Starting phenix.real_space_refine on Fri Mar 22 16:02:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tqt_26071/03_2024/7tqt_26071_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tqt_26071/03_2024/7tqt_26071.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tqt_26071/03_2024/7tqt_26071.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tqt_26071/03_2024/7tqt_26071.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tqt_26071/03_2024/7tqt_26071_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tqt_26071/03_2024/7tqt_26071_updated.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 210 5.16 5 C 21454 2.51 5 N 5744 2.21 5 O 6469 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "a GLU 26": "OE1" <-> "OE2" Residue "a TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 167": "OD1" <-> "OD2" Residue "a TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 259": "OE1" <-> "OE2" Residue "c ASP 17": "OD1" <-> "OD2" Residue "c PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 59": "OD1" <-> "OD2" Residue "c TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 69": "OE1" <-> "OE2" Residue "e PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 167": "OD1" <-> "OD2" Residue "e TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 259": "OE1" <-> "OE2" Residue "g PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 259": "OE1" <-> "OE2" Residue "j PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 95": "OE1" <-> "OE2" Residue "m PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 55": "OE1" <-> "OE2" Residue "q TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r GLU 67": "OE1" <-> "OE2" Residue "r TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ASP 17": "OD1" <-> "OD2" Residue "s PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ASP 181": "OD1" <-> "OD2" Residue "s PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 33877 Number of models: 1 Model: "" Number of chains: 27 Chain: "L" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 490 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 98} Link IDs: {'TRANS': 97} Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 294 Unresolved non-hydrogen dihedrals: 98 Planarities with less than four sites: {'UNK:plan-1': 98} Unresolved non-hydrogen planarities: 98 Chain: "H" Number of atoms: 540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 540 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 108} Link IDs: {'TRANS': 107} Unresolved non-hydrogen bonds: 216 Unresolved non-hydrogen angles: 324 Unresolved non-hydrogen dihedrals: 108 Planarities with less than four sites: {'UNK:plan-1': 108} Unresolved non-hydrogen planarities: 108 Chain: "a" Number of atoms: 2213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2213 Classifications: {'peptide': 281} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 260} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PHE%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "b" Number of atoms: 2053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2053 Classifications: {'peptide': 264} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 247} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLN%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "c" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1848 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 20, 'TRANS': 218} Chain: "d" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 512 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 3, 'TRANS': 64} Chain: "e" Number of atoms: 2219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2219 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 20, 'TRANS': 261} Chain: "f" Number of atoms: 2008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2008 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 16, 'TRANS': 241} Chain breaks: 1 Chain: "g" Number of atoms: 1810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1810 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 20, 'TRANS': 213} Chain: "h" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 512 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 3, 'TRANS': 64} Chain: "i" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2226 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 20, 'TRANS': 262} Chain: "j" Number of atoms: 2003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2003 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 16, 'TRANS': 240} Chain breaks: 2 Chain: "k" Number of atoms: 1801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1801 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 20, 'TRANS': 212} Chain: "l" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 512 Classifications: {'peptide': 68} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 64} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ASN%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "m" Number of atoms: 2176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2176 Classifications: {'peptide': 276} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 256} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PHE%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "n" Number of atoms: 2029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2029 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 16, 'TRANS': 244} Chain breaks: 1 Chain: "o" Number of atoms: 1810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1810 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 20, 'TRANS': 213} Chain: "p" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 504 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "q" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2226 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 20, 'TRANS': 262} Chain: "r" Number of atoms: 1975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1975 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 16, 'TRANS': 236} Chain breaks: 2 Chain: "s" Number of atoms: 1818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1818 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 20, 'TRANS': 214} Chain: "t" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 512 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 3, 'TRANS': 64} Chain: "a" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'MYR': 1} Classifications: {'undetermined': 1} Chain: "e" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'MYR': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'MYR': 1} Classifications: {'undetermined': 1} Chain: "m" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'MYR': 1} Classifications: {'undetermined': 1} Chain: "q" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'MYR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 17.95, per 1000 atoms: 0.53 Number of scatterers: 33877 At special positions: 0 Unit cell: (125.4, 179.74, 158.84, 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 210 16.00 O 6469 8.00 N 5744 7.00 C 21454 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.39 Conformation dependent library (CDL) restraints added in 6.0 seconds 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8326 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 105 helices and 59 sheets defined 11.8% alpha, 20.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.39 Creating SS restraints... Processing helix chain 'a' and resid 42 through 44 No H-bonds generated for 'chain 'a' and resid 42 through 44' Processing helix chain 'a' and resid 52 through 55 No H-bonds generated for 'chain 'a' and resid 52 through 55' Processing helix chain 'a' and resid 68 through 70 No H-bonds generated for 'chain 'a' and resid 68 through 70' Processing helix chain 'a' and resid 72 through 75 No H-bonds generated for 'chain 'a' and resid 72 through 75' Processing helix chain 'a' and resid 96 through 99 Processing helix chain 'a' and resid 111 through 119 removed outlier: 3.661A pdb=" N PHE a 119 " --> pdb=" O ARG a 115 " (cutoff:3.500A) Processing helix chain 'a' and resid 168 through 171 Processing helix chain 'a' and resid 226 through 229 Processing helix chain 'a' and resid 283 through 285 No H-bonds generated for 'chain 'a' and resid 283 through 285' Processing helix chain 'b' and resid 34 through 36 No H-bonds generated for 'chain 'b' and resid 34 through 36' Processing helix chain 'b' and resid 44 through 46 No H-bonds generated for 'chain 'b' and resid 44 through 46' Processing helix chain 'b' and resid 57 through 59 No H-bonds generated for 'chain 'b' and resid 57 through 59' Processing helix chain 'b' and resid 82 through 88 removed outlier: 4.955A pdb=" N ASP b 88 " --> pdb=" O ASP b 84 " (cutoff:3.500A) Processing helix chain 'b' and resid 90 through 98 Processing helix chain 'b' and resid 145 through 148 No H-bonds generated for 'chain 'b' and resid 145 through 148' Processing helix chain 'b' and resid 151 through 153 No H-bonds generated for 'chain 'b' and resid 151 through 153' Processing helix chain 'b' and resid 168 through 170 No H-bonds generated for 'chain 'b' and resid 168 through 170' Processing helix chain 'b' and resid 187 through 192 removed outlier: 4.436A pdb=" N PHE b 191 " --> pdb=" O GLY b 188 " (cutoff:3.500A) Processing helix chain 'c' and resid 43 through 47 Processing helix chain 'c' and resid 65 through 68 Processing helix chain 'c' and resid 98 through 105 removed outlier: 3.998A pdb=" N TYR c 105 " --> pdb=" O GLU c 101 " (cutoff:3.500A) Processing helix chain 'c' and resid 144 through 147 No H-bonds generated for 'chain 'c' and resid 144 through 147' Processing helix chain 'd' and resid 36 through 38 No H-bonds generated for 'chain 'd' and resid 36 through 38' Processing helix chain 'd' and resid 50 through 54 removed outlier: 3.549A pdb=" N THR d 54 " --> pdb=" O SER d 51 " (cutoff:3.500A) Processing helix chain 'e' and resid 52 through 55 No H-bonds generated for 'chain 'e' and resid 52 through 55' Processing helix chain 'e' and resid 72 through 75 No H-bonds generated for 'chain 'e' and resid 72 through 75' Processing helix chain 'e' and resid 93 through 99 removed outlier: 5.193A pdb=" N LYS e 97 " --> pdb=" O GLY e 94 " (cutoff:3.500A) Processing helix chain 'e' and resid 111 through 119 removed outlier: 3.856A pdb=" N LYS e 116 " --> pdb=" O GLN e 112 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N PHE e 119 " --> pdb=" O ARG e 115 " (cutoff:3.500A) Processing helix chain 'e' and resid 168 through 171 Processing helix chain 'e' and resid 226 through 229 No H-bonds generated for 'chain 'e' and resid 226 through 229' Processing helix chain 'f' and resid 34 through 36 No H-bonds generated for 'chain 'f' and resid 34 through 36' Processing helix chain 'f' and resid 44 through 46 No H-bonds generated for 'chain 'f' and resid 44 through 46' Processing helix chain 'f' and resid 57 through 59 No H-bonds generated for 'chain 'f' and resid 57 through 59' Processing helix chain 'f' and resid 82 through 88 removed outlier: 4.453A pdb=" N ASP f 88 " --> pdb=" O ASP f 84 " (cutoff:3.500A) Processing helix chain 'f' and resid 90 through 97 removed outlier: 3.908A pdb=" N TYR f 97 " --> pdb=" O GLY f 93 " (cutoff:3.500A) Processing helix chain 'f' and resid 145 through 148 No H-bonds generated for 'chain 'f' and resid 145 through 148' Processing helix chain 'f' and resid 187 through 192 removed outlier: 4.539A pdb=" N PHE f 191 " --> pdb=" O GLY f 188 " (cutoff:3.500A) Processing helix chain 'g' and resid 43 through 47 Processing helix chain 'g' and resid 65 through 68 Processing helix chain 'g' and resid 98 through 105 removed outlier: 3.650A pdb=" N TYR g 105 " --> pdb=" O GLU g 101 " (cutoff:3.500A) Processing helix chain 'g' and resid 144 through 149 Processing helix chain 'h' and resid 36 through 38 No H-bonds generated for 'chain 'h' and resid 36 through 38' Processing helix chain 'h' and resid 50 through 54 Processing helix chain 'i' and resid 42 through 44 No H-bonds generated for 'chain 'i' and resid 42 through 44' Processing helix chain 'i' and resid 52 through 54 No H-bonds generated for 'chain 'i' and resid 52 through 54' Processing helix chain 'i' and resid 68 through 70 No H-bonds generated for 'chain 'i' and resid 68 through 70' Processing helix chain 'i' and resid 72 through 75 No H-bonds generated for 'chain 'i' and resid 72 through 75' Processing helix chain 'i' and resid 96 through 98 No H-bonds generated for 'chain 'i' and resid 96 through 98' Processing helix chain 'i' and resid 111 through 119 removed outlier: 3.635A pdb=" N PHE i 119 " --> pdb=" O ARG i 115 " (cutoff:3.500A) Processing helix chain 'i' and resid 169 through 171 No H-bonds generated for 'chain 'i' and resid 169 through 171' Processing helix chain 'i' and resid 226 through 228 No H-bonds generated for 'chain 'i' and resid 226 through 228' Processing helix chain 'i' and resid 283 through 285 No H-bonds generated for 'chain 'i' and resid 283 through 285' Processing helix chain 'j' and resid 34 through 36 No H-bonds generated for 'chain 'j' and resid 34 through 36' Processing helix chain 'j' and resid 57 through 60 No H-bonds generated for 'chain 'j' and resid 57 through 60' Processing helix chain 'j' and resid 82 through 85 No H-bonds generated for 'chain 'j' and resid 82 through 85' Processing helix chain 'j' and resid 90 through 98 Processing helix chain 'j' and resid 151 through 153 No H-bonds generated for 'chain 'j' and resid 151 through 153' Processing helix chain 'j' and resid 187 through 192 removed outlier: 4.432A pdb=" N PHE j 191 " --> pdb=" O GLY j 188 " (cutoff:3.500A) Processing helix chain 'k' and resid 43 through 47 Processing helix chain 'k' and resid 65 through 68 Processing helix chain 'k' and resid 98 through 105 removed outlier: 3.981A pdb=" N TYR k 105 " --> pdb=" O GLU k 101 " (cutoff:3.500A) Processing helix chain 'k' and resid 144 through 149 Processing helix chain 'l' and resid 36 through 38 No H-bonds generated for 'chain 'l' and resid 36 through 38' Processing helix chain 'l' and resid 50 through 54 Processing helix chain 'm' and resid 42 through 44 No H-bonds generated for 'chain 'm' and resid 42 through 44' Processing helix chain 'm' and resid 52 through 55 No H-bonds generated for 'chain 'm' and resid 52 through 55' Processing helix chain 'm' and resid 72 through 75 No H-bonds generated for 'chain 'm' and resid 72 through 75' Processing helix chain 'm' and resid 93 through 99 removed outlier: 4.900A pdb=" N LYS m 97 " --> pdb=" O GLY m 94 " (cutoff:3.500A) Processing helix chain 'm' and resid 111 through 119 removed outlier: 3.611A pdb=" N PHE m 119 " --> pdb=" O ARG m 115 " (cutoff:3.500A) Processing helix chain 'm' and resid 168 through 171 Processing helix chain 'm' and resid 226 through 229 Processing helix chain 'n' and resid 34 through 36 No H-bonds generated for 'chain 'n' and resid 34 through 36' Processing helix chain 'n' and resid 57 through 59 No H-bonds generated for 'chain 'n' and resid 57 through 59' Processing helix chain 'n' and resid 82 through 85 No H-bonds generated for 'chain 'n' and resid 82 through 85' Processing helix chain 'n' and resid 90 through 98 Processing helix chain 'n' and resid 145 through 148 No H-bonds generated for 'chain 'n' and resid 145 through 148' Processing helix chain 'n' and resid 187 through 192 removed outlier: 4.317A pdb=" N PHE n 191 " --> pdb=" O GLY n 188 " (cutoff:3.500A) Processing helix chain 'o' and resid 43 through 47 Processing helix chain 'o' and resid 65 through 68 Processing helix chain 'o' and resid 94 through 96 No H-bonds generated for 'chain 'o' and resid 94 through 96' Processing helix chain 'o' and resid 98 through 105 removed outlier: 3.945A pdb=" N TYR o 105 " --> pdb=" O GLU o 101 " (cutoff:3.500A) Processing helix chain 'o' and resid 144 through 147 No H-bonds generated for 'chain 'o' and resid 144 through 147' Processing helix chain 'p' and resid 36 through 38 No H-bonds generated for 'chain 'p' and resid 36 through 38' Processing helix chain 'p' and resid 50 through 54 Processing helix chain 'q' and resid 52 through 55 No H-bonds generated for 'chain 'q' and resid 52 through 55' Processing helix chain 'q' and resid 72 through 75 No H-bonds generated for 'chain 'q' and resid 72 through 75' Processing helix chain 'q' and resid 93 through 99 removed outlier: 4.867A pdb=" N LYS q 97 " --> pdb=" O GLY q 94 " (cutoff:3.500A) Processing helix chain 'q' and resid 111 through 119 removed outlier: 3.604A pdb=" N LYS q 116 " --> pdb=" O GLN q 112 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE q 119 " --> pdb=" O ARG q 115 " (cutoff:3.500A) Processing helix chain 'q' and resid 169 through 171 No H-bonds generated for 'chain 'q' and resid 169 through 171' Processing helix chain 'q' and resid 226 through 229 Processing helix chain 'q' and resid 283 through 285 No H-bonds generated for 'chain 'q' and resid 283 through 285' Processing helix chain 'r' and resid 34 through 36 No H-bonds generated for 'chain 'r' and resid 34 through 36' Processing helix chain 'r' and resid 44 through 46 No H-bonds generated for 'chain 'r' and resid 44 through 46' Processing helix chain 'r' and resid 57 through 59 No H-bonds generated for 'chain 'r' and resid 57 through 59' Processing helix chain 'r' and resid 82 through 88 removed outlier: 3.768A pdb=" N LYS r 87 " --> pdb=" O PRO r 83 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N ASP r 88 " --> pdb=" O ASP r 84 " (cutoff:3.500A) Processing helix chain 'r' and resid 90 through 98 removed outlier: 3.681A pdb=" N TYR r 97 " --> pdb=" O GLY r 93 " (cutoff:3.500A) Processing helix chain 'r' and resid 151 through 153 No H-bonds generated for 'chain 'r' and resid 151 through 153' Processing helix chain 'r' and resid 187 through 192 removed outlier: 4.346A pdb=" N PHE r 191 " --> pdb=" O GLY r 188 " (cutoff:3.500A) Processing helix chain 's' and resid 43 through 47 Processing helix chain 's' and resid 65 through 68 Processing helix chain 's' and resid 92 through 95 No H-bonds generated for 'chain 's' and resid 92 through 95' Processing helix chain 's' and resid 98 through 105 removed outlier: 4.053A pdb=" N TYR s 105 " --> pdb=" O GLU s 101 " (cutoff:3.500A) Processing helix chain 's' and resid 146 through 148 No H-bonds generated for 'chain 's' and resid 146 through 148' Processing helix chain 't' and resid 36 through 38 No H-bonds generated for 'chain 't' and resid 36 through 38' Processing helix chain 't' and resid 50 through 54 removed outlier: 3.509A pdb=" N THR t 54 " --> pdb=" O SER t 51 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'L' and resid 4 through 6 Processing sheet with id= B, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.781A pdb=" N UNK L 96 " --> pdb=" O UNK L 11 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'L' and resid 34 through 37 removed outlier: 4.323A pdb=" N UNK L 80 " --> pdb=" O UNK L 37 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'H' and resid 19 through 22 removed outlier: 4.156A pdb=" N UNK H 73 " --> pdb=" O UNK H 19 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'H' and resid 34 through 37 Processing sheet with id= F, first strand: chain 'H' and resid 46 through 48 Processing sheet with id= G, first strand: chain 'a' and resid 100 through 104 Processing sheet with id= H, first strand: chain 'a' and resid 122 through 124 Processing sheet with id= I, first strand: chain 'a' and resid 188 through 191 removed outlier: 3.784A pdb=" N THR a 83 " --> pdb=" O VAL a 254 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N MET a 256 " --> pdb=" O CYS a 81 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N CYS a 81 " --> pdb=" O MET a 256 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'b' and resid 14 through 18 Processing sheet with id= K, first strand: chain 'b' and resid 63 through 65 Processing sheet with id= L, first strand: chain 'b' and resid 69 through 71 Processing sheet with id= M, first strand: chain 'b' and resid 78 through 81 removed outlier: 6.218A pdb=" N ALA b 121 " --> pdb=" O LEU b 234 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'b' and resid 101 through 103 Processing sheet with id= O, first strand: chain 'c' and resid 70 through 73 Processing sheet with id= P, first strand: chain 'c' and resid 151 through 156 removed outlier: 5.465A pdb=" N LEU c 130 " --> pdb=" O TYR c 193 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N TYR c 193 " --> pdb=" O LEU c 130 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N SER c 132 " --> pdb=" O CYS c 191 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N CYS c 191 " --> pdb=" O SER c 132 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N SER c 134 " --> pdb=" O ILE c 189 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ILE c 189 " --> pdb=" O SER c 134 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE c 82 " --> pdb=" O CYS c 191 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N TYR c 193 " --> pdb=" O PRO c 80 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'd' and resid 4 through 7 Processing sheet with id= R, first strand: chain 'e' and resid 100 through 104 Processing sheet with id= S, first strand: chain 'e' and resid 122 through 124 Processing sheet with id= T, first strand: chain 'e' and resid 188 through 191 removed outlier: 6.047A pdb=" N MET e 256 " --> pdb=" O CYS e 81 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N CYS e 81 " --> pdb=" O MET e 256 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'f' and resid 14 through 18 Processing sheet with id= V, first strand: chain 'f' and resid 63 through 65 Processing sheet with id= W, first strand: chain 'f' and resid 69 through 72 Processing sheet with id= X, first strand: chain 'f' and resid 78 through 81 removed outlier: 6.141A pdb=" N ALA f 121 " --> pdb=" O LEU f 234 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'f' and resid 101 through 103 Processing sheet with id= Z, first strand: chain 'g' and resid 70 through 73 Processing sheet with id= AA, first strand: chain 'g' and resid 151 through 156 Processing sheet with id= AB, first strand: chain 'h' and resid 4 through 6 Processing sheet with id= AC, first strand: chain 'i' and resid 100 through 104 Processing sheet with id= AD, first strand: chain 'i' and resid 122 through 124 Processing sheet with id= AE, first strand: chain 'i' and resid 188 through 191 removed outlier: 6.136A pdb=" N MET i 256 " --> pdb=" O CYS i 81 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N CYS i 81 " --> pdb=" O MET i 256 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'j' and resid 14 through 18 Processing sheet with id= AG, first strand: chain 'j' and resid 63 through 65 Processing sheet with id= AH, first strand: chain 'j' and resid 69 through 71 Processing sheet with id= AI, first strand: chain 'j' and resid 78 through 81 removed outlier: 6.230A pdb=" N ALA j 121 " --> pdb=" O LEU j 234 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'j' and resid 101 through 103 Processing sheet with id= AK, first strand: chain 'k' and resid 70 through 73 Processing sheet with id= AL, first strand: chain 'k' and resid 82 through 85 removed outlier: 3.672A pdb=" N PHE k 82 " --> pdb=" O CYS k 191 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LYS k 128 " --> pdb=" O GLN k 194 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'l' and resid 4 through 6 Processing sheet with id= AN, first strand: chain 'm' and resid 100 through 104 Processing sheet with id= AO, first strand: chain 'm' and resid 188 through 191 removed outlier: 6.141A pdb=" N MET m 256 " --> pdb=" O CYS m 81 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N CYS m 81 " --> pdb=" O MET m 256 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'n' and resid 14 through 18 Processing sheet with id= AQ, first strand: chain 'n' and resid 63 through 65 Processing sheet with id= AR, first strand: chain 'n' and resid 69 through 71 Processing sheet with id= AS, first strand: chain 'n' and resid 78 through 81 removed outlier: 6.278A pdb=" N ALA n 121 " --> pdb=" O LEU n 234 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'n' and resid 101 through 103 Processing sheet with id= AU, first strand: chain 'o' and resid 70 through 73 Processing sheet with id= AV, first strand: chain 'o' and resid 151 through 156 removed outlier: 3.561A pdb=" N PHE o 82 " --> pdb=" O CYS o 191 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N TYR o 193 " --> pdb=" O PRO o 80 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'p' and resid 4 through 7 Processing sheet with id= AX, first strand: chain 'q' and resid 100 through 104 Processing sheet with id= AY, first strand: chain 'q' and resid 122 through 124 Processing sheet with id= AZ, first strand: chain 'q' and resid 188 through 191 removed outlier: 6.025A pdb=" N MET q 256 " --> pdb=" O CYS q 81 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N CYS q 81 " --> pdb=" O MET q 256 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'r' and resid 14 through 18 Processing sheet with id= BB, first strand: chain 'r' and resid 69 through 71 Processing sheet with id= BC, first strand: chain 'r' and resid 78 through 81 removed outlier: 6.288A pdb=" N ALA r 121 " --> pdb=" O LEU r 234 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'r' and resid 101 through 103 Processing sheet with id= BE, first strand: chain 's' and resid 70 through 72 removed outlier: 3.972A pdb=" N PHE s 208 " --> pdb=" O CYS s 120 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 's' and resid 151 through 156 removed outlier: 4.120A pdb=" N LYS s 128 " --> pdb=" O THR s 195 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N LEU s 130 " --> pdb=" O TYR s 193 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N TYR s 193 " --> pdb=" O LEU s 130 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N SER s 132 " --> pdb=" O CYS s 191 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N CYS s 191 " --> pdb=" O SER s 132 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N SER s 134 " --> pdb=" O ILE s 189 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N ILE s 189 " --> pdb=" O SER s 134 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE s 82 " --> pdb=" O CYS s 191 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N TYR s 193 " --> pdb=" O PRO s 80 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 't' and resid 4 through 7 730 hydrogen bonds defined for protein. 1746 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.45 Time building geometry restraints manager: 14.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 6064 1.31 - 1.44: 10258 1.44 - 1.57: 18001 1.57 - 1.71: 73 1.71 - 1.84: 338 Bond restraints: 34734 Sorted by residual: bond pdb=" CB HIS b 224 " pdb=" CG HIS b 224 " ideal model delta sigma weight residual 1.497 1.342 0.155 1.40e-02 5.10e+03 1.22e+02 bond pdb=" CD ARG b 103 " pdb=" NE ARG b 103 " ideal model delta sigma weight residual 1.458 1.367 0.091 1.40e-02 5.10e+03 4.20e+01 bond pdb=" CD ARG q 238 " pdb=" NE ARG q 238 " ideal model delta sigma weight residual 1.458 1.370 0.088 1.40e-02 5.10e+03 3.98e+01 bond pdb=" CB HIS e 246 " pdb=" CG HIS e 246 " ideal model delta sigma weight residual 1.497 1.409 0.088 1.40e-02 5.10e+03 3.92e+01 bond pdb=" CB HIS r 224 " pdb=" CG HIS r 224 " ideal model delta sigma weight residual 1.497 1.410 0.087 1.40e-02 5.10e+03 3.85e+01 ... (remaining 34729 not shown) Histogram of bond angle deviations from ideal: 95.48 - 103.50: 724 103.50 - 111.52: 14292 111.52 - 119.54: 15075 119.54 - 127.56: 16976 127.56 - 135.59: 312 Bond angle restraints: 47379 Sorted by residual: angle pdb=" C PRO g 135 " pdb=" N PRO g 136 " pdb=" CA PRO g 136 " ideal model delta sigma weight residual 120.21 129.18 -8.97 9.60e-01 1.09e+00 8.73e+01 angle pdb=" C PRO o 135 " pdb=" N PRO o 136 " pdb=" CA PRO o 136 " ideal model delta sigma weight residual 120.03 129.14 -9.11 9.90e-01 1.02e+00 8.46e+01 angle pdb=" C PRO s 135 " pdb=" N PRO s 136 " pdb=" CA PRO s 136 " ideal model delta sigma weight residual 120.21 128.95 -8.74 9.60e-01 1.09e+00 8.29e+01 angle pdb=" C PRO k 135 " pdb=" N PRO k 136 " pdb=" CA PRO k 136 " ideal model delta sigma weight residual 119.92 129.66 -9.74 1.07e+00 8.73e-01 8.28e+01 angle pdb=" CA ASP o 17 " pdb=" CB ASP o 17 " pdb=" CG ASP o 17 " ideal model delta sigma weight residual 112.60 121.56 -8.96 1.00e+00 1.00e+00 8.02e+01 ... (remaining 47374 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 20025 17.74 - 35.48: 513 35.48 - 53.22: 114 53.22 - 70.96: 46 70.96 - 88.70: 18 Dihedral angle restraints: 20716 sinusoidal: 7815 harmonic: 12901 Sorted by residual: dihedral pdb=" C TYR i 274 " pdb=" N TYR i 274 " pdb=" CA TYR i 274 " pdb=" CB TYR i 274 " ideal model delta harmonic sigma weight residual -122.60 -107.83 -14.77 0 2.50e+00 1.60e-01 3.49e+01 dihedral pdb=" CA ARG c 222 " pdb=" C ARG c 222 " pdb=" N LEU c 223 " pdb=" CA LEU c 223 " ideal model delta harmonic sigma weight residual -180.00 -152.55 -27.45 0 5.00e+00 4.00e-02 3.01e+01 dihedral pdb=" C ARG c 222 " pdb=" N ARG c 222 " pdb=" CA ARG c 222 " pdb=" CB ARG c 222 " ideal model delta harmonic sigma weight residual -122.60 -111.28 -11.32 0 2.50e+00 1.60e-01 2.05e+01 ... (remaining 20713 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 3902 0.104 - 0.208: 1240 0.208 - 0.312: 156 0.312 - 0.416: 20 0.416 - 0.519: 4 Chirality restraints: 5322 Sorted by residual: chirality pdb=" CG LEU s 235 " pdb=" CB LEU s 235 " pdb=" CD1 LEU s 235 " pdb=" CD2 LEU s 235 " both_signs ideal model delta sigma weight residual False -2.59 -3.11 0.52 2.00e-01 2.50e+01 6.74e+00 chirality pdb=" CB VAL q 16 " pdb=" CA VAL q 16 " pdb=" CG1 VAL q 16 " pdb=" CG2 VAL q 16 " both_signs ideal model delta sigma weight residual False -2.63 -3.11 0.49 2.00e-01 2.50e+01 5.89e+00 chirality pdb=" CA TRP m 264 " pdb=" N TRP m 264 " pdb=" C TRP m 264 " pdb=" CB TRP m 264 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.52e+00 ... (remaining 5319 not shown) Planarity restraints: 6150 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP r 79 " 0.064 2.00e-02 2.50e+03 3.18e-02 2.53e+01 pdb=" CG TRP r 79 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TRP r 79 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP r 79 " -0.025 2.00e-02 2.50e+03 pdb=" NE1 TRP r 79 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 TRP r 79 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP r 79 " -0.044 2.00e-02 2.50e+03 pdb=" CZ2 TRP r 79 " 0.035 2.00e-02 2.50e+03 pdb=" CZ3 TRP r 79 " -0.016 2.00e-02 2.50e+03 pdb=" CH2 TRP r 79 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR m 150 " 0.059 2.00e-02 2.50e+03 3.14e-02 1.97e+01 pdb=" CG TYR m 150 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR m 150 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR m 150 " -0.024 2.00e-02 2.50e+03 pdb=" CE1 TYR m 150 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 TYR m 150 " -0.019 2.00e-02 2.50e+03 pdb=" CZ TYR m 150 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR m 150 " 0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR r 98 " 0.060 2.00e-02 2.50e+03 3.14e-02 1.97e+01 pdb=" CG TYR r 98 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR r 98 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR r 98 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 TYR r 98 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR r 98 " -0.015 2.00e-02 2.50e+03 pdb=" CZ TYR r 98 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR r 98 " 0.043 2.00e-02 2.50e+03 ... (remaining 6147 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 10380 2.82 - 3.34: 32451 3.34 - 3.86: 60136 3.86 - 4.38: 74796 4.38 - 4.90: 118223 Nonbonded interactions: 295986 Sorted by model distance: nonbonded pdb=" N ASP f 11 " pdb=" OD1 ASP f 11 " model vdw 2.300 2.520 nonbonded pdb=" NH2 ARG q 115 " pdb=" OE1 GLU s 101 " model vdw 2.366 2.520 nonbonded pdb=" N ASP m 221 " pdb=" OD1 ASP m 221 " model vdw 2.374 2.520 nonbonded pdb=" NZ LYS h 34 " pdb=" OD2 ASP k 18 " model vdw 2.377 2.520 nonbonded pdb=" ND2 ASN e 241 " pdb=" OG1 THR i 134 " model vdw 2.393 2.520 ... (remaining 295981 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 'H' and resid 12 through 109) selection = chain 'L' } ncs_group { reference = (chain 'a' and (resid 19 through 213 or resid 218 through 298 or resid 300)) selection = (chain 'e' and (resid 19 through 213 or resid 218 through 298 or resid 300)) selection = (chain 'i' and (resid 19 through 213 or resid 218 through 298 or resid 300)) selection = chain 'm' selection = (chain 'q' and (resid 19 through 213 or resid 218 through 298 or resid 300)) } ncs_group { reference = (chain 'b' and (resid 10 through 164 or resid 170 through 239 or resid 245 throu \ gh 271)) selection = (chain 'f' and (resid 10 through 164 or resid 170 through 239 or resid 245 throu \ gh 271)) selection = (chain 'j' and (resid 10 through 164 or resid 170 through 239 or resid 245 throu \ gh 271)) selection = (chain 'n' and (resid 10 through 164 or resid 170 through 239 or resid 245 throu \ gh 271)) selection = (chain 'r' and (resid 10 through 239 or resid 245 through 271)) } ncs_group { reference = (chain 'c' and resid 1 through 233) selection = (chain 'g' and resid 1 through 233) selection = chain 'k' selection = (chain 'o' and resid 1 through 233) selection = (chain 's' and resid 1 through 233) } ncs_group { reference = (chain 'd' and resid 2 through 68) selection = (chain 'h' and resid 2 through 68) selection = (chain 'l' and resid 2 through 68) selection = chain 'p' selection = (chain 't' and resid 2 through 68) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 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: 0.020 Extract box with map and model: 6.800 Check model and map are aligned: 0.480 Set scattering table: 0.320 Process input model: 87.330 Find NCS groups from input model: 3.150 Set up NCS constraints: 0.160 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: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 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 : 0.021 0.160 34734 Z= 1.370 Angle : 1.842 12.421 47379 Z= 1.247 Chirality : 0.097 0.519 5322 Planarity : 0.009 0.065 6150 Dihedral : 9.913 88.698 12390 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.07 % 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: 0.55 (0.12), residues: 4158 helix: -2.98 (0.18), residues: 418 sheet: 1.54 (0.15), residues: 1016 loop : 0.58 (0.11), residues: 2724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.009 TRP r 79 HIS 0.017 0.003 HIS i 99 PHE 0.041 0.006 PHE q 120 TYR 0.060 0.009 TYR r 98 ARG 0.018 0.001 ARG q 114 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1898 residues out of total 3659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1898 time to evaluate : 3.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN b 272 " (corrupted residue). Skipping it. 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 TARDY: cannot create tardy model for: "PHE m 298 " (corrupted residue). Skipping it. 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 40 THR cc_start: 0.8637 (t) cc_final: 0.8329 (t) REVERT: a 49 GLN cc_start: 0.9088 (mm-40) cc_final: 0.8726 (mm110) REVERT: a 66 THR cc_start: 0.9064 (t) cc_final: 0.8829 (p) REVERT: a 69 GLU cc_start: 0.8119 (mp0) cc_final: 0.7918 (mp0) REVERT: a 107 TYR cc_start: 0.9131 (p90) cc_final: 0.8825 (p90) REVERT: a 118 GLU cc_start: 0.8424 (mt-10) cc_final: 0.8180 (mt-10) REVERT: a 127 LEU cc_start: 0.8896 (tp) cc_final: 0.8400 (tt) REVERT: a 132 VAL cc_start: 0.9563 (t) cc_final: 0.9336 (p) REVERT: a 150 TYR cc_start: 0.8734 (m-80) cc_final: 0.8532 (m-80) REVERT: a 151 GLN cc_start: 0.8865 (tt0) cc_final: 0.8564 (tt0) REVERT: a 165 TRP cc_start: 0.8187 (p-90) cc_final: 0.7806 (p-90) REVERT: a 171 GLN cc_start: 0.8595 (mt0) cc_final: 0.8330 (mt0) REVERT: a 178 ILE cc_start: 0.9536 (mt) cc_final: 0.9239 (mm) REVERT: a 182 TYR cc_start: 0.8398 (t80) cc_final: 0.8040 (t80) REVERT: a 194 VAL cc_start: 0.9215 (m) cc_final: 0.8907 (p) REVERT: a 287 LEU cc_start: 0.9065 (mt) cc_final: 0.8816 (pt) REVERT: a 291 LYS cc_start: 0.8844 (ptmt) cc_final: 0.8274 (ptpt) REVERT: b 42 ILE cc_start: 0.8934 (mt) cc_final: 0.8633 (mt) REVERT: b 99 HIS cc_start: 0.8694 (m90) cc_final: 0.8126 (m170) REVERT: b 112 CYS cc_start: 0.8716 (t) cc_final: 0.8364 (t) REVERT: b 223 LYS cc_start: 0.8781 (mtmt) cc_final: 0.8399 (mttm) REVERT: b 249 ILE cc_start: 0.9169 (mt) cc_final: 0.8750 (mm) REVERT: c 55 MET cc_start: 0.8728 (ttm) cc_final: 0.8273 (ttm) REVERT: c 70 ILE cc_start: 0.9061 (mt) cc_final: 0.8471 (mt) REVERT: c 159 LEU cc_start: 0.8816 (mt) cc_final: 0.8440 (mt) REVERT: c 160 GLN cc_start: 0.8470 (mm-40) cc_final: 0.8254 (mm110) REVERT: c 193 TYR cc_start: 0.8753 (m-80) cc_final: 0.8514 (m-80) REVERT: c 209 MET cc_start: 0.7897 (ttp) cc_final: 0.7667 (ttp) REVERT: c 219 PHE cc_start: 0.8512 (t80) cc_final: 0.8285 (t80) REVERT: c 224 LEU cc_start: 0.8497 (mt) cc_final: 0.8213 (mt) REVERT: e 32 ASN cc_start: 0.8021 (m-40) cc_final: 0.7803 (m-40) REVERT: e 51 ILE cc_start: 0.9285 (pt) cc_final: 0.9004 (pt) REVERT: e 57 GLU cc_start: 0.5486 (mp0) cc_final: 0.4832 (mp0) REVERT: e 101 ASN cc_start: 0.8812 (t0) cc_final: 0.8411 (t0) REVERT: e 111 VAL cc_start: 0.9167 (m) cc_final: 0.8810 (p) REVERT: e 128 GLU cc_start: 0.7577 (tt0) cc_final: 0.6838 (tt0) REVERT: e 171 GLN cc_start: 0.9061 (mt0) cc_final: 0.8688 (mt0) REVERT: e 188 ARG cc_start: 0.8566 (ttm170) cc_final: 0.8282 (ttt180) REVERT: e 194 VAL cc_start: 0.9156 (m) cc_final: 0.8860 (p) REVERT: e 241 ASN cc_start: 0.8165 (m110) cc_final: 0.7522 (m110) REVERT: e 255 TYR cc_start: 0.9127 (m-80) cc_final: 0.8851 (m-10) REVERT: e 267 ARG cc_start: 0.9363 (mtp85) cc_final: 0.9142 (mtt-85) REVERT: e 280 ASP cc_start: 0.8185 (m-30) cc_final: 0.7302 (t0) REVERT: e 295 ILE cc_start: 0.8456 (mt) cc_final: 0.8168 (mt) REVERT: f 80 TRP cc_start: 0.9121 (m-90) cc_final: 0.8760 (m-90) REVERT: f 100 TYR cc_start: 0.8171 (t80) cc_final: 0.7664 (t80) REVERT: f 149 ASN cc_start: 0.8713 (m-40) cc_final: 0.8421 (m-40) REVERT: f 199 ASN cc_start: 0.8707 (t0) cc_final: 0.7792 (p0) REVERT: f 218 ILE cc_start: 0.9564 (tt) cc_final: 0.9345 (mt) REVERT: f 252 THR cc_start: 0.9370 (m) cc_final: 0.9150 (p) REVERT: g 41 LYS cc_start: 0.8867 (mttm) cc_final: 0.8593 (mmmm) REVERT: g 44 MET cc_start: 0.9189 (mmp) cc_final: 0.8933 (mmm) REVERT: g 55 MET cc_start: 0.7998 (tpt) cc_final: 0.7697 (tpt) REVERT: g 85 SER cc_start: 0.9049 (m) cc_final: 0.8410 (p) REVERT: g 91 ASP cc_start: 0.8302 (t0) cc_final: 0.7428 (t0) REVERT: g 112 SER cc_start: 0.8581 (m) cc_final: 0.8146 (p) REVERT: g 118 LEU cc_start: 0.8919 (tp) cc_final: 0.8461 (tt) REVERT: g 148 MET cc_start: 0.7738 (ttm) cc_final: 0.7356 (ttt) REVERT: g 155 TRP cc_start: 0.9220 (t60) cc_final: 0.8994 (t60) REVERT: g 169 TRP cc_start: 0.9085 (t-100) cc_final: 0.8453 (t-100) REVERT: g 207 MET cc_start: 0.8109 (pmm) cc_final: 0.7628 (pmm) REVERT: g 216 CYS cc_start: 0.8413 (m) cc_final: 0.8029 (m) REVERT: g 225 ARG cc_start: 0.8761 (ptt90) cc_final: 0.8249 (ptt-90) REVERT: g 230 ILE cc_start: 0.9249 (tt) cc_final: 0.8796 (tt) REVERT: i 54 ASP cc_start: 0.8084 (m-30) cc_final: 0.7848 (m-30) REVERT: i 75 PHE cc_start: 0.9232 (t80) cc_final: 0.9029 (t80) REVERT: i 83 THR cc_start: 0.9234 (t) cc_final: 0.9006 (m) REVERT: i 131 PHE cc_start: 0.8929 (m-80) cc_final: 0.8719 (m-80) REVERT: i 169 THR cc_start: 0.9043 (p) cc_final: 0.8669 (t) REVERT: i 298 PHE cc_start: 0.8329 (m-80) cc_final: 0.7637 (m-80) REVERT: j 99 HIS cc_start: 0.8433 (m90) cc_final: 0.8014 (m90) REVERT: j 147 ASN cc_start: 0.7684 (m-40) cc_final: 0.7276 (t0) REVERT: j 149 ASN cc_start: 0.8670 (m-40) cc_final: 0.8346 (m-40) REVERT: j 213 VAL cc_start: 0.9031 (t) cc_final: 0.8684 (m) REVERT: j 252 THR cc_start: 0.9120 (m) cc_final: 0.8900 (m) REVERT: k 11 ASN cc_start: 0.9167 (m-40) cc_final: 0.8941 (m-40) REVERT: k 43 MET cc_start: 0.8843 (mmm) cc_final: 0.8279 (mmm) REVERT: k 51 THR cc_start: 0.8967 (p) cc_final: 0.8656 (p) REVERT: k 112 SER cc_start: 0.8736 (m) cc_final: 0.8236 (p) REVERT: k 116 THR cc_start: 0.9197 (m) cc_final: 0.8923 (t) REVERT: k 118 LEU cc_start: 0.8516 (tp) cc_final: 0.8181 (tt) REVERT: k 130 LEU cc_start: 0.8875 (tp) cc_final: 0.8463 (tt) REVERT: k 154 ILE cc_start: 0.8556 (mm) cc_final: 0.8241 (mt) REVERT: k 216 CYS cc_start: 0.8601 (m) cc_final: 0.7516 (m) REVERT: k 218 ASP cc_start: 0.8441 (p0) cc_final: 0.8170 (p0) REVERT: l 25 ILE cc_start: 0.8479 (mm) cc_final: 0.8129 (mm) REVERT: l 64 THR cc_start: 0.9005 (p) cc_final: 0.7580 (p) REVERT: m 49 GLN cc_start: 0.8625 (mm-40) cc_final: 0.7726 (mm110) REVERT: m 57 GLU cc_start: 0.6906 (mp0) cc_final: 0.6666 (mp0) REVERT: m 70 SER cc_start: 0.9180 (p) cc_final: 0.8509 (t) REVERT: m 71 CYS cc_start: 0.8709 (m) cc_final: 0.8167 (t) REVERT: m 105 ILE cc_start: 0.9123 (mm) cc_final: 0.8889 (mm) REVERT: m 128 GLU cc_start: 0.7892 (tt0) cc_final: 0.7322 (tt0) REVERT: m 151 GLN cc_start: 0.8845 (tt0) cc_final: 0.7751 (tt0) REVERT: m 170 TRP cc_start: 0.8821 (m100) cc_final: 0.8292 (m100) REVERT: m 180 TYR cc_start: 0.9343 (t80) cc_final: 0.9050 (t80) REVERT: m 203 PHE cc_start: 0.8883 (m-80) cc_final: 0.8466 (m-10) REVERT: m 223 PHE cc_start: 0.7189 (m-80) cc_final: 0.6963 (m-10) REVERT: m 281 MET cc_start: 0.8158 (mtm) cc_final: 0.7303 (mtm) REVERT: n 50 VAL cc_start: 0.9251 (m) cc_final: 0.8979 (t) REVERT: n 61 ASN cc_start: 0.9017 (m-40) cc_final: 0.8423 (m110) REVERT: n 74 THR cc_start: 0.8076 (p) cc_final: 0.7776 (t) REVERT: n 84 ASP cc_start: 0.7467 (t70) cc_final: 0.6913 (t0) REVERT: n 87 LYS cc_start: 0.8684 (pttt) cc_final: 0.8329 (ptmt) REVERT: n 113 ASN cc_start: 0.8425 (m-40) cc_final: 0.8096 (t0) REVERT: n 129 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7644 (mm-30) REVERT: n 130 PHE cc_start: 0.8804 (t80) cc_final: 0.8531 (t80) REVERT: n 149 ASN cc_start: 0.8833 (m-40) cc_final: 0.8150 (m110) REVERT: n 178 ASP cc_start: 0.7955 (p0) cc_final: 0.7584 (p0) REVERT: n 212 TYR cc_start: 0.9216 (t80) cc_final: 0.8781 (t80) REVERT: n 219 ASP cc_start: 0.8569 (t0) cc_final: 0.8358 (t0) REVERT: o 10 SER cc_start: 0.9286 (m) cc_final: 0.8800 (p) REVERT: o 36 ILE cc_start: 0.9596 (mt) cc_final: 0.9295 (mt) REVERT: o 41 LYS cc_start: 0.8930 (mmtt) cc_final: 0.8388 (mmtp) REVERT: o 43 MET cc_start: 0.9015 (mmm) cc_final: 0.8733 (mmm) REVERT: o 44 MET cc_start: 0.9136 (mmp) cc_final: 0.8792 (mmm) REVERT: o 53 ILE cc_start: 0.9140 (mt) cc_final: 0.8788 (mt) REVERT: o 70 ILE cc_start: 0.9364 (mt) cc_final: 0.8989 (mt) REVERT: o 74 ASP cc_start: 0.7951 (p0) cc_final: 0.7556 (p0) REVERT: o 93 ARG cc_start: 0.8833 (mtm-85) cc_final: 0.8373 (mtm-85) REVERT: o 94 LEU cc_start: 0.9407 (mt) cc_final: 0.9169 (mm) REVERT: o 104 ASN cc_start: 0.8063 (m-40) cc_final: 0.7252 (m-40) REVERT: o 120 CYS cc_start: 0.7712 (m) cc_final: 0.7293 (m) REVERT: o 146 ASP cc_start: 0.8642 (m-30) cc_final: 0.8439 (m-30) REVERT: o 156 ASP cc_start: 0.5333 (m-30) cc_final: 0.5052 (m-30) REVERT: o 169 TRP cc_start: 0.8538 (t-100) cc_final: 0.7931 (t-100) REVERT: o 182 ASP cc_start: 0.7917 (m-30) cc_final: 0.7543 (m-30) REVERT: o 208 PHE cc_start: 0.8024 (m-80) cc_final: 0.7803 (m-80) REVERT: o 216 CYS cc_start: 0.7619 (m) cc_final: 0.7006 (m) REVERT: o 218 ASP cc_start: 0.8786 (p0) cc_final: 0.8537 (p0) REVERT: o 234 LYS cc_start: 0.7791 (tttm) cc_final: 0.7552 (ttpt) REVERT: p 7 THR cc_start: 0.9190 (m) cc_final: 0.8880 (p) REVERT: p 33 TYR cc_start: 0.9030 (m-80) cc_final: 0.8818 (m-10) REVERT: p 54 THR cc_start: 0.9227 (p) cc_final: 0.8114 (m) REVERT: q 54 ASP cc_start: 0.8219 (m-30) cc_final: 0.7879 (m-30) REVERT: q 55 VAL cc_start: 0.9128 (m) cc_final: 0.8799 (t) REVERT: q 189 MET cc_start: 0.8536 (ptt) cc_final: 0.8300 (ptm) REVERT: q 203 PHE cc_start: 0.9131 (m-80) cc_final: 0.8558 (m-80) REVERT: q 226 LEU cc_start: 0.9257 (tp) cc_final: 0.8986 (tp) REVERT: q 257 LYS cc_start: 0.9104 (ttpt) cc_final: 0.8590 (ptmt) REVERT: q 279 VAL cc_start: 0.9308 (m) cc_final: 0.8972 (p) REVERT: r 89 MET cc_start: 0.8897 (mmt) cc_final: 0.8674 (mmm) REVERT: r 122 LEU cc_start: 0.9321 (mt) cc_final: 0.9083 (mt) REVERT: s 18 ASP cc_start: 0.7376 (t0) cc_final: 0.6969 (t0) REVERT: s 27 ASN cc_start: 0.8945 (m-40) cc_final: 0.8660 (t0) REVERT: s 73 ASN cc_start: 0.9000 (p0) cc_final: 0.8581 (m-40) REVERT: s 75 ASN cc_start: 0.8103 (t0) cc_final: 0.7550 (p0) REVERT: s 166 VAL cc_start: 0.9697 (t) cc_final: 0.9477 (m) REVERT: s 173 THR cc_start: 0.9070 (p) cc_final: 0.8797 (p) REVERT: s 216 CYS cc_start: 0.8401 (m) cc_final: 0.8069 (m) REVERT: s 218 ASP cc_start: 0.8706 (p0) cc_final: 0.8352 (p0) REVERT: s 223 LEU cc_start: 0.8753 (tp) cc_final: 0.8025 (tp) REVERT: s 226 ASP cc_start: 0.7117 (m-30) cc_final: 0.6426 (m-30) REVERT: t 42 THR cc_start: 0.8529 (p) cc_final: 0.8320 (t) REVERT: t 44 GLN cc_start: 0.8759 (pt0) cc_final: 0.8413 (pt0) REVERT: t 54 THR cc_start: 0.9246 (p) cc_final: 0.9017 (t) outliers start: 0 outliers final: 0 residues processed: 1898 average time/residue: 0.4590 time to fit residues: 1387.8790 Evaluate side-chains 1316 residues out of total 3659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1316 time to evaluate : 3.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 363 optimal weight: 5.9990 chunk 325 optimal weight: 6.9990 chunk 180 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 chunk 219 optimal weight: 1.9990 chunk 174 optimal weight: 5.9990 chunk 337 optimal weight: 8.9990 chunk 130 optimal weight: 7.9990 chunk 204 optimal weight: 7.9990 chunk 250 optimal weight: 5.9990 chunk 390 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 99 HIS ** a 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 35 HIS ** c 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 194 GLN ** c 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 49 GLN e 60 HIS ** e 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 43 ASN f 226 ASN f 246 GLN f 261 ASN ** g 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 27 ASN ** g 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 160 GLN g 232 GLN h 26 ASN ** j 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 196 GLN j 271 HIS ** k 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 75 ASN k 108 HIS m 32 ASN n 15 GLN n 118 HIS ** n 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 27 ASN o 96 HIS p 4 GLN p 17 ASN p 31 ASN q 101 ASN q 112 GLN q 184 ASN q 198 ASN q 202 HIS ** q 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 118 HIS ** r 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 162 ASN r 224 HIS ** s 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 34734 Z= 0.340 Angle : 0.730 12.874 47379 Z= 0.386 Chirality : 0.047 0.197 5322 Planarity : 0.006 0.117 6150 Dihedral : 6.138 66.781 4820 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.08 % Allowed : 3.42 % Favored : 96.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.12), residues: 4158 helix: -2.24 (0.22), residues: 395 sheet: 1.12 (0.15), residues: 1055 loop : 0.20 (0.11), residues: 2708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP r 80 HIS 0.016 0.002 HIS c 229 PHE 0.039 0.003 PHE j 174 TYR 0.032 0.003 TYR c 175 ARG 0.015 0.001 ARG e 238 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1559 residues out of total 3659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1556 time to evaluate : 3.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE a 298 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN b 272 " (corrupted residue). Skipping it. 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 TARDY: cannot create tardy model for: "ASN l 69 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE m 298 " (corrupted residue). Skipping it. 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 66 THR cc_start: 0.9220 (t) cc_final: 0.8947 (m) REVERT: a 73 GLU cc_start: 0.8657 (tp30) cc_final: 0.8431 (tp30) REVERT: a 98 LYS cc_start: 0.8836 (mmmt) cc_final: 0.8423 (tppt) REVERT: a 127 LEU cc_start: 0.9279 (tp) cc_final: 0.8316 (tt) REVERT: a 171 GLN cc_start: 0.8618 (mt0) cc_final: 0.8105 (mt0) REVERT: a 194 VAL cc_start: 0.9271 (m) cc_final: 0.9050 (p) REVERT: a 291 LYS cc_start: 0.9076 (ptmt) cc_final: 0.8201 (ptpt) REVERT: b 42 ILE cc_start: 0.8725 (mt) cc_final: 0.8365 (mt) REVERT: b 50 VAL cc_start: 0.8709 (m) cc_final: 0.8369 (p) REVERT: b 64 TYR cc_start: 0.8987 (m-80) cc_final: 0.8764 (m-10) REVERT: b 84 ASP cc_start: 0.7652 (t0) cc_final: 0.7430 (t70) REVERT: b 112 CYS cc_start: 0.8729 (t) cc_final: 0.8422 (t) REVERT: b 223 LYS cc_start: 0.9042 (mtmt) cc_final: 0.8527 (mttm) REVERT: b 249 ILE cc_start: 0.9254 (mt) cc_final: 0.8767 (mm) REVERT: b 259 GLU cc_start: 0.8206 (pt0) cc_final: 0.7698 (pt0) REVERT: c 44 MET cc_start: 0.9096 (mmm) cc_final: 0.8881 (mmm) REVERT: c 55 MET cc_start: 0.8688 (ttm) cc_final: 0.8233 (ttm) REVERT: c 69 GLN cc_start: 0.8789 (mt0) cc_final: 0.8540 (mp10) REVERT: c 70 ILE cc_start: 0.9014 (mt) cc_final: 0.8535 (mt) REVERT: c 118 LEU cc_start: 0.9101 (tp) cc_final: 0.8625 (tt) REVERT: c 157 LEU cc_start: 0.9158 (mt) cc_final: 0.8946 (mt) REVERT: c 163 CYS cc_start: 0.8268 (p) cc_final: 0.8046 (p) REVERT: c 164 SER cc_start: 0.9555 (p) cc_final: 0.9327 (m) REVERT: d 38 SER cc_start: 0.9201 (m) cc_final: 0.8970 (p) REVERT: e 35 GLU cc_start: 0.8837 (mp0) cc_final: 0.8273 (mp0) REVERT: e 54 ASP cc_start: 0.8698 (m-30) cc_final: 0.8313 (m-30) REVERT: e 57 GLU cc_start: 0.5553 (mp0) cc_final: 0.4597 (mp0) REVERT: e 69 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7505 (tt0) REVERT: e 115 ARG cc_start: 0.8233 (ttt90) cc_final: 0.7828 (ttt90) REVERT: e 122 TYR cc_start: 0.9303 (m-10) cc_final: 0.9010 (m-10) REVERT: e 179 PHE cc_start: 0.8568 (m-80) cc_final: 0.8193 (m-80) REVERT: e 188 ARG cc_start: 0.8617 (ttm170) cc_final: 0.8389 (ttm170) REVERT: e 231 ASP cc_start: 0.7260 (t0) cc_final: 0.7001 (t0) REVERT: e 241 ASN cc_start: 0.8358 (m110) cc_final: 0.7909 (m110) REVERT: e 275 ARG cc_start: 0.7033 (ttt-90) cc_final: 0.6206 (ttm-80) REVERT: e 280 ASP cc_start: 0.7859 (m-30) cc_final: 0.7525 (t0) REVERT: e 295 ILE cc_start: 0.8407 (mt) cc_final: 0.8098 (mt) REVERT: f 101 LEU cc_start: 0.9427 (mt) cc_final: 0.9187 (mp) REVERT: f 126 LEU cc_start: 0.9294 (mt) cc_final: 0.9009 (mt) REVERT: f 127 ILE cc_start: 0.9307 (mp) cc_final: 0.9006 (mt) REVERT: f 162 ASN cc_start: 0.8268 (m-40) cc_final: 0.7825 (p0) REVERT: f 196 GLN cc_start: 0.9014 (mt0) cc_final: 0.8764 (mt0) REVERT: f 221 MET cc_start: 0.8648 (mmm) cc_final: 0.8436 (mmm) REVERT: g 44 MET cc_start: 0.9117 (mmp) cc_final: 0.8821 (mmm) REVERT: g 112 SER cc_start: 0.8794 (m) cc_final: 0.8193 (p) REVERT: g 128 LYS cc_start: 0.7860 (mppt) cc_final: 0.7288 (mmtm) REVERT: g 148 MET cc_start: 0.7576 (ttm) cc_final: 0.7087 (ttt) REVERT: g 162 SER cc_start: 0.9111 (m) cc_final: 0.8889 (p) REVERT: g 163 CYS cc_start: 0.8701 (p) cc_final: 0.8281 (p) REVERT: g 169 TRP cc_start: 0.8945 (t-100) cc_final: 0.8664 (t-100) REVERT: g 171 SER cc_start: 0.8901 (t) cc_final: 0.8664 (m) REVERT: g 216 CYS cc_start: 0.8529 (m) cc_final: 0.8159 (m) REVERT: g 225 ARG cc_start: 0.8721 (ptt90) cc_final: 0.8077 (ptt-90) REVERT: h 8 GLN cc_start: 0.7710 (mt0) cc_final: 0.7346 (mt0) REVERT: i 75 PHE cc_start: 0.9353 (t80) cc_final: 0.9073 (t80) REVERT: i 120 PHE cc_start: 0.8639 (m-80) cc_final: 0.8347 (m-10) REVERT: i 166 ASP cc_start: 0.8244 (p0) cc_final: 0.7570 (p0) REVERT: i 169 THR cc_start: 0.8999 (p) cc_final: 0.8622 (t) REVERT: i 182 TYR cc_start: 0.9090 (t80) cc_final: 0.8857 (t80) REVERT: i 250 THR cc_start: 0.8007 (m) cc_final: 0.7299 (m) REVERT: i 264 TRP cc_start: 0.9090 (m-90) cc_final: 0.8810 (m-90) REVERT: i 274 TYR cc_start: 0.8412 (m-80) cc_final: 0.7868 (m-80) REVERT: j 32 ILE cc_start: 0.9154 (mm) cc_final: 0.8906 (mm) REVERT: j 109 HIS cc_start: 0.8161 (t70) cc_final: 0.7940 (t-90) REVERT: j 111 GLN cc_start: 0.7861 (pm20) cc_final: 0.7219 (tt0) REVERT: j 132 MET cc_start: 0.7989 (mtt) cc_final: 0.7685 (mmt) REVERT: j 147 ASN cc_start: 0.7739 (m-40) cc_final: 0.7479 (t0) REVERT: j 152 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7665 (mt-10) REVERT: j 213 VAL cc_start: 0.8965 (t) cc_final: 0.8680 (m) REVERT: k 2 LEU cc_start: 0.9496 (tp) cc_final: 0.9223 (tp) REVERT: k 11 ASN cc_start: 0.9276 (m-40) cc_final: 0.9039 (m-40) REVERT: k 14 LEU cc_start: 0.9365 (tp) cc_final: 0.9141 (tp) REVERT: k 27 ASN cc_start: 0.9059 (m110) cc_final: 0.8675 (m110) REVERT: k 36 ILE cc_start: 0.9130 (mt) cc_final: 0.8498 (mt) REVERT: k 43 MET cc_start: 0.9163 (mmm) cc_final: 0.8630 (mmm) REVERT: k 56 ASN cc_start: 0.8895 (t0) cc_final: 0.8513 (t0) REVERT: k 65 MET cc_start: 0.8024 (tpp) cc_final: 0.7753 (tpp) REVERT: k 112 SER cc_start: 0.8888 (m) cc_final: 0.8415 (p) REVERT: k 116 THR cc_start: 0.9035 (m) cc_final: 0.8744 (t) REVERT: k 169 TRP cc_start: 0.8537 (t-100) cc_final: 0.8004 (t-100) REVERT: k 171 SER cc_start: 0.8665 (t) cc_final: 0.8345 (p) REVERT: k 216 CYS cc_start: 0.8453 (m) cc_final: 0.7501 (m) REVERT: k 218 ASP cc_start: 0.8766 (p0) cc_final: 0.8453 (p0) REVERT: l 38 SER cc_start: 0.9516 (m) cc_final: 0.9160 (t) REVERT: m 70 SER cc_start: 0.9134 (p) cc_final: 0.8401 (t) REVERT: m 71 CYS cc_start: 0.8517 (m) cc_final: 0.8300 (t) REVERT: m 105 ILE cc_start: 0.8812 (mm) cc_final: 0.8489 (tp) REVERT: m 170 TRP cc_start: 0.8626 (m100) cc_final: 0.8211 (m100) REVERT: n 50 VAL cc_start: 0.9201 (m) cc_final: 0.8944 (t) REVERT: n 61 ASN cc_start: 0.8911 (m-40) cc_final: 0.8610 (m-40) REVERT: n 74 THR cc_start: 0.8109 (p) cc_final: 0.7800 (t) REVERT: n 84 ASP cc_start: 0.7842 (t70) cc_final: 0.7325 (t0) REVERT: n 106 TYR cc_start: 0.8311 (m-80) cc_final: 0.7900 (m-80) REVERT: n 174 PHE cc_start: 0.8606 (m-80) cc_final: 0.8304 (m-80) REVERT: n 178 ASP cc_start: 0.8261 (p0) cc_final: 0.8004 (p0) REVERT: n 183 SER cc_start: 0.8896 (p) cc_final: 0.8207 (t) REVERT: n 199 ASN cc_start: 0.8899 (t0) cc_final: 0.8602 (t0) REVERT: n 216 LEU cc_start: 0.9085 (mt) cc_final: 0.8866 (mt) REVERT: n 257 CYS cc_start: 0.8394 (m) cc_final: 0.8181 (m) REVERT: o 10 SER cc_start: 0.9080 (m) cc_final: 0.8801 (p) REVERT: o 39 GLU cc_start: 0.8726 (tm-30) cc_final: 0.8494 (tm-30) REVERT: o 44 MET cc_start: 0.9129 (mmp) cc_final: 0.8739 (mmm) REVERT: o 94 LEU cc_start: 0.9509 (mt) cc_final: 0.9290 (mm) REVERT: o 95 SER cc_start: 0.8710 (p) cc_final: 0.8286 (t) REVERT: o 104 ASN cc_start: 0.8095 (m-40) cc_final: 0.7423 (m-40) REVERT: o 120 CYS cc_start: 0.8589 (m) cc_final: 0.8291 (m) REVERT: o 151 THR cc_start: 0.9285 (m) cc_final: 0.8951 (t) REVERT: o 216 CYS cc_start: 0.7842 (m) cc_final: 0.7196 (m) REVERT: o 224 LEU cc_start: 0.8898 (tp) cc_final: 0.8611 (tp) REVERT: o 234 LYS cc_start: 0.7457 (tttm) cc_final: 0.7245 (ttmt) REVERT: q 112 GLN cc_start: 0.7289 (tt0) cc_final: 0.6997 (tt0) REVERT: q 126 ASP cc_start: 0.8568 (m-30) cc_final: 0.8358 (m-30) REVERT: q 151 GLN cc_start: 0.8493 (tt0) cc_final: 0.8286 (tt0) REVERT: q 173 SER cc_start: 0.9312 (m) cc_final: 0.8863 (p) REVERT: q 257 LYS cc_start: 0.9146 (ttpt) cc_final: 0.8786 (ptmt) REVERT: r 20 ASN cc_start: 0.9038 (p0) cc_final: 0.8788 (p0) REVERT: s 18 ASP cc_start: 0.7721 (t0) cc_final: 0.7281 (t0) REVERT: s 34 ILE cc_start: 0.9208 (pt) cc_final: 0.8812 (pt) REVERT: s 50 ASP cc_start: 0.7839 (m-30) cc_final: 0.7591 (m-30) REVERT: s 107 THR cc_start: 0.9017 (p) cc_final: 0.8400 (t) REVERT: s 128 LYS cc_start: 0.7912 (mmtp) cc_final: 0.7702 (mmtp) REVERT: s 194 GLN cc_start: 0.8220 (mm110) cc_final: 0.7947 (tp-100) REVERT: s 218 ASP cc_start: 0.8664 (p0) cc_final: 0.8220 (p0) REVERT: t 6 SER cc_start: 0.8948 (p) cc_final: 0.8711 (p) REVERT: t 44 GLN cc_start: 0.8710 (pt0) cc_final: 0.8436 (pt0) outliers start: 3 outliers final: 1 residues processed: 1557 average time/residue: 0.4422 time to fit residues: 1113.9330 Evaluate side-chains 1242 residues out of total 3659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1241 time to evaluate : 3.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 217 optimal weight: 20.0000 chunk 121 optimal weight: 0.1980 chunk 324 optimal weight: 8.9990 chunk 265 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 391 optimal weight: 5.9990 chunk 422 optimal weight: 2.9990 chunk 348 optimal weight: 0.0470 chunk 387 optimal weight: 9.9990 chunk 133 optimal weight: 20.0000 chunk 313 optimal weight: 6.9990 overall best weight: 3.2484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 147 ASN ** b 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 149 ASN ** c 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 11 ASN e 148 GLN ** e 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 30 ASN f 43 ASN f 149 ASN ** g 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 11 ASN g 27 ASN ** g 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 112 GLN i 151 GLN i 184 ASN ** j 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 196 GLN ** j 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 226 ASN k 96 HIS m 175 ASN n 94 GLN n 147 ASN ** n 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 27 ASN p 4 GLN p 31 ASN q 49 GLN q 198 ASN ** r 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 108 HIS s 232 GLN t 44 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.3944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 34734 Z= 0.254 Angle : 0.639 12.859 47379 Z= 0.334 Chirality : 0.045 0.181 5322 Planarity : 0.005 0.100 6150 Dihedral : 5.754 59.808 4820 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.03 % Allowed : 2.81 % Favored : 97.16 % 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: -0.03 (0.12), residues: 4158 helix: -2.27 (0.22), residues: 414 sheet: 0.91 (0.15), residues: 1061 loop : 0.05 (0.12), residues: 2683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP m 103 HIS 0.011 0.001 HIS r 109 PHE 0.036 0.002 PHE q 120 TYR 0.027 0.002 TYR i 274 ARG 0.010 0.001 ARG i 114 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1561 residues out of total 3659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1560 time to evaluate : 3.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE a 298 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN b 272 " (corrupted residue). Skipping it. 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 TARDY: cannot create tardy model for: "ASN l 69 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE m 298 " (corrupted residue). Skipping it. 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 98 LYS cc_start: 0.8787 (mmmt) cc_final: 0.8388 (tppt) REVERT: a 127 LEU cc_start: 0.8980 (tp) cc_final: 0.8329 (tt) REVERT: a 194 VAL cc_start: 0.9168 (m) cc_final: 0.8960 (p) REVERT: a 205 ASP cc_start: 0.7543 (t70) cc_final: 0.7265 (t0) REVERT: b 80 TRP cc_start: 0.8852 (m-90) cc_final: 0.8344 (m-90) REVERT: b 87 LYS cc_start: 0.8252 (pttp) cc_final: 0.7974 (pttt) REVERT: b 214 ASN cc_start: 0.8700 (t0) cc_final: 0.8464 (t0) REVERT: b 223 LYS cc_start: 0.9078 (mtmt) cc_final: 0.8520 (mttm) REVERT: b 259 GLU cc_start: 0.8175 (pt0) cc_final: 0.7887 (pt0) REVERT: c 43 MET cc_start: 0.8919 (mmm) cc_final: 0.8710 (mmm) REVERT: c 55 MET cc_start: 0.8762 (ttm) cc_final: 0.8293 (ttm) REVERT: c 70 ILE cc_start: 0.9038 (mt) cc_final: 0.8570 (mt) REVERT: c 209 MET cc_start: 0.7509 (ttp) cc_final: 0.7182 (ttp) REVERT: c 222 ARG cc_start: 0.7932 (mmm-85) cc_final: 0.7722 (mmm160) REVERT: d 38 SER cc_start: 0.9189 (m) cc_final: 0.8915 (p) REVERT: e 34 GLN cc_start: 0.8370 (mt0) cc_final: 0.8047 (mt0) REVERT: e 35 GLU cc_start: 0.8859 (mp0) cc_final: 0.8308 (mp0) REVERT: e 54 ASP cc_start: 0.8752 (m-30) cc_final: 0.8484 (m-30) REVERT: e 57 GLU cc_start: 0.5480 (mp0) cc_final: 0.4472 (mp0) REVERT: e 69 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7872 (tt0) REVERT: e 111 VAL cc_start: 0.9161 (m) cc_final: 0.8946 (p) REVERT: e 115 ARG cc_start: 0.8098 (ttt90) cc_final: 0.7672 (ttt90) REVERT: e 128 GLU cc_start: 0.7517 (tt0) cc_final: 0.7316 (tt0) REVERT: e 150 TYR cc_start: 0.9186 (m-80) cc_final: 0.8982 (m-80) REVERT: f 15 GLN cc_start: 0.7490 (tt0) cc_final: 0.7123 (mt0) REVERT: f 55 GLU cc_start: 0.8694 (pp20) cc_final: 0.8295 (pp20) REVERT: f 126 LEU cc_start: 0.9296 (mt) cc_final: 0.8943 (mt) REVERT: f 127 ILE cc_start: 0.9271 (mp) cc_final: 0.8952 (mt) REVERT: f 142 TYR cc_start: 0.7579 (t80) cc_final: 0.7256 (t80) REVERT: f 196 GLN cc_start: 0.9073 (mt0) cc_final: 0.8797 (mt0) REVERT: f 209 VAL cc_start: 0.9071 (t) cc_final: 0.8816 (p) REVERT: f 212 TYR cc_start: 0.9030 (t80) cc_final: 0.8154 (t80) REVERT: f 234 LEU cc_start: 0.8645 (mm) cc_final: 0.8432 (mm) REVERT: g 18 ASP cc_start: 0.7785 (t0) cc_final: 0.7571 (t0) REVERT: g 112 SER cc_start: 0.8751 (m) cc_final: 0.8253 (p) REVERT: g 148 MET cc_start: 0.7493 (ttm) cc_final: 0.6964 (ttt) REVERT: g 163 CYS cc_start: 0.8729 (p) cc_final: 0.8264 (p) REVERT: g 169 TRP cc_start: 0.8927 (t-100) cc_final: 0.8349 (t-100) REVERT: g 216 CYS cc_start: 0.8546 (m) cc_final: 0.8264 (m) REVERT: g 225 ARG cc_start: 0.8889 (ptt90) cc_final: 0.8619 (ptt-90) REVERT: h 27 TYR cc_start: 0.8716 (p90) cc_final: 0.8407 (p90) REVERT: h 33 TYR cc_start: 0.8785 (m-10) cc_final: 0.8564 (m-10) REVERT: i 71 CYS cc_start: 0.8252 (p) cc_final: 0.8007 (p) REVERT: i 75 PHE cc_start: 0.9308 (t80) cc_final: 0.9088 (t80) REVERT: i 151 GLN cc_start: 0.9231 (tt0) cc_final: 0.8803 (tt0) REVERT: i 166 ASP cc_start: 0.8347 (p0) cc_final: 0.7589 (p0) REVERT: i 169 THR cc_start: 0.8886 (p) cc_final: 0.8454 (t) REVERT: i 180 TYR cc_start: 0.8582 (t80) cc_final: 0.8311 (t80) REVERT: i 182 TYR cc_start: 0.9145 (t80) cc_final: 0.8580 (t80) REVERT: i 250 THR cc_start: 0.7492 (m) cc_final: 0.7109 (m) REVERT: i 264 TRP cc_start: 0.9129 (m-90) cc_final: 0.8829 (m-90) REVERT: j 111 GLN cc_start: 0.7576 (pm20) cc_final: 0.7190 (tt0) REVERT: j 132 MET cc_start: 0.8013 (mtt) cc_final: 0.7546 (mmt) REVERT: j 145 TYR cc_start: 0.9158 (t80) cc_final: 0.8750 (t80) REVERT: j 196 GLN cc_start: 0.8798 (tt0) cc_final: 0.8112 (tt0) REVERT: j 213 VAL cc_start: 0.9169 (t) cc_final: 0.8938 (m) REVERT: k 27 ASN cc_start: 0.9079 (m110) cc_final: 0.8674 (m110) REVERT: k 36 ILE cc_start: 0.9202 (mt) cc_final: 0.8425 (mt) REVERT: k 43 MET cc_start: 0.9105 (mmm) cc_final: 0.8507 (mmm) REVERT: k 56 ASN cc_start: 0.8885 (t0) cc_final: 0.8293 (t0) REVERT: k 112 SER cc_start: 0.8845 (m) cc_final: 0.8521 (p) REVERT: k 124 MET cc_start: 0.7512 (mmm) cc_final: 0.7294 (mtt) REVERT: k 133 TYR cc_start: 0.8659 (t80) cc_final: 0.8258 (t80) REVERT: k 169 TRP cc_start: 0.8401 (t-100) cc_final: 0.8073 (t-100) REVERT: k 171 SER cc_start: 0.8708 (t) cc_final: 0.8494 (p) REVERT: k 176 ARG cc_start: 0.8807 (mtt-85) cc_final: 0.8481 (mtt-85) REVERT: k 188 PHE cc_start: 0.8519 (m-80) cc_final: 0.8108 (m-80) REVERT: k 216 CYS cc_start: 0.8457 (m) cc_final: 0.7614 (m) REVERT: k 218 ASP cc_start: 0.8757 (p0) cc_final: 0.8423 (p0) REVERT: l 25 ILE cc_start: 0.8820 (mm) cc_final: 0.8488 (mm) REVERT: l 38 SER cc_start: 0.9526 (m) cc_final: 0.9170 (t) REVERT: l 42 THR cc_start: 0.8782 (p) cc_final: 0.8504 (t) REVERT: m 70 SER cc_start: 0.9099 (p) cc_final: 0.8353 (t) REVERT: m 89 ASN cc_start: 0.8255 (t0) cc_final: 0.7925 (t0) REVERT: m 105 ILE cc_start: 0.8763 (mm) cc_final: 0.8344 (tp) REVERT: m 110 THR cc_start: 0.8307 (p) cc_final: 0.8098 (p) REVERT: m 165 TRP cc_start: 0.8572 (p-90) cc_final: 0.8189 (p-90) REVERT: m 169 THR cc_start: 0.9455 (p) cc_final: 0.9125 (t) REVERT: m 170 TRP cc_start: 0.8681 (m100) cc_final: 0.8251 (m100) REVERT: m 175 ASN cc_start: 0.8237 (m-40) cc_final: 0.7846 (m110) REVERT: n 61 ASN cc_start: 0.8946 (m-40) cc_final: 0.8593 (m-40) REVERT: n 74 THR cc_start: 0.8111 (p) cc_final: 0.7842 (t) REVERT: n 84 ASP cc_start: 0.7836 (t70) cc_final: 0.6156 (t0) REVERT: n 87 LYS cc_start: 0.8366 (pttt) cc_final: 0.7932 (ptpp) REVERT: n 174 PHE cc_start: 0.8506 (m-80) cc_final: 0.8098 (m-80) REVERT: n 183 SER cc_start: 0.8751 (p) cc_final: 0.8084 (t) REVERT: n 199 ASN cc_start: 0.8927 (t0) cc_final: 0.8528 (t0) REVERT: n 215 SER cc_start: 0.9355 (p) cc_final: 0.9126 (t) REVERT: n 219 ASP cc_start: 0.9036 (t0) cc_final: 0.8748 (t0) REVERT: n 257 CYS cc_start: 0.8421 (m) cc_final: 0.8218 (m) REVERT: o 10 SER cc_start: 0.9162 (m) cc_final: 0.8525 (t) REVERT: o 39 GLU cc_start: 0.8722 (tm-30) cc_final: 0.8504 (tm-30) REVERT: o 44 MET cc_start: 0.9144 (mmp) cc_final: 0.8892 (mmm) REVERT: o 84 LEU cc_start: 0.9301 (tp) cc_final: 0.9099 (tp) REVERT: o 95 SER cc_start: 0.8613 (p) cc_final: 0.8269 (t) REVERT: o 104 ASN cc_start: 0.8040 (m-40) cc_final: 0.7441 (m-40) REVERT: o 120 CYS cc_start: 0.8523 (m) cc_final: 0.8184 (m) REVERT: o 151 THR cc_start: 0.9286 (m) cc_final: 0.8934 (t) REVERT: o 169 TRP cc_start: 0.8165 (t-100) cc_final: 0.7132 (t-100) REVERT: o 216 CYS cc_start: 0.7406 (m) cc_final: 0.6725 (m) REVERT: o 224 LEU cc_start: 0.8887 (tp) cc_final: 0.8679 (tp) REVERT: o 232 GLN cc_start: 0.8203 (pp30) cc_final: 0.7428 (pp30) REVERT: o 234 LYS cc_start: 0.7609 (tttm) cc_final: 0.7348 (ttmt) REVERT: p 16 GLN cc_start: 0.6580 (mp10) cc_final: 0.6312 (mp10) REVERT: q 95 GLU cc_start: 0.8229 (mm-30) cc_final: 0.6857 (mm-30) REVERT: q 135 GLU cc_start: 0.7115 (mt-10) cc_final: 0.6660 (mt-10) REVERT: q 151 GLN cc_start: 0.8420 (tt0) cc_final: 0.8125 (tt0) REVERT: q 173 SER cc_start: 0.9304 (m) cc_final: 0.9050 (p) REVERT: q 189 MET cc_start: 0.8326 (ptt) cc_final: 0.7994 (ptm) REVERT: q 198 ASN cc_start: 0.8985 (m110) cc_final: 0.8728 (m-40) REVERT: q 209 ARG cc_start: 0.8073 (pmt-80) cc_final: 0.7809 (ptt90) REVERT: q 257 LYS cc_start: 0.9021 (ttpt) cc_final: 0.8473 (ptmt) REVERT: q 286 ILE cc_start: 0.9317 (pt) cc_final: 0.8759 (mt) REVERT: r 20 ASN cc_start: 0.9004 (p0) cc_final: 0.8770 (p0) REVERT: s 18 ASP cc_start: 0.7418 (t0) cc_final: 0.7129 (t0) REVERT: s 34 ILE cc_start: 0.9059 (pt) cc_final: 0.8710 (pt) REVERT: s 173 THR cc_start: 0.9309 (p) cc_final: 0.8856 (p) REVERT: s 194 GLN cc_start: 0.8311 (mm110) cc_final: 0.8049 (tp-100) REVERT: s 209 MET cc_start: 0.8180 (ttm) cc_final: 0.7828 (mtp) REVERT: s 223 LEU cc_start: 0.8859 (tp) cc_final: 0.8468 (tp) REVERT: s 225 ARG cc_start: 0.8574 (ptt180) cc_final: 0.8334 (ptt90) REVERT: s 226 ASP cc_start: 0.7313 (m-30) cc_final: 0.6383 (m-30) outliers start: 1 outliers final: 0 residues processed: 1561 average time/residue: 0.4583 time to fit residues: 1152.7133 Evaluate side-chains 1241 residues out of total 3659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1241 time to evaluate : 3.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 386 optimal weight: 20.0000 chunk 294 optimal weight: 30.0000 chunk 203 optimal weight: 20.0000 chunk 43 optimal weight: 30.0000 chunk 186 optimal weight: 9.9990 chunk 262 optimal weight: 1.9990 chunk 392 optimal weight: 10.0000 chunk 415 optimal weight: 0.2980 chunk 205 optimal weight: 20.0000 chunk 372 optimal weight: 1.9990 chunk 112 optimal weight: 10.0000 overall best weight: 4.8590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 226 ASN c 11 ASN ** c 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 4 GLN e 49 GLN ** e 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 43 ASN ** g 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 226 ASN ** k 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 32 ASN m 49 GLN ** n 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 196 GLN o 27 ASN ** p 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 31 ASN q 49 GLN q 112 GLN ** r 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 224 HIS ** s 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 44 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.4441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 34734 Z= 0.302 Angle : 0.641 14.034 47379 Z= 0.332 Chirality : 0.045 0.249 5322 Planarity : 0.005 0.070 6150 Dihedral : 5.684 56.706 4820 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.05 % Allowed : 3.06 % Favored : 96.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.13), residues: 4158 helix: -2.19 (0.22), residues: 423 sheet: 0.72 (0.15), residues: 1055 loop : -0.12 (0.12), residues: 2680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP m 103 HIS 0.010 0.001 HIS c 96 PHE 0.029 0.002 PHE j 174 TYR 0.024 0.002 TYR g 175 ARG 0.014 0.001 ARG r 264 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1479 residues out of total 3659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1477 time to evaluate : 3.777 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE a 298 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN b 272 " (corrupted residue). Skipping it. 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 TARDY: cannot create tardy model for: "ASN l 69 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "PHE m 298 " (corrupted residue). Skipping it. 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 127 LEU cc_start: 0.9132 (tp) cc_final: 0.8364 (tt) REVERT: a 192 PRO cc_start: 0.9557 (Cg_endo) cc_final: 0.9289 (Cg_exo) REVERT: a 205 ASP cc_start: 0.7317 (t70) cc_final: 0.6984 (t0) REVERT: b 80 TRP cc_start: 0.8944 (m-90) cc_final: 0.8525 (m-90) REVERT: b 99 HIS cc_start: 0.8348 (m170) cc_final: 0.8059 (m170) REVERT: b 214 ASN cc_start: 0.8857 (t0) cc_final: 0.8569 (t0) REVERT: b 216 LEU cc_start: 0.8874 (mt) cc_final: 0.8661 (mt) REVERT: b 260 PHE cc_start: 0.8991 (m-80) cc_final: 0.8760 (m-10) REVERT: c 42 ASN cc_start: 0.9350 (t0) cc_final: 0.9116 (t0) REVERT: c 43 MET cc_start: 0.8958 (mmm) cc_final: 0.8622 (mmm) REVERT: c 59 ASP cc_start: 0.8733 (m-30) cc_final: 0.8235 (m-30) REVERT: c 133 TYR cc_start: 0.8765 (t80) cc_final: 0.7923 (t80) REVERT: c 136 PRO cc_start: 0.9002 (Cg_exo) cc_final: 0.8793 (Cg_endo) REVERT: c 225 ARG cc_start: 0.8511 (ptt180) cc_final: 0.7836 (ptt180) REVERT: d 32 TYR cc_start: 0.9126 (m-10) cc_final: 0.8891 (m-10) REVERT: d 38 SER cc_start: 0.9091 (m) cc_final: 0.8841 (p) REVERT: e 54 ASP cc_start: 0.8863 (m-30) cc_final: 0.8636 (m-30) REVERT: e 57 GLU cc_start: 0.5489 (mp0) cc_final: 0.4608 (mp0) REVERT: e 69 GLU cc_start: 0.8263 (mt-10) cc_final: 0.7794 (tt0) REVERT: e 111 VAL cc_start: 0.9193 (m) cc_final: 0.8912 (p) REVERT: e 175 ASN cc_start: 0.9088 (m110) cc_final: 0.8306 (m-40) REVERT: e 180 TYR cc_start: 0.8912 (t80) cc_final: 0.8524 (t80) REVERT: f 15 GLN cc_start: 0.7476 (tt0) cc_final: 0.7087 (mt0) REVERT: f 55 GLU cc_start: 0.8544 (pp20) cc_final: 0.8306 (pp20) REVERT: f 126 LEU cc_start: 0.9283 (mt) cc_final: 0.8963 (mt) REVERT: f 127 ILE cc_start: 0.9276 (mp) cc_final: 0.8980 (mt) REVERT: f 149 ASN cc_start: 0.8891 (m110) cc_final: 0.8670 (m-40) REVERT: f 212 TYR cc_start: 0.8877 (t80) cc_final: 0.8226 (t80) REVERT: g 18 ASP cc_start: 0.7661 (t0) cc_final: 0.7194 (t0) REVERT: g 55 MET cc_start: 0.8474 (tpt) cc_final: 0.8245 (tpt) REVERT: g 90 SER cc_start: 0.8121 (p) cc_final: 0.7558 (t) REVERT: g 101 GLU cc_start: 0.8385 (tp30) cc_final: 0.7895 (mm-30) REVERT: g 112 SER cc_start: 0.8875 (m) cc_final: 0.8292 (p) REVERT: g 148 MET cc_start: 0.7149 (ttm) cc_final: 0.6542 (ttt) REVERT: g 163 CYS cc_start: 0.8761 (p) cc_final: 0.8306 (p) REVERT: g 169 TRP cc_start: 0.9068 (t-100) cc_final: 0.8103 (t-100) REVERT: g 216 CYS cc_start: 0.8572 (m) cc_final: 0.8302 (m) REVERT: h 7 THR cc_start: 0.9027 (m) cc_final: 0.8778 (m) REVERT: h 27 TYR cc_start: 0.8824 (p90) cc_final: 0.8244 (p90) REVERT: i 120 PHE cc_start: 0.8779 (m-80) cc_final: 0.8501 (m-80) REVERT: i 151 GLN cc_start: 0.9321 (tt0) cc_final: 0.9001 (tt0) REVERT: i 166 ASP cc_start: 0.8387 (p0) cc_final: 0.7717 (p0) REVERT: i 169 THR cc_start: 0.8992 (p) cc_final: 0.8695 (t) REVERT: i 180 TYR cc_start: 0.8684 (t80) cc_final: 0.8418 (t80) REVERT: i 182 TYR cc_start: 0.9191 (t80) cc_final: 0.8789 (t80) REVERT: i 198 ASN cc_start: 0.8731 (m110) cc_final: 0.8477 (m110) REVERT: i 250 THR cc_start: 0.7612 (m) cc_final: 0.7115 (m) REVERT: i 264 TRP cc_start: 0.9147 (m-90) cc_final: 0.8837 (m-90) REVERT: j 109 HIS cc_start: 0.8214 (t-90) cc_final: 0.7962 (t-90) REVERT: j 111 GLN cc_start: 0.7736 (pm20) cc_final: 0.7244 (tt0) REVERT: j 116 LYS cc_start: 0.8138 (mtmt) cc_final: 0.7931 (mtmt) REVERT: j 129 GLU cc_start: 0.8810 (mm-30) cc_final: 0.8509 (mm-30) REVERT: j 132 MET cc_start: 0.8218 (mtt) cc_final: 0.7691 (mmt) REVERT: j 145 TYR cc_start: 0.9201 (t80) cc_final: 0.8995 (t80) REVERT: j 258 THR cc_start: 0.8815 (m) cc_final: 0.8352 (m) REVERT: k 2 LEU cc_start: 0.9354 (tp) cc_final: 0.9141 (tp) REVERT: k 27 ASN cc_start: 0.9027 (m110) cc_final: 0.8658 (m110) REVERT: k 36 ILE cc_start: 0.9282 (mt) cc_final: 0.8517 (mt) REVERT: k 56 ASN cc_start: 0.8891 (t0) cc_final: 0.8385 (t0) REVERT: k 65 MET cc_start: 0.8195 (tpp) cc_final: 0.7917 (tpp) REVERT: k 112 SER cc_start: 0.8851 (m) cc_final: 0.8536 (p) REVERT: k 124 MET cc_start: 0.7374 (mmm) cc_final: 0.7118 (mtt) REVERT: k 169 TRP cc_start: 0.8315 (t-100) cc_final: 0.8086 (t-100) REVERT: k 188 PHE cc_start: 0.8595 (m-80) cc_final: 0.8196 (m-80) REVERT: k 203 THR cc_start: 0.9088 (p) cc_final: 0.8811 (p) REVERT: k 216 CYS cc_start: 0.8480 (m) cc_final: 0.7636 (m) REVERT: k 218 ASP cc_start: 0.8842 (p0) cc_final: 0.8458 (p0) REVERT: k 226 ASP cc_start: 0.7181 (m-30) cc_final: 0.6840 (m-30) REVERT: l 25 ILE cc_start: 0.8693 (mm) cc_final: 0.8427 (mm) REVERT: l 38 SER cc_start: 0.9531 (m) cc_final: 0.9173 (t) REVERT: l 42 THR cc_start: 0.8815 (p) cc_final: 0.8546 (t) REVERT: l 43 ARG cc_start: 0.8673 (ptt180) cc_final: 0.8208 (ptt180) REVERT: m 70 SER cc_start: 0.9132 (p) cc_final: 0.8710 (t) REVERT: m 97 LYS cc_start: 0.8739 (pttp) cc_final: 0.8506 (ptmt) REVERT: m 105 ILE cc_start: 0.8813 (mm) cc_final: 0.8439 (tp) REVERT: m 169 THR cc_start: 0.9527 (p) cc_final: 0.9148 (t) REVERT: m 223 PHE cc_start: 0.7639 (m-80) cc_final: 0.7147 (m-10) REVERT: m 281 MET cc_start: 0.8349 (mtp) cc_final: 0.7900 (mtm) REVERT: n 61 ASN cc_start: 0.8884 (m-40) cc_final: 0.8531 (m-40) REVERT: n 74 THR cc_start: 0.8076 (p) cc_final: 0.7802 (t) REVERT: n 149 ASN cc_start: 0.9034 (m-40) cc_final: 0.8667 (m-40) REVERT: n 174 PHE cc_start: 0.8538 (m-80) cc_final: 0.8108 (m-80) REVERT: n 183 SER cc_start: 0.8976 (p) cc_final: 0.8148 (t) REVERT: n 198 ILE cc_start: 0.9375 (mt) cc_final: 0.9109 (pt) REVERT: n 199 ASN cc_start: 0.8901 (t0) cc_final: 0.8398 (t0) REVERT: n 214 ASN cc_start: 0.8814 (t0) cc_final: 0.8495 (t0) REVERT: n 215 SER cc_start: 0.9400 (p) cc_final: 0.9093 (t) REVERT: n 219 ASP cc_start: 0.8993 (t0) cc_final: 0.8678 (t0) REVERT: o 10 SER cc_start: 0.9183 (m) cc_final: 0.8537 (t) REVERT: o 17 ASP cc_start: 0.8385 (t0) cc_final: 0.6671 (t0) REVERT: o 18 ASP cc_start: 0.8209 (p0) cc_final: 0.7993 (p0) REVERT: o 39 GLU cc_start: 0.8798 (tm-30) cc_final: 0.8460 (tm-30) REVERT: o 55 MET cc_start: 0.8285 (ttm) cc_final: 0.7840 (ttm) REVERT: o 70 ILE cc_start: 0.9477 (mt) cc_final: 0.8633 (mt) REVERT: o 95 SER cc_start: 0.8839 (p) cc_final: 0.8201 (t) REVERT: o 104 ASN cc_start: 0.8293 (m-40) cc_final: 0.7538 (m-40) REVERT: o 120 CYS cc_start: 0.8593 (m) cc_final: 0.8182 (m) REVERT: o 185 GLU cc_start: 0.7298 (mm-30) cc_final: 0.6961 (mm-30) REVERT: o 216 CYS cc_start: 0.7461 (m) cc_final: 0.6813 (m) REVERT: o 232 GLN cc_start: 0.8296 (pp30) cc_final: 0.7337 (pp30) REVERT: p 54 THR cc_start: 0.9067 (m) cc_final: 0.8567 (m) REVERT: q 89 ASN cc_start: 0.8981 (t0) cc_final: 0.8255 (t0) REVERT: q 95 GLU cc_start: 0.8610 (mm-30) cc_final: 0.7965 (mm-30) REVERT: q 118 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7954 (mp0) REVERT: q 126 ASP cc_start: 0.8501 (m-30) cc_final: 0.7935 (m-30) REVERT: q 127 LEU cc_start: 0.9186 (tp) cc_final: 0.8783 (tp) REVERT: q 173 SER cc_start: 0.9322 (m) cc_final: 0.9040 (p) REVERT: q 202 HIS cc_start: 0.8534 (m90) cc_final: 0.8065 (m90) REVERT: q 209 ARG cc_start: 0.8147 (pmt-80) cc_final: 0.7849 (ptt90) REVERT: q 257 LYS cc_start: 0.9050 (ttpt) cc_final: 0.8339 (ptmt) REVERT: q 286 ILE cc_start: 0.9347 (pt) cc_final: 0.8867 (mt) REVERT: r 20 ASN cc_start: 0.9083 (p0) cc_final: 0.8853 (p0) REVERT: r 89 MET cc_start: 0.8757 (mmm) cc_final: 0.8079 (tpp) REVERT: r 122 LEU cc_start: 0.9358 (mt) cc_final: 0.9121 (mt) REVERT: r 223 LYS cc_start: 0.9215 (mttm) cc_final: 0.8954 (mttm) REVERT: s 18 ASP cc_start: 0.7315 (t0) cc_final: 0.7103 (t0) REVERT: s 84 LEU cc_start: 0.9184 (mt) cc_final: 0.8965 (mt) REVERT: s 157 LEU cc_start: 0.8998 (mm) cc_final: 0.8669 (mt) REVERT: s 184 THR cc_start: 0.8525 (m) cc_final: 0.8096 (p) REVERT: s 190 THR cc_start: 0.8625 (p) cc_final: 0.8378 (t) REVERT: s 226 ASP cc_start: 0.7128 (m-30) cc_final: 0.6807 (m-30) outliers start: 2 outliers final: 1 residues processed: 1479 average time/residue: 0.4444 time to fit residues: 1069.2651 Evaluate side-chains 1229 residues out of total 3659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1228 time to evaluate : 3.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 346 optimal weight: 20.0000 chunk 235 optimal weight: 5.9990 chunk 6 optimal weight: 30.0000 chunk 309 optimal weight: 30.0000 chunk 171 optimal weight: 10.0000 chunk 354 optimal weight: 10.0000 chunk 287 optimal weight: 20.0000 chunk 0 optimal weight: 40.0000 chunk 212 optimal weight: 20.0000 chunk 373 optimal weight: 7.9990 chunk 104 optimal weight: 6.9990 overall best weight: 8.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 108 HIS ** c 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 4 GLN ** d 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 175 ASN ** e 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 43 ASN ** g 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 112 GLN ** j 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 195 HIS j 226 ASN ** k 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 27 ASN ** k 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 194 GLN ** l 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 15 GLN o 27 ASN o 104 ASN ** o 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 4 GLN p 31 ASN q 49 GLN ** q 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 232 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.4880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.117 34734 Z= 0.435 Angle : 0.716 9.113 47379 Z= 0.370 Chirality : 0.047 0.270 5322 Planarity : 0.005 0.059 6150 Dihedral : 5.950 52.285 4820 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 19.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % 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: -0.56 (0.12), residues: 4158 helix: -2.19 (0.22), residues: 413 sheet: 0.41 (0.15), residues: 1056 loop : -0.35 (0.12), residues: 2689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP b 227 HIS 0.008 0.002 HIS c 96 PHE 0.032 0.003 PHE q 120 TYR 0.035 0.002 TYR g 175 ARG 0.012 0.001 ARG i 188 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1377 residues out of total 3659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1377 time to evaluate : 3.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN b 272 " (corrupted residue). Skipping it. 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 TARDY: cannot create tardy model for: "ASN l 69 " (corrupted residue). Skipping it. 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 127 LEU cc_start: 0.9154 (tp) cc_final: 0.8323 (tt) REVERT: b 18 LEU cc_start: 0.9428 (mt) cc_final: 0.9123 (mp) REVERT: b 80 TRP cc_start: 0.8971 (m-90) cc_final: 0.8542 (m-90) REVERT: b 99 HIS cc_start: 0.8537 (m170) cc_final: 0.8325 (m170) REVERT: b 178 ASP cc_start: 0.9072 (p0) cc_final: 0.8813 (p0) REVERT: b 214 ASN cc_start: 0.8849 (t0) cc_final: 0.8510 (t0) REVERT: b 216 LEU cc_start: 0.8929 (mt) cc_final: 0.8617 (mt) REVERT: b 260 PHE cc_start: 0.8959 (m-80) cc_final: 0.8573 (m-10) REVERT: c 43 MET cc_start: 0.8912 (mmm) cc_final: 0.8706 (tpp) REVERT: c 139 LYS cc_start: 0.9101 (ptmm) cc_final: 0.8708 (ptpp) REVERT: c 163 CYS cc_start: 0.8039 (p) cc_final: 0.7476 (p) REVERT: c 218 ASP cc_start: 0.8612 (p0) cc_final: 0.8245 (p0) REVERT: c 225 ARG cc_start: 0.8407 (ptt180) cc_final: 0.7893 (ptt180) REVERT: d 31 ASN cc_start: 0.8766 (m-40) cc_final: 0.8451 (m110) REVERT: d 36 SER cc_start: 0.8919 (p) cc_final: 0.8256 (p) REVERT: e 49 GLN cc_start: 0.8688 (mm110) cc_final: 0.8298 (mm-40) REVERT: e 54 ASP cc_start: 0.8912 (m-30) cc_final: 0.8701 (m-30) REVERT: e 57 GLU cc_start: 0.5768 (mp0) cc_final: 0.5451 (mp0) REVERT: e 69 GLU cc_start: 0.8318 (mt-10) cc_final: 0.7818 (tt0) REVERT: f 15 GLN cc_start: 0.7534 (tt0) cc_final: 0.7054 (pt0) REVERT: f 55 GLU cc_start: 0.8620 (pp20) cc_final: 0.8254 (pp20) REVERT: f 126 LEU cc_start: 0.9236 (mt) cc_final: 0.9028 (mt) REVERT: f 149 ASN cc_start: 0.8880 (m110) cc_final: 0.8670 (m110) REVERT: f 212 TYR cc_start: 0.9121 (t80) cc_final: 0.8712 (t80) REVERT: f 232 LEU cc_start: 0.8962 (mt) cc_final: 0.8524 (mp) REVERT: g 12 GLN cc_start: 0.8694 (pp30) cc_final: 0.8057 (pp30) REVERT: g 112 SER cc_start: 0.8965 (m) cc_final: 0.8477 (p) REVERT: g 120 CYS cc_start: 0.8987 (m) cc_final: 0.8765 (m) REVERT: g 133 TYR cc_start: 0.9096 (t80) cc_final: 0.8735 (t80) REVERT: g 148 MET cc_start: 0.6922 (ttm) cc_final: 0.6688 (ttt) REVERT: g 163 CYS cc_start: 0.8691 (p) cc_final: 0.8282 (p) REVERT: g 169 TRP cc_start: 0.9070 (t-100) cc_final: 0.8103 (t-100) REVERT: g 216 CYS cc_start: 0.8549 (m) cc_final: 0.8338 (m) REVERT: h 8 GLN cc_start: 0.7745 (mt0) cc_final: 0.7126 (mt0) REVERT: i 120 PHE cc_start: 0.8892 (m-80) cc_final: 0.8608 (m-80) REVERT: i 151 GLN cc_start: 0.9377 (tt0) cc_final: 0.9102 (tt0) REVERT: i 166 ASP cc_start: 0.8446 (p0) cc_final: 0.7511 (p0) REVERT: i 169 THR cc_start: 0.9117 (p) cc_final: 0.8779 (t) REVERT: i 175 ASN cc_start: 0.8214 (m110) cc_final: 0.8007 (m110) REVERT: i 180 TYR cc_start: 0.8641 (t80) cc_final: 0.8382 (t80) REVERT: i 250 THR cc_start: 0.7758 (m) cc_final: 0.7454 (m) REVERT: j 60 SER cc_start: 0.9113 (m) cc_final: 0.8571 (p) REVERT: j 84 ASP cc_start: 0.8130 (t0) cc_final: 0.7803 (t0) REVERT: j 111 GLN cc_start: 0.7973 (pm20) cc_final: 0.7529 (tt0) REVERT: j 129 GLU cc_start: 0.8883 (mm-30) cc_final: 0.8676 (mm-30) REVERT: j 132 MET cc_start: 0.8285 (mtt) cc_final: 0.7808 (mmt) REVERT: j 213 VAL cc_start: 0.9246 (t) cc_final: 0.8912 (m) REVERT: j 249 ILE cc_start: 0.8773 (mm) cc_final: 0.8565 (mm) REVERT: k 2 LEU cc_start: 0.9364 (tp) cc_final: 0.9123 (tp) REVERT: k 27 ASN cc_start: 0.9101 (m-40) cc_final: 0.8757 (m110) REVERT: k 29 ASP cc_start: 0.9193 (t0) cc_final: 0.8794 (t0) REVERT: k 56 ASN cc_start: 0.9033 (t0) cc_final: 0.8512 (t0) REVERT: k 65 MET cc_start: 0.8222 (tpp) cc_final: 0.7990 (tpp) REVERT: k 70 ILE cc_start: 0.9517 (mm) cc_final: 0.9287 (mm) REVERT: k 112 SER cc_start: 0.8835 (m) cc_final: 0.8439 (p) REVERT: k 124 MET cc_start: 0.7736 (mmm) cc_final: 0.7175 (mtt) REVERT: k 169 TRP cc_start: 0.8462 (t-100) cc_final: 0.8075 (t-100) REVERT: k 180 ARG cc_start: 0.8201 (tpt-90) cc_final: 0.7963 (tpp80) REVERT: k 188 PHE cc_start: 0.8710 (m-80) cc_final: 0.8297 (m-80) REVERT: k 216 CYS cc_start: 0.8594 (m) cc_final: 0.7909 (m) REVERT: k 218 ASP cc_start: 0.8765 (p0) cc_final: 0.8453 (p0) REVERT: l 25 ILE cc_start: 0.8812 (mm) cc_final: 0.8581 (mm) REVERT: l 38 SER cc_start: 0.9544 (m) cc_final: 0.9150 (t) REVERT: m 70 SER cc_start: 0.9187 (p) cc_final: 0.8953 (t) REVERT: m 97 LYS cc_start: 0.8723 (pttp) cc_final: 0.8384 (ptmt) REVERT: m 105 ILE cc_start: 0.9041 (mm) cc_final: 0.8540 (tp) REVERT: m 110 THR cc_start: 0.8261 (p) cc_final: 0.8001 (p) REVERT: m 127 LEU cc_start: 0.8958 (tp) cc_final: 0.8660 (tp) REVERT: m 169 THR cc_start: 0.9568 (p) cc_final: 0.9154 (t) REVERT: m 223 PHE cc_start: 0.7843 (m-80) cc_final: 0.7554 (m-80) REVERT: n 14 ARG cc_start: 0.3000 (tpm170) cc_final: 0.1231 (mmp-170) REVERT: n 61 ASN cc_start: 0.8924 (m-40) cc_final: 0.8532 (m-40) REVERT: n 74 THR cc_start: 0.8151 (p) cc_final: 0.7892 (t) REVERT: n 84 ASP cc_start: 0.8147 (t70) cc_final: 0.7437 (t0) REVERT: n 132 MET cc_start: 0.8814 (mmm) cc_final: 0.8539 (mmm) REVERT: n 183 SER cc_start: 0.9128 (p) cc_final: 0.8484 (t) REVERT: n 198 ILE cc_start: 0.9375 (mt) cc_final: 0.8994 (tp) REVERT: n 199 ASN cc_start: 0.8963 (t0) cc_final: 0.8235 (t0) REVERT: n 215 SER cc_start: 0.9272 (p) cc_final: 0.9033 (p) REVERT: o 10 SER cc_start: 0.9221 (m) cc_final: 0.8955 (p) REVERT: o 17 ASP cc_start: 0.8562 (t0) cc_final: 0.6830 (t0) REVERT: o 39 GLU cc_start: 0.8903 (tm-30) cc_final: 0.8530 (tm-30) REVERT: o 95 SER cc_start: 0.9052 (p) cc_final: 0.8369 (t) REVERT: o 120 CYS cc_start: 0.8570 (m) cc_final: 0.8112 (m) REVERT: o 139 LYS cc_start: 0.8748 (tmmt) cc_final: 0.8371 (tttt) REVERT: o 185 GLU cc_start: 0.7575 (mm-30) cc_final: 0.7158 (mm-30) REVERT: o 216 CYS cc_start: 0.7697 (m) cc_final: 0.7048 (m) REVERT: p 24 THR cc_start: 0.9173 (p) cc_final: 0.8894 (t) REVERT: p 54 THR cc_start: 0.8889 (m) cc_final: 0.8221 (m) REVERT: p 55 GLU cc_start: 0.7847 (mp0) cc_final: 0.7515 (mp0) REVERT: q 95 GLU cc_start: 0.8549 (mm-30) cc_final: 0.7957 (mm-30) REVERT: q 118 GLU cc_start: 0.8302 (mt-10) cc_final: 0.7726 (mt-10) REVERT: q 126 ASP cc_start: 0.8514 (m-30) cc_final: 0.7954 (m-30) REVERT: q 127 LEU cc_start: 0.9143 (tp) cc_final: 0.8920 (tp) REVERT: q 202 HIS cc_start: 0.8612 (m90) cc_final: 0.8102 (m90) REVERT: q 218 ASP cc_start: 0.7316 (t0) cc_final: 0.7065 (t0) REVERT: q 286 ILE cc_start: 0.9290 (pt) cc_final: 0.8855 (mt) REVERT: r 20 ASN cc_start: 0.9057 (p0) cc_final: 0.8852 (p0) REVERT: r 89 MET cc_start: 0.8745 (mmm) cc_final: 0.8094 (tpp) REVERT: r 196 GLN cc_start: 0.9006 (mt0) cc_final: 0.8697 (mm-40) REVERT: r 199 ASN cc_start: 0.9039 (t0) cc_final: 0.8833 (t0) REVERT: s 18 ASP cc_start: 0.7350 (t0) cc_final: 0.7145 (t0) REVERT: s 181 ASP cc_start: 0.8242 (p0) cc_final: 0.7923 (p0) REVERT: s 184 THR cc_start: 0.8586 (m) cc_final: 0.8237 (p) REVERT: s 209 MET cc_start: 0.8352 (ttm) cc_final: 0.7867 (mtp) REVERT: s 226 ASP cc_start: 0.7432 (m-30) cc_final: 0.7080 (m-30) REVERT: t 13 HIS cc_start: 0.8948 (t70) cc_final: 0.8712 (t70) outliers start: 0 outliers final: 0 residues processed: 1377 average time/residue: 0.4533 time to fit residues: 1010.0644 Evaluate side-chains 1169 residues out of total 3659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1169 time to evaluate : 3.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 139 optimal weight: 5.9990 chunk 374 optimal weight: 30.0000 chunk 82 optimal weight: 20.0000 chunk 244 optimal weight: 0.1980 chunk 102 optimal weight: 5.9990 chunk 416 optimal weight: 10.0000 chunk 345 optimal weight: 20.0000 chunk 192 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 137 optimal weight: 0.8980 chunk 218 optimal weight: 10.0000 overall best weight: 2.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 23 GLN ** a 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 271 HIS ** c 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 4 GLN ** d 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 89 ASN ** e 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 244 ASN f 43 ASN ** g 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 195 HIS ** k 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 32 ASN ** m 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 30 ASN n 196 GLN ** o 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 4 GLN ** p 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 49 GLN ** q 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 224 HIS ** s 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.5122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 34734 Z= 0.231 Angle : 0.621 8.970 47379 Z= 0.320 Chirality : 0.045 0.271 5322 Planarity : 0.005 0.051 6150 Dihedral : 5.658 54.319 4820 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 16.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.05 % Allowed : 1.59 % Favored : 98.36 % 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: -0.52 (0.13), residues: 4158 helix: -2.06 (0.23), residues: 391 sheet: 0.34 (0.15), residues: 1071 loop : -0.32 (0.12), residues: 2696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP b 227 HIS 0.008 0.001 HIS f 195 PHE 0.032 0.002 PHE a 120 TYR 0.027 0.002 TYR b 179 ARG 0.021 0.001 ARG r 264 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1431 residues out of total 3659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1429 time to evaluate : 3.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN b 272 " (corrupted residue). Skipping it. 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 TARDY: cannot create tardy model for: "ASN l 69 " (corrupted residue). Skipping it. 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 118 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8247 (mt-10) REVERT: a 127 LEU cc_start: 0.9041 (tp) cc_final: 0.8468 (tt) REVERT: a 171 GLN cc_start: 0.8285 (mt0) cc_final: 0.7818 (mt0) REVERT: b 80 TRP cc_start: 0.8987 (m-90) cc_final: 0.8569 (m-90) REVERT: b 84 ASP cc_start: 0.7661 (t70) cc_final: 0.7160 (t70) REVERT: b 99 HIS cc_start: 0.8433 (m170) cc_final: 0.8105 (m170) REVERT: b 112 CYS cc_start: 0.8641 (t) cc_final: 0.8111 (t) REVERT: b 249 ILE cc_start: 0.9122 (mt) cc_final: 0.8572 (mm) REVERT: c 70 ILE cc_start: 0.9152 (mm) cc_final: 0.8835 (mm) REVERT: c 163 CYS cc_start: 0.7815 (p) cc_final: 0.7518 (p) REVERT: c 218 ASP cc_start: 0.8559 (p0) cc_final: 0.8242 (p0) REVERT: e 49 GLN cc_start: 0.8512 (mm110) cc_final: 0.8277 (mm-40) REVERT: e 57 GLU cc_start: 0.5836 (mp0) cc_final: 0.4897 (mp0) REVERT: e 66 THR cc_start: 0.8551 (m) cc_final: 0.8175 (p) REVERT: e 69 GLU cc_start: 0.8311 (mt-10) cc_final: 0.7974 (tt0) REVERT: e 111 VAL cc_start: 0.9106 (m) cc_final: 0.8889 (p) REVERT: f 15 GLN cc_start: 0.7449 (tt0) cc_final: 0.7061 (pt0) REVERT: f 55 GLU cc_start: 0.8495 (pp20) cc_final: 0.8247 (pp20) REVERT: f 100 TYR cc_start: 0.8512 (t80) cc_final: 0.8229 (t80) REVERT: f 126 LEU cc_start: 0.9222 (mt) cc_final: 0.8922 (mt) REVERT: f 127 ILE cc_start: 0.9371 (mp) cc_final: 0.8975 (mt) REVERT: f 149 ASN cc_start: 0.8926 (m110) cc_final: 0.8715 (m110) REVERT: g 12 GLN cc_start: 0.8579 (pp30) cc_final: 0.7947 (pp30) REVERT: g 55 MET cc_start: 0.8259 (tpt) cc_final: 0.7979 (tpp) REVERT: g 101 GLU cc_start: 0.8515 (mm-30) cc_final: 0.7998 (mm-30) REVERT: g 112 SER cc_start: 0.8942 (m) cc_final: 0.8474 (p) REVERT: g 120 CYS cc_start: 0.8956 (m) cc_final: 0.8655 (m) REVERT: g 133 TYR cc_start: 0.9171 (t80) cc_final: 0.8754 (t80) REVERT: g 163 CYS cc_start: 0.8673 (p) cc_final: 0.8231 (p) REVERT: g 169 TRP cc_start: 0.8965 (t-100) cc_final: 0.7912 (t-100) REVERT: g 216 CYS cc_start: 0.8666 (m) cc_final: 0.8430 (m) REVERT: g 226 ASP cc_start: 0.7771 (m-30) cc_final: 0.7453 (m-30) REVERT: i 151 GLN cc_start: 0.9312 (tt0) cc_final: 0.8941 (tt0) REVERT: i 166 ASP cc_start: 0.8535 (p0) cc_final: 0.7587 (p0) REVERT: i 169 THR cc_start: 0.9010 (p) cc_final: 0.8727 (t) REVERT: i 250 THR cc_start: 0.7705 (m) cc_final: 0.7316 (m) REVERT: i 262 ARG cc_start: 0.8944 (ttp80) cc_final: 0.8155 (ttm170) REVERT: j 60 SER cc_start: 0.8948 (m) cc_final: 0.8508 (p) REVERT: j 84 ASP cc_start: 0.7786 (t0) cc_final: 0.7313 (t0) REVERT: j 111 GLN cc_start: 0.8030 (pm20) cc_final: 0.7419 (tt0) REVERT: j 117 PHE cc_start: 0.8421 (m-80) cc_final: 0.8180 (m-80) REVERT: j 127 ILE cc_start: 0.8877 (mt) cc_final: 0.8653 (mt) REVERT: j 129 GLU cc_start: 0.8812 (mm-30) cc_final: 0.8609 (mm-30) REVERT: j 132 MET cc_start: 0.8301 (mtt) cc_final: 0.7801 (mmt) REVERT: j 260 PHE cc_start: 0.8901 (m-80) cc_final: 0.8488 (m-80) REVERT: k 2 LEU cc_start: 0.9323 (tp) cc_final: 0.9109 (tp) REVERT: k 14 LEU cc_start: 0.9294 (tp) cc_final: 0.9039 (tp) REVERT: k 27 ASN cc_start: 0.9022 (m-40) cc_final: 0.8685 (m110) REVERT: k 29 ASP cc_start: 0.9079 (t0) cc_final: 0.8622 (t0) REVERT: k 65 MET cc_start: 0.8086 (tpp) cc_final: 0.7882 (tpp) REVERT: k 98 MET cc_start: 0.9003 (tpp) cc_final: 0.8762 (ttp) REVERT: k 112 SER cc_start: 0.8826 (m) cc_final: 0.8228 (p) REVERT: k 119 PHE cc_start: 0.8536 (t80) cc_final: 0.8133 (t80) REVERT: k 124 MET cc_start: 0.7413 (mmm) cc_final: 0.7022 (mtt) REVERT: k 169 TRP cc_start: 0.8287 (t-100) cc_final: 0.7806 (t-100) REVERT: k 188 PHE cc_start: 0.8790 (m-80) cc_final: 0.8374 (m-80) REVERT: k 216 CYS cc_start: 0.8416 (m) cc_final: 0.7590 (m) REVERT: l 21 ASN cc_start: 0.8346 (p0) cc_final: 0.7968 (p0) REVERT: l 25 ILE cc_start: 0.8706 (mm) cc_final: 0.8424 (mm) REVERT: l 38 SER cc_start: 0.9524 (m) cc_final: 0.9107 (t) REVERT: l 42 THR cc_start: 0.8826 (p) cc_final: 0.8591 (t) REVERT: m 97 LYS cc_start: 0.8775 (pttp) cc_final: 0.8466 (ptmt) REVERT: m 105 ILE cc_start: 0.8953 (mm) cc_final: 0.8432 (tp) REVERT: m 110 THR cc_start: 0.8423 (p) cc_final: 0.8015 (p) REVERT: m 128 GLU cc_start: 0.8108 (tt0) cc_final: 0.7651 (tt0) REVERT: m 169 THR cc_start: 0.9495 (p) cc_final: 0.9081 (t) REVERT: m 262 ARG cc_start: 0.9221 (ptm160) cc_final: 0.8933 (ptp-170) REVERT: n 14 ARG cc_start: 0.2906 (tpm170) cc_final: 0.0893 (tpm170) REVERT: n 61 ASN cc_start: 0.8888 (m-40) cc_final: 0.8546 (m-40) REVERT: n 74 THR cc_start: 0.8089 (p) cc_final: 0.7847 (t) REVERT: n 132 MET cc_start: 0.8651 (mmm) cc_final: 0.8426 (mmp) REVERT: n 149 ASN cc_start: 0.8967 (m-40) cc_final: 0.8525 (m-40) REVERT: n 183 SER cc_start: 0.8923 (p) cc_final: 0.8343 (t) REVERT: n 198 ILE cc_start: 0.9367 (mt) cc_final: 0.9103 (pt) REVERT: n 199 ASN cc_start: 0.8767 (t0) cc_final: 0.8045 (t0) REVERT: n 214 ASN cc_start: 0.8957 (t0) cc_final: 0.8495 (t0) REVERT: n 219 ASP cc_start: 0.9000 (t0) cc_final: 0.8739 (t0) REVERT: n 221 MET cc_start: 0.7088 (mtm) cc_final: 0.6744 (mtm) REVERT: o 10 SER cc_start: 0.9134 (m) cc_final: 0.8865 (p) REVERT: o 17 ASP cc_start: 0.8546 (t0) cc_final: 0.7121 (t0) REVERT: o 39 GLU cc_start: 0.8776 (tm-30) cc_final: 0.8506 (tm-30) REVERT: o 55 MET cc_start: 0.8070 (ttm) cc_final: 0.7666 (ttm) REVERT: o 70 ILE cc_start: 0.9430 (mt) cc_final: 0.8572 (mt) REVERT: o 95 SER cc_start: 0.8938 (p) cc_final: 0.8225 (t) REVERT: o 153 ILE cc_start: 0.9056 (pt) cc_final: 0.8826 (pt) REVERT: o 154 ILE cc_start: 0.7838 (mm) cc_final: 0.7231 (pt) REVERT: o 185 GLU cc_start: 0.7455 (mm-30) cc_final: 0.7113 (mm-30) REVERT: o 216 CYS cc_start: 0.7653 (m) cc_final: 0.6896 (m) REVERT: o 218 ASP cc_start: 0.8941 (p0) cc_final: 0.8738 (p0) REVERT: o 223 LEU cc_start: 0.8633 (tp) cc_final: 0.8386 (tp) REVERT: o 224 LEU cc_start: 0.8932 (tp) cc_final: 0.8661 (tp) REVERT: p 24 THR cc_start: 0.9127 (p) cc_final: 0.8892 (t) REVERT: p 54 THR cc_start: 0.8775 (m) cc_final: 0.8230 (m) REVERT: p 55 GLU cc_start: 0.7865 (mp0) cc_final: 0.7385 (mp0) REVERT: q 89 ASN cc_start: 0.8865 (t0) cc_final: 0.8175 (t0) REVERT: q 90 SER cc_start: 0.8842 (t) cc_final: 0.8578 (t) REVERT: q 95 GLU cc_start: 0.8526 (mm-30) cc_final: 0.7951 (mm-30) REVERT: q 148 GLN cc_start: 0.8581 (mm-40) cc_final: 0.8320 (mm110) REVERT: q 171 GLN cc_start: 0.8353 (mt0) cc_final: 0.8073 (mt0) REVERT: q 198 ASN cc_start: 0.9303 (m110) cc_final: 0.8925 (m-40) REVERT: q 202 HIS cc_start: 0.8533 (m90) cc_final: 0.8183 (m90) REVERT: q 218 ASP cc_start: 0.7137 (t0) cc_final: 0.6597 (t70) REVERT: r 20 ASN cc_start: 0.9061 (p0) cc_final: 0.8841 (p0) REVERT: r 196 GLN cc_start: 0.9010 (mt0) cc_final: 0.8691 (mm-40) REVERT: r 199 ASN cc_start: 0.8967 (t0) cc_final: 0.8732 (t0) REVERT: s 18 ASP cc_start: 0.7194 (t0) cc_final: 0.6879 (t0) REVERT: s 34 ILE cc_start: 0.9150 (pt) cc_final: 0.8609 (pt) REVERT: s 55 MET cc_start: 0.8335 (tpp) cc_final: 0.7938 (tpp) REVERT: s 67 MET cc_start: 0.9255 (tmm) cc_final: 0.8457 (ttt) REVERT: s 181 ASP cc_start: 0.8171 (p0) cc_final: 0.7924 (p0) REVERT: s 184 THR cc_start: 0.8588 (m) cc_final: 0.8254 (p) REVERT: s 209 MET cc_start: 0.8308 (ttm) cc_final: 0.7868 (mtp) REVERT: s 226 ASP cc_start: 0.7616 (m-30) cc_final: 0.7309 (m-30) REVERT: t 13 HIS cc_start: 0.8897 (t70) cc_final: 0.8646 (t70) outliers start: 2 outliers final: 2 residues processed: 1430 average time/residue: 0.4679 time to fit residues: 1097.1261 Evaluate side-chains 1203 residues out of total 3659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1201 time to evaluate : 4.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 401 optimal weight: 9.9990 chunk 46 optimal weight: 0.4980 chunk 237 optimal weight: 10.0000 chunk 303 optimal weight: 4.9990 chunk 235 optimal weight: 10.0000 chunk 350 optimal weight: 6.9990 chunk 232 optimal weight: 10.0000 chunk 414 optimal weight: 2.9990 chunk 259 optimal weight: 10.0000 chunk 252 optimal weight: 20.0000 chunk 191 optimal weight: 30.0000 overall best weight: 5.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 23 GLN ** a 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 249 HIS ** b 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 4 GLN ** d 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 184 ASN f 43 ASN ** g 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 112 GLN ** i 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 195 HIS j 226 ASN ** k 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 44 GLN ** m 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 27 ASN o 35 HIS ** o 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 232 GLN p 4 GLN ** p 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 31 ASN ** q 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 265 ASN ** s 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 160 GLN t 26 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.5352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 34734 Z= 0.312 Angle : 0.662 9.858 47379 Z= 0.337 Chirality : 0.046 0.272 5322 Planarity : 0.005 0.083 6150 Dihedral : 5.715 57.863 4820 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 17.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.08 % Allowed : 1.50 % Favored : 98.41 % 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: -0.65 (0.13), residues: 4158 helix: -2.04 (0.23), residues: 390 sheet: 0.26 (0.15), residues: 1067 loop : -0.43 (0.12), residues: 2701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP b 227 HIS 0.008 0.001 HIS g 96 PHE 0.034 0.002 PHE i 120 TYR 0.029 0.002 TYR k 175 ARG 0.013 0.001 ARG r 264 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1383 residues out of total 3659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1380 time to evaluate : 3.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN b 272 " (corrupted residue). Skipping it. 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 TARDY: cannot create tardy model for: "ASN l 69 " (corrupted residue). Skipping it. 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 65 LYS cc_start: 0.9100 (mtmm) cc_final: 0.8727 (mtmt) REVERT: a 127 LEU cc_start: 0.9196 (tp) cc_final: 0.8477 (tt) REVERT: a 264 TRP cc_start: 0.9368 (m-90) cc_final: 0.8871 (m-90) REVERT: b 99 HIS cc_start: 0.8586 (m170) cc_final: 0.8273 (m170) REVERT: b 214 ASN cc_start: 0.8881 (t0) cc_final: 0.8509 (t0) REVERT: b 216 LEU cc_start: 0.8891 (mt) cc_final: 0.8564 (mt) REVERT: b 249 ILE cc_start: 0.9170 (mt) cc_final: 0.8896 (mm) REVERT: b 260 PHE cc_start: 0.8711 (m-10) cc_final: 0.8350 (m-10) REVERT: b 266 ILE cc_start: 0.8864 (tp) cc_final: 0.8424 (tp) REVERT: c 72 LEU cc_start: 0.8021 (mp) cc_final: 0.7664 (mt) REVERT: c 155 TRP cc_start: 0.9065 (t60) cc_final: 0.8784 (t60) REVERT: c 163 CYS cc_start: 0.7808 (p) cc_final: 0.6850 (p) REVERT: d 13 HIS cc_start: 0.8752 (t-90) cc_final: 0.8344 (t70) REVERT: e 54 ASP cc_start: 0.8748 (m-30) cc_final: 0.8444 (m-30) REVERT: e 57 GLU cc_start: 0.5829 (mp0) cc_final: 0.5196 (mp0) REVERT: e 69 GLU cc_start: 0.8455 (mt-10) cc_final: 0.7902 (tt0) REVERT: f 15 GLN cc_start: 0.7536 (tt0) cc_final: 0.7048 (pt0) REVERT: f 55 GLU cc_start: 0.8639 (pp20) cc_final: 0.8318 (pp20) REVERT: f 70 SER cc_start: 0.8777 (m) cc_final: 0.8503 (p) REVERT: f 126 LEU cc_start: 0.9179 (mt) cc_final: 0.8887 (mt) REVERT: f 127 ILE cc_start: 0.9326 (mp) cc_final: 0.8987 (mt) REVERT: f 149 ASN cc_start: 0.8920 (m110) cc_final: 0.8720 (m110) REVERT: f 199 ASN cc_start: 0.8978 (t0) cc_final: 0.8716 (t0) REVERT: g 12 GLN cc_start: 0.8748 (pp30) cc_final: 0.7986 (pp30) REVERT: g 55 MET cc_start: 0.8288 (tpt) cc_final: 0.7962 (tpp) REVERT: g 101 GLU cc_start: 0.8558 (mm-30) cc_final: 0.8329 (mm-30) REVERT: g 112 SER cc_start: 0.9016 (m) cc_final: 0.8525 (p) REVERT: g 114 ARG cc_start: 0.8918 (ttp-110) cc_final: 0.8426 (ttm170) REVERT: g 120 CYS cc_start: 0.8971 (m) cc_final: 0.8640 (m) REVERT: g 133 TYR cc_start: 0.9238 (t80) cc_final: 0.8845 (t80) REVERT: g 155 TRP cc_start: 0.9208 (t60) cc_final: 0.8638 (t60) REVERT: g 163 CYS cc_start: 0.8752 (p) cc_final: 0.8009 (p) REVERT: g 169 TRP cc_start: 0.9012 (t-100) cc_final: 0.8026 (t-100) REVERT: g 225 ARG cc_start: 0.8706 (ptt-90) cc_final: 0.8379 (ptt-90) REVERT: i 35 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7537 (tt0) REVERT: i 78 ARG cc_start: 0.8788 (mmt90) cc_final: 0.8568 (mmt-90) REVERT: i 151 GLN cc_start: 0.9381 (tt0) cc_final: 0.8885 (tt0) REVERT: i 166 ASP cc_start: 0.8520 (p0) cc_final: 0.7638 (p0) REVERT: i 169 THR cc_start: 0.9057 (p) cc_final: 0.8742 (t) REVERT: i 180 TYR cc_start: 0.8754 (t80) cc_final: 0.8482 (t80) REVERT: i 262 ARG cc_start: 0.9002 (ttp80) cc_final: 0.8349 (ttm170) REVERT: j 60 SER cc_start: 0.9012 (m) cc_final: 0.8612 (p) REVERT: j 84 ASP cc_start: 0.7891 (t70) cc_final: 0.7506 (t0) REVERT: j 132 MET cc_start: 0.8347 (mtt) cc_final: 0.7923 (mmt) REVERT: k 2 LEU cc_start: 0.9333 (tp) cc_final: 0.9104 (tp) REVERT: k 27 ASN cc_start: 0.9004 (m-40) cc_final: 0.8626 (m110) REVERT: k 29 ASP cc_start: 0.9074 (t0) cc_final: 0.8738 (t0) REVERT: k 66 GLU cc_start: 0.8577 (mp0) cc_final: 0.8219 (mp0) REVERT: k 112 SER cc_start: 0.8747 (m) cc_final: 0.8239 (p) REVERT: k 119 PHE cc_start: 0.8461 (t80) cc_final: 0.8110 (t80) REVERT: k 124 MET cc_start: 0.7461 (mmm) cc_final: 0.7075 (mtt) REVERT: k 169 TRP cc_start: 0.8251 (t-100) cc_final: 0.7844 (t-100) REVERT: k 188 PHE cc_start: 0.8897 (m-80) cc_final: 0.8464 (m-80) REVERT: k 216 CYS cc_start: 0.8335 (m) cc_final: 0.7603 (m) REVERT: k 218 ASP cc_start: 0.8810 (p0) cc_final: 0.8582 (p0) REVERT: k 226 ASP cc_start: 0.7896 (m-30) cc_final: 0.7644 (m-30) REVERT: k 232 GLN cc_start: 0.8149 (mt0) cc_final: 0.7504 (mm110) REVERT: l 25 ILE cc_start: 0.8662 (mm) cc_final: 0.8418 (mm) REVERT: l 38 SER cc_start: 0.9559 (m) cc_final: 0.9153 (t) REVERT: l 42 THR cc_start: 0.8852 (p) cc_final: 0.8551 (t) REVERT: l 43 ARG cc_start: 0.8485 (ptt180) cc_final: 0.8282 (ptt180) REVERT: l 64 THR cc_start: 0.8685 (t) cc_final: 0.6992 (t) REVERT: m 66 THR cc_start: 0.8742 (m) cc_final: 0.8464 (p) REVERT: m 97 LYS cc_start: 0.8690 (pttp) cc_final: 0.8378 (ptmt) REVERT: m 105 ILE cc_start: 0.9069 (mm) cc_final: 0.8614 (tp) REVERT: m 165 TRP cc_start: 0.8301 (p-90) cc_final: 0.8078 (p-90) REVERT: m 169 THR cc_start: 0.9490 (p) cc_final: 0.9041 (t) REVERT: m 223 PHE cc_start: 0.7538 (m-80) cc_final: 0.7029 (m-10) REVERT: m 262 ARG cc_start: 0.9225 (ptm160) cc_final: 0.9009 (ptm160) REVERT: n 14 ARG cc_start: 0.3160 (tpm170) cc_final: 0.1494 (tpm170) REVERT: n 61 ASN cc_start: 0.8891 (m-40) cc_final: 0.8525 (m-40) REVERT: n 74 THR cc_start: 0.8123 (p) cc_final: 0.7890 (t) REVERT: n 132 MET cc_start: 0.8601 (mmm) cc_final: 0.8359 (mmm) REVERT: n 183 SER cc_start: 0.8940 (p) cc_final: 0.8475 (t) REVERT: n 198 ILE cc_start: 0.9321 (mt) cc_final: 0.8950 (tp) REVERT: n 199 ASN cc_start: 0.8794 (t0) cc_final: 0.8002 (t0) REVERT: n 214 ASN cc_start: 0.8861 (t0) cc_final: 0.8321 (m-40) REVERT: n 215 SER cc_start: 0.9288 (p) cc_final: 0.9036 (p) REVERT: n 219 ASP cc_start: 0.9035 (t0) cc_final: 0.8697 (t0) REVERT: n 226 ASN cc_start: 0.8151 (m110) cc_final: 0.7728 (m110) REVERT: n 257 CYS cc_start: 0.8640 (m) cc_final: 0.8418 (m) REVERT: o 10 SER cc_start: 0.9183 (m) cc_final: 0.8782 (t) REVERT: o 39 GLU cc_start: 0.8889 (tm-30) cc_final: 0.8559 (tm-30) REVERT: o 55 MET cc_start: 0.8101 (ttm) cc_final: 0.7703 (ttm) REVERT: o 70 ILE cc_start: 0.9397 (mt) cc_final: 0.8524 (mt) REVERT: o 95 SER cc_start: 0.8969 (p) cc_final: 0.8169 (t) REVERT: o 120 CYS cc_start: 0.8556 (m) cc_final: 0.8142 (m) REVERT: o 128 LYS cc_start: 0.8499 (mmpt) cc_final: 0.8157 (mmmt) REVERT: o 139 LYS cc_start: 0.8852 (tmmt) cc_final: 0.8493 (tttt) REVERT: o 154 ILE cc_start: 0.8375 (mm) cc_final: 0.7460 (pt) REVERT: o 185 GLU cc_start: 0.7586 (mm-30) cc_final: 0.7245 (mm-30) REVERT: o 216 CYS cc_start: 0.7758 (m) cc_final: 0.7010 (m) REVERT: o 218 ASP cc_start: 0.9057 (p0) cc_final: 0.8786 (p0) REVERT: o 223 LEU cc_start: 0.8652 (tp) cc_final: 0.8434 (tp) REVERT: p 24 THR cc_start: 0.9133 (p) cc_final: 0.8800 (t) REVERT: p 54 THR cc_start: 0.8734 (m) cc_final: 0.8227 (m) REVERT: p 55 GLU cc_start: 0.7937 (mp0) cc_final: 0.7592 (mp0) REVERT: q 89 ASN cc_start: 0.8959 (t0) cc_final: 0.8526 (t0) REVERT: q 112 GLN cc_start: 0.7809 (tt0) cc_final: 0.7359 (tt0) REVERT: q 118 GLU cc_start: 0.8372 (mt-10) cc_final: 0.8168 (mt-10) REVERT: q 148 GLN cc_start: 0.8618 (mm-40) cc_final: 0.8251 (mm110) REVERT: q 151 GLN cc_start: 0.8531 (tt0) cc_final: 0.8150 (tt0) REVERT: q 171 GLN cc_start: 0.8290 (mt0) cc_final: 0.7989 (mt0) REVERT: q 198 ASN cc_start: 0.9346 (m110) cc_final: 0.8918 (m-40) REVERT: q 202 HIS cc_start: 0.8546 (m90) cc_final: 0.8202 (m90) REVERT: q 218 ASP cc_start: 0.7506 (t0) cc_final: 0.7103 (t70) REVERT: r 20 ASN cc_start: 0.9048 (p0) cc_final: 0.8836 (p0) REVERT: r 185 VAL cc_start: 0.9387 (t) cc_final: 0.8935 (m) REVERT: r 196 GLN cc_start: 0.9002 (mt0) cc_final: 0.8719 (mm-40) REVERT: r 199 ASN cc_start: 0.8945 (t0) cc_final: 0.8665 (t0) REVERT: s 18 ASP cc_start: 0.7147 (t0) cc_final: 0.6786 (t0) REVERT: s 34 ILE cc_start: 0.9128 (pt) cc_final: 0.8614 (pt) REVERT: s 159 LEU cc_start: 0.8806 (mm) cc_final: 0.8482 (mt) REVERT: s 209 MET cc_start: 0.8142 (ttm) cc_final: 0.7724 (mtp) REVERT: s 226 ASP cc_start: 0.7650 (m-30) cc_final: 0.7371 (m-30) REVERT: t 13 HIS cc_start: 0.8931 (t70) cc_final: 0.8708 (t70) outliers start: 3 outliers final: 1 residues processed: 1381 average time/residue: 0.4413 time to fit residues: 989.8395 Evaluate side-chains 1169 residues out of total 3659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1168 time to evaluate : 3.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 256 optimal weight: 5.9990 chunk 165 optimal weight: 8.9990 chunk 247 optimal weight: 7.9990 chunk 124 optimal weight: 20.0000 chunk 81 optimal weight: 9.9990 chunk 80 optimal weight: 5.9990 chunk 263 optimal weight: 9.9990 chunk 282 optimal weight: 5.9990 chunk 204 optimal weight: 5.9990 chunk 38 optimal weight: 20.0000 chunk 325 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 23 GLN ** a 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 271 HIS ** c 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 4 GLN ** d 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 49 GLN ** e 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 43 ASN ** g 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 152 HIS ** h 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 34 GLN ** i 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 195 HIS ** k 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 32 ASN ** m 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 27 ASN ** o 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 49 GLN ** q 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 224 HIS r 265 ASN ** s 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 108 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.5518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 34734 Z= 0.364 Angle : 0.682 9.040 47379 Z= 0.347 Chirality : 0.046 0.279 5322 Planarity : 0.005 0.084 6150 Dihedral : 5.802 59.118 4820 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 19.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.11 % Allowed : 1.31 % Favored : 98.58 % Cbeta Deviations : 0.00 % 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: -0.76 (0.13), residues: 4158 helix: -2.06 (0.23), residues: 385 sheet: 0.18 (0.15), residues: 1063 loop : -0.52 (0.12), residues: 2710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP b 227 HIS 0.008 0.001 HIS g 96 PHE 0.028 0.002 PHE a 120 TYR 0.023 0.002 TYR n 193 ARG 0.012 0.001 ARG s 177 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1339 residues out of total 3659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1335 time to evaluate : 3.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN b 272 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASN l 69 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 120 PHE cc_start: 0.8434 (m-10) cc_final: 0.8202 (m-10) REVERT: a 127 LEU cc_start: 0.9215 (tp) cc_final: 0.8509 (tp) REVERT: a 150 TYR cc_start: 0.8999 (m-80) cc_final: 0.8677 (m-10) REVERT: a 264 TRP cc_start: 0.9373 (m-90) cc_final: 0.8855 (m-90) REVERT: b 145 TYR cc_start: 0.8639 (t80) cc_final: 0.8422 (t80) REVERT: b 214 ASN cc_start: 0.8986 (t0) cc_final: 0.8623 (t0) REVERT: b 216 LEU cc_start: 0.8873 (mt) cc_final: 0.8560 (mt) REVERT: b 249 ILE cc_start: 0.9193 (mt) cc_final: 0.8921 (mm) REVERT: b 260 PHE cc_start: 0.8708 (m-10) cc_final: 0.8449 (m-10) REVERT: c 123 MET cc_start: 0.9018 (tpp) cc_final: 0.8809 (tpp) REVERT: c 139 LYS cc_start: 0.9044 (ptmm) cc_final: 0.8750 (ptpp) REVERT: c 163 CYS cc_start: 0.7697 (p) cc_final: 0.7232 (p) REVERT: e 54 ASP cc_start: 0.8732 (m-30) cc_final: 0.8387 (m-30) REVERT: e 57 GLU cc_start: 0.5777 (mp0) cc_final: 0.5155 (mp0) REVERT: e 69 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8021 (tt0) REVERT: f 15 GLN cc_start: 0.7508 (tt0) cc_final: 0.6987 (pt0) REVERT: f 55 GLU cc_start: 0.8672 (pp20) cc_final: 0.8290 (pp20) REVERT: f 96 MET cc_start: 0.8780 (ptm) cc_final: 0.8316 (tmm) REVERT: f 126 LEU cc_start: 0.9112 (mt) cc_final: 0.8856 (mt) REVERT: f 127 ILE cc_start: 0.9290 (mp) cc_final: 0.8998 (mt) REVERT: f 199 ASN cc_start: 0.9023 (t0) cc_final: 0.8769 (t0) REVERT: g 12 GLN cc_start: 0.8705 (pp30) cc_final: 0.7948 (pp30) REVERT: g 112 SER cc_start: 0.9053 (m) cc_final: 0.8488 (p) REVERT: g 114 ARG cc_start: 0.9058 (ttp-110) cc_final: 0.8490 (ttm170) REVERT: g 120 CYS cc_start: 0.8997 (m) cc_final: 0.8668 (m) REVERT: g 133 TYR cc_start: 0.9235 (t80) cc_final: 0.8876 (t80) REVERT: g 155 TRP cc_start: 0.9244 (t60) cc_final: 0.8616 (t60) REVERT: g 163 CYS cc_start: 0.8796 (p) cc_final: 0.8054 (p) REVERT: g 169 TRP cc_start: 0.9009 (t-100) cc_final: 0.8012 (t-100) REVERT: g 216 CYS cc_start: 0.8628 (m) cc_final: 0.8405 (m) REVERT: g 225 ARG cc_start: 0.8602 (ptt90) cc_final: 0.8211 (ptt-90) REVERT: h 8 GLN cc_start: 0.7771 (mt0) cc_final: 0.7311 (mt0) REVERT: h 27 TYR cc_start: 0.8846 (p90) cc_final: 0.8506 (p90) REVERT: i 35 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7670 (tt0) REVERT: i 151 GLN cc_start: 0.9404 (tt0) cc_final: 0.8986 (tt0) REVERT: i 166 ASP cc_start: 0.8487 (p0) cc_final: 0.7663 (p0) REVERT: i 169 THR cc_start: 0.9061 (p) cc_final: 0.8744 (t) REVERT: i 262 ARG cc_start: 0.9042 (ttp80) cc_final: 0.8281 (ttm170) REVERT: i 264 TRP cc_start: 0.9144 (m-90) cc_final: 0.8533 (m-10) REVERT: j 60 SER cc_start: 0.8939 (m) cc_final: 0.8520 (p) REVERT: j 84 ASP cc_start: 0.7982 (t70) cc_final: 0.7621 (t0) REVERT: j 132 MET cc_start: 0.8320 (mtt) cc_final: 0.7877 (mmt) REVERT: k 2 LEU cc_start: 0.9330 (tp) cc_final: 0.9110 (tp) REVERT: k 29 ASP cc_start: 0.9053 (t0) cc_final: 0.8743 (t0) REVERT: k 36 ILE cc_start: 0.9214 (mt) cc_final: 0.8341 (mt) REVERT: k 98 MET cc_start: 0.9040 (tpp) cc_final: 0.8806 (ttp) REVERT: k 112 SER cc_start: 0.8784 (m) cc_final: 0.8228 (p) REVERT: k 119 PHE cc_start: 0.8488 (t80) cc_final: 0.8172 (t80) REVERT: k 169 TRP cc_start: 0.8218 (t-100) cc_final: 0.7832 (t-100) REVERT: k 188 PHE cc_start: 0.8908 (m-80) cc_final: 0.8639 (m-80) REVERT: k 216 CYS cc_start: 0.8387 (m) cc_final: 0.7670 (m) REVERT: k 218 ASP cc_start: 0.8848 (p0) cc_final: 0.8602 (p0) REVERT: l 38 SER cc_start: 0.9535 (m) cc_final: 0.9155 (t) REVERT: l 42 THR cc_start: 0.8895 (p) cc_final: 0.8572 (t) REVERT: l 43 ARG cc_start: 0.8603 (ptt180) cc_final: 0.8402 (ptt180) REVERT: m 66 THR cc_start: 0.8779 (m) cc_final: 0.8497 (p) REVERT: m 97 LYS cc_start: 0.8762 (pttp) cc_final: 0.8377 (ptmt) REVERT: m 105 ILE cc_start: 0.9124 (mm) cc_final: 0.8681 (tp) REVERT: m 127 LEU cc_start: 0.9005 (tp) cc_final: 0.8113 (tp) REVERT: m 204 TYR cc_start: 0.8418 (t80) cc_final: 0.8117 (t80) REVERT: m 229 ILE cc_start: 0.8487 (pt) cc_final: 0.8276 (pt) REVERT: n 60 SER cc_start: 0.9062 (m) cc_final: 0.8847 (m) REVERT: n 61 ASN cc_start: 0.8889 (m-40) cc_final: 0.8556 (m-40) REVERT: n 74 THR cc_start: 0.8158 (p) cc_final: 0.7933 (t) REVERT: n 87 LYS cc_start: 0.8315 (pttt) cc_final: 0.7965 (pttt) REVERT: n 132 MET cc_start: 0.8661 (mmm) cc_final: 0.8377 (tpp) REVERT: n 149 ASN cc_start: 0.8871 (m-40) cc_final: 0.8481 (m-40) REVERT: n 183 SER cc_start: 0.8913 (p) cc_final: 0.8453 (t) REVERT: n 199 ASN cc_start: 0.8753 (t0) cc_final: 0.8007 (t0) REVERT: n 214 ASN cc_start: 0.8936 (t0) cc_final: 0.8616 (t0) REVERT: n 221 MET cc_start: 0.7209 (mtm) cc_final: 0.6741 (mtm) REVERT: n 257 CYS cc_start: 0.8676 (m) cc_final: 0.8412 (m) REVERT: o 10 SER cc_start: 0.9144 (m) cc_final: 0.8914 (p) REVERT: o 17 ASP cc_start: 0.8571 (t0) cc_final: 0.7030 (t0) REVERT: o 39 GLU cc_start: 0.8928 (tm-30) cc_final: 0.8534 (tm-30) REVERT: o 55 MET cc_start: 0.8095 (ttm) cc_final: 0.7686 (ttm) REVERT: o 70 ILE cc_start: 0.9402 (mt) cc_final: 0.8506 (mt) REVERT: o 120 CYS cc_start: 0.8617 (m) cc_final: 0.8224 (m) REVERT: o 128 LYS cc_start: 0.8560 (mmpt) cc_final: 0.8260 (mmmt) REVERT: o 139 LYS cc_start: 0.8864 (tmmt) cc_final: 0.8464 (tttt) REVERT: o 154 ILE cc_start: 0.8613 (mm) cc_final: 0.7723 (pt) REVERT: o 185 GLU cc_start: 0.7629 (mm-30) cc_final: 0.7273 (mm-30) REVERT: o 216 CYS cc_start: 0.7879 (m) cc_final: 0.7205 (m) REVERT: o 218 ASP cc_start: 0.9073 (p0) cc_final: 0.8762 (p0) REVERT: p 24 THR cc_start: 0.9086 (p) cc_final: 0.8791 (t) REVERT: p 54 THR cc_start: 0.8818 (m) cc_final: 0.8253 (m) REVERT: p 55 GLU cc_start: 0.7977 (mp0) cc_final: 0.7619 (mp0) REVERT: q 89 ASN cc_start: 0.8893 (t0) cc_final: 0.8598 (t0) REVERT: q 112 GLN cc_start: 0.7743 (tt0) cc_final: 0.7279 (tt0) REVERT: q 127 LEU cc_start: 0.9156 (tp) cc_final: 0.8919 (tp) REVERT: q 148 GLN cc_start: 0.8603 (mm-40) cc_final: 0.8321 (mm110) REVERT: q 151 GLN cc_start: 0.8555 (tt0) cc_final: 0.8166 (tt0) REVERT: q 165 TRP cc_start: 0.8832 (p-90) cc_final: 0.8608 (p-90) REVERT: q 171 GLN cc_start: 0.8321 (mt0) cc_final: 0.7976 (mt0) REVERT: q 198 ASN cc_start: 0.9369 (m110) cc_final: 0.8942 (m-40) REVERT: q 202 HIS cc_start: 0.8461 (m90) cc_final: 0.8133 (m90) REVERT: r 55 GLU cc_start: 0.8751 (mm-30) cc_final: 0.7909 (pm20) REVERT: r 196 GLN cc_start: 0.8990 (mt0) cc_final: 0.8690 (mm-40) REVERT: r 199 ASN cc_start: 0.8885 (t0) cc_final: 0.8593 (t0) REVERT: s 18 ASP cc_start: 0.7236 (t0) cc_final: 0.6865 (t0) REVERT: s 34 ILE cc_start: 0.9155 (pt) cc_final: 0.8614 (pt) REVERT: s 209 MET cc_start: 0.8196 (ttm) cc_final: 0.7674 (mtp) REVERT: s 223 LEU cc_start: 0.8900 (tt) cc_final: 0.8552 (tt) REVERT: s 224 LEU cc_start: 0.9220 (mt) cc_final: 0.8932 (mt) REVERT: s 226 ASP cc_start: 0.7676 (m-30) cc_final: 0.7339 (m-30) outliers start: 4 outliers final: 1 residues processed: 1336 average time/residue: 0.4385 time to fit residues: 952.5992 Evaluate side-chains 1150 residues out of total 3659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1149 time to evaluate : 3.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 377 optimal weight: 20.0000 chunk 397 optimal weight: 0.9990 chunk 362 optimal weight: 30.0000 chunk 386 optimal weight: 20.0000 chunk 396 optimal weight: 10.0000 chunk 232 optimal weight: 0.0970 chunk 168 optimal weight: 0.9980 chunk 303 optimal weight: 7.9990 chunk 118 optimal weight: 10.0000 chunk 349 optimal weight: 0.6980 chunk 365 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 23 GLN ** a 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 119 GLN c 11 ASN c 63 ASN d 4 GLN ** d 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 49 GLN ** e 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 43 ASN f 94 GLN ** g 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 11 ASN ** h 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 112 GLN j 149 ASN ** k 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 49 GLN ** m 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 31 ASN q 49 GLN ** q 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 108 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.5667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 34734 Z= 0.184 Angle : 0.627 9.818 47379 Z= 0.318 Chirality : 0.045 0.267 5322 Planarity : 0.005 0.061 6150 Dihedral : 5.548 57.608 4820 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.08 % Allowed : 0.52 % Favored : 99.40 % Cbeta Deviations : 0.00 % 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: -0.65 (0.13), residues: 4158 helix: -2.22 (0.22), residues: 397 sheet: 0.32 (0.15), residues: 1044 loop : -0.42 (0.12), residues: 2717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP b 80 HIS 0.011 0.001 HIS f 195 PHE 0.028 0.002 PHE i 120 TYR 0.031 0.002 TYR i 180 ARG 0.012 0.001 ARG f 103 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1413 residues out of total 3659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1410 time to evaluate : 3.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN b 272 " (corrupted residue). Skipping it. 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 TARDY: cannot create tardy model for: "ASN l 69 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "PHE m 298 " (corrupted residue). Skipping it. 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 118 GLU cc_start: 0.8646 (mt-10) cc_final: 0.8272 (mt-10) REVERT: a 127 LEU cc_start: 0.9175 (tp) cc_final: 0.8476 (tp) REVERT: a 150 TYR cc_start: 0.8916 (m-80) cc_final: 0.8639 (m-10) REVERT: a 264 TRP cc_start: 0.9323 (m-90) cc_final: 0.8793 (m-90) REVERT: a 286 ILE cc_start: 0.9081 (pt) cc_final: 0.8729 (pt) REVERT: b 71 TRP cc_start: 0.8575 (t60) cc_final: 0.8303 (t60) REVERT: b 72 LYS cc_start: 0.8554 (mmpt) cc_final: 0.8076 (mmpt) REVERT: b 96 MET cc_start: 0.8694 (tpp) cc_final: 0.8374 (tpt) REVERT: b 99 HIS cc_start: 0.8265 (m170) cc_final: 0.8026 (m170) REVERT: b 142 TYR cc_start: 0.7115 (t80) cc_final: 0.6805 (t80) REVERT: b 214 ASN cc_start: 0.8948 (t0) cc_final: 0.8659 (t0) REVERT: b 216 LEU cc_start: 0.8827 (mt) cc_final: 0.8376 (mt) REVERT: b 249 ILE cc_start: 0.9132 (mt) cc_final: 0.8883 (mm) REVERT: b 266 ILE cc_start: 0.8569 (tp) cc_final: 0.8185 (tp) REVERT: c 163 CYS cc_start: 0.7423 (p) cc_final: 0.7129 (p) REVERT: c 171 SER cc_start: 0.9018 (t) cc_final: 0.8560 (p) REVERT: e 57 GLU cc_start: 0.5701 (mp0) cc_final: 0.5115 (mp0) REVERT: e 69 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8237 (tt0) REVERT: e 113 LEU cc_start: 0.9097 (tp) cc_final: 0.8748 (tp) REVERT: e 115 ARG cc_start: 0.7995 (ttt-90) cc_final: 0.7217 (ttt90) REVERT: f 15 GLN cc_start: 0.7471 (tt0) cc_final: 0.7004 (pt0) REVERT: f 55 GLU cc_start: 0.8587 (pp20) cc_final: 0.8197 (pp20) REVERT: f 57 ASP cc_start: 0.8760 (t70) cc_final: 0.8536 (t70) REVERT: f 96 MET cc_start: 0.8638 (ptm) cc_final: 0.8311 (tmm) REVERT: f 126 LEU cc_start: 0.9166 (mt) cc_final: 0.8924 (mt) REVERT: f 127 ILE cc_start: 0.9270 (mp) cc_final: 0.9014 (mt) REVERT: f 149 ASN cc_start: 0.9037 (m110) cc_final: 0.8766 (m-40) REVERT: f 199 ASN cc_start: 0.8920 (t0) cc_final: 0.8646 (t0) REVERT: f 249 ILE cc_start: 0.9196 (mm) cc_final: 0.8794 (mm) REVERT: g 12 GLN cc_start: 0.8792 (pp30) cc_final: 0.8167 (pp30) REVERT: g 27 ASN cc_start: 0.8398 (m-40) cc_final: 0.8085 (m-40) REVERT: g 55 MET cc_start: 0.8080 (tpt) cc_final: 0.7763 (tpt) REVERT: g 95 SER cc_start: 0.8895 (p) cc_final: 0.8074 (m) REVERT: g 101 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7507 (mm-30) REVERT: g 112 SER cc_start: 0.8993 (m) cc_final: 0.8391 (p) REVERT: g 114 ARG cc_start: 0.8793 (ttp-110) cc_final: 0.8245 (ttm170) REVERT: g 120 CYS cc_start: 0.8802 (m) cc_final: 0.8541 (m) REVERT: g 133 TYR cc_start: 0.9137 (t80) cc_final: 0.8817 (t80) REVERT: g 155 TRP cc_start: 0.9144 (t60) cc_final: 0.8659 (t60) REVERT: g 163 CYS cc_start: 0.8684 (p) cc_final: 0.7984 (p) REVERT: g 169 TRP cc_start: 0.8857 (t-100) cc_final: 0.7797 (t-100) REVERT: g 205 THR cc_start: 0.9285 (p) cc_final: 0.8877 (t) REVERT: g 216 CYS cc_start: 0.8556 (m) cc_final: 0.8350 (m) REVERT: g 225 ARG cc_start: 0.8555 (ptt90) cc_final: 0.8276 (ptt-90) REVERT: g 226 ASP cc_start: 0.7453 (m-30) cc_final: 0.7239 (m-30) REVERT: h 4 GLN cc_start: 0.8567 (mt0) cc_final: 0.8337 (mt0) REVERT: h 27 TYR cc_start: 0.8782 (p90) cc_final: 0.8334 (p90) REVERT: i 35 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7418 (tt0) REVERT: i 151 GLN cc_start: 0.9290 (tt0) cc_final: 0.8661 (tt0) REVERT: i 166 ASP cc_start: 0.8391 (p0) cc_final: 0.7570 (p0) REVERT: i 169 THR cc_start: 0.8983 (p) cc_final: 0.8684 (t) REVERT: j 55 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8405 (mm-30) REVERT: j 60 SER cc_start: 0.8928 (m) cc_final: 0.8483 (p) REVERT: j 84 ASP cc_start: 0.7796 (t70) cc_final: 0.7399 (t0) REVERT: j 122 LEU cc_start: 0.8971 (mt) cc_final: 0.8738 (mt) REVERT: j 129 GLU cc_start: 0.9117 (mm-30) cc_final: 0.8814 (mm-30) REVERT: j 132 MET cc_start: 0.8395 (mtt) cc_final: 0.8183 (tpp) REVERT: j 249 ILE cc_start: 0.8777 (mm) cc_final: 0.8527 (mm) REVERT: j 259 GLU cc_start: 0.8229 (tt0) cc_final: 0.8022 (tt0) REVERT: k 2 LEU cc_start: 0.9330 (tp) cc_final: 0.9125 (tp) REVERT: k 29 ASP cc_start: 0.8879 (t0) cc_final: 0.8460 (t0) REVERT: k 56 ASN cc_start: 0.8791 (t0) cc_final: 0.8479 (t0) REVERT: k 107 THR cc_start: 0.9296 (p) cc_final: 0.9079 (p) REVERT: k 112 SER cc_start: 0.8697 (m) cc_final: 0.8160 (p) REVERT: k 119 PHE cc_start: 0.8435 (t80) cc_final: 0.8074 (t80) REVERT: k 124 MET cc_start: 0.7529 (mmm) cc_final: 0.7282 (mtt) REVERT: k 169 TRP cc_start: 0.8062 (t-100) cc_final: 0.7652 (t-100) REVERT: k 188 PHE cc_start: 0.8866 (m-80) cc_final: 0.8494 (m-80) REVERT: k 216 CYS cc_start: 0.8439 (m) cc_final: 0.7651 (m) REVERT: k 218 ASP cc_start: 0.8865 (p0) cc_final: 0.8583 (p0) REVERT: k 219 PHE cc_start: 0.7707 (t80) cc_final: 0.7360 (t80) REVERT: k 226 ASP cc_start: 0.7836 (m-30) cc_final: 0.7532 (m-30) REVERT: k 232 GLN cc_start: 0.7974 (mt0) cc_final: 0.7766 (mm110) REVERT: l 25 ILE cc_start: 0.8522 (mm) cc_final: 0.8298 (mm) REVERT: l 38 SER cc_start: 0.9554 (m) cc_final: 0.9134 (t) REVERT: l 42 THR cc_start: 0.8847 (p) cc_final: 0.8479 (t) REVERT: l 64 THR cc_start: 0.8747 (t) cc_final: 0.7269 (t) REVERT: m 66 THR cc_start: 0.8678 (m) cc_final: 0.8468 (p) REVERT: m 97 LYS cc_start: 0.8720 (pttp) cc_final: 0.8440 (ptmt) REVERT: m 105 ILE cc_start: 0.8966 (mm) cc_final: 0.8500 (tp) REVERT: m 127 LEU cc_start: 0.8837 (tp) cc_final: 0.8126 (tp) REVERT: m 171 GLN cc_start: 0.8532 (mt0) cc_final: 0.7688 (mt0) REVERT: m 223 PHE cc_start: 0.7218 (m-80) cc_final: 0.6792 (m-10) REVERT: m 281 MET cc_start: 0.8123 (mtt) cc_final: 0.7894 (mtt) REVERT: n 14 ARG cc_start: 0.3072 (tpm170) cc_final: 0.1449 (tpm170) REVERT: n 61 ASN cc_start: 0.8786 (m-40) cc_final: 0.8397 (m-40) REVERT: n 72 LYS cc_start: 0.7813 (tttm) cc_final: 0.7608 (mtpt) REVERT: n 74 THR cc_start: 0.8070 (p) cc_final: 0.7859 (t) REVERT: n 161 TYR cc_start: 0.7987 (t80) cc_final: 0.7778 (t80) REVERT: n 183 SER cc_start: 0.8720 (p) cc_final: 0.8227 (t) REVERT: n 199 ASN cc_start: 0.8624 (t0) cc_final: 0.8028 (t0) REVERT: n 214 ASN cc_start: 0.8858 (t0) cc_final: 0.8515 (t0) REVERT: n 219 ASP cc_start: 0.8949 (t0) cc_final: 0.8691 (t0) REVERT: n 221 MET cc_start: 0.7192 (mtm) cc_final: 0.6834 (mtm) REVERT: n 257 CYS cc_start: 0.8595 (m) cc_final: 0.8236 (m) REVERT: o 10 SER cc_start: 0.9147 (m) cc_final: 0.8711 (t) REVERT: o 39 GLU cc_start: 0.8876 (tm-30) cc_final: 0.8578 (tm-30) REVERT: o 41 LYS cc_start: 0.8511 (mmtm) cc_final: 0.8216 (mmtm) REVERT: o 55 MET cc_start: 0.8026 (ttm) cc_final: 0.7685 (ttm) REVERT: o 70 ILE cc_start: 0.9407 (mt) cc_final: 0.8556 (mt) REVERT: o 95 SER cc_start: 0.8900 (p) cc_final: 0.7932 (t) REVERT: o 120 CYS cc_start: 0.8378 (m) cc_final: 0.7980 (m) REVERT: o 139 LYS cc_start: 0.8770 (tmmt) cc_final: 0.8342 (tttt) REVERT: o 148 MET cc_start: 0.6793 (ttt) cc_final: 0.6576 (ttt) REVERT: o 154 ILE cc_start: 0.7879 (mm) cc_final: 0.7086 (pt) REVERT: o 185 GLU cc_start: 0.7321 (mm-30) cc_final: 0.7098 (mm-30) REVERT: o 198 VAL cc_start: 0.8178 (t) cc_final: 0.7960 (p) REVERT: o 216 CYS cc_start: 0.7951 (m) cc_final: 0.7342 (m) REVERT: o 218 ASP cc_start: 0.9002 (p0) cc_final: 0.8754 (p0) REVERT: o 222 ARG cc_start: 0.8613 (mmm-85) cc_final: 0.8308 (mtp180) REVERT: o 224 LEU cc_start: 0.8924 (tp) cc_final: 0.8682 (tp) REVERT: p 24 THR cc_start: 0.9068 (p) cc_final: 0.8780 (t) REVERT: q 23 GLN cc_start: 0.8262 (tp40) cc_final: 0.8040 (tp-100) REVERT: q 89 ASN cc_start: 0.8790 (t0) cc_final: 0.7838 (t0) REVERT: q 90 SER cc_start: 0.8682 (t) cc_final: 0.8383 (t) REVERT: q 97 LYS cc_start: 0.9297 (mptt) cc_final: 0.8967 (mptt) REVERT: q 198 ASN cc_start: 0.9259 (m110) cc_final: 0.8817 (m-40) REVERT: r 55 GLU cc_start: 0.8606 (mm-30) cc_final: 0.7629 (pm20) REVERT: r 178 ASP cc_start: 0.9297 (p0) cc_final: 0.9086 (p0) REVERT: r 185 VAL cc_start: 0.9398 (t) cc_final: 0.8911 (m) REVERT: r 199 ASN cc_start: 0.8809 (t0) cc_final: 0.8545 (t0) REVERT: s 18 ASP cc_start: 0.7037 (t0) cc_final: 0.6524 (t0) REVERT: s 19 PHE cc_start: 0.8413 (m-80) cc_final: 0.8049 (m-80) REVERT: s 34 ILE cc_start: 0.9118 (pt) cc_final: 0.8643 (pt) REVERT: s 44 MET cc_start: 0.8694 (mmm) cc_final: 0.8470 (mmm) REVERT: s 139 LYS cc_start: 0.8409 (tptm) cc_final: 0.7810 (ttpt) REVERT: s 155 TRP cc_start: 0.8389 (t60) cc_final: 0.8025 (t60) REVERT: s 159 LEU cc_start: 0.8716 (mm) cc_final: 0.8367 (mt) REVERT: s 209 MET cc_start: 0.8070 (ttm) cc_final: 0.7759 (mtp) REVERT: s 223 LEU cc_start: 0.8640 (tt) cc_final: 0.8244 (tt) REVERT: s 226 ASP cc_start: 0.7406 (m-30) cc_final: 0.7019 (m-30) REVERT: t 13 HIS cc_start: 0.8799 (t70) cc_final: 0.8584 (t70) outliers start: 3 outliers final: 2 residues processed: 1412 average time/residue: 0.4378 time to fit residues: 1003.8208 Evaluate side-chains 1195 residues out of total 3659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1193 time to evaluate : 3.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 384 optimal weight: 9.9990 chunk 253 optimal weight: 4.9990 chunk 408 optimal weight: 10.0000 chunk 249 optimal weight: 20.0000 chunk 193 optimal weight: 10.0000 chunk 283 optimal weight: 9.9990 chunk 428 optimal weight: 20.0000 chunk 394 optimal weight: 10.0000 chunk 341 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 263 optimal weight: 20.0000 overall best weight: 8.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 23 GLN ** a 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 111 GLN b 226 ASN b 271 HIS d 4 GLN ** d 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 112 GLN i 171 GLN j 195 HIS k 56 ASN k 108 HIS ** l 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 32 ASN ** m 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 4 GLN ** p 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 108 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.5816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.151 34734 Z= 0.483 Angle : 0.789 12.834 47379 Z= 0.401 Chirality : 0.049 0.314 5322 Planarity : 0.006 0.076 6150 Dihedral : 6.190 58.224 4820 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 21.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.03 % Allowed : 0.44 % Favored : 99.54 % 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: -0.97 (0.13), residues: 4158 helix: -2.23 (0.22), residues: 384 sheet: -0.04 (0.15), residues: 1048 loop : -0.63 (0.12), residues: 2726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.003 TRP b 227 HIS 0.011 0.002 HIS s 108 PHE 0.029 0.003 PHE k 19 TYR 0.047 0.003 TYR a 255 ARG 0.011 0.001 ARG c 222 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1307 residues out of total 3659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1306 time to evaluate : 4.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN b 272 " (corrupted residue). Skipping it. 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 TARDY: cannot create tardy model for: "ASN l 69 " (corrupted residue). Skipping it. 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 85 LEU cc_start: 0.9114 (mt) cc_final: 0.8896 (mt) REVERT: a 120 PHE cc_start: 0.8568 (m-10) cc_final: 0.8302 (m-10) REVERT: a 264 TRP cc_start: 0.9347 (m-90) cc_final: 0.8792 (m-90) REVERT: b 95 ASN cc_start: 0.7980 (m-40) cc_final: 0.7731 (m-40) REVERT: b 99 HIS cc_start: 0.8577 (m170) cc_final: 0.8095 (m170) REVERT: b 142 TYR cc_start: 0.7161 (t80) cc_final: 0.6852 (t80) REVERT: b 214 ASN cc_start: 0.8979 (t0) cc_final: 0.8662 (t0) REVERT: b 216 LEU cc_start: 0.8904 (mt) cc_final: 0.8493 (mt) REVERT: b 249 ILE cc_start: 0.9212 (mt) cc_final: 0.8984 (mm) REVERT: b 260 PHE cc_start: 0.8787 (m-10) cc_final: 0.8490 (m-10) REVERT: b 266 ILE cc_start: 0.8676 (tp) cc_final: 0.8219 (tp) REVERT: c 2 LEU cc_start: 0.9410 (tp) cc_final: 0.9188 (tp) REVERT: c 17 ASP cc_start: 0.8486 (t70) cc_final: 0.8183 (t0) REVERT: c 55 MET cc_start: 0.9293 (ppp) cc_final: 0.8988 (ppp) REVERT: c 155 TRP cc_start: 0.9035 (t60) cc_final: 0.8794 (t60) REVERT: c 163 CYS cc_start: 0.7737 (p) cc_final: 0.6948 (p) REVERT: d 52 LYS cc_start: 0.9334 (mtmt) cc_final: 0.9129 (mttp) REVERT: e 57 GLU cc_start: 0.5604 (mp0) cc_final: 0.4948 (mp0) REVERT: e 69 GLU cc_start: 0.8480 (mt-10) cc_final: 0.8083 (tt0) REVERT: e 115 ARG cc_start: 0.8277 (ttt-90) cc_final: 0.7792 (ttt-90) REVERT: f 55 GLU cc_start: 0.8714 (pp20) cc_final: 0.8278 (pp20) REVERT: f 96 MET cc_start: 0.8843 (ptm) cc_final: 0.8412 (tmm) REVERT: f 100 TYR cc_start: 0.8440 (t80) cc_final: 0.8196 (t80) REVERT: f 149 ASN cc_start: 0.8961 (m110) cc_final: 0.8720 (m110) REVERT: f 199 ASN cc_start: 0.9068 (t0) cc_final: 0.8817 (t0) REVERT: g 2 LEU cc_start: 0.9562 (tp) cc_final: 0.9341 (tp) REVERT: g 12 GLN cc_start: 0.8728 (pp30) cc_final: 0.8147 (pp30) REVERT: g 27 ASN cc_start: 0.8685 (m-40) cc_final: 0.8350 (m-40) REVERT: g 112 SER cc_start: 0.9045 (m) cc_final: 0.8390 (p) REVERT: g 114 ARG cc_start: 0.8990 (ttp-110) cc_final: 0.8472 (ttm170) REVERT: g 120 CYS cc_start: 0.9055 (m) cc_final: 0.8718 (m) REVERT: g 133 TYR cc_start: 0.9229 (t80) cc_final: 0.8337 (t80) REVERT: g 163 CYS cc_start: 0.8767 (p) cc_final: 0.8544 (p) REVERT: g 169 TRP cc_start: 0.9005 (t-100) cc_final: 0.8021 (t-100) REVERT: g 216 CYS cc_start: 0.8581 (m) cc_final: 0.8349 (m) REVERT: g 225 ARG cc_start: 0.8688 (ptt90) cc_final: 0.8321 (ptt-90) REVERT: g 226 ASP cc_start: 0.7827 (m-30) cc_final: 0.7366 (m-30) REVERT: h 8 GLN cc_start: 0.7844 (mt0) cc_final: 0.7475 (mt0) REVERT: h 27 TYR cc_start: 0.8899 (p90) cc_final: 0.8585 (p90) REVERT: i 35 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7577 (tt0) REVERT: i 166 ASP cc_start: 0.8367 (p0) cc_final: 0.7524 (p0) REVERT: i 169 THR cc_start: 0.9135 (p) cc_final: 0.8751 (t) REVERT: i 264 TRP cc_start: 0.9168 (m-90) cc_final: 0.8820 (m-10) REVERT: j 35 TYR cc_start: 0.8966 (m-80) cc_final: 0.8693 (m-10) REVERT: j 60 SER cc_start: 0.8959 (m) cc_final: 0.8641 (p) REVERT: j 84 ASP cc_start: 0.8047 (t70) cc_final: 0.7632 (t0) REVERT: j 132 MET cc_start: 0.8426 (mtt) cc_final: 0.8205 (tpp) REVERT: j 213 VAL cc_start: 0.9311 (t) cc_final: 0.8981 (m) REVERT: j 259 GLU cc_start: 0.8313 (tt0) cc_final: 0.8113 (tt0) REVERT: k 2 LEU cc_start: 0.9302 (tp) cc_final: 0.9082 (tp) REVERT: k 29 ASP cc_start: 0.9066 (t0) cc_final: 0.8663 (t0) REVERT: k 36 ILE cc_start: 0.9231 (mt) cc_final: 0.8285 (mt) REVERT: k 112 SER cc_start: 0.8778 (m) cc_final: 0.8333 (p) REVERT: k 119 PHE cc_start: 0.8519 (t80) cc_final: 0.8207 (t80) REVERT: k 188 PHE cc_start: 0.8943 (m-80) cc_final: 0.8732 (m-80) REVERT: k 216 CYS cc_start: 0.8592 (m) cc_final: 0.7787 (m) REVERT: k 218 ASP cc_start: 0.8836 (p0) cc_final: 0.8471 (p0) REVERT: k 226 ASP cc_start: 0.8069 (m-30) cc_final: 0.7827 (m-30) REVERT: l 21 ASN cc_start: 0.8657 (p0) cc_final: 0.8359 (p0) REVERT: l 25 ILE cc_start: 0.8736 (mm) cc_final: 0.8501 (mm) REVERT: l 38 SER cc_start: 0.9547 (m) cc_final: 0.9149 (t) REVERT: l 42 THR cc_start: 0.8921 (p) cc_final: 0.8549 (t) REVERT: l 43 ARG cc_start: 0.8694 (ptt180) cc_final: 0.8436 (ptt180) REVERT: l 64 THR cc_start: 0.8886 (t) cc_final: 0.7212 (t) REVERT: m 34 GLN cc_start: 0.8602 (pm20) cc_final: 0.7534 (tm-30) REVERT: m 97 LYS cc_start: 0.8829 (pttp) cc_final: 0.8413 (ptmt) REVERT: m 105 ILE cc_start: 0.9136 (mm) cc_final: 0.8729 (tp) REVERT: m 110 THR cc_start: 0.8607 (p) cc_final: 0.8373 (p) REVERT: m 223 PHE cc_start: 0.7714 (m-80) cc_final: 0.7347 (m-80) REVERT: m 229 ILE cc_start: 0.8502 (pt) cc_final: 0.8251 (pt) REVERT: n 61 ASN cc_start: 0.8869 (m-40) cc_final: 0.8607 (m-40) REVERT: n 72 LYS cc_start: 0.7946 (tttm) cc_final: 0.7717 (mtpt) REVERT: n 74 THR cc_start: 0.8209 (p) cc_final: 0.7946 (t) REVERT: n 106 TYR cc_start: 0.8295 (m-80) cc_final: 0.8006 (m-80) REVERT: n 149 ASN cc_start: 0.8691 (m-40) cc_final: 0.8317 (m-40) REVERT: n 183 SER cc_start: 0.8694 (p) cc_final: 0.8197 (t) REVERT: n 199 ASN cc_start: 0.8759 (t0) cc_final: 0.8054 (t0) REVERT: n 214 ASN cc_start: 0.8950 (t0) cc_final: 0.8700 (t0) REVERT: n 216 LEU cc_start: 0.9323 (mt) cc_final: 0.9104 (mt) REVERT: n 221 MET cc_start: 0.7372 (mtm) cc_final: 0.6849 (mtm) REVERT: n 257 CYS cc_start: 0.8873 (m) cc_final: 0.8635 (m) REVERT: o 10 SER cc_start: 0.9130 (m) cc_final: 0.8865 (p) REVERT: o 17 ASP cc_start: 0.8738 (t0) cc_final: 0.7109 (t0) REVERT: o 39 GLU cc_start: 0.8990 (tm-30) cc_final: 0.8588 (tm-30) REVERT: o 55 MET cc_start: 0.8112 (ttm) cc_final: 0.7760 (ttm) REVERT: o 70 ILE cc_start: 0.9377 (mt) cc_final: 0.8394 (mt) REVERT: o 102 ILE cc_start: 0.9585 (mt) cc_final: 0.9381 (mt) REVERT: o 120 CYS cc_start: 0.8377 (m) cc_final: 0.8043 (m) REVERT: o 139 LYS cc_start: 0.8783 (tmmt) cc_final: 0.8335 (tttt) REVERT: o 148 MET cc_start: 0.6785 (ttt) cc_final: 0.6575 (ttt) REVERT: o 185 GLU cc_start: 0.7606 (mm-30) cc_final: 0.7236 (mm-30) REVERT: o 216 CYS cc_start: 0.8089 (m) cc_final: 0.7520 (m) REVERT: o 218 ASP cc_start: 0.9082 (p0) cc_final: 0.8681 (p0) REVERT: p 21 ASN cc_start: 0.7987 (m110) cc_final: 0.7751 (m110) REVERT: p 24 THR cc_start: 0.9146 (p) cc_final: 0.8715 (t) REVERT: q 89 ASN cc_start: 0.8809 (t0) cc_final: 0.8473 (t0) REVERT: q 118 GLU cc_start: 0.8504 (mt-10) cc_final: 0.8251 (mt-10) REVERT: q 154 TYR cc_start: 0.8479 (t80) cc_final: 0.8182 (t80) REVERT: q 189 MET cc_start: 0.7706 (ptm) cc_final: 0.7501 (ptm) REVERT: q 212 LEU cc_start: 0.8786 (pt) cc_final: 0.8500 (pt) REVERT: r 55 GLU cc_start: 0.8790 (mm-30) cc_final: 0.7902 (pm20) REVERT: r 106 TYR cc_start: 0.8592 (m-80) cc_final: 0.8347 (m-80) REVERT: r 170 GLU cc_start: 0.8583 (mm-30) cc_final: 0.8223 (tp30) REVERT: r 199 ASN cc_start: 0.8847 (t0) cc_final: 0.8585 (t0) REVERT: s 18 ASP cc_start: 0.7257 (t0) cc_final: 0.7054 (t0) REVERT: s 34 ILE cc_start: 0.9193 (pt) cc_final: 0.8812 (pt) REVERT: s 209 MET cc_start: 0.8202 (ttm) cc_final: 0.7806 (mtp) REVERT: s 218 ASP cc_start: 0.8857 (p0) cc_final: 0.8647 (p0) REVERT: s 223 LEU cc_start: 0.8872 (tt) cc_final: 0.8334 (tt) outliers start: 1 outliers final: 1 residues processed: 1307 average time/residue: 0.4477 time to fit residues: 947.8558 Evaluate side-chains 1093 residues out of total 3659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1092 time to evaluate : 3.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 209 optimal weight: 2.9990 chunk 270 optimal weight: 3.9990 chunk 363 optimal weight: 7.9990 chunk 104 optimal weight: 10.0000 chunk 314 optimal weight: 20.0000 chunk 50 optimal weight: 30.0000 chunk 94 optimal weight: 7.9990 chunk 341 optimal weight: 2.9990 chunk 142 optimal weight: 8.9990 chunk 350 optimal weight: 7.9990 chunk 43 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 23 GLN ** a 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 260 HIS b 111 GLN d 4 GLN ** d 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 49 GLN ** e 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 225 ASN ** g 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 112 GLN ** i 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 135 ASN j 195 HIS k 108 HIS ** l 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 27 ASN p 13 HIS p 31 ASN ** q 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.113057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.101820 restraints weight = 79604.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.104763 restraints weight = 39753.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.106737 restraints weight = 23348.577| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.5955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 34734 Z= 0.319 Angle : 0.693 10.950 47379 Z= 0.353 Chirality : 0.047 0.296 5322 Planarity : 0.005 0.078 6150 Dihedral : 6.059 56.374 4820 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 19.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.03 % Allowed : 0.33 % Favored : 99.64 % Cbeta Deviations : 0.00 % 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: -0.97 (0.13), residues: 4158 helix: -2.28 (0.22), residues: 387 sheet: -0.04 (0.15), residues: 1050 loop : -0.61 (0.12), residues: 2721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP b 227 HIS 0.010 0.001 HIS k 108 PHE 0.048 0.002 PHE r 130 TYR 0.053 0.003 TYR a 255 ARG 0.012 0.001 ARG s 114 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13790.30 seconds wall clock time: 244 minutes 52.12 seconds (14692.12 seconds total)