Starting phenix.real_space_refine on Wed Mar 20 22:04:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p1g_13158/03_2024/7p1g_13158_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p1g_13158/03_2024/7p1g_13158.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p1g_13158/03_2024/7p1g_13158_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p1g_13158/03_2024/7p1g_13158_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p1g_13158/03_2024/7p1g_13158_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p1g_13158/03_2024/7p1g_13158.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p1g_13158/03_2024/7p1g_13158.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p1g_13158/03_2024/7p1g_13158_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p1g_13158/03_2024/7p1g_13158_updated.pdb" } resolution = 3.2 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= 0.001 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 30 5.49 5 Mg 10 5.21 5 S 175 5.16 5 C 17855 2.51 5 N 5035 2.21 5 O 5475 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "M ARG 64": "NH1" <-> "NH2" Residue "M GLU 67": "OE1" <-> "OE2" Residue "M GLU 76": "OE1" <-> "OE2" Residue "M PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 102": "OD1" <-> "OD2" Residue "M ASP 110": "OD1" <-> "OD2" Residue "M ASP 112": "OD1" <-> "OD2" Residue "M ASP 136": "OD1" <-> "OD2" Residue "M GLU 146": "OE1" <-> "OE2" Residue "M PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 156": "OD1" <-> "OD2" Residue "M GLU 177": "OE1" <-> "OE2" Residue "M ASP 212": "OD1" <-> "OD2" Residue "M TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 214": "OD1" <-> "OD2" Residue "M PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 252": "OD1" <-> "OD2" Residue "M ARG 257": "NH1" <-> "NH2" Residue "M GLU 258": "OE1" <-> "OE2" Residue "M GLU 284": "OE1" <-> "OE2" Residue "M GLU 287": "OE1" <-> "OE2" Residue "M ASP 293": "OD1" <-> "OD2" Residue "M ASP 294": "OD1" <-> "OD2" Residue "M PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 329": "OE1" <-> "OE2" Residue "M GLU 344": "OE1" <-> "OE2" Residue "M TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 369": "OE1" <-> "OE2" Residue "M ARG 376": "NH1" <-> "NH2" Residue "C PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 56": "OD1" <-> "OD2" Residue "C GLU 72": "OE1" <-> "OE2" Residue "C GLU 83": "OE1" <-> "OE2" Residue "C TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 99": "OE1" <-> "OE2" Residue "C TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 205": "OE1" <-> "OE2" Residue "C GLU 226": "OE1" <-> "OE2" Residue "C GLU 241": "OE1" <-> "OE2" Residue "C GLU 253": "OE1" <-> "OE2" Residue "C GLU 270": "OE1" <-> "OE2" Residue "C ASP 286": "OD1" <-> "OD2" Residue "C ASP 288": "OD1" <-> "OD2" Residue "C TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 316": "OE1" <-> "OE2" Residue "C GLU 334": "OE1" <-> "OE2" Residue "C TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 64": "NH1" <-> "NH2" Residue "K GLU 67": "OE1" <-> "OE2" Residue "K GLU 76": "OE1" <-> "OE2" Residue "K PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 102": "OD1" <-> "OD2" Residue "K ASP 110": "OD1" <-> "OD2" Residue "K ASP 112": "OD1" <-> "OD2" Residue "K ASP 136": "OD1" <-> "OD2" Residue "K GLU 146": "OE1" <-> "OE2" Residue "K PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 156": "OD1" <-> "OD2" Residue "K GLU 177": "OE1" <-> "OE2" Residue "K ASP 212": "OD1" <-> "OD2" Residue "K TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 214": "OD1" <-> "OD2" Residue "K PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 252": "OD1" <-> "OD2" Residue "K ARG 257": "NH1" <-> "NH2" Residue "K GLU 258": "OE1" <-> "OE2" Residue "K GLU 284": "OE1" <-> "OE2" Residue "K GLU 287": "OE1" <-> "OE2" Residue "K ASP 293": "OD1" <-> "OD2" Residue "K ASP 294": "OD1" <-> "OD2" Residue "K PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 329": "OE1" <-> "OE2" Residue "K GLU 344": "OE1" <-> "OE2" Residue "K TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 369": "OE1" <-> "OE2" Residue "K ARG 376": "NH1" <-> "NH2" Residue "A PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 56": "OD1" <-> "OD2" Residue "A GLU 72": "OE1" <-> "OE2" Residue "A GLU 83": "OE1" <-> "OE2" Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 99": "OE1" <-> "OE2" Residue "A TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 205": "OE1" <-> "OE2" Residue "A GLU 226": "OE1" <-> "OE2" Residue "A GLU 241": "OE1" <-> "OE2" Residue "A GLU 253": "OE1" <-> "OE2" Residue "A GLU 270": "OE1" <-> "OE2" Residue "A ASP 286": "OD1" <-> "OD2" Residue "A ASP 288": "OD1" <-> "OD2" Residue "A TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 316": "OE1" <-> "OE2" Residue "A GLU 334": "OE1" <-> "OE2" Residue "A TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 64": "NH1" <-> "NH2" Residue "L GLU 67": "OE1" <-> "OE2" Residue "L GLU 76": "OE1" <-> "OE2" Residue "L PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 102": "OD1" <-> "OD2" Residue "L ASP 110": "OD1" <-> "OD2" Residue "L ASP 112": "OD1" <-> "OD2" Residue "L ASP 136": "OD1" <-> "OD2" Residue "L GLU 146": "OE1" <-> "OE2" Residue "L PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 156": "OD1" <-> "OD2" Residue "L GLU 177": "OE1" <-> "OE2" Residue "L ASP 212": "OD1" <-> "OD2" Residue "L TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 214": "OD1" <-> "OD2" Residue "L PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 252": "OD1" <-> "OD2" Residue "L ARG 257": "NH1" <-> "NH2" Residue "L GLU 258": "OE1" <-> "OE2" Residue "L GLU 284": "OE1" <-> "OE2" Residue "L GLU 287": "OE1" <-> "OE2" Residue "L ASP 293": "OD1" <-> "OD2" Residue "L ASP 294": "OD1" <-> "OD2" Residue "L PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 329": "OE1" <-> "OE2" Residue "L GLU 344": "OE1" <-> "OE2" Residue "L TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 369": "OE1" <-> "OE2" Residue "L ARG 376": "NH1" <-> "NH2" Residue "B PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 56": "OD1" <-> "OD2" Residue "B GLU 72": "OE1" <-> "OE2" Residue "B GLU 83": "OE1" <-> "OE2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 99": "OE1" <-> "OE2" Residue "B TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 205": "OE1" <-> "OE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B GLU 241": "OE1" <-> "OE2" Residue "B GLU 253": "OE1" <-> "OE2" Residue "B GLU 270": "OE1" <-> "OE2" Residue "B ASP 286": "OD1" <-> "OD2" Residue "B ASP 288": "OD1" <-> "OD2" Residue "B TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 316": "OE1" <-> "OE2" Residue "B GLU 334": "OE1" <-> "OE2" Residue "B TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 64": "NH1" <-> "NH2" Residue "N GLU 67": "OE1" <-> "OE2" Residue "N GLU 76": "OE1" <-> "OE2" Residue "N PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 102": "OD1" <-> "OD2" Residue "N ASP 110": "OD1" <-> "OD2" Residue "N ASP 112": "OD1" <-> "OD2" Residue "N ASP 136": "OD1" <-> "OD2" Residue "N GLU 146": "OE1" <-> "OE2" Residue "N PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 156": "OD1" <-> "OD2" Residue "N GLU 177": "OE1" <-> "OE2" Residue "N ASP 212": "OD1" <-> "OD2" Residue "N TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 214": "OD1" <-> "OD2" Residue "N PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 252": "OD1" <-> "OD2" Residue "N ARG 257": "NH1" <-> "NH2" Residue "N GLU 258": "OE1" <-> "OE2" Residue "N GLU 284": "OE1" <-> "OE2" Residue "N GLU 287": "OE1" <-> "OE2" Residue "N ASP 293": "OD1" <-> "OD2" Residue "N ASP 294": "OD1" <-> "OD2" Residue "N PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 329": "OE1" <-> "OE2" Residue "N GLU 344": "OE1" <-> "OE2" Residue "N TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 369": "OE1" <-> "OE2" Residue "N ARG 376": "NH1" <-> "NH2" Residue "D PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 56": "OD1" <-> "OD2" Residue "D GLU 72": "OE1" <-> "OE2" Residue "D GLU 83": "OE1" <-> "OE2" Residue "D TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 99": "OE1" <-> "OE2" Residue "D TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 205": "OE1" <-> "OE2" Residue "D GLU 226": "OE1" <-> "OE2" Residue "D GLU 241": "OE1" <-> "OE2" Residue "D GLU 253": "OE1" <-> "OE2" Residue "D GLU 270": "OE1" <-> "OE2" Residue "D ASP 286": "OD1" <-> "OD2" Residue "D ASP 288": "OD1" <-> "OD2" Residue "D TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 316": "OE1" <-> "OE2" Residue "D GLU 334": "OE1" <-> "OE2" Residue "D TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 64": "NH1" <-> "NH2" Residue "O GLU 67": "OE1" <-> "OE2" Residue "O GLU 76": "OE1" <-> "OE2" Residue "O PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 102": "OD1" <-> "OD2" Residue "O ASP 110": "OD1" <-> "OD2" Residue "O ASP 112": "OD1" <-> "OD2" Residue "O ASP 136": "OD1" <-> "OD2" Residue "O GLU 146": "OE1" <-> "OE2" Residue "O PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 156": "OD1" <-> "OD2" Residue "O GLU 177": "OE1" <-> "OE2" Residue "O ASP 212": "OD1" <-> "OD2" Residue "O TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 214": "OD1" <-> "OD2" Residue "O PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 252": "OD1" <-> "OD2" Residue "O ARG 257": "NH1" <-> "NH2" Residue "O GLU 258": "OE1" <-> "OE2" Residue "O GLU 284": "OE1" <-> "OE2" Residue "O GLU 287": "OE1" <-> "OE2" Residue "O ASP 293": "OD1" <-> "OD2" Residue "O ASP 294": "OD1" <-> "OD2" Residue "O PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 329": "OE1" <-> "OE2" Residue "O GLU 344": "OE1" <-> "OE2" Residue "O TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 369": "OE1" <-> "OE2" Residue "O ARG 376": "NH1" <-> "NH2" Residue "E PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 56": "OD1" <-> "OD2" Residue "E GLU 72": "OE1" <-> "OE2" Residue "E GLU 83": "OE1" <-> "OE2" Residue "E TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 99": "OE1" <-> "OE2" Residue "E TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 205": "OE1" <-> "OE2" Residue "E GLU 226": "OE1" <-> "OE2" Residue "E GLU 241": "OE1" <-> "OE2" Residue "E GLU 253": "OE1" <-> "OE2" Residue "E GLU 270": "OE1" <-> "OE2" Residue "E ASP 286": "OD1" <-> "OD2" Residue "E ASP 288": "OD1" <-> "OD2" Residue "E TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 316": "OE1" <-> "OE2" Residue "E GLU 334": "OE1" <-> "OE2" Residue "E TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 28580 Number of models: 1 Model: "" Number of chains: 25 Chain: "M" Number of atoms: 2697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2697 Classifications: {'peptide': 347} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 328} Chain breaks: 1 Chain: "C" Number of atoms: 2899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2899 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain: "H" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "K" Number of atoms: 2697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2697 Classifications: {'peptide': 347} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 328} Chain breaks: 1 Chain: "A" Number of atoms: 2899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2899 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain: "F" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "L" Number of atoms: 2697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2697 Classifications: {'peptide': 347} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 328} Chain breaks: 1 Chain: "B" Number of atoms: 2899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2899 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain: "G" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "N" Number of atoms: 2697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2697 Classifications: {'peptide': 347} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 328} Chain breaks: 1 Chain: "D" Number of atoms: 2899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2899 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain: "I" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "O" Number of atoms: 2697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2697 Classifications: {'peptide': 347} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 328} Chain breaks: 1 Chain: "E" Number of atoms: 2899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2899 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain: "J" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "M" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'GH3': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'GH3': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'GH3': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'GH3': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "O" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'GH3': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 14.16, per 1000 atoms: 0.50 Number of scatterers: 28580 At special positions: 0 Unit cell: (170.5, 127.6, 204.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 175 16.00 P 30 15.00 Mg 10 11.99 O 5475 8.00 N 5035 7.00 C 17855 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.51 Conformation dependent library (CDL) restraints added in 5.5 seconds 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTH H 4 " pdb=" CB DTH F 4 " pdb=" CB DTH G 4 " pdb=" CB DTH I 4 " pdb=" CB DTH J 4 " Number of C-beta restraints generated: 6630 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 160 helices and 35 sheets defined 37.6% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.64 Creating SS restraints... Processing helix chain 'M' and resid 25 through 38 removed outlier: 3.535A pdb=" N ASP M 33 " --> pdb=" O ARG M 29 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN M 38 " --> pdb=" O LEU M 34 " (cutoff:3.500A) Processing helix chain 'M' and resid 44 through 57 removed outlier: 4.135A pdb=" N ARG M 49 " --> pdb=" O GLU M 45 " (cutoff:3.500A) Processing helix chain 'M' and resid 71 through 76 Processing helix chain 'M' and resid 105 through 107 No H-bonds generated for 'chain 'M' and resid 105 through 107' Processing helix chain 'M' and resid 113 through 128 removed outlier: 3.827A pdb=" N ARG M 117 " --> pdb=" O THR M 113 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASN M 120 " --> pdb=" O ILE M 116 " (cutoff:3.500A) Processing helix chain 'M' and resid 141 through 151 Processing helix chain 'M' and resid 244 through 246 No H-bonds generated for 'chain 'M' and resid 244 through 246' Processing helix chain 'M' and resid 251 through 257 removed outlier: 4.137A pdb=" N ARG M 257 " --> pdb=" O GLY M 253 " (cutoff:3.500A) Processing helix chain 'M' and resid 267 through 278 removed outlier: 4.050A pdb=" N ASN M 277 " --> pdb=" O VAL M 273 " (cutoff:3.500A) Processing helix chain 'M' and resid 294 through 296 No H-bonds generated for 'chain 'M' and resid 294 through 296' Processing helix chain 'M' and resid 302 through 304 No H-bonds generated for 'chain 'M' and resid 302 through 304' Processing helix chain 'M' and resid 336 through 349 Processing helix chain 'M' and resid 365 through 375 removed outlier: 3.881A pdb=" N ALA M 370 " --> pdb=" O SER M 366 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE M 373 " --> pdb=" O GLU M 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 59 removed outlier: 3.550A pdb=" N GLN C 59 " --> pdb=" O ASP C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 91 Processing helix chain 'C' and resid 113 through 125 Processing helix chain 'C' and resid 137 through 145 removed outlier: 3.754A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 182 through 194 removed outlier: 3.578A pdb=" N LYS C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 213 Processing helix chain 'C' and resid 223 through 232 Processing helix chain 'C' and resid 251 through 256 removed outlier: 3.568A pdb=" N PHE C 255 " --> pdb=" O ASN C 252 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG C 256 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 264 through 267 Processing helix chain 'C' and resid 274 through 283 Processing helix chain 'C' and resid 287 through 294 removed outlier: 4.846A pdb=" N LYS C 291 " --> pdb=" O ASP C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 305 Processing helix chain 'C' and resid 309 through 320 removed outlier: 5.519A pdb=" N GLN C 314 " --> pdb=" O ALA C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 348 removed outlier: 4.215A pdb=" N LYS C 336 " --> pdb=" O PRO C 333 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N VAL C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY C 342 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA C 347 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 352 No H-bonds generated for 'chain 'C' and resid 350 through 352' Processing helix chain 'C' and resid 359 through 365 Processing helix chain 'C' and resid 367 through 371 Processing helix chain 'K' and resid 25 through 38 removed outlier: 3.534A pdb=" N ASP K 33 " --> pdb=" O ARG K 29 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN K 38 " --> pdb=" O LEU K 34 " (cutoff:3.500A) Processing helix chain 'K' and resid 44 through 57 removed outlier: 4.134A pdb=" N ARG K 49 " --> pdb=" O GLU K 45 " (cutoff:3.500A) Processing helix chain 'K' and resid 71 through 76 Processing helix chain 'K' and resid 105 through 107 No H-bonds generated for 'chain 'K' and resid 105 through 107' Processing helix chain 'K' and resid 113 through 128 removed outlier: 3.827A pdb=" N ARG K 117 " --> pdb=" O THR K 113 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASN K 120 " --> pdb=" O ILE K 116 " (cutoff:3.500A) Processing helix chain 'K' and resid 141 through 151 Processing helix chain 'K' and resid 244 through 246 No H-bonds generated for 'chain 'K' and resid 244 through 246' Processing helix chain 'K' and resid 251 through 257 removed outlier: 4.137A pdb=" N ARG K 257 " --> pdb=" O GLY K 253 " (cutoff:3.500A) Processing helix chain 'K' and resid 267 through 278 removed outlier: 4.049A pdb=" N ASN K 277 " --> pdb=" O VAL K 273 " (cutoff:3.500A) Processing helix chain 'K' and resid 294 through 296 No H-bonds generated for 'chain 'K' and resid 294 through 296' Processing helix chain 'K' and resid 302 through 304 No H-bonds generated for 'chain 'K' and resid 302 through 304' Processing helix chain 'K' and resid 336 through 349 Processing helix chain 'K' and resid 365 through 375 removed outlier: 3.882A pdb=" N ALA K 370 " --> pdb=" O SER K 366 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE K 373 " --> pdb=" O GLU K 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 59 removed outlier: 3.550A pdb=" N GLN A 59 " --> pdb=" O ASP A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 91 Processing helix chain 'A' and resid 113 through 125 Processing helix chain 'A' and resid 137 through 145 removed outlier: 3.754A pdb=" N LEU A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 182 through 194 removed outlier: 3.578A pdb=" N LYS A 191 " --> pdb=" O ASP A 187 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 213 Processing helix chain 'A' and resid 223 through 232 Processing helix chain 'A' and resid 251 through 256 removed outlier: 3.568A pdb=" N PHE A 255 " --> pdb=" O ASN A 252 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG A 256 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 264 through 267 Processing helix chain 'A' and resid 274 through 283 Processing helix chain 'A' and resid 287 through 294 removed outlier: 4.847A pdb=" N LYS A 291 " --> pdb=" O ASP A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 305 Processing helix chain 'A' and resid 309 through 320 removed outlier: 5.519A pdb=" N GLN A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 348 removed outlier: 4.215A pdb=" N LYS A 336 " --> pdb=" O PRO A 333 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N VAL A 339 " --> pdb=" O LYS A 336 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY A 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA A 347 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 352 No H-bonds generated for 'chain 'A' and resid 350 through 352' Processing helix chain 'A' and resid 359 through 365 Processing helix chain 'A' and resid 367 through 371 Processing helix chain 'L' and resid 25 through 38 removed outlier: 3.534A pdb=" N ASP L 33 " --> pdb=" O ARG L 29 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN L 38 " --> pdb=" O LEU L 34 " (cutoff:3.500A) Processing helix chain 'L' and resid 44 through 57 removed outlier: 4.135A pdb=" N ARG L 49 " --> pdb=" O GLU L 45 " (cutoff:3.500A) Processing helix chain 'L' and resid 71 through 76 Processing helix chain 'L' and resid 105 through 107 No H-bonds generated for 'chain 'L' and resid 105 through 107' Processing helix chain 'L' and resid 113 through 128 removed outlier: 3.827A pdb=" N ARG L 117 " --> pdb=" O THR L 113 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASN L 120 " --> pdb=" O ILE L 116 " (cutoff:3.500A) Processing helix chain 'L' and resid 141 through 151 Processing helix chain 'L' and resid 244 through 246 No H-bonds generated for 'chain 'L' and resid 244 through 246' Processing helix chain 'L' and resid 251 through 257 removed outlier: 4.137A pdb=" N ARG L 257 " --> pdb=" O GLY L 253 " (cutoff:3.500A) Processing helix chain 'L' and resid 267 through 278 removed outlier: 4.050A pdb=" N ASN L 277 " --> pdb=" O VAL L 273 " (cutoff:3.500A) Processing helix chain 'L' and resid 294 through 296 No H-bonds generated for 'chain 'L' and resid 294 through 296' Processing helix chain 'L' and resid 302 through 304 No H-bonds generated for 'chain 'L' and resid 302 through 304' Processing helix chain 'L' and resid 336 through 349 Processing helix chain 'L' and resid 365 through 375 removed outlier: 3.881A pdb=" N ALA L 370 " --> pdb=" O SER L 366 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE L 373 " --> pdb=" O GLU L 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 59 removed outlier: 3.550A pdb=" N GLN B 59 " --> pdb=" O ASP B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 91 Processing helix chain 'B' and resid 113 through 125 Processing helix chain 'B' and resid 137 through 145 removed outlier: 3.754A pdb=" N LEU B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 182 through 194 removed outlier: 3.578A pdb=" N LYS B 191 " --> pdb=" O ASP B 187 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 213 Processing helix chain 'B' and resid 223 through 232 Processing helix chain 'B' and resid 251 through 256 removed outlier: 3.569A pdb=" N PHE B 255 " --> pdb=" O ASN B 252 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG B 256 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 262 Processing helix chain 'B' and resid 264 through 267 Processing helix chain 'B' and resid 274 through 283 Processing helix chain 'B' and resid 287 through 294 removed outlier: 4.847A pdb=" N LYS B 291 " --> pdb=" O ASP B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 305 Processing helix chain 'B' and resid 309 through 320 removed outlier: 5.519A pdb=" N GLN B 314 " --> pdb=" O ALA B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 348 removed outlier: 4.215A pdb=" N LYS B 336 " --> pdb=" O PRO B 333 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N VAL B 339 " --> pdb=" O LYS B 336 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY B 342 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA B 347 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 352 No H-bonds generated for 'chain 'B' and resid 350 through 352' Processing helix chain 'B' and resid 359 through 365 Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'N' and resid 25 through 38 removed outlier: 3.535A pdb=" N ASP N 33 " --> pdb=" O ARG N 29 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN N 38 " --> pdb=" O LEU N 34 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 57 removed outlier: 4.135A pdb=" N ARG N 49 " --> pdb=" O GLU N 45 " (cutoff:3.500A) Processing helix chain 'N' and resid 71 through 76 Processing helix chain 'N' and resid 105 through 107 No H-bonds generated for 'chain 'N' and resid 105 through 107' Processing helix chain 'N' and resid 113 through 128 removed outlier: 3.827A pdb=" N ARG N 117 " --> pdb=" O THR N 113 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASN N 120 " --> pdb=" O ILE N 116 " (cutoff:3.500A) Processing helix chain 'N' and resid 141 through 151 Processing helix chain 'N' and resid 244 through 246 No H-bonds generated for 'chain 'N' and resid 244 through 246' Processing helix chain 'N' and resid 251 through 257 removed outlier: 4.137A pdb=" N ARG N 257 " --> pdb=" O GLY N 253 " (cutoff:3.500A) Processing helix chain 'N' and resid 267 through 278 removed outlier: 4.049A pdb=" N ASN N 277 " --> pdb=" O VAL N 273 " (cutoff:3.500A) Processing helix chain 'N' and resid 294 through 296 No H-bonds generated for 'chain 'N' and resid 294 through 296' Processing helix chain 'N' and resid 302 through 304 No H-bonds generated for 'chain 'N' and resid 302 through 304' Processing helix chain 'N' and resid 336 through 349 Processing helix chain 'N' and resid 365 through 375 removed outlier: 3.881A pdb=" N ALA N 370 " --> pdb=" O SER N 366 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE N 373 " --> pdb=" O GLU N 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 59 removed outlier: 3.551A pdb=" N GLN D 59 " --> pdb=" O ASP D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 91 Processing helix chain 'D' and resid 113 through 125 Processing helix chain 'D' and resid 137 through 145 removed outlier: 3.753A pdb=" N LEU D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 174 No H-bonds generated for 'chain 'D' and resid 172 through 174' Processing helix chain 'D' and resid 182 through 194 removed outlier: 3.578A pdb=" N LYS D 191 " --> pdb=" O ASP D 187 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 213 Processing helix chain 'D' and resid 223 through 232 Processing helix chain 'D' and resid 251 through 256 removed outlier: 3.568A pdb=" N PHE D 255 " --> pdb=" O ASN D 252 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG D 256 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 262 Processing helix chain 'D' and resid 264 through 267 Processing helix chain 'D' and resid 274 through 283 Processing helix chain 'D' and resid 287 through 294 removed outlier: 4.847A pdb=" N LYS D 291 " --> pdb=" O ASP D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 305 Processing helix chain 'D' and resid 309 through 320 removed outlier: 5.520A pdb=" N GLN D 314 " --> pdb=" O ALA D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 348 removed outlier: 4.215A pdb=" N LYS D 336 " --> pdb=" O PRO D 333 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N VAL D 339 " --> pdb=" O LYS D 336 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY D 342 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA D 347 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 352 No H-bonds generated for 'chain 'D' and resid 350 through 352' Processing helix chain 'D' and resid 359 through 365 Processing helix chain 'D' and resid 367 through 371 Processing helix chain 'O' and resid 25 through 38 removed outlier: 3.535A pdb=" N ASP O 33 " --> pdb=" O ARG O 29 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN O 38 " --> pdb=" O LEU O 34 " (cutoff:3.500A) Processing helix chain 'O' and resid 44 through 57 removed outlier: 4.135A pdb=" N ARG O 49 " --> pdb=" O GLU O 45 " (cutoff:3.500A) Processing helix chain 'O' and resid 71 through 76 Processing helix chain 'O' and resid 105 through 107 No H-bonds generated for 'chain 'O' and resid 105 through 107' Processing helix chain 'O' and resid 113 through 128 removed outlier: 3.827A pdb=" N ARG O 117 " --> pdb=" O THR O 113 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASN O 120 " --> pdb=" O ILE O 116 " (cutoff:3.500A) Processing helix chain 'O' and resid 141 through 151 Processing helix chain 'O' and resid 244 through 246 No H-bonds generated for 'chain 'O' and resid 244 through 246' Processing helix chain 'O' and resid 251 through 257 removed outlier: 4.137A pdb=" N ARG O 257 " --> pdb=" O GLY O 253 " (cutoff:3.500A) Processing helix chain 'O' and resid 267 through 278 removed outlier: 4.050A pdb=" N ASN O 277 " --> pdb=" O VAL O 273 " (cutoff:3.500A) Processing helix chain 'O' and resid 294 through 296 No H-bonds generated for 'chain 'O' and resid 294 through 296' Processing helix chain 'O' and resid 302 through 304 No H-bonds generated for 'chain 'O' and resid 302 through 304' Processing helix chain 'O' and resid 336 through 349 Processing helix chain 'O' and resid 365 through 375 removed outlier: 3.881A pdb=" N ALA O 370 " --> pdb=" O SER O 366 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE O 373 " --> pdb=" O GLU O 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 59 removed outlier: 3.550A pdb=" N GLN E 59 " --> pdb=" O ASP E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 91 Processing helix chain 'E' and resid 113 through 125 Processing helix chain 'E' and resid 137 through 145 removed outlier: 3.753A pdb=" N LEU E 142 " --> pdb=" O ALA E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 174 No H-bonds generated for 'chain 'E' and resid 172 through 174' Processing helix chain 'E' and resid 182 through 194 removed outlier: 3.578A pdb=" N LYS E 191 " --> pdb=" O ASP E 187 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 213 Processing helix chain 'E' and resid 223 through 232 Processing helix chain 'E' and resid 251 through 256 removed outlier: 3.568A pdb=" N PHE E 255 " --> pdb=" O ASN E 252 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG E 256 " --> pdb=" O GLU E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 262 Processing helix chain 'E' and resid 264 through 267 Processing helix chain 'E' and resid 274 through 283 Processing helix chain 'E' and resid 287 through 294 removed outlier: 4.847A pdb=" N LYS E 291 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 305 Processing helix chain 'E' and resid 309 through 320 removed outlier: 5.519A pdb=" N GLN E 314 " --> pdb=" O ALA E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 348 removed outlier: 4.215A pdb=" N LYS E 336 " --> pdb=" O PRO E 333 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N VAL E 339 " --> pdb=" O LYS E 336 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY E 342 " --> pdb=" O VAL E 339 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA E 347 " --> pdb=" O SER E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 352 No H-bonds generated for 'chain 'E' and resid 350 through 352' Processing helix chain 'E' and resid 359 through 365 Processing helix chain 'E' and resid 367 through 371 Processing sheet with id= A, first strand: chain 'M' and resid 218 through 220 removed outlier: 3.624A pdb=" N PHE M 61 " --> pdb=" O TYR M 311 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'M' and resid 132 through 134 removed outlier: 3.554A pdb=" N GLN M 134 " --> pdb=" O VAL M 199 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'M' and resid 154 through 158 removed outlier: 3.806A pdb=" N ALA M 166 " --> pdb=" O TYR M 174 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 132 through 136 removed outlier: 6.247A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 52 through 54 Processing sheet with id= F, first strand: chain 'C' and resid 150 through 155 Processing sheet with id= G, first strand: chain 'C' and resid 239 through 241 Processing sheet with id= H, first strand: chain 'K' and resid 218 through 220 removed outlier: 3.624A pdb=" N PHE K 61 " --> pdb=" O TYR K 311 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'K' and resid 132 through 134 removed outlier: 3.555A pdb=" N GLN K 134 " --> pdb=" O VAL K 199 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'K' and resid 154 through 158 removed outlier: 3.806A pdb=" N ALA K 166 " --> pdb=" O TYR K 174 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 132 through 136 removed outlier: 6.247A pdb=" N THR A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 52 through 54 Processing sheet with id= M, first strand: chain 'A' and resid 150 through 155 Processing sheet with id= N, first strand: chain 'A' and resid 239 through 241 Processing sheet with id= O, first strand: chain 'L' and resid 218 through 220 removed outlier: 3.625A pdb=" N PHE L 61 " --> pdb=" O TYR L 311 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'L' and resid 132 through 134 removed outlier: 3.554A pdb=" N GLN L 134 " --> pdb=" O VAL L 199 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'L' and resid 154 through 158 removed outlier: 3.805A pdb=" N ALA L 166 " --> pdb=" O TYR L 174 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 132 through 136 removed outlier: 6.247A pdb=" N THR B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ALA B 135 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 52 through 54 Processing sheet with id= T, first strand: chain 'B' and resid 150 through 155 Processing sheet with id= U, first strand: chain 'B' and resid 239 through 241 Processing sheet with id= V, first strand: chain 'N' and resid 218 through 220 removed outlier: 3.624A pdb=" N PHE N 61 " --> pdb=" O TYR N 311 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'N' and resid 132 through 134 removed outlier: 3.554A pdb=" N GLN N 134 " --> pdb=" O VAL N 199 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'N' and resid 154 through 158 removed outlier: 3.806A pdb=" N ALA N 166 " --> pdb=" O TYR N 174 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 132 through 136 removed outlier: 6.247A pdb=" N THR D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ALA D 135 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU D 105 " --> pdb=" O ALA D 135 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'D' and resid 52 through 54 Processing sheet with id= AA, first strand: chain 'D' and resid 150 through 155 Processing sheet with id= AB, first strand: chain 'D' and resid 239 through 241 Processing sheet with id= AC, first strand: chain 'O' and resid 218 through 220 removed outlier: 3.624A pdb=" N PHE O 61 " --> pdb=" O TYR O 311 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'O' and resid 132 through 134 removed outlier: 3.555A pdb=" N GLN O 134 " --> pdb=" O VAL O 199 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'O' and resid 154 through 158 removed outlier: 3.805A pdb=" N ALA O 166 " --> pdb=" O TYR O 174 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'E' and resid 132 through 136 removed outlier: 6.247A pdb=" N THR E 103 " --> pdb=" O TYR E 133 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ALA E 135 " --> pdb=" O THR E 103 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU E 105 " --> pdb=" O ALA E 135 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'E' and resid 52 through 54 Processing sheet with id= AH, first strand: chain 'E' and resid 150 through 155 Processing sheet with id= AI, first strand: chain 'E' and resid 239 through 241 930 hydrogen bonds defined for protein. 2310 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.27 Time building geometry restraints manager: 12.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 4790 1.30 - 1.42: 7637 1.42 - 1.55: 16363 1.55 - 1.68: 70 1.68 - 1.81: 325 Bond restraints: 29185 Sorted by residual: bond pdb=" O4' GH3 K 402 " pdb=" C1' GH3 K 402 " ideal model delta sigma weight residual 1.297 1.692 -0.395 2.00e-02 2.50e+03 3.90e+02 bond pdb=" O4' GH3 N 402 " pdb=" C1' GH3 N 402 " ideal model delta sigma weight residual 1.297 1.692 -0.395 2.00e-02 2.50e+03 3.89e+02 bond pdb=" O4' GH3 L 402 " pdb=" C1' GH3 L 402 " ideal model delta sigma weight residual 1.297 1.692 -0.395 2.00e-02 2.50e+03 3.89e+02 bond pdb=" O4' GH3 M 402 " pdb=" C1' GH3 M 402 " ideal model delta sigma weight residual 1.297 1.692 -0.395 2.00e-02 2.50e+03 3.89e+02 bond pdb=" O4' GH3 O 402 " pdb=" C1' GH3 O 402 " ideal model delta sigma weight residual 1.297 1.691 -0.394 2.00e-02 2.50e+03 3.89e+02 ... (remaining 29180 not shown) Histogram of bond angle deviations from ideal: 93.89 - 102.17: 179 102.17 - 110.45: 8823 110.45 - 118.74: 14470 118.74 - 127.02: 15709 127.02 - 135.31: 389 Bond angle restraints: 39570 Sorted by residual: angle pdb=" C TRP I 1 " pdb=" CA TRP I 1 " pdb=" CB TRP I 1 " ideal model delta sigma weight residual 110.10 98.76 11.34 1.90e+00 2.77e-01 3.56e+01 angle pdb=" C TRP H 1 " pdb=" CA TRP H 1 " pdb=" CB TRP H 1 " ideal model delta sigma weight residual 110.10 98.78 11.32 1.90e+00 2.77e-01 3.55e+01 angle pdb=" C TRP F 1 " pdb=" CA TRP F 1 " pdb=" CB TRP F 1 " ideal model delta sigma weight residual 110.10 98.79 11.31 1.90e+00 2.77e-01 3.55e+01 angle pdb=" C TRP J 1 " pdb=" CA TRP J 1 " pdb=" CB TRP J 1 " ideal model delta sigma weight residual 110.10 98.80 11.30 1.90e+00 2.77e-01 3.54e+01 angle pdb=" C TRP G 1 " pdb=" CA TRP G 1 " pdb=" CB TRP G 1 " ideal model delta sigma weight residual 110.10 98.81 11.29 1.90e+00 2.77e-01 3.53e+01 ... (remaining 39565 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.97: 16821 26.97 - 53.94: 549 53.94 - 80.92: 105 80.92 - 107.89: 10 107.89 - 134.86: 10 Dihedral angle restraints: 17495 sinusoidal: 7140 harmonic: 10355 Sorted by residual: dihedral pdb=" C TRP I 1 " pdb=" N TRP I 1 " pdb=" CA TRP I 1 " pdb=" CB TRP I 1 " ideal model delta harmonic sigma weight residual -122.60 -104.35 -18.25 0 2.50e+00 1.60e-01 5.33e+01 dihedral pdb=" C TRP F 1 " pdb=" N TRP F 1 " pdb=" CA TRP F 1 " pdb=" CB TRP F 1 " ideal model delta harmonic sigma weight residual -122.60 -104.35 -18.25 0 2.50e+00 1.60e-01 5.33e+01 dihedral pdb=" C TRP H 1 " pdb=" N TRP H 1 " pdb=" CA TRP H 1 " pdb=" CB TRP H 1 " ideal model delta harmonic sigma weight residual -122.60 -104.36 -18.24 0 2.50e+00 1.60e-01 5.32e+01 ... (remaining 17492 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 2811 0.076 - 0.153: 1229 0.153 - 0.229: 220 0.229 - 0.306: 24 0.306 - 0.382: 11 Chirality restraints: 4295 Sorted by residual: chirality pdb=" C2' GH3 M 402 " pdb=" C3' GH3 M 402 " pdb=" O2' GH3 M 402 " pdb=" C1' GH3 M 402 " both_signs ideal model delta sigma weight residual False -2.44 -2.82 0.38 2.00e-01 2.50e+01 3.65e+00 chirality pdb=" C2' GH3 O 402 " pdb=" C3' GH3 O 402 " pdb=" O2' GH3 O 402 " pdb=" C1' GH3 O 402 " both_signs ideal model delta sigma weight residual False -2.44 -2.82 0.38 2.00e-01 2.50e+01 3.63e+00 chirality pdb=" C2' GH3 K 402 " pdb=" C3' GH3 K 402 " pdb=" O2' GH3 K 402 " pdb=" C1' GH3 K 402 " both_signs ideal model delta sigma weight residual False -2.44 -2.82 0.38 2.00e-01 2.50e+01 3.62e+00 ... (remaining 4292 not shown) Planarity restraints: 5150 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 62 " 0.090 9.50e-02 1.11e+02 4.91e-02 1.08e+01 pdb=" NE ARG B 62 " -0.023 2.00e-02 2.50e+03 pdb=" CZ ARG B 62 " 0.053 2.00e-02 2.50e+03 pdb=" NH1 ARG B 62 " -0.019 2.00e-02 2.50e+03 pdb=" NH2 ARG B 62 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 62 " -0.089 9.50e-02 1.11e+02 4.87e-02 1.08e+01 pdb=" NE ARG C 62 " 0.023 2.00e-02 2.50e+03 pdb=" CZ ARG C 62 " -0.053 2.00e-02 2.50e+03 pdb=" NH1 ARG C 62 " 0.019 2.00e-02 2.50e+03 pdb=" NH2 ARG C 62 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 62 " -0.088 9.50e-02 1.11e+02 4.84e-02 1.08e+01 pdb=" NE ARG E 62 " 0.023 2.00e-02 2.50e+03 pdb=" CZ ARG E 62 " -0.053 2.00e-02 2.50e+03 pdb=" NH1 ARG E 62 " 0.019 2.00e-02 2.50e+03 pdb=" NH2 ARG E 62 " 0.015 2.00e-02 2.50e+03 ... (remaining 5147 not shown) Histogram of nonbonded interaction distances: 1.31 - 2.03: 25 2.03 - 2.75: 4945 2.75 - 3.46: 41090 3.46 - 4.18: 73571 4.18 - 4.90: 131248 Nonbonded interactions: 250879 Sorted by model distance: nonbonded pdb=" N TRP G 1 " pdb=" C ALA G 7 " model vdw 1.310 3.350 nonbonded pdb=" N TRP F 1 " pdb=" C ALA F 7 " model vdw 1.311 3.350 nonbonded pdb=" N TRP I 1 " pdb=" C ALA I 7 " model vdw 1.311 3.350 nonbonded pdb=" N TRP J 1 " pdb=" C ALA J 7 " model vdw 1.311 3.350 nonbonded pdb=" N TRP H 1 " pdb=" C ALA H 7 " model vdw 1.311 3.350 ... (remaining 250874 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 7.250 Check model and map are aligned: 0.440 Set scattering table: 0.280 Process input model: 73.470 Find NCS groups from input model: 1.970 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 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 : 0.022 0.395 29185 Z= 1.446 Angle : 1.362 16.052 39570 Z= 0.736 Chirality : 0.084 0.382 4295 Planarity : 0.008 0.049 5150 Dihedral : 15.089 134.860 10865 Min Nonbonded Distance : 1.310 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 0.17 % Allowed : 5.03 % Favored : 94.80 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.12), residues: 3560 helix: -2.80 (0.09), residues: 1295 sheet: -1.83 (0.25), residues: 420 loop : -1.13 (0.14), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.006 TRP E 340 HIS 0.018 0.004 HIS B 40 PHE 0.037 0.005 PHE E 200 TYR 0.029 0.007 TYR L 174 ARG 0.054 0.008 ARG E 62 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 740 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 735 time to evaluate : 2.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 26 MET cc_start: 0.6983 (tmt) cc_final: 0.6634 (tmm) REVERT: M 79 PRO cc_start: 0.7917 (Cg_exo) cc_final: 0.7701 (Cg_endo) REVERT: M 285 HIS cc_start: 0.6882 (m-70) cc_final: 0.6671 (m-70) REVERT: M 294 ASP cc_start: 0.8482 (t70) cc_final: 0.8231 (t0) REVERT: C 355 MET cc_start: 0.8006 (mmm) cc_final: 0.7654 (mtt) REVERT: K 147 LEU cc_start: 0.7049 (mt) cc_final: 0.6708 (tt) REVERT: K 264 ASN cc_start: 0.8309 (t0) cc_final: 0.7890 (t0) REVERT: K 329 GLU cc_start: 0.6808 (mp0) cc_final: 0.6059 (pm20) REVERT: A 190 MET cc_start: 0.8385 (ttt) cc_final: 0.8069 (mtp) REVERT: A 280 ASN cc_start: 0.7929 (m-40) cc_final: 0.7663 (m-40) REVERT: B 210 ARG cc_start: 0.8162 (ttp80) cc_final: 0.7808 (ttp-170) REVERT: B 227 MET cc_start: 0.7844 (mmm) cc_final: 0.7599 (mmm) REVERT: B 246 GLN cc_start: 0.8501 (mt0) cc_final: 0.8245 (mt0) REVERT: B 355 MET cc_start: 0.7360 (mmm) cc_final: 0.7155 (mtp) REVERT: N 32 GLN cc_start: 0.7701 (tp40) cc_final: 0.7178 (tp40) REVERT: N 120 ASN cc_start: 0.6712 (t0) cc_final: 0.6367 (m-40) REVERT: D 12 ASN cc_start: 0.8352 (m110) cc_final: 0.7584 (p0) REVERT: D 82 MET cc_start: 0.8045 (mmm) cc_final: 0.7688 (tpt) REVERT: D 244 ASP cc_start: 0.8342 (p0) cc_final: 0.7958 (p0) REVERT: D 355 MET cc_start: 0.7573 (mmm) cc_final: 0.7328 (mtp) REVERT: O 288 MET cc_start: 0.6300 (mmm) cc_final: 0.6092 (mmt) REVERT: O 316 MET cc_start: 0.2886 (tpt) cc_final: 0.2127 (tpt) REVERT: E 116 ARG cc_start: 0.6896 (mtm-85) cc_final: 0.6473 (mtp85) REVERT: E 123 MET cc_start: 0.7765 (mmt) cc_final: 0.7311 (mmt) REVERT: E 227 MET cc_start: 0.6848 (mmm) cc_final: 0.6523 (mmm) outliers start: 5 outliers final: 5 residues processed: 739 average time/residue: 0.4366 time to fit residues: 490.6985 Evaluate side-chains 418 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 413 time to evaluate : 3.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS Chi-restraints excluded: chain F residue 5 CYS Chi-restraints excluded: chain G residue 5 CYS Chi-restraints excluded: chain I residue 5 CYS Chi-restraints excluded: chain J residue 5 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 299 optimal weight: 20.0000 chunk 269 optimal weight: 1.9990 chunk 149 optimal weight: 7.9990 chunk 91 optimal weight: 0.9980 chunk 181 optimal weight: 0.8980 chunk 143 optimal weight: 0.9990 chunk 278 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 169 optimal weight: 9.9990 chunk 207 optimal weight: 0.9980 chunk 322 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 103 GLN M 290 HIS M 360 ASN C 12 ASN C 92 ASN C 252 ASN A 92 ASN A 246 GLN A 252 ASN L 38 GLN L 103 GLN L 360 ASN B 12 ASN B 246 GLN B 252 ASN N 91 ASN D 92 ASN D 162 ASN D 246 GLN D 353 GLN O 56 GLN O 285 HIS E 92 ASN E 162 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 29185 Z= 0.231 Angle : 0.683 10.256 39570 Z= 0.344 Chirality : 0.047 0.333 4295 Planarity : 0.005 0.042 5150 Dihedral : 10.742 125.753 4145 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.21 % Allowed : 10.30 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.14), residues: 3560 helix: -1.07 (0.13), residues: 1305 sheet: -1.09 (0.26), residues: 395 loop : -0.20 (0.15), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP I 1 HIS 0.006 0.001 HIS A 88 PHE 0.014 0.001 PHE O 151 TYR 0.015 0.001 TYR K 311 ARG 0.008 0.001 ARG L 376 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 520 time to evaluate : 3.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 258 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7622 (mt-10) REVERT: M 316 MET cc_start: 0.4349 (tpt) cc_final: 0.4107 (tpp) REVERT: C 355 MET cc_start: 0.7891 (mmm) cc_final: 0.7559 (mtt) REVERT: K 264 ASN cc_start: 0.8452 (t0) cc_final: 0.7862 (t0) REVERT: K 286 ARG cc_start: 0.6382 (mtp180) cc_final: 0.5876 (mtp180) REVERT: K 316 MET cc_start: 0.3141 (tpt) cc_final: 0.2479 (tpp) REVERT: A 192 ILE cc_start: 0.8182 (mm) cc_final: 0.7904 (pt) REVERT: L 360 ASN cc_start: 0.7798 (OUTLIER) cc_final: 0.7488 (m-40) REVERT: B 176 MET cc_start: 0.8290 (mmm) cc_final: 0.8075 (mmp) REVERT: N 293 ASP cc_start: 0.8573 (p0) cc_final: 0.8364 (p0) REVERT: N 351 TYR cc_start: 0.8740 (m-80) cc_final: 0.8072 (m-80) REVERT: D 12 ASN cc_start: 0.8090 (m110) cc_final: 0.7452 (p0) REVERT: D 44 MET cc_start: 0.7711 (mmp) cc_final: 0.7422 (mmm) REVERT: D 305 MET cc_start: 0.8074 (mmm) cc_final: 0.7834 (mmm) REVERT: O 78 PHE cc_start: 0.6897 (m-10) cc_final: 0.6647 (m-10) REVERT: J 5 CYS cc_start: 0.5633 (OUTLIER) cc_final: 0.5408 (t) outliers start: 66 outliers final: 36 residues processed: 563 average time/residue: 0.3864 time to fit residues: 345.9853 Evaluate side-chains 427 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 389 time to evaluate : 2.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 189 SER Chi-restraints excluded: chain M residue 329 GLU Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 215 LYS Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 89 SER Chi-restraints excluded: chain K residue 344 GLU Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain F residue 5 CYS Chi-restraints excluded: chain L residue 360 ASN Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain N residue 53 VAL Chi-restraints excluded: chain N residue 80 THR Chi-restraints excluded: chain N residue 366 SER Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain I residue 5 CYS Chi-restraints excluded: chain O residue 53 VAL Chi-restraints excluded: chain O residue 285 HIS Chi-restraints excluded: chain O residue 341 LEU Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 191 LYS Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 286 ASP Chi-restraints excluded: chain J residue 5 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 179 optimal weight: 0.7980 chunk 100 optimal weight: 6.9990 chunk 268 optimal weight: 2.9990 chunk 219 optimal weight: 5.9990 chunk 88 optimal weight: 10.0000 chunk 322 optimal weight: 0.6980 chunk 348 optimal weight: 0.7980 chunk 287 optimal weight: 0.9990 chunk 320 optimal weight: 0.8980 chunk 110 optimal weight: 4.9990 chunk 259 optimal weight: 0.0870 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN C 41 GLN C 162 ASN K 290 HIS A 115 ASN A 162 ASN L 38 GLN B 78 ASN ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 HIS ** D 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 ASN ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 HIS ** O 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 ASN ** E 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 173 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29185 Z= 0.186 Angle : 0.618 11.140 39570 Z= 0.306 Chirality : 0.045 0.315 4295 Planarity : 0.004 0.040 5150 Dihedral : 9.666 134.494 4143 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.18 % Allowed : 12.92 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.37 (0.14), residues: 3560 helix: -0.25 (0.14), residues: 1275 sheet: -1.31 (0.23), residues: 460 loop : 0.27 (0.15), residues: 1825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP L 359 HIS 0.020 0.001 HIS O 285 PHE 0.010 0.001 PHE K 310 TYR 0.013 0.001 TYR M 311 ARG 0.009 0.000 ARG O 376 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 423 time to evaluate : 2.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 50 MET cc_start: 0.7299 (mtm) cc_final: 0.7086 (mtm) REVERT: M 316 MET cc_start: 0.4130 (tpt) cc_final: 0.3576 (tpp) REVERT: C 355 MET cc_start: 0.7860 (mmm) cc_final: 0.7556 (mtt) REVERT: K 26 MET cc_start: 0.6610 (tmm) cc_final: 0.6388 (tmm) REVERT: K 316 MET cc_start: 0.3212 (tpt) cc_final: 0.2934 (tpp) REVERT: A 82 MET cc_start: 0.8448 (tpt) cc_final: 0.8214 (tpt) REVERT: A 205 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7649 (mt-10) REVERT: L 26 MET cc_start: 0.6826 (tmm) cc_final: 0.5499 (ptp) REVERT: L 258 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7184 (mt-10) REVERT: L 369 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6357 (mt-10) REVERT: B 246 GLN cc_start: 0.8631 (mt0) cc_final: 0.8269 (mt0) REVERT: B 313 MET cc_start: 0.7649 (tpp) cc_final: 0.7416 (mmm) REVERT: N 288 MET cc_start: 0.8288 (mmm) cc_final: 0.8056 (mmp) REVERT: D 12 ASN cc_start: 0.7990 (m110) cc_final: 0.7325 (p0) REVERT: D 44 MET cc_start: 0.7743 (mmp) cc_final: 0.7512 (mmm) REVERT: D 283 MET cc_start: 0.8008 (mmm) cc_final: 0.7422 (mmt) REVERT: O 288 MET cc_start: 0.6372 (tpp) cc_final: 0.6148 (tpp) outliers start: 65 outliers final: 42 residues processed: 464 average time/residue: 0.3910 time to fit residues: 290.0493 Evaluate side-chains 420 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 376 time to evaluate : 2.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 189 SER Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 215 LYS Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 90 SER Chi-restraints excluded: chain K residue 120 ASN Chi-restraints excluded: chain K residue 236 THR Chi-restraints excluded: chain K residue 344 GLU Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain F residue 5 CYS Chi-restraints excluded: chain L residue 45 GLU Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 369 GLU Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain N residue 80 THR Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 154 VAL Chi-restraints excluded: chain O residue 341 LEU Chi-restraints excluded: chain O residue 361 VAL Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 239 SER Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 286 ASP Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 355 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 319 optimal weight: 0.4980 chunk 242 optimal weight: 7.9990 chunk 167 optimal weight: 4.9990 chunk 35 optimal weight: 0.0870 chunk 154 optimal weight: 4.9990 chunk 216 optimal weight: 2.9990 chunk 324 optimal weight: 1.9990 chunk 343 optimal weight: 3.9990 chunk 169 optimal weight: 8.9990 chunk 307 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.7164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 115 ASN B 297 ASN B 314 GLN ** N 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 285 HIS ** O 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 ASN ** E 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.3941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 29185 Z= 0.304 Angle : 0.641 11.329 39570 Z= 0.316 Chirality : 0.047 0.329 4295 Planarity : 0.004 0.042 5150 Dihedral : 8.914 125.976 4141 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.65 % Allowed : 13.56 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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 (0.14), residues: 3560 helix: -0.11 (0.14), residues: 1295 sheet: -1.06 (0.22), residues: 505 loop : 0.29 (0.16), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 340 HIS 0.010 0.001 HIS O 356 PHE 0.014 0.002 PHE K 310 TYR 0.020 0.001 TYR M 311 ARG 0.005 0.000 ARG N 239 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 413 time to evaluate : 3.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 316 MET cc_start: 0.3590 (tpt) cc_final: 0.3363 (tpp) REVERT: C 157 ASP cc_start: 0.8099 (t70) cc_final: 0.7775 (t70) REVERT: K 75 GLU cc_start: 0.6992 (tm-30) cc_final: 0.6743 (tm-30) REVERT: K 264 ASN cc_start: 0.8480 (t0) cc_final: 0.8198 (t0) REVERT: K 316 MET cc_start: 0.3020 (tpt) cc_final: 0.2645 (tpp) REVERT: A 205 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7732 (mt-10) REVERT: L 26 MET cc_start: 0.6960 (tmm) cc_final: 0.5672 (ptp) REVERT: L 369 GLU cc_start: 0.7113 (OUTLIER) cc_final: 0.6264 (mp0) REVERT: N 297 ASN cc_start: 0.8686 (t0) cc_final: 0.8191 (t0) REVERT: D 12 ASN cc_start: 0.8151 (m110) cc_final: 0.7471 (p0) REVERT: D 44 MET cc_start: 0.7744 (mmp) cc_final: 0.7514 (mmm) REVERT: D 283 MET cc_start: 0.8099 (mmm) cc_final: 0.7592 (mmt) REVERT: O 265 ILE cc_start: 0.8759 (tp) cc_final: 0.8536 (tp) REVERT: O 294 ASP cc_start: 0.7211 (t70) cc_final: 0.6968 (t70) REVERT: O 316 MET cc_start: 0.4849 (tpt) cc_final: 0.3084 (tpt) REVERT: E 191 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.8137 (ttmm) REVERT: E 335 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.6521 (ptp-170) outliers start: 79 outliers final: 51 residues processed: 467 average time/residue: 0.3848 time to fit residues: 291.8599 Evaluate side-chains 423 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 368 time to evaluate : 3.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 189 SER Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 215 LYS Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 120 ASN Chi-restraints excluded: chain K residue 214 ASP Chi-restraints excluded: chain K residue 236 THR Chi-restraints excluded: chain K residue 344 GLU Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain F residue 5 CYS Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 369 GLU Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain N residue 80 THR Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 154 VAL Chi-restraints excluded: chain O residue 285 HIS Chi-restraints excluded: chain O residue 341 LEU Chi-restraints excluded: chain O residue 361 VAL Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 191 LYS Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 286 ASP Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 335 ARG Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 355 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 285 optimal weight: 0.9980 chunk 194 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 255 optimal weight: 0.6980 chunk 141 optimal weight: 3.9990 chunk 292 optimal weight: 30.0000 chunk 237 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 175 optimal weight: 0.0770 chunk 307 optimal weight: 10.0000 chunk 86 optimal weight: 5.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 356 HIS C 92 ASN A 115 ASN L 46 HIS B 162 ASN N 46 HIS ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.4322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 29185 Z= 0.176 Angle : 0.591 11.131 39570 Z= 0.287 Chirality : 0.044 0.304 4295 Planarity : 0.004 0.054 5150 Dihedral : 8.338 100.425 4141 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.35 % Allowed : 14.50 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.08 (0.14), residues: 3560 helix: 0.20 (0.14), residues: 1270 sheet: -1.03 (0.23), residues: 455 loop : 0.22 (0.16), residues: 1835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 359 HIS 0.014 0.001 HIS O 285 PHE 0.008 0.001 PHE K 310 TYR 0.014 0.001 TYR M 311 ARG 0.011 0.000 ARG L 376 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 409 time to evaluate : 3.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 209 MET cc_start: 0.6308 (mtm) cc_final: 0.5960 (mtm) REVERT: M 316 MET cc_start: 0.3509 (tpt) cc_final: 0.3268 (tpp) REVERT: C 157 ASP cc_start: 0.8070 (t70) cc_final: 0.7780 (t70) REVERT: K 26 MET cc_start: 0.6745 (tmm) cc_final: 0.6439 (tmm) REVERT: K 75 GLU cc_start: 0.7037 (tm-30) cc_final: 0.6782 (tm-30) REVERT: K 264 ASN cc_start: 0.8425 (t0) cc_final: 0.8117 (t0) REVERT: K 316 MET cc_start: 0.2717 (tpt) cc_final: 0.2045 (tpt) REVERT: A 82 MET cc_start: 0.8501 (tpt) cc_final: 0.8261 (tpt) REVERT: L 26 MET cc_start: 0.6847 (tmm) cc_final: 0.5662 (ptp) REVERT: L 369 GLU cc_start: 0.7149 (OUTLIER) cc_final: 0.6220 (mp0) REVERT: N 239 ARG cc_start: 0.7589 (ttm-80) cc_final: 0.7378 (tpp80) REVERT: D 12 ASN cc_start: 0.8139 (m110) cc_final: 0.7443 (p0) REVERT: D 44 MET cc_start: 0.7742 (mmp) cc_final: 0.7446 (mmm) REVERT: D 283 MET cc_start: 0.7963 (mmm) cc_final: 0.7547 (mmt) REVERT: O 316 MET cc_start: 0.4710 (tpt) cc_final: 0.3005 (tpt) REVERT: E 57 GLU cc_start: 0.7013 (OUTLIER) cc_final: 0.6593 (tt0) outliers start: 70 outliers final: 50 residues processed: 453 average time/residue: 0.3874 time to fit residues: 283.4277 Evaluate side-chains 430 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 378 time to evaluate : 2.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 189 SER Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 215 LYS Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 253 GLU Chi-restraints excluded: chain K residue 53 VAL Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 120 ASN Chi-restraints excluded: chain K residue 214 ASP Chi-restraints excluded: chain K residue 344 GLU Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain F residue 5 CYS Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 369 GLU Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain G residue 5 CYS Chi-restraints excluded: chain N residue 80 THR Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain O residue 53 VAL Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 154 VAL Chi-restraints excluded: chain O residue 341 LEU Chi-restraints excluded: chain O residue 361 VAL Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 286 ASP Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 355 MET Chi-restraints excluded: chain J residue 5 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 115 optimal weight: 3.9990 chunk 309 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 201 optimal weight: 4.9990 chunk 84 optimal weight: 7.9990 chunk 343 optimal weight: 0.5980 chunk 285 optimal weight: 0.9990 chunk 159 optimal weight: 7.9990 chunk 28 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 chunk 180 optimal weight: 4.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 92 ASN K 46 HIS A 115 ASN B 40 HIS ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 73 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.4563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 29185 Z= 0.190 Angle : 0.585 11.136 39570 Z= 0.284 Chirality : 0.044 0.306 4295 Planarity : 0.004 0.044 5150 Dihedral : 8.019 85.057 4141 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.38 % Allowed : 15.30 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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 (0.14), residues: 3560 helix: 0.15 (0.14), residues: 1330 sheet: -0.98 (0.23), residues: 455 loop : 0.04 (0.16), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 356 HIS 0.007 0.001 HIS O 356 PHE 0.010 0.001 PHE A 200 TYR 0.015 0.001 TYR O 240 ARG 0.011 0.000 ARG L 376 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 413 time to evaluate : 3.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 157 ASP cc_start: 0.8042 (t70) cc_final: 0.7725 (t70) REVERT: K 75 GLU cc_start: 0.7018 (tm-30) cc_final: 0.6760 (tm-30) REVERT: K 264 ASN cc_start: 0.8330 (t0) cc_final: 0.8045 (t0) REVERT: K 316 MET cc_start: 0.2721 (tpt) cc_final: 0.2025 (tpt) REVERT: A 82 MET cc_start: 0.8483 (tpt) cc_final: 0.8237 (tpt) REVERT: A 190 MET cc_start: 0.8050 (mtp) cc_final: 0.7722 (mtm) REVERT: L 369 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.6114 (mp0) REVERT: B 283 MET cc_start: 0.7831 (mmm) cc_final: 0.7554 (mmm) REVERT: N 183 ASP cc_start: 0.0809 (OUTLIER) cc_final: 0.0607 (p0) REVERT: N 304 ASP cc_start: 0.7683 (t70) cc_final: 0.7365 (t0) REVERT: D 12 ASN cc_start: 0.8012 (m110) cc_final: 0.7379 (p0) REVERT: D 283 MET cc_start: 0.8009 (mmm) cc_final: 0.7613 (mmt) REVERT: D 334 GLU cc_start: 0.7043 (pm20) cc_final: 0.6839 (pm20) REVERT: O 316 MET cc_start: 0.4667 (tpt) cc_final: 0.3171 (tpt) outliers start: 71 outliers final: 56 residues processed: 460 average time/residue: 0.3691 time to fit residues: 278.5249 Evaluate side-chains 445 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 387 time to evaluate : 2.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 189 SER Chi-restraints excluded: chain M residue 354 THR Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 215 LYS Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 120 ASN Chi-restraints excluded: chain K residue 214 ASP Chi-restraints excluded: chain K residue 236 THR Chi-restraints excluded: chain K residue 344 GLU Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain F residue 5 CYS Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 369 GLU Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain G residue 5 CYS Chi-restraints excluded: chain N residue 80 THR Chi-restraints excluded: chain N residue 183 ASP Chi-restraints excluded: chain N residue 210 THR Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain O residue 53 VAL Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 207 LEU Chi-restraints excluded: chain O residue 341 LEU Chi-restraints excluded: chain O residue 361 VAL Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 191 LYS Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 286 ASP Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 355 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 331 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 195 optimal weight: 0.9980 chunk 250 optimal weight: 0.1980 chunk 194 optimal weight: 0.6980 chunk 289 optimal weight: 5.9990 chunk 191 optimal weight: 0.7980 chunk 342 optimal weight: 3.9990 chunk 214 optimal weight: 0.9980 chunk 208 optimal weight: 2.9990 chunk 157 optimal weight: 7.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 46 HIS ** A 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 101 HIS A 115 ASN ** L 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 285 HIS O 356 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.4723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 29185 Z= 0.173 Angle : 0.578 11.158 39570 Z= 0.279 Chirality : 0.044 0.303 4295 Planarity : 0.004 0.045 5150 Dihedral : 7.858 81.489 4141 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.28 % Allowed : 15.91 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.11 (0.14), residues: 3560 helix: 0.26 (0.14), residues: 1330 sheet: -0.89 (0.24), residues: 455 loop : 0.06 (0.16), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 340 HIS 0.007 0.001 HIS A 101 PHE 0.008 0.001 PHE K 151 TYR 0.016 0.001 TYR O 240 ARG 0.012 0.000 ARG L 376 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 410 time to evaluate : 3.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 162 ARG cc_start: 0.6542 (tpt170) cc_final: 0.6186 (tpt170) REVERT: C 157 ASP cc_start: 0.8020 (t70) cc_final: 0.7725 (t70) REVERT: C 355 MET cc_start: 0.7878 (mtm) cc_final: 0.7667 (mtm) REVERT: K 26 MET cc_start: 0.6730 (tmm) cc_final: 0.6362 (tmm) REVERT: K 75 GLU cc_start: 0.7100 (tm-30) cc_final: 0.6822 (tm-30) REVERT: K 264 ASN cc_start: 0.8317 (t0) cc_final: 0.8027 (t0) REVERT: K 316 MET cc_start: 0.2693 (tpt) cc_final: 0.1997 (tpt) REVERT: A 82 MET cc_start: 0.8469 (tpt) cc_final: 0.8232 (tpt) REVERT: A 190 MET cc_start: 0.8003 (OUTLIER) cc_final: 0.7742 (mtm) REVERT: A 335 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.7417 (ptp-170) REVERT: L 26 MET cc_start: 0.7110 (tmm) cc_final: 0.5655 (ptp) REVERT: L 369 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.6121 (mp0) REVERT: B 283 MET cc_start: 0.7809 (mmm) cc_final: 0.7543 (mmm) REVERT: B 313 MET cc_start: 0.7556 (tpp) cc_final: 0.7339 (mmm) REVERT: N 304 ASP cc_start: 0.7713 (t70) cc_final: 0.7394 (t0) REVERT: D 12 ASN cc_start: 0.7969 (m110) cc_final: 0.7324 (p0) REVERT: D 283 MET cc_start: 0.7997 (mmm) cc_final: 0.7625 (mmt) REVERT: D 334 GLU cc_start: 0.6984 (pm20) cc_final: 0.6729 (pm20) REVERT: O 78 PHE cc_start: 0.7053 (OUTLIER) cc_final: 0.6156 (m-10) REVERT: O 316 MET cc_start: 0.4835 (tpt) cc_final: 0.3456 (tpt) REVERT: E 306 TYR cc_start: 0.8302 (m-80) cc_final: 0.7727 (m-10) REVERT: E 335 ARG cc_start: 0.7727 (OUTLIER) cc_final: 0.5938 (ptp-170) outliers start: 68 outliers final: 46 residues processed: 452 average time/residue: 0.3714 time to fit residues: 271.9606 Evaluate side-chains 443 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 392 time to evaluate : 3.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 189 SER Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 215 LYS Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 253 GLU Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 120 ASN Chi-restraints excluded: chain K residue 236 THR Chi-restraints excluded: chain K residue 344 GLU Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 335 ARG Chi-restraints excluded: chain F residue 5 CYS Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 369 GLU Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain G residue 5 CYS Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain O residue 53 VAL Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 78 PHE Chi-restraints excluded: chain O residue 341 LEU Chi-restraints excluded: chain O residue 361 VAL Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 191 LYS Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 286 ASP Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 335 ARG Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 355 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 211 optimal weight: 4.9990 chunk 136 optimal weight: 6.9990 chunk 204 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 217 optimal weight: 5.9990 chunk 233 optimal weight: 6.9990 chunk 169 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 268 optimal weight: 0.0030 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 115 ASN ** L 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 356 HIS ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 285 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.4871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 29185 Z= 0.179 Angle : 0.581 11.163 39570 Z= 0.279 Chirality : 0.044 0.304 4295 Planarity : 0.004 0.042 5150 Dihedral : 7.756 82.578 4141 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.01 % Allowed : 16.48 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.07 (0.14), residues: 3560 helix: 0.34 (0.14), residues: 1330 sheet: -0.82 (0.24), residues: 455 loop : 0.03 (0.16), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 340 HIS 0.008 0.001 HIS O 285 PHE 0.009 0.001 PHE K 306 TYR 0.017 0.001 TYR O 240 ARG 0.008 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 418 time to evaluate : 3.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 162 ARG cc_start: 0.6441 (tpt170) cc_final: 0.6093 (tpt170) REVERT: M 209 MET cc_start: 0.6177 (mtm) cc_final: 0.5963 (mtm) REVERT: C 157 ASP cc_start: 0.8017 (t70) cc_final: 0.7730 (t70) REVERT: C 355 MET cc_start: 0.7860 (mtm) cc_final: 0.7646 (mtm) REVERT: K 26 MET cc_start: 0.6717 (tmm) cc_final: 0.6419 (tmm) REVERT: K 75 GLU cc_start: 0.7078 (tm-30) cc_final: 0.6794 (tm-30) REVERT: K 147 LEU cc_start: 0.7390 (mt) cc_final: 0.7174 (tt) REVERT: K 264 ASN cc_start: 0.8312 (t0) cc_final: 0.8021 (t0) REVERT: K 316 MET cc_start: 0.2853 (tpt) cc_final: 0.2191 (tpt) REVERT: A 82 MET cc_start: 0.8473 (tpt) cc_final: 0.8264 (tpt) REVERT: A 190 MET cc_start: 0.7993 (OUTLIER) cc_final: 0.7749 (mtm) REVERT: L 26 MET cc_start: 0.7091 (tmm) cc_final: 0.5686 (ptp) REVERT: L 369 GLU cc_start: 0.7054 (OUTLIER) cc_final: 0.6160 (mp0) REVERT: B 283 MET cc_start: 0.7855 (mmm) cc_final: 0.7575 (mmm) REVERT: N 304 ASP cc_start: 0.7700 (t70) cc_final: 0.7404 (t0) REVERT: D 12 ASN cc_start: 0.8134 (m110) cc_final: 0.7431 (p0) REVERT: D 283 MET cc_start: 0.7994 (mmm) cc_final: 0.7638 (mmt) REVERT: D 334 GLU cc_start: 0.6972 (pm20) cc_final: 0.6718 (pm20) REVERT: O 78 PHE cc_start: 0.7238 (OUTLIER) cc_final: 0.6275 (m-10) REVERT: O 316 MET cc_start: 0.4845 (tpt) cc_final: 0.3469 (tpt) REVERT: E 306 TYR cc_start: 0.8343 (m-80) cc_final: 0.7677 (m-10) REVERT: E 335 ARG cc_start: 0.7701 (OUTLIER) cc_final: 0.5957 (ptp-170) outliers start: 60 outliers final: 45 residues processed: 456 average time/residue: 0.3696 time to fit residues: 274.5748 Evaluate side-chains 440 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 391 time to evaluate : 3.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 189 SER Chi-restraints excluded: chain M residue 354 THR Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 215 LYS Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 120 ASN Chi-restraints excluded: chain K residue 214 ASP Chi-restraints excluded: chain K residue 236 THR Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 369 GLU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain G residue 5 CYS Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain O residue 53 VAL Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 78 PHE Chi-restraints excluded: chain O residue 341 LEU Chi-restraints excluded: chain O residue 361 VAL Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 286 ASP Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 335 ARG Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 311 optimal weight: 7.9990 chunk 327 optimal weight: 0.2980 chunk 299 optimal weight: 0.0570 chunk 318 optimal weight: 0.9990 chunk 191 optimal weight: 0.8980 chunk 138 optimal weight: 2.9990 chunk 250 optimal weight: 0.9980 chunk 97 optimal weight: 9.9990 chunk 288 optimal weight: 0.6980 chunk 301 optimal weight: 8.9990 chunk 317 optimal weight: 3.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 352 HIS C 101 HIS ** A 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 285 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.5053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 29185 Z= 0.163 Angle : 0.577 11.683 39570 Z= 0.277 Chirality : 0.043 0.299 4295 Planarity : 0.004 0.043 5150 Dihedral : 7.606 84.736 4140 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.78 % Allowed : 16.68 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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 (0.14), residues: 3560 helix: 0.38 (0.14), residues: 1335 sheet: -0.67 (0.24), residues: 450 loop : 0.09 (0.16), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP O 359 HIS 0.009 0.001 HIS O 285 PHE 0.018 0.001 PHE O 83 TYR 0.017 0.001 TYR O 240 ARG 0.007 0.000 ARG C 372 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 432 time to evaluate : 4.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 223 GLU cc_start: 0.7129 (mp0) cc_final: 0.6928 (mm-30) REVERT: C 157 ASP cc_start: 0.8015 (t70) cc_final: 0.7727 (t70) REVERT: C 355 MET cc_start: 0.7883 (mtm) cc_final: 0.7531 (mtm) REVERT: K 26 MET cc_start: 0.6716 (tmm) cc_final: 0.6406 (tmm) REVERT: K 75 GLU cc_start: 0.7082 (tm-30) cc_final: 0.6796 (tm-30) REVERT: K 147 LEU cc_start: 0.7376 (mt) cc_final: 0.7151 (tt) REVERT: K 264 ASN cc_start: 0.8283 (t0) cc_final: 0.7990 (t0) REVERT: A 82 MET cc_start: 0.8480 (tpt) cc_final: 0.8255 (tpt) REVERT: A 190 MET cc_start: 0.7946 (OUTLIER) cc_final: 0.7719 (mtm) REVERT: A 335 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.7139 (ptp-170) REVERT: L 26 MET cc_start: 0.7070 (tmm) cc_final: 0.5681 (ptp) REVERT: L 369 GLU cc_start: 0.7157 (OUTLIER) cc_final: 0.6232 (mp0) REVERT: B 283 MET cc_start: 0.7807 (mmm) cc_final: 0.7531 (mmm) REVERT: N 55 ARG cc_start: 0.8096 (ttm-80) cc_final: 0.7667 (ttp80) REVERT: N 75 GLU cc_start: 0.6472 (tm-30) cc_final: 0.6139 (tm-30) REVERT: N 286 ARG cc_start: 0.7422 (OUTLIER) cc_final: 0.7050 (mtt-85) REVERT: N 304 ASP cc_start: 0.7680 (t70) cc_final: 0.7390 (t0) REVERT: D 12 ASN cc_start: 0.8011 (m110) cc_final: 0.7356 (p0) REVERT: D 283 MET cc_start: 0.7998 (mmm) cc_final: 0.7615 (mmt) REVERT: D 305 MET cc_start: 0.7706 (mmm) cc_final: 0.7488 (mmt) REVERT: O 78 PHE cc_start: 0.7165 (OUTLIER) cc_final: 0.6256 (m-10) REVERT: O 316 MET cc_start: 0.4873 (tpt) cc_final: 0.3508 (tpt) REVERT: E 306 TYR cc_start: 0.8308 (m-80) cc_final: 0.7641 (m-10) REVERT: E 335 ARG cc_start: 0.7588 (OUTLIER) cc_final: 0.5869 (ptp-170) outliers start: 53 outliers final: 42 residues processed: 463 average time/residue: 0.3884 time to fit residues: 290.0330 Evaluate side-chains 455 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 407 time to evaluate : 3.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 215 LYS Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 253 GLU Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 120 ASN Chi-restraints excluded: chain K residue 214 ASP Chi-restraints excluded: chain K residue 236 THR Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 335 ARG Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 369 GLU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain G residue 5 CYS Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 286 ARG Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain O residue 53 VAL Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 78 PHE Chi-restraints excluded: chain O residue 154 VAL Chi-restraints excluded: chain O residue 341 LEU Chi-restraints excluded: chain O residue 361 VAL Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 286 ASP Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 335 ARG Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 209 optimal weight: 1.9990 chunk 337 optimal weight: 5.9990 chunk 205 optimal weight: 0.9980 chunk 159 optimal weight: 0.8980 chunk 234 optimal weight: 4.9990 chunk 353 optimal weight: 4.9990 chunk 325 optimal weight: 0.9980 chunk 281 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 217 optimal weight: 0.0870 chunk 172 optimal weight: 10.0000 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 352 HIS C 101 HIS C 297 ASN K 352 HIS ** A 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 115 ASN ** L 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 285 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.5158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29185 Z= 0.176 Angle : 0.583 10.945 39570 Z= 0.283 Chirality : 0.044 0.301 4295 Planarity : 0.004 0.043 5150 Dihedral : 7.536 86.649 4140 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.71 % Allowed : 17.01 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.01 (0.14), residues: 3560 helix: 0.41 (0.14), residues: 1325 sheet: -0.63 (0.25), residues: 415 loop : 0.01 (0.15), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 79 HIS 0.010 0.001 HIS M 352 PHE 0.024 0.001 PHE O 83 TYR 0.017 0.001 TYR O 240 ARG 0.007 0.000 ARG C 372 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 420 time to evaluate : 3.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 162 ARG cc_start: 0.6546 (tpt170) cc_final: 0.6195 (tpt170) REVERT: C 54 VAL cc_start: 0.8988 (t) cc_final: 0.8787 (t) REVERT: C 157 ASP cc_start: 0.8021 (t70) cc_final: 0.7709 (t70) REVERT: C 355 MET cc_start: 0.7944 (mtm) cc_final: 0.7733 (mtm) REVERT: K 26 MET cc_start: 0.6623 (tmm) cc_final: 0.6311 (tmm) REVERT: K 75 GLU cc_start: 0.7082 (tm-30) cc_final: 0.6794 (tm-30) REVERT: K 147 LEU cc_start: 0.7380 (mt) cc_final: 0.7158 (tt) REVERT: K 264 ASN cc_start: 0.8272 (t0) cc_final: 0.7969 (t0) REVERT: K 316 MET cc_start: 0.2525 (tpt) cc_final: 0.2014 (tpt) REVERT: A 335 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.7166 (ptp-170) REVERT: L 26 MET cc_start: 0.7064 (tmm) cc_final: 0.5685 (ptp) REVERT: L 369 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6230 (mp0) REVERT: B 283 MET cc_start: 0.7840 (mmm) cc_final: 0.7564 (mmm) REVERT: N 75 GLU cc_start: 0.6530 (tm-30) cc_final: 0.6193 (tm-30) REVERT: N 286 ARG cc_start: 0.7366 (OUTLIER) cc_final: 0.6992 (mtt-85) REVERT: N 304 ASP cc_start: 0.7700 (t70) cc_final: 0.7424 (t0) REVERT: D 12 ASN cc_start: 0.8010 (m110) cc_final: 0.7379 (p0) REVERT: D 283 MET cc_start: 0.7986 (mmm) cc_final: 0.7618 (mmt) REVERT: O 78 PHE cc_start: 0.7154 (OUTLIER) cc_final: 0.6173 (m-10) REVERT: O 316 MET cc_start: 0.4909 (tpt) cc_final: 0.3514 (tpt) REVERT: E 306 TYR cc_start: 0.8316 (m-80) cc_final: 0.7660 (m-10) REVERT: E 335 ARG cc_start: 0.7605 (OUTLIER) cc_final: 0.5942 (ptp-170) outliers start: 51 outliers final: 44 residues processed: 450 average time/residue: 0.3697 time to fit residues: 270.2387 Evaluate side-chains 457 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 408 time to evaluate : 3.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 215 LYS Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 253 GLU Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 120 ASN Chi-restraints excluded: chain K residue 214 ASP Chi-restraints excluded: chain K residue 236 THR Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 335 ARG Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 302 MET Chi-restraints excluded: chain L residue 369 GLU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain G residue 5 CYS Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 286 ARG Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain O residue 53 VAL Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 78 PHE Chi-restraints excluded: chain O residue 341 LEU Chi-restraints excluded: chain O residue 361 VAL Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 335 ARG Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 223 optimal weight: 20.0000 chunk 300 optimal weight: 7.9990 chunk 86 optimal weight: 7.9990 chunk 259 optimal weight: 0.0870 chunk 41 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 chunk 282 optimal weight: 0.8980 chunk 118 optimal weight: 0.5980 chunk 289 optimal weight: 7.9990 chunk 35 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 352 HIS C 92 ASN C 101 HIS ** A 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 115 ASN ** L 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 285 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.180048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.140455 restraints weight = 34183.972| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 1.71 r_work: 0.3438 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.5227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 29185 Z= 0.181 Angle : 0.585 12.181 39570 Z= 0.284 Chirality : 0.044 0.301 4295 Planarity : 0.004 0.062 5150 Dihedral : 7.515 88.356 4140 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.74 % Allowed : 17.11 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.01 (0.14), residues: 3560 helix: 0.44 (0.14), residues: 1330 sheet: -0.81 (0.24), residues: 465 loop : 0.03 (0.16), residues: 1765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP O 359 HIS 0.009 0.001 HIS M 352 PHE 0.021 0.001 PHE O 83 TYR 0.017 0.001 TYR O 240 ARG 0.015 0.000 ARG D 372 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6768.09 seconds wall clock time: 122 minutes 28.24 seconds (7348.24 seconds total)