunk 372 optimal weight: 1.9990 chunk 477 optimal weight: 3.9990 chunk 370 optimal weight: 0.7980 chunk 550 optimal weight: 3.9990 chunk 365 optimal weight: 0.9990 chunk 651 optimal weight: 0.0030 chunk 407 optimal weight: 4.9990 chunk 397 optimal weight: 2.9990 chunk 300 optimal weight: 0.9980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 11 GLN D 111 ASN D 132 GLN E 33 GLN E 78 GLN ** F 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 132 GLN ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 ASN ** G 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 132 GLN K 15 GLN K 53 ASN L 11 GLN L 68 GLN L 132 GLN M 78 GLN M 139 ASN ** Q 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 47 ASN Q 68 GLN Q 139 ASN ** S 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 146 ASN U 15 GLN V 111 ASN V 146 ASN ** W 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 61 ASN c 68 GLN ** c 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 15 GLN h 68 GLN j 132 GLN ** k 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 270 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 55108 Z= 0.169 Angle : 0.560 12.997 74959 Z= 0.265 Chirality : 0.035 0.222 8198 Planarity : 0.004 0.218 9826 Dihedral : 10.390 88.526 10012 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 2.33 % Allowed : 15.35 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.10), residues: 6771 helix: 1.86 (0.07), residues: 5295 sheet: 0.39 (0.60), residues: 49 loop : -0.42 (0.16), residues: 1427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP l 146 HIS 0.008 0.002 HIS M 140 PHE 0.013 0.001 PHE b 98 TYR 0.026 0.001 TYR L 74 ARG 0.031 0.000 ARG m 61 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13542 Ramachandran restraints generated. 6771 Oldfield, 0 Emsley, 6771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13542 Ramachandran restraints generated. 6771 Oldfield, 0 Emsley, 6771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1077 residues out of total 5289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 954 time to evaluate : 4.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LYS cc_start: 0.8238 (tmtt) cc_final: 0.8037 (tttp) REVERT: A 116 ASP cc_start: 0.7280 (m-30) cc_final: 0.6973 (m-30) REVERT: B 115 GLU cc_start: 0.8068 (mp0) cc_final: 0.7714 (mp0) REVERT: C 13 ASP cc_start: 0.7454 (t0) cc_final: 0.7164 (t0) REVERT: C 46 ASP cc_start: 0.6950 (m-30) cc_final: 0.6455 (m-30) REVERT: C 50 SER cc_start: 0.8216 (OUTLIER) cc_final: 0.7950 (p) REVERT: D 15 ARG cc_start: 0.7403 (OUTLIER) cc_final: 0.7000 (ttm-80) REVERT: D 115 GLU cc_start: 0.6934 (mm-30) cc_final: 0.6533 (mm-30) REVERT: E 165 ASP cc_start: 0.7441 (m-30) cc_final: 0.7134 (m-30) REVERT: F 74 TYR cc_start: 0.8437 (t80) cc_final: 0.8134 (t80) REVERT: F 166 ARG cc_start: 0.7345 (ttm-80) cc_final: 0.6567 (tpp-160) REVERT: G 3 THR cc_start: 0.8319 (p) cc_final: 0.8030 (t) REVERT: G 131 GLU cc_start: 0.7971 (tp30) cc_final: 0.7608 (tp30) REVERT: G 147 ARG cc_start: 0.8159 (ttp-110) cc_final: 0.7904 (tmm-80) REVERT: G 169 ASN cc_start: 0.8463 (m-40) cc_final: 0.8204 (m110) REVERT: H 11 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.6604 (mt0) REVERT: H 19 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7690 (mp) REVERT: H 62 GLU cc_start: 0.7014 (OUTLIER) cc_final: 0.6738 (pt0) REVERT: H 86 MET cc_start: 0.8148 (mtp) cc_final: 0.7360 (mtt) REVERT: H 134 MET cc_start: 0.8670 (mtm) cc_final: 0.8131 (mtm) REVERT: I 49 GLN cc_start: 0.6956 (tp-100) cc_final: 0.6307 (pm20) REVERT: I 50 SER cc_start: 0.8445 (t) cc_final: 0.7946 (p) REVERT: I 143 SER cc_start: 0.7181 (p) cc_final: 0.6776 (m) REVERT: I 145 ASP cc_start: 0.7216 (m-30) cc_final: 0.6990 (m-30) REVERT: J 115 GLU cc_start: 0.7875 (mp0) cc_final: 0.7529 (mp0) REVERT: K 67 THR cc_start: 0.8282 (m) cc_final: 0.7973 (p) REVERT: K 68 GLN cc_start: 0.6881 (mp10) cc_final: 0.6541 (mm110) REVERT: K 137 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.7958 (mtmm) REVERT: L 25 ASP cc_start: 0.6996 (m-30) cc_final: 0.6454 (m-30) REVERT: M 49 GLN cc_start: 0.7916 (tp-100) cc_final: 0.7402 (pm20) REVERT: M 68 GLN cc_start: 0.7691 (OUTLIER) cc_final: 0.7357 (pt0) REVERT: N 107 ASP cc_start: 0.7698 (m-30) cc_final: 0.7358 (m-30) REVERT: N 115 GLU cc_start: 0.7122 (mp0) cc_final: 0.6831 (mp0) REVERT: O 68 GLN cc_start: 0.7775 (OUTLIER) cc_final: 0.7566 (mp10) REVERT: P 22 SER cc_start: 0.8557 (OUTLIER) cc_final: 0.8345 (t) REVERT: Q 108 ASP cc_start: 0.8458 (m-30) cc_final: 0.8251 (m-30) REVERT: R 1 MET cc_start: 0.7845 (ptp) cc_final: 0.7432 (ptp) REVERT: S 35 ASN cc_start: 0.8743 (m-40) cc_final: 0.8487 (m-40) REVERT: S 116 ASP cc_start: 0.7251 (OUTLIER) cc_final: 0.6749 (m-30) REVERT: S 137 LYS cc_start: 0.8397 (OUTLIER) cc_final: 0.7699 (mttp) REVERT: T 8 VAL cc_start: 0.8591 (OUTLIER) cc_final: 0.8342 (m) REVERT: U 77 ASP cc_start: 0.7938 (OUTLIER) cc_final: 0.7644 (p0) REVERT: V 152 ASP cc_start: 0.7391 (t0) cc_final: 0.6939 (t0) REVERT: X 25 ASP cc_start: 0.6778 (m-30) cc_final: 0.6529 (m-30) REVERT: X 86 MET cc_start: 0.7814 (mtm) cc_final: 0.7545 (mtp) REVERT: X 132 GLN cc_start: 0.7675 (mm110) cc_final: 0.7432 (mm-40) REVERT: Y 39 GLN cc_start: 0.7537 (OUTLIER) cc_final: 0.7272 (mt0) REVERT: Y 68 GLN cc_start: 0.7806 (OUTLIER) cc_final: 0.6989 (mt0) REVERT: Z 17 GLU cc_start: 0.7428 (pm20) cc_final: 0.6723 (tm-30) REVERT: Z 85 ASP cc_start: 0.8394 (m-30) cc_final: 0.8094 (m-30) REVERT: Z 106 GLU cc_start: 0.6833 (mt-10) cc_final: 0.6302 (mt-10) REVERT: a 65 TYR cc_start: 0.8101 (p90) cc_final: 0.7691 (p90) REVERT: a 109 GLU cc_start: 0.7425 (tm-30) cc_final: 0.6863 (tm-30) REVERT: a 159 GLU cc_start: 0.6796 (tt0) cc_final: 0.6542 (tt0) REVERT: b 22 SER cc_start: 0.7947 (p) cc_final: 0.7611 (m) REVERT: b 106 GLU cc_start: 0.6812 (mm-30) cc_final: 0.6213 (mm-30) REVERT: c 11 THR cc_start: 0.8426 (t) cc_final: 0.8197 (m) REVERT: c 49 GLN cc_start: 0.7734 (tp-100) cc_final: 0.7179 (pm20) REVERT: c 53 ASN cc_start: 0.8345 (m-40) cc_final: 0.7959 (m110) REVERT: d 136 GLU cc_start: 0.7022 (OUTLIER) cc_final: 0.6682 (mt-10) REVERT: d 140 ASP cc_start: 0.6671 (OUTLIER) cc_final: 0.6283 (m-30) REVERT: d 159 GLU cc_start: 0.7780 (tt0) cc_final: 0.7532 (tt0) REVERT: e 42 LYS cc_start: 0.7851 (ttpt) cc_final: 0.7396 (tptp) REVERT: e 78 GLN cc_start: 0.7310 (tp40) cc_final: 0.7045 (tp-100) REVERT: e 123 ASP cc_start: 0.7381 (t0) cc_final: 0.6993 (t0) REVERT: f 86 MET cc_start: 0.8235 (mtp) cc_final: 0.7922 (mtp) REVERT: g 131 GLU cc_start: 0.7266 (tp30) cc_final: 0.6931 (tp30) REVERT: h 79 MET cc_start: 0.8893 (tpp) cc_final: 0.8501 (tpp) REVERT: i 42 LYS cc_start: 0.7573 (tttm) cc_final: 0.7342 (tptt) REVERT: i 50 SER cc_start: 0.7729 (t) cc_final: 0.7515 (p) REVERT: i 70 GLN cc_start: 0.7105 (mm-40) cc_final: 0.6773 (mm110) REVERT: j 25 ASP cc_start: 0.6554 (m-30) cc_final: 0.6230 (m-30) REVERT: k 19 ARG cc_start: 0.7332 (OUTLIER) cc_final: 0.6972 (mmt90) REVERT: l 41 ARG cc_start: 0.7955 (OUTLIER) cc_final: 0.7594 (ttt-90) REVERT: l 206 SER cc_start: 0.7760 (OUTLIER) cc_final: 0.7424 (t) REVERT: m 11 SER cc_start: 0.7341 (m) cc_final: 0.6958 (t) REVERT: m 19 ARG cc_start: 0.7697 (OUTLIER) cc_final: 0.6906 (tpm170) REVERT: m 25 VAL cc_start: 0.8395 (m) cc_final: 0.8159 (t) REVERT: m 66 MET cc_start: 0.6879 (mtm) cc_final: 0.6537 (mtm) REVERT: n 55 ASN cc_start: 0.8105 (m-40) cc_final: 0.7706 (t0) REVERT: n 134 LYS cc_start: 0.7619 (mttp) cc_final: 0.7233 (mttp) outliers start: 123 outliers final: 59 residues processed: 1017 average time/residue: 1.5236 time to fit residues: 1914.8477 Evaluate side-chains 995 residues out of total 5289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 915 time to evaluate : 4.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain D residue 15 ARG Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain G residue 116 ASP Chi-restraints excluded: chain H residue 11 GLN Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 141 ILE Chi-restraints excluded: chain H residue 154 SER Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain K residue 50 SER Chi-restraints excluded: chain K residue 137 LYS Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain M residue 50 SER Chi-restraints excluded: chain M residue 68 GLN Chi-restraints excluded: chain M residue 70 GLN Chi-restraints excluded: chain O residue 68 GLN Chi-restraints excluded: chain O residue 116 ASP Chi-restraints excluded: chain P residue 22 SER Chi-restraints excluded: chain P residue 103 SER Chi-restraints excluded: chain Q residue 10 SER Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 166 ARG Chi-restraints excluded: chain S residue 32 ARG Chi-restraints excluded: chain S residue 50 SER Chi-restraints excluded: chain S residue 116 ASP Chi-restraints excluded: chain S residue 137 LYS Chi-restraints excluded: chain T residue 8 VAL Chi-restraints excluded: chain T residue 149 THR Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 77 ASP Chi-restraints excluded: chain U residue 116 ASP Chi-restraints excluded: chain V residue 28 SER Chi-restraints excluded: chain V residue 135 LYS Chi-restraints excluded: chain W residue 3 THR Chi-restraints excluded: chain W residue 50 SER Chi-restraints excluded: chain W residue 125 SER Chi-restraints excluded: chain Y residue 2 LYS Chi-restraints excluded: chain Y residue 39 GLN Chi-restraints excluded: chain Y residue 67 THR Chi-restraints excluded: chain Y residue 68 GLN Chi-restraints excluded: chain a residue 162 SER Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain d residue 136 GLU Chi-restraints excluded: chain d residue 140 ASP Chi-restraints excluded: chain e residue 20 SER Chi-restraints excluded: chain e residue 134 LYS Chi-restraints excluded: chain e residue 159 GLU Chi-restraints excluded: chain f residue 115 GLU Chi-restraints excluded: chain f residue 166 ARG Chi-restraints excluded: chain g residue 10 SER Chi-restraints excluded: chain g residue 50 SER Chi-restraints excluded: chain i residue 31 LEU Chi-restraints excluded: chain j residue 4 VAL Chi-restraints excluded: chain j residue 22 SER Chi-restraints excluded: chain j residue 30 THR Chi-restraints excluded: chain j residue 75 THR Chi-restraints excluded: chain j residue 106 GLU Chi-restraints excluded: chain j residue 149 THR Chi-restraints excluded: chain k residue 19 ARG Chi-restraints excluded: chain k residue 207 SER Chi-restraints excluded: chain l residue 41 ARG Chi-restraints excluded: chain l residue 206 SER Chi-restraints excluded: chain l residue 251 ASP Chi-restraints excluded: chain m residue 19 ARG Chi-restraints excluded: chain m residue 41 ILE Chi-restraints excluded: chain m residue 46 SER Chi-restraints excluded: chain m residue 47 THR Chi-restraints excluded: chain m residue 56 MET Chi-restraints excluded: chain m residue 64 THR Chi-restraints excluded: chain n residue 44 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 676 random chunks: chunk 403 optimal weight: 6.9990 chunk 260 optimal weight: 2.9990 chunk 389 optimal weight: 5.9990 chunk 196 optimal weight: 0.9980 chunk 128 optimal weight: 0.7980 chunk 126 optimal weight: 0.0370 chunk 414 optimal weight: 9.9990 chunk 443 optimal weight: 0.5980 chunk 322 optimal weight: 0.5980 chunk 60 optimal weight: 7.9990 chunk 512 optimal weight: 4.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 11 GLN D 23 GLN D 111 ASN D 132 GLN E 33 GLN ** F 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 132 GLN ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 ASN G 78 GLN ** G 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 15 GLN ** I 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 132 GLN K 15 GLN K 53 ASN L 11 GLN L 68 GLN M 78 GLN M 139 ASN Q 15 GLN Q 47 ASN Q 68 GLN Q 139 ASN ** S 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 15 GLN V 111 ASN V 146 ASN ** W 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 39 GLN ** Y 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 11 GLN a 61 ASN c 68 GLN ** c 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 132 GLN e 15 GLN h 68 GLN j 132 GLN ** k 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 270 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 55108 Z= 0.165 Angle : 0.555 12.434 74959 Z= 0.263 Chirality : 0.035 0.243 8198 Planarity : 0.005 0.383 9826 Dihedral : 10.356 88.657 10012 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.42 % Allowed : 15.56 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.10), residues: 6771 helix: 1.94 (0.07), residues: 5288 sheet: 0.37 (0.60), residues: 49 loop : -0.40 (0.16), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP l 146 HIS 0.008 0.002 HIS M 140 PHE 0.013 0.001 PHE b 98 TYR 0.027 0.001 TYR a 90 ARG 0.040 0.000 ARG m 61 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13542 Ramachandran restraints generated. 6771 Oldfield, 0 Emsley, 6771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13542 Ramachandran restraints generated. 6771 Oldfield, 0 Emsley, 6771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1079 residues out of total 5289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 951 time to evaluate : 5.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LYS cc_start: 0.8246 (tmtt) cc_final: 0.8022 (tttp) REVERT: A 116 ASP cc_start: 0.7291 (m-30) cc_final: 0.6987 (m-30) REVERT: B 115 GLU cc_start: 0.8065 (mp0) cc_final: 0.7711 (mp0) REVERT: C 13 ASP cc_start: 0.7408 (t0) cc_final: 0.7144 (t0) REVERT: C 46 ASP cc_start: 0.6952 (m-30) cc_final: 0.6454 (m-30) REVERT: C 50 SER cc_start: 0.8211 (OUTLIER) cc_final: 0.7954 (p) REVERT: D 15 ARG cc_start: 0.7294 (OUTLIER) cc_final: 0.6934 (ttm-80) REVERT: D 94 THR cc_start: 0.8586 (m) cc_final: 0.8066 (p) REVERT: D 115 GLU cc_start: 0.6934 (mm-30) cc_final: 0.6522 (mm-30) REVERT: E 165 ASP cc_start: 0.7369 (m-30) cc_final: 0.7059 (m-30) REVERT: F 74 TYR cc_start: 0.8412 (t80) cc_final: 0.7857 (t80) REVERT: F 166 ARG cc_start: 0.7320 (ttm-80) cc_final: 0.6565 (tpp-160) REVERT: G 131 GLU cc_start: 0.7966 (tp30) cc_final: 0.7598 (tp30) REVERT: G 147 ARG cc_start: 0.8177 (ttp-110) cc_final: 0.7932 (tmm-80) REVERT: G 169 ASN cc_start: 0.8436 (m-40) cc_final: 0.8172 (m110) REVERT: H 11 GLN cc_start: 0.7898 (OUTLIER) cc_final: 0.6584 (mt0) REVERT: H 19 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7693 (mp) REVERT: H 62 GLU cc_start: 0.6990 (OUTLIER) cc_final: 0.6704 (pt0) REVERT: H 86 MET cc_start: 0.8184 (mtp) cc_final: 0.7386 (mtt) REVERT: H 134 MET cc_start: 0.8697 (mtm) cc_final: 0.8136 (mtm) REVERT: I 49 GLN cc_start: 0.6975 (tp-100) cc_final: 0.6309 (pm20) REVERT: I 143 SER cc_start: 0.7135 (p) cc_final: 0.6750 (m) REVERT: I 145 ASP cc_start: 0.7194 (m-30) cc_final: 0.6976 (m-30) REVERT: J 115 GLU cc_start: 0.7868 (mp0) cc_final: 0.7517 (mp0) REVERT: J 150 ARG cc_start: 0.6547 (mmt90) cc_final: 0.6341 (tpt170) REVERT: K 67 THR cc_start: 0.8388 (m) cc_final: 0.8025 (p) REVERT: K 68 GLN cc_start: 0.6874 (mp10) cc_final: 0.6546 (mm110) REVERT: K 137 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.7965 (mtmm) REVERT: L 25 ASP cc_start: 0.6990 (m-30) cc_final: 0.6460 (m-30) REVERT: M 49 GLN cc_start: 0.7927 (tp-100) cc_final: 0.7394 (pm20) REVERT: M 68 GLN cc_start: 0.7631 (OUTLIER) cc_final: 0.7319 (pt0) REVERT: N 107 ASP cc_start: 0.7660 (m-30) cc_final: 0.7349 (m-30) REVERT: N 115 GLU cc_start: 0.7085 (mp0) cc_final: 0.6786 (mp0) REVERT: P 22 SER cc_start: 0.8546 (OUTLIER) cc_final: 0.8344 (t) REVERT: R 1 MET cc_start: 0.7858 (ptp) cc_final: 0.7384 (ptp) REVERT: S 35 ASN cc_start: 0.8661 (m-40) cc_final: 0.8406 (m-40) REVERT: S 116 ASP cc_start: 0.7177 (OUTLIER) cc_final: 0.6745 (m-30) REVERT: S 137 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.7704 (mttp) REVERT: T 8 VAL cc_start: 0.8579 (OUTLIER) cc_final: 0.8333 (m) REVERT: U 77 ASP cc_start: 0.7906 (OUTLIER) cc_final: 0.7604 (p0) REVERT: U 116 ASP cc_start: 0.7148 (OUTLIER) cc_final: 0.6830 (p0) REVERT: U 117 GLU cc_start: 0.7350 (mp0) cc_final: 0.6855 (mp0) REVERT: V 62 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7214 (pt0) REVERT: V 106 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7421 (mm-30) REVERT: V 150 ARG cc_start: 0.7443 (mmm-85) cc_final: 0.7241 (mmm-85) REVERT: V 152 ASP cc_start: 0.7409 (t0) cc_final: 0.6959 (t0) REVERT: W 78 GLN cc_start: 0.7857 (tp40) cc_final: 0.7298 (tp40) REVERT: X 25 ASP cc_start: 0.6774 (m-30) cc_final: 0.6520 (m-30) REVERT: X 86 MET cc_start: 0.7815 (mtm) cc_final: 0.7545 (mtp) REVERT: X 132 GLN cc_start: 0.7654 (mm110) cc_final: 0.6875 (mm-40) REVERT: Y 39 GLN cc_start: 0.7538 (OUTLIER) cc_final: 0.7288 (mt0) REVERT: Y 68 GLN cc_start: 0.7729 (OUTLIER) cc_final: 0.6933 (mt0) REVERT: Z 17 GLU cc_start: 0.7401 (pm20) cc_final: 0.6720 (tm-30) REVERT: Z 106 GLU cc_start: 0.6866 (mt-10) cc_final: 0.6591 (mt-10) REVERT: a 65 TYR cc_start: 0.8152 (p90) cc_final: 0.7739 (p90) REVERT: a 109 GLU cc_start: 0.7442 (tm-30) cc_final: 0.6905 (tm-30) REVERT: a 134 LYS cc_start: 0.8554 (mmtp) cc_final: 0.8247 (mttt) REVERT: a 159 GLU cc_start: 0.6792 (tt0) cc_final: 0.6538 (tt0) REVERT: b 15 ARG cc_start: 0.6756 (mtm110) cc_final: 0.6414 (mtm110) REVERT: b 22 SER cc_start: 0.7760 (p) cc_final: 0.7467 (m) REVERT: b 106 GLU cc_start: 0.6804 (mm-30) cc_final: 0.6196 (mm-30) REVERT: c 11 THR cc_start: 0.8421 (t) cc_final: 0.8207 (m) REVERT: c 49 GLN cc_start: 0.7718 (tp-100) cc_final: 0.7153 (pm20) REVERT: c 53 ASN cc_start: 0.8342 (m-40) cc_final: 0.7952 (m110) REVERT: d 133 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8535 (mttp) REVERT: d 136 GLU cc_start: 0.7002 (OUTLIER) cc_final: 0.6686 (mt-10) REVERT: d 140 ASP cc_start: 0.6697 (OUTLIER) cc_final: 0.6317 (m-30) REVERT: d 159 GLU cc_start: 0.7776 (tt0) cc_final: 0.7505 (tt0) REVERT: e 42 LYS cc_start: 0.7892 (ttpt) cc_final: 0.7459 (tttp) REVERT: e 78 GLN cc_start: 0.7308 (tp40) cc_final: 0.7055 (tp-100) REVERT: e 123 ASP cc_start: 0.7379 (t0) cc_final: 0.6985 (t0) REVERT: f 86 MET cc_start: 0.8243 (mtp) cc_final: 0.7957 (mtp) REVERT: g 131 GLU cc_start: 0.7264 (tp30) cc_final: 0.6933 (tp30) REVERT: h 79 MET cc_start: 0.8885 (tpp) cc_final: 0.8488 (tpp) REVERT: h 150 ARG cc_start: 0.7171 (tpp-160) cc_final: 0.6568 (tpp-160) REVERT: i 15 GLN cc_start: 0.7563 (mp10) cc_final: 0.7325 (mp10) REVERT: i 42 LYS cc_start: 0.7579 (tttm) cc_final: 0.7328 (tptt) REVERT: i 50 SER cc_start: 0.7792 (t) cc_final: 0.7567 (p) REVERT: i 70 GLN cc_start: 0.7104 (mm-40) cc_final: 0.6771 (mm110) REVERT: j 25 ASP cc_start: 0.6551 (m-30) cc_final: 0.6220 (m-30) REVERT: k 19 ARG cc_start: 0.7321 (OUTLIER) cc_final: 0.6959 (mmt90) REVERT: k 161 THR cc_start: 0.8633 (OUTLIER) cc_final: 0.8383 (m) REVERT: l 41 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.7594 (ttt-90) REVERT: l 206 SER cc_start: 0.7753 (OUTLIER) cc_final: 0.7405 (t) REVERT: m 11 SER cc_start: 0.7283 (m) cc_final: 0.6949 (t) REVERT: m 19 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.6828 (tpm170) REVERT: n 55 ASN cc_start: 0.8079 (m-40) cc_final: 0.7695 (t0) REVERT: n 134 LYS cc_start: 0.7633 (mttp) cc_final: 0.7211 (mttp) REVERT: n 156 ASP cc_start: 0.7570 (OUTLIER) cc_final: 0.7268 (m-30) outliers start: 128 outliers final: 64 residues processed: 1019 average time/residue: 1.5405 time to fit residues: 1940.3025 Evaluate side-chains 998 residues out of total 5289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 909 time to evaluate : 4.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain C residue 7 GLU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain D residue 15 ARG Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain H residue 11 GLN Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 141 ILE Chi-restraints excluded: chain H residue 154 SER Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 15 GLN Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain K residue 50 SER Chi-restraints excluded: chain K residue 137 LYS Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain M residue 50 SER Chi-restraints excluded: chain M residue 68 GLN Chi-restraints excluded: chain M residue 70 GLN Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain P residue 22 SER Chi-restraints excluded: chain P residue 103 SER Chi-restraints excluded: chain Q residue 10 SER Chi-restraints excluded: chain Q residue 15 GLN Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 166 ARG Chi-restraints excluded: chain S residue 32 ARG Chi-restraints excluded: chain S residue 50 SER Chi-restraints excluded: chain S residue 116 ASP Chi-restraints excluded: chain S residue 137 LYS Chi-restraints excluded: chain T residue 8 VAL Chi-restraints excluded: chain T residue 149 THR Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 77 ASP Chi-restraints excluded: chain U residue 116 ASP Chi-restraints excluded: chain V residue 28 SER Chi-restraints excluded: chain V residue 62 GLU Chi-restraints excluded: chain W residue 3 THR Chi-restraints excluded: chain W residue 50 SER Chi-restraints excluded: chain W residue 125 SER Chi-restraints excluded: chain Y residue 2 LYS Chi-restraints excluded: chain Y residue 39 GLN Chi-restraints excluded: chain Y residue 67 THR Chi-restraints excluded: chain Y residue 68 GLN Chi-restraints excluded: chain a residue 162 SER Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain d residue 133 LYS Chi-restraints excluded: chain d residue 136 GLU Chi-restraints excluded: chain d residue 140 ASP Chi-restraints excluded: chain d residue 150 ARG Chi-restraints excluded: chain e residue 20 SER Chi-restraints excluded: chain e residue 134 LYS Chi-restraints excluded: chain f residue 115 GLU Chi-restraints excluded: chain f residue 166 ARG Chi-restraints excluded: chain g residue 10 SER Chi-restraints excluded: chain g residue 50 SER Chi-restraints excluded: chain g residue 145 ASP Chi-restraints excluded: chain i residue 31 LEU Chi-restraints excluded: chain j residue 4 VAL Chi-restraints excluded: chain j residue 22 SER Chi-restraints excluded: chain j residue 30 THR Chi-restraints excluded: chain j residue 75 THR Chi-restraints excluded: chain j residue 106 GLU Chi-restraints excluded: chain j residue 149 THR Chi-restraints excluded: chain k residue 19 ARG Chi-restraints excluded: chain k residue 47 ASP Chi-restraints excluded: chain k residue 161 THR Chi-restraints excluded: chain k residue 207 SER Chi-restraints excluded: chain l residue 41 ARG Chi-restraints excluded: chain l residue 141 GLU Chi-restraints excluded: chain l residue 206 SER Chi-restraints excluded: chain l residue 251 ASP Chi-restraints excluded: chain l residue 266 THR Chi-restraints excluded: chain m residue 19 ARG Chi-restraints excluded: chain m residue 41 ILE Chi-restraints excluded: chain m residue 46 SER Chi-restraints excluded: chain m residue 47 THR Chi-restraints excluded: chain m residue 56 MET Chi-restraints excluded: chain m residue 64 THR Chi-restraints excluded: chain n residue 44 ASN Chi-restraints excluded: chain n residue 156 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 676 random chunks: chunk 592 optimal weight: 4.9990 chunk 624 optimal weight: 6.9990 chunk 569 optimal weight: 4.9990 chunk 607 optimal weight: 3.9990 chunk 365 optimal weight: 4.9990 chunk 264 optimal weight: 7.9990 chunk 476 optimal weight: 3.9990 chunk 186 optimal weight: 4.9990 chunk 548 optimal weight: 3.9990 chunk 574 optimal weight: 0.9990 chunk 605 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 11 GLN D 23 GLN D 111 ASN D 132 GLN E 33 GLN E 78 GLN ** F 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 47 ASN F 132 GLN ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 ASN ** G 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 161 ASN I 15 GLN ** I 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 132 GLN K 15 GLN K 47 ASN K 53 ASN L 11 GLN L 132 GLN M 139 ASN N 132 GLN O 68 GLN ** O 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 47 ASN Q 68 GLN Q 139 ASN R 35 ASN ** S 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 68 GLN ** S 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 47 ASN U 15 GLN V 111 ASN V 146 ASN W 33 GLN W 140 HIS ** X 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 47 ASN ** Y 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 61 ASN b 132 GLN c 68 GLN c 140 HIS d 132 GLN e 15 GLN f 143 ASN g 57 GLN g 61 ASN h 68 GLN j 132 GLN ** k 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 270 GLN l 259 GLN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 55108 Z= 0.415 Angle : 0.732 15.222 74959 Z= 0.352 Chirality : 0.044 0.313 8198 Planarity : 0.006 0.149 9826 Dihedral : 10.640 89.192 10012 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.61 % Allowed : 15.60 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 1.60 (0.10), residues: 6771 helix: 1.52 (0.07), residues: 5298 sheet: 0.66 (0.60), residues: 48 loop : -0.50 (0.16), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP S 128 HIS 0.011 0.003 HIS U 140 PHE 0.025 0.003 PHE O 122 TYR 0.030 0.002 TYR a 90 ARG 0.029 0.001 ARG m 61 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13542 Ramachandran restraints generated. 6771 Oldfield, 0 Emsley, 6771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13542 Ramachandran restraints generated. 6771 Oldfield, 0 Emsley, 6771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1072 residues out of total 5289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 934 time to evaluate : 4.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LYS cc_start: 0.8348 (tmtt) cc_final: 0.8135 (tttp) REVERT: A 116 ASP cc_start: 0.7367 (m-30) cc_final: 0.7083 (m-30) REVERT: B 1 MET cc_start: 0.7675 (ptp) cc_final: 0.7453 (pmm) REVERT: B 115 GLU cc_start: 0.8119 (mp0) cc_final: 0.7771 (mp0) REVERT: B 135 LYS cc_start: 0.8294 (ttpt) cc_final: 0.7732 (ttpt) REVERT: C 13 ASP cc_start: 0.7676 (t0) cc_final: 0.7352 (t0) REVERT: C 46 ASP cc_start: 0.7022 (m-30) cc_final: 0.6532 (m-30) REVERT: C 70 GLN cc_start: 0.7490 (OUTLIER) cc_final: 0.6393 (tp40) REVERT: D 15 ARG cc_start: 0.7401 (OUTLIER) cc_final: 0.7148 (ttm-80) REVERT: D 115 GLU cc_start: 0.7054 (mm-30) cc_final: 0.6645 (mm-30) REVERT: D 131 VAL cc_start: 0.8717 (t) cc_final: 0.8505 (t) REVERT: F 74 TYR cc_start: 0.8555 (t80) cc_final: 0.8266 (t80) REVERT: F 166 ARG cc_start: 0.7387 (ttm-80) cc_final: 0.6581 (tpp-160) REVERT: G 147 ARG cc_start: 0.8328 (ttp-110) cc_final: 0.8088 (tmm-80) REVERT: G 169 ASN cc_start: 0.8516 (m-40) cc_final: 0.8178 (m110) REVERT: H 11 GLN cc_start: 0.8074 (OUTLIER) cc_final: 0.6869 (mt0) REVERT: H 62 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.7280 (pt0) REVERT: H 134 MET cc_start: 0.8731 (mtm) cc_final: 0.8203 (mtm) REVERT: I 49 GLN cc_start: 0.7088 (tp-100) cc_final: 0.6320 (pm20) REVERT: I 50 SER cc_start: 0.8395 (t) cc_final: 0.7857 (p) REVERT: I 143 SER cc_start: 0.7214 (p) cc_final: 0.6870 (m) REVERT: I 145 ASP cc_start: 0.7352 (m-30) cc_final: 0.7079 (m-30) REVERT: J 33 GLU cc_start: 0.7209 (tp30) cc_final: 0.6730 (tp30) REVERT: J 115 GLU cc_start: 0.7902 (mp0) cc_final: 0.7545 (mp0) REVERT: K 67 THR cc_start: 0.8445 (m) cc_final: 0.8137 (p) REVERT: K 68 GLN cc_start: 0.6990 (mp10) cc_final: 0.6767 (mm110) REVERT: K 137 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.7942 (mtmm) REVERT: L 17 GLU cc_start: 0.7471 (mt-10) cc_final: 0.7239 (mm-30) REVERT: L 25 ASP cc_start: 0.7017 (m-30) cc_final: 0.6493 (m-30) REVERT: M 49 GLN cc_start: 0.8040 (tp-100) cc_final: 0.7420 (pm20) REVERT: M 68 GLN cc_start: 0.7828 (OUTLIER) cc_final: 0.7428 (pt0) REVERT: M 70 GLN cc_start: 0.7417 (OUTLIER) cc_final: 0.7142 (mm-40) REVERT: N 107 ASP cc_start: 0.7858 (m-30) cc_final: 0.7505 (m-30) REVERT: N 115 GLU cc_start: 0.7164 (mp0) cc_final: 0.6883 (mp0) REVERT: N 134 MET cc_start: 0.8860 (mtm) cc_final: 0.8412 (mtm) REVERT: O 109 GLU cc_start: 0.7304 (tt0) cc_final: 0.7070 (tt0) REVERT: R 1 MET cc_start: 0.7896 (ptp) cc_final: 0.7426 (ptp) REVERT: S 35 ASN cc_start: 0.8829 (m-40) cc_final: 0.8534 (m-40) REVERT: S 116 ASP cc_start: 0.7307 (OUTLIER) cc_final: 0.6795 (m-30) REVERT: S 137 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.7669 (mttp) REVERT: T 86 MET cc_start: 0.8230 (mmm) cc_final: 0.7906 (mmm) REVERT: U 77 ASP cc_start: 0.7948 (OUTLIER) cc_final: 0.7630 (p0) REVERT: U 116 ASP cc_start: 0.7135 (OUTLIER) cc_final: 0.6901 (p0) REVERT: U 117 GLU cc_start: 0.7389 (mp0) cc_final: 0.7080 (mp0) REVERT: V 1 MET cc_start: 0.7040 (tpt) cc_final: 0.6739 (tmt) REVERT: V 106 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7419 (mm-30) REVERT: V 152 ASP cc_start: 0.7424 (t0) cc_final: 0.7017 (t70) REVERT: X 25 ASP cc_start: 0.6960 (m-30) cc_final: 0.6673 (m-30) REVERT: X 87 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7251 (tm-30) REVERT: X 132 GLN cc_start: 0.7744 (mm110) cc_final: 0.7461 (mm-40) REVERT: X 143 ASN cc_start: 0.7745 (m-40) cc_final: 0.7495 (m-40) REVERT: Y 39 GLN cc_start: 0.7583 (OUTLIER) cc_final: 0.7228 (mt0) REVERT: Y 68 GLN cc_start: 0.7755 (OUTLIER) cc_final: 0.6995 (mt0) REVERT: a 65 TYR cc_start: 0.8169 (p90) cc_final: 0.7794 (p90) REVERT: a 109 GLU cc_start: 0.7604 (tm-30) cc_final: 0.7100 (tm-30) REVERT: b 22 SER cc_start: 0.8025 (p) cc_final: 0.7737 (m) REVERT: b 106 GLU cc_start: 0.6936 (mm-30) cc_final: 0.6324 (mm-30) REVERT: c 11 THR cc_start: 0.8535 (t) cc_final: 0.8198 (m) REVERT: c 53 ASN cc_start: 0.8369 (m-40) cc_final: 0.7891 (m110) REVERT: d 134 MET cc_start: 0.8824 (mtm) cc_final: 0.8532 (mtm) REVERT: d 136 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6946 (pt0) REVERT: d 140 ASP cc_start: 0.6797 (OUTLIER) cc_final: 0.6470 (m-30) REVERT: d 159 GLU cc_start: 0.7800 (tt0) cc_final: 0.7538 (tt0) REVERT: e 42 LYS cc_start: 0.7983 (ttpt) cc_final: 0.7551 (tttp) REVERT: e 78 GLN cc_start: 0.7437 (tp40) cc_final: 0.7174 (tp-100) REVERT: e 123 ASP cc_start: 0.7402 (t0) cc_final: 0.7008 (t0) REVERT: f 86 MET cc_start: 0.8249 (mtp) cc_final: 0.7971 (mtp) REVERT: g 117 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.6920 (mp0) REVERT: g 131 GLU cc_start: 0.7346 (tp30) cc_final: 0.7025 (tp30) REVERT: h 79 MET cc_start: 0.8922 (tpp) cc_final: 0.8691 (tpp) REVERT: h 150 ARG cc_start: 0.7401 (tpp-160) cc_final: 0.6830 (tpp-160) REVERT: i 15 GLN cc_start: 0.7676 (mp10) cc_final: 0.7440 (mp10) REVERT: i 42 LYS cc_start: 0.7589 (tttm) cc_final: 0.7370 (tptt) REVERT: i 50 SER cc_start: 0.7707 (t) cc_final: 0.7443 (p) REVERT: i 70 GLN cc_start: 0.7154 (mm-40) cc_final: 0.6773 (mm110) REVERT: i 111 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8538 (tt) REVERT: j 25 ASP cc_start: 0.6712 (m-30) cc_final: 0.6375 (m-30) REVERT: k 19 ARG cc_start: 0.7337 (OUTLIER) cc_final: 0.6991 (mmt90) REVERT: k 34 MET cc_start: 0.7345 (mmm) cc_final: 0.7061 (mmm) REVERT: l 41 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.7706 (ttt-90) REVERT: l 206 SER cc_start: 0.7864 (OUTLIER) cc_final: 0.7497 (t) REVERT: m 11 SER cc_start: 0.7521 (m) cc_final: 0.7309 (t) REVERT: m 19 ARG cc_start: 0.7814 (OUTLIER) cc_final: 0.6953 (tpm170) REVERT: n 55 ASN cc_start: 0.8194 (m-40) cc_final: 0.7785 (t0) REVERT: n 134 LYS cc_start: 0.7658 (mttp) cc_final: 0.7053 (mtpp) outliers start: 138 outliers final: 72 residues processed: 1010 average time/residue: 1.5430 time to fit residues: 1924.5176 Evaluate side-chains 998 residues out of total 5289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 904 time to evaluate : 4.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 70 GLN Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain D residue 15 ARG Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain G residue 116 ASP Chi-restraints excluded: chain G residue 162 SER Chi-restraints excluded: chain H residue 11 GLN Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 141 ILE Chi-restraints excluded: chain H residue 154 SER Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain K residue 50 SER Chi-restraints excluded: chain K residue 137 LYS Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain M residue 50 SER Chi-restraints excluded: chain M residue 68 GLN Chi-restraints excluded: chain M residue 70 GLN Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain P residue 103 SER Chi-restraints excluded: chain P residue 154 SER Chi-restraints excluded: chain Q residue 10 SER Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 166 ARG Chi-restraints excluded: chain S residue 32 ARG Chi-restraints excluded: chain S residue 116 ASP Chi-restraints excluded: chain S residue 137 LYS Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 8 VAL Chi-restraints excluded: chain T residue 146 ASN Chi-restraints excluded: chain T residue 149 THR Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 50 SER Chi-restraints excluded: chain U residue 77 ASP Chi-restraints excluded: chain U residue 116 ASP Chi-restraints excluded: chain V residue 9 VAL Chi-restraints excluded: chain V residue 28 SER Chi-restraints excluded: chain W residue 3 THR Chi-restraints excluded: chain W residue 50 SER Chi-restraints excluded: chain W residue 125 SER Chi-restraints excluded: chain X residue 87 GLU Chi-restraints excluded: chain Y residue 2 LYS Chi-restraints excluded: chain Y residue 39 GLN Chi-restraints excluded: chain Y residue 67 THR Chi-restraints excluded: chain Y residue 68 GLN Chi-restraints excluded: chain a residue 70 GLN Chi-restraints excluded: chain a residue 162 SER Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain d residue 136 GLU Chi-restraints excluded: chain d residue 140 ASP Chi-restraints excluded: chain d residue 150 ARG Chi-restraints excluded: chain e residue 20 SER Chi-restraints excluded: chain e residue 118 ILE Chi-restraints excluded: chain e residue 134 LYS Chi-restraints excluded: chain f residue 33 GLU Chi-restraints excluded: chain f residue 115 GLU Chi-restraints excluded: chain f residue 166 ARG Chi-restraints excluded: chain g residue 10 SER Chi-restraints excluded: chain g residue 50 SER Chi-restraints excluded: chain g residue 117 GLU Chi-restraints excluded: chain g residue 145 ASP Chi-restraints excluded: chain h residue 111 ASN Chi-restraints excluded: chain i residue 31 LEU Chi-restraints excluded: chain i residue 111 LEU Chi-restraints excluded: chain j residue 4 VAL Chi-restraints excluded: chain j residue 30 THR Chi-restraints excluded: chain j residue 75 THR Chi-restraints excluded: chain j residue 106 GLU Chi-restraints excluded: chain j residue 149 THR Chi-restraints excluded: chain k residue 19 ARG Chi-restraints excluded: chain k residue 47 ASP Chi-restraints excluded: chain k residue 161 THR Chi-restraints excluded: chain k residue 207 SER Chi-restraints excluded: chain l residue 41 ARG Chi-restraints excluded: chain l residue 141 GLU Chi-restraints excluded: chain l residue 206 SER Chi-restraints excluded: chain l residue 251 ASP Chi-restraints excluded: chain l residue 266 THR Chi-restraints excluded: chain m residue 19 ARG Chi-restraints excluded: chain m residue 41 ILE Chi-restraints excluded: chain m residue 46 SER Chi-restraints excluded: chain m residue 47 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 676 random chunks: chunk 398 optimal weight: 3.9990 chunk 642 optimal weight: 1.9990 chunk 391 optimal weight: 0.6980 chunk 304 optimal weight: 3.9990 chunk 446 optimal weight: 2.9990 chunk 673 optimal weight: 4.9990 chunk 619 optimal weight: 0.9980 chunk 536 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 414 optimal weight: 5.9990 chunk 328 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 11 GLN D 23 GLN D 111 ASN D 132 GLN E 33 GLN E 78 GLN ** F 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 132 GLN ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 ASN G 169 ASN I 15 GLN ** I 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 132 GLN K 15 GLN K 53 ASN L 11 GLN M 78 GLN M 139 ASN N 132 GLN O 68 GLN ** O 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 47 ASN Q 68 GLN Q 139 ASN ** S 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 15 GLN V 111 ASN V 146 ASN W 68 GLN ** X 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 47 ASN ** Y 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 132 GLN ** c 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 68 GLN d 132 GLN e 15 GLN g 57 GLN g 61 ASN h 68 GLN j 132 GLN ** k 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 270 GLN l 259 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 55108 Z= 0.242 Angle : 0.630 13.258 74959 Z= 0.301 Chirality : 0.038 0.291 8198 Planarity : 0.005 0.312 9826 Dihedral : 10.621 88.499 10012 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.08 % Allowed : 16.45 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 1.82 (0.10), residues: 6771 helix: 1.70 (0.07), residues: 5279 sheet: 0.62 (0.59), residues: 48 loop : -0.51 (0.15), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP l 146 HIS 0.008 0.003 HIS C 140 PHE 0.017 0.002 PHE R 98 TYR 0.027 0.002 TYR a 90 ARG 0.048 0.001 ARG m 61 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13542 Ramachandran restraints generated. 6771 Oldfield, 0 Emsley, 6771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13542 Ramachandran restraints generated. 6771 Oldfield, 0 Emsley, 6771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1049 residues out of total 5289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 939 time to evaluate : 4.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LYS cc_start: 0.8345 (tmtt) cc_final: 0.8100 (tttp) REVERT: A 116 ASP cc_start: 0.7383 (m-30) cc_final: 0.7064 (m-30) REVERT: B 1 MET cc_start: 0.7677 (ptp) cc_final: 0.7468 (pmm) REVERT: B 115 GLU cc_start: 0.8067 (mp0) cc_final: 0.7729 (mp0) REVERT: B 135 LYS cc_start: 0.8272 (ttpt) cc_final: 0.7721 (ttpt) REVERT: C 46 ASP cc_start: 0.6958 (m-30) cc_final: 0.6474 (m-30) REVERT: C 50 SER cc_start: 0.8309 (OUTLIER) cc_final: 0.8007 (p) REVERT: D 15 ARG cc_start: 0.7417 (OUTLIER) cc_final: 0.7086 (ttm-80) REVERT: D 94 THR cc_start: 0.8625 (m) cc_final: 0.8106 (p) REVERT: D 115 GLU cc_start: 0.7018 (mm-30) cc_final: 0.6607 (mm-30) REVERT: F 159 GLU cc_start: 0.7517 (tt0) cc_final: 0.7296 (tt0) REVERT: F 166 ARG cc_start: 0.7394 (ttm-80) cc_final: 0.6572 (tpp-160) REVERT: G 131 GLU cc_start: 0.7937 (tp30) cc_final: 0.7631 (tp30) REVERT: G 147 ARG cc_start: 0.8308 (ttp-110) cc_final: 0.8078 (tmm-80) REVERT: G 169 ASN cc_start: 0.8498 (m110) cc_final: 0.8290 (m110) REVERT: H 11 GLN cc_start: 0.8004 (OUTLIER) cc_final: 0.6758 (mt0) REVERT: H 62 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.7037 (pt0) REVERT: H 86 MET cc_start: 0.8191 (mtp) cc_final: 0.7889 (mtp) REVERT: H 134 MET cc_start: 0.8715 (mtm) cc_final: 0.8173 (mtm) REVERT: I 49 GLN cc_start: 0.7058 (tp-100) cc_final: 0.6378 (pm20) REVERT: I 50 SER cc_start: 0.8420 (t) cc_final: 0.7909 (p) REVERT: I 143 SER cc_start: 0.7175 (p) cc_final: 0.6836 (m) REVERT: I 145 ASP cc_start: 0.7313 (m-30) cc_final: 0.7058 (m-30) REVERT: J 33 GLU cc_start: 0.7099 (tp30) cc_final: 0.6607 (tp30) REVERT: J 115 GLU cc_start: 0.7892 (mp0) cc_final: 0.7534 (mp0) REVERT: J 150 ARG cc_start: 0.6496 (mmt90) cc_final: 0.5899 (mmt180) REVERT: K 67 THR cc_start: 0.8403 (m) cc_final: 0.8102 (p) REVERT: K 137 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.7924 (mtmm) REVERT: L 17 GLU cc_start: 0.7477 (mt-10) cc_final: 0.7249 (mm-30) REVERT: L 25 ASP cc_start: 0.7020 (m-30) cc_final: 0.6477 (m-30) REVERT: L 136 GLU cc_start: 0.7032 (mm-30) cc_final: 0.6817 (mm-30) REVERT: M 49 GLN cc_start: 0.7971 (tp-100) cc_final: 0.7395 (pm20) REVERT: M 68 GLN cc_start: 0.7774 (OUTLIER) cc_final: 0.7434 (pt0) REVERT: M 70 GLN cc_start: 0.7378 (OUTLIER) cc_final: 0.7093 (mm-40) REVERT: N 107 ASP cc_start: 0.7773 (m-30) cc_final: 0.7439 (m-30) REVERT: N 115 GLU cc_start: 0.7187 (mp0) cc_final: 0.6909 (mp0) REVERT: N 134 MET cc_start: 0.8830 (mtm) cc_final: 0.8324 (mtm) REVERT: N 150 ARG cc_start: 0.7141 (tpp-160) cc_final: 0.6876 (tpp-160) REVERT: R 1 MET cc_start: 0.7868 (ptp) cc_final: 0.7376 (ptp) REVERT: S 35 ASN cc_start: 0.8785 (m-40) cc_final: 0.8528 (m-40) REVERT: S 116 ASP cc_start: 0.7227 (OUTLIER) cc_final: 0.6708 (m-30) REVERT: T 8 VAL cc_start: 0.8665 (OUTLIER) cc_final: 0.8422 (m) REVERT: T 86 MET cc_start: 0.8235 (mmm) cc_final: 0.7871 (mmm) REVERT: U 77 ASP cc_start: 0.7939 (OUTLIER) cc_final: 0.7653 (p0) REVERT: U 116 ASP cc_start: 0.7116 (OUTLIER) cc_final: 0.6887 (p0) REVERT: U 117 GLU cc_start: 0.7367 (mp0) cc_final: 0.7049 (mp0) REVERT: V 150 ARG cc_start: 0.7512 (mmm-85) cc_final: 0.7163 (tpt-90) REVERT: V 152 ASP cc_start: 0.7379 (t0) cc_final: 0.6972 (t70) REVERT: W 78 GLN cc_start: 0.7728 (tp40) cc_final: 0.7124 (tp40) REVERT: X 25 ASP cc_start: 0.6977 (m-30) cc_final: 0.6727 (m-30) REVERT: X 86 MET cc_start: 0.7778 (mtm) cc_final: 0.7558 (mtp) REVERT: X 132 GLN cc_start: 0.7716 (mm110) cc_final: 0.7461 (mm-40) REVERT: X 143 ASN cc_start: 0.7684 (m-40) cc_final: 0.7416 (m-40) REVERT: Y 39 GLN cc_start: 0.7509 (OUTLIER) cc_final: 0.7260 (mt0) REVERT: Y 68 GLN cc_start: 0.7830 (OUTLIER) cc_final: 0.6981 (mt0) REVERT: Z 17 GLU cc_start: 0.7399 (pm20) cc_final: 0.6653 (tm-30) REVERT: a 65 TYR cc_start: 0.8148 (p90) cc_final: 0.7737 (p90) REVERT: a 109 GLU cc_start: 0.7556 (tm-30) cc_final: 0.7076 (tm-30) REVERT: a 134 LYS cc_start: 0.8518 (mmtp) cc_final: 0.8246 (mttt) REVERT: b 106 GLU cc_start: 0.6942 (mm-30) cc_final: 0.6361 (mm-30) REVERT: c 11 THR cc_start: 0.8425 (t) cc_final: 0.8187 (m) REVERT: c 49 GLN cc_start: 0.7722 (tp40) cc_final: 0.7285 (pm20) REVERT: c 53 ASN cc_start: 0.8314 (m-40) cc_final: 0.7969 (m110) REVERT: d 134 MET cc_start: 0.8820 (mtm) cc_final: 0.8569 (mtm) REVERT: d 136 GLU cc_start: 0.7072 (OUTLIER) cc_final: 0.6751 (mt-10) REVERT: d 140 ASP cc_start: 0.6739 (OUTLIER) cc_final: 0.6359 (m-30) REVERT: d 159 GLU cc_start: 0.7784 (tt0) cc_final: 0.7534 (tt0) REVERT: e 42 LYS cc_start: 0.7965 (ttpt) cc_final: 0.7501 (tttp) REVERT: e 78 GLN cc_start: 0.7402 (tp40) cc_final: 0.7130 (tp-100) REVERT: e 123 ASP cc_start: 0.7390 (t0) cc_final: 0.6999 (t0) REVERT: f 86 MET cc_start: 0.8223 (mtp) cc_final: 0.7904 (mtp) REVERT: g 117 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.6968 (mt-10) REVERT: g 131 GLU cc_start: 0.7301 (tp30) cc_final: 0.6955 (tp30) REVERT: h 79 MET cc_start: 0.8921 (tpp) cc_final: 0.8557 (tpp) REVERT: h 150 ARG cc_start: 0.7330 (tpp-160) cc_final: 0.6801 (tpp-160) REVERT: i 15 GLN cc_start: 0.7650 (mp10) cc_final: 0.7435 (mp10) REVERT: i 42 LYS cc_start: 0.7585 (tttm) cc_final: 0.7358 (tptt) REVERT: i 50 SER cc_start: 0.7735 (t) cc_final: 0.7496 (p) REVERT: i 70 GLN cc_start: 0.7149 (mm-40) cc_final: 0.6768 (mm110) REVERT: i 111 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8459 (tt) REVERT: j 25 ASP cc_start: 0.6713 (m-30) cc_final: 0.6344 (m-30) REVERT: k 19 ARG cc_start: 0.7349 (OUTLIER) cc_final: 0.7011 (mmt90) REVERT: l 41 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7639 (ttm-80) REVERT: l 206 SER cc_start: 0.7817 (OUTLIER) cc_final: 0.7440 (t) REVERT: m 19 ARG cc_start: 0.7814 (OUTLIER) cc_final: 0.6948 (tpm170) REVERT: n 55 ASN cc_start: 0.8192 (m-40) cc_final: 0.7813 (t0) REVERT: n 134 LYS cc_start: 0.7617 (mttp) cc_final: 0.7017 (mtpp) outliers start: 110 outliers final: 66 residues processed: 997 average time/residue: 1.5940 time to fit residues: 1978.9855 Evaluate side-chains 1002 residues out of total 5289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 915 time to evaluate : 4.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 120 ARG Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain D residue 15 ARG Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain G residue 116 ASP Chi-restraints excluded: chain G residue 162 SER Chi-restraints excluded: chain H residue 11 GLN Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 141 ILE Chi-restraints excluded: chain H residue 154 SER Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 15 GLN Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain K residue 50 SER Chi-restraints excluded: chain K residue 137 LYS Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain M residue 50 SER Chi-restraints excluded: chain M residue 68 GLN Chi-restraints excluded: chain M residue 70 GLN Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain P residue 103 SER Chi-restraints excluded: chain P residue 154 SER Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 166 ARG Chi-restraints excluded: chain S residue 32 ARG Chi-restraints excluded: chain S residue 116 ASP Chi-restraints excluded: chain T residue 8 VAL Chi-restraints excluded: chain T residue 146 ASN Chi-restraints excluded: chain T residue 149 THR Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 50 SER Chi-restraints excluded: chain U residue 77 ASP Chi-restraints excluded: chain U residue 116 ASP Chi-restraints excluded: chain V residue 28 SER Chi-restraints excluded: chain V residue 136 GLU Chi-restraints excluded: chain W residue 3 THR Chi-restraints excluded: chain W residue 50 SER Chi-restraints excluded: chain W residue 125 SER Chi-restraints excluded: chain Y residue 39 GLN Chi-restraints excluded: chain Y residue 47 ASN Chi-restraints excluded: chain Y residue 67 THR Chi-restraints excluded: chain Y residue 68 GLN Chi-restraints excluded: chain a residue 162 SER Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain d residue 136 GLU Chi-restraints excluded: chain d residue 140 ASP Chi-restraints excluded: chain d residue 150 ARG Chi-restraints excluded: chain e residue 20 SER Chi-restraints excluded: chain e residue 134 LYS Chi-restraints excluded: chain f residue 115 GLU Chi-restraints excluded: chain f residue 166 ARG Chi-restraints excluded: chain g residue 10 SER Chi-restraints excluded: chain g residue 50 SER Chi-restraints excluded: chain g residue 57 GLN Chi-restraints excluded: chain g residue 117 GLU Chi-restraints excluded: chain g residue 145 ASP Chi-restraints excluded: chain i residue 31 LEU Chi-restraints excluded: chain i residue 111 LEU Chi-restraints excluded: chain j residue 4 VAL Chi-restraints excluded: chain j residue 30 THR Chi-restraints excluded: chain j residue 75 THR Chi-restraints excluded: chain j residue 106 GLU Chi-restraints excluded: chain j residue 149 THR Chi-restraints excluded: chain k residue 19 ARG Chi-restraints excluded: chain k residue 47 ASP Chi-restraints excluded: chain k residue 161 THR Chi-restraints excluded: chain k residue 207 SER Chi-restraints excluded: chain l residue 41 ARG Chi-restraints excluded: chain l residue 206 SER Chi-restraints excluded: chain l residue 251 ASP Chi-restraints excluded: chain l residue 266 THR Chi-restraints excluded: chain m residue 19 ARG Chi-restraints excluded: chain m residue 41 ILE Chi-restraints excluded: chain m residue 46 SER Chi-restraints excluded: chain m residue 47 THR Chi-restraints excluded: chain m residue 64 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 676 random chunks: chunk 425 optimal weight: 2.9990 chunk 571 optimal weight: 1.9990 chunk 164 optimal weight: 0.6980 chunk 494 optimal weight: 1.9990 chunk 79 optimal weight: 0.0970 chunk 149 optimal weight: 0.0670 chunk 537 optimal weight: 1.9990 chunk 224 optimal weight: 0.9990 chunk 551 optimal weight: 0.7980 chunk 68 optimal weight: 8.9990 chunk 98 optimal weight: 1.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 47 ASN ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 ASN D 11 GLN D 23 GLN D 111 ASN D 132 GLN E 33 GLN ** F 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 132 GLN ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 ASN I 39 GLN ** I 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 132 GLN K 15 GLN K 53 ASN L 11 GLN M 78 GLN M 139 ASN N 132 GLN O 33 GLN O 68 GLN ** O 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 47 ASN Q 68 GLN Q 139 ASN ** S 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 15 GLN V 111 ASN V 146 ASN ** X 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 132 GLN ** c 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 68 GLN d 132 GLN e 15 GLN ** g 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 61 ASN h 68 GLN j 132 GLN ** k 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 270 GLN l 259 GLN ** n 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.103911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.093880 restraints weight = 73793.545| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 0.88 r_work: 0.2994 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.282 55108 Z= 0.291 Angle : 0.781 59.198 74959 Z= 0.414 Chirality : 0.039 0.938 8198 Planarity : 0.006 0.317 9826 Dihedral : 10.618 88.526 10012 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.02 % Allowed : 16.68 % Favored : 81.30 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 1.83 (0.10), residues: 6771 helix: 1.70 (0.07), residues: 5279 sheet: 0.61 (0.59), residues: 48 loop : -0.51 (0.15), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP l 146 HIS 0.008 0.002 HIS C 140 PHE 0.016 0.002 PHE R 98 TYR 0.026 0.001 TYR a 90 ARG 0.066 0.001 ARG m 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25703.23 seconds wall clock time: 444 minutes 3.38 seconds (26643.38 seconds total)