Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 29 13:43:36 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7res_24438/04_2023/7res_24438_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7res_24438/04_2023/7res_24438.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7res_24438/04_2023/7res_24438.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7res_24438/04_2023/7res_24438.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7res_24438/04_2023/7res_24438_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7res_24438/04_2023/7res_24438_updated.pdb" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.256 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: 5 Type Number sf(0) Gaussians P 72 5.49 5 S 184 5.16 5 C 18768 2.51 5 N 5152 2.21 5 O 5912 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 15": "OE1" <-> "OE2" Residue "A TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 43": "OD1" <-> "OD2" Residue "A ASP 47": "OD1" <-> "OD2" Residue "A ASP 50": "OD1" <-> "OD2" Residue "A GLU 75": "OE1" <-> "OE2" Residue "A PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 111": "OE1" <-> "OE2" Residue "A GLU 132": "OE1" <-> "OE2" Residue "A ARG 136": "NH1" <-> "NH2" Residue "A GLU 146": "OE1" <-> "OE2" Residue "A GLU 168": "OE1" <-> "OE2" Residue "A GLU 199": "OE1" <-> "OE2" Residue "A ARG 203": "NH1" <-> "NH2" Residue "A ARG 231": "NH1" <-> "NH2" Residue "A ASP 232": "OD1" <-> "OD2" Residue "A TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 255": "OD1" <-> "OD2" Residue "A ASP 261": "OD1" <-> "OD2" Residue "A GLU 335": "OE1" <-> "OE2" Residue "A ARG 356": "NH1" <-> "NH2" Residue "A ASP 364": "OD1" <-> "OD2" Residue "A GLU 395": "OE1" <-> "OE2" Residue "A PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 407": "NH1" <-> "NH2" Residue "A TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 412": "NH1" <-> "NH2" Residue "A GLU 421": "OE1" <-> "OE2" Residue "A ASP 470": "OD1" <-> "OD2" Residue "A GLU 500": "OE1" <-> "OE2" Residue "A ARG 512": "NH1" <-> "NH2" Residue "A TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 15": "OE1" <-> "OE2" Residue "B TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 43": "OD1" <-> "OD2" Residue "B ASP 50": "OD1" <-> "OD2" Residue "B GLU 75": "OE1" <-> "OE2" Residue "B PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 132": "OE1" <-> "OE2" Residue "B ARG 136": "NH1" <-> "NH2" Residue "B GLU 146": "OE1" <-> "OE2" Residue "B GLU 168": "OE1" <-> "OE2" Residue "B ARG 203": "NH1" <-> "NH2" Residue "B ARG 231": "NH1" <-> "NH2" Residue "B ASP 232": "OD1" <-> "OD2" Residue "B TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 239": "OD1" <-> "OD2" Residue "B ASP 255": "OD1" <-> "OD2" Residue "B ASP 261": "OD1" <-> "OD2" Residue "B ASP 269": "OD1" <-> "OD2" Residue "B GLU 335": "OE1" <-> "OE2" Residue "B ARG 356": "NH1" <-> "NH2" Residue "B ASP 364": "OD1" <-> "OD2" Residue "B GLU 395": "OE1" <-> "OE2" Residue "B GLU 399": "OE1" <-> "OE2" Residue "B PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 404": "OD1" <-> "OD2" Residue "B ARG 407": "NH1" <-> "NH2" Residue "B TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 412": "NH1" <-> "NH2" Residue "B ASP 470": "OD1" <-> "OD2" Residue "B GLU 500": "OE1" <-> "OE2" Residue "B ARG 512": "NH1" <-> "NH2" Residue "B TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 43": "OD1" <-> "OD2" Residue "C ASP 50": "OD1" <-> "OD2" Residue "C GLU 75": "OE1" <-> "OE2" Residue "C PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 136": "NH1" <-> "NH2" Residue "C GLU 146": "OE1" <-> "OE2" Residue "C GLU 168": "OE1" <-> "OE2" Residue "C GLU 196": "OE1" <-> "OE2" Residue "C ARG 203": "NH1" <-> "NH2" Residue "C ASP 214": "OD1" <-> "OD2" Residue "C ARG 231": "NH1" <-> "NH2" Residue "C ASP 232": "OD1" <-> "OD2" Residue "C TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 255": "OD1" <-> "OD2" Residue "C ASP 261": "OD1" <-> "OD2" Residue "C ASP 274": "OD1" <-> "OD2" Residue "C ASP 319": "OD1" <-> "OD2" Residue "C GLU 335": "OE1" <-> "OE2" Residue "C ARG 356": "NH1" <-> "NH2" Residue "C ASP 364": "OD1" <-> "OD2" Residue "C GLU 395": "OE1" <-> "OE2" Residue "C PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 407": "NH1" <-> "NH2" Residue "C TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 412": "NH1" <-> "NH2" Residue "C GLU 421": "OE1" <-> "OE2" Residue "C ASP 470": "OD1" <-> "OD2" Residue "C GLU 500": "OE1" <-> "OE2" Residue "C ARG 512": "NH1" <-> "NH2" Residue "C TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 43": "OD1" <-> "OD2" Residue "D ASP 47": "OD1" <-> "OD2" Residue "D ASP 50": "OD1" <-> "OD2" Residue "D GLU 75": "OE1" <-> "OE2" Residue "D PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 111": "OE1" <-> "OE2" Residue "D GLU 132": "OE1" <-> "OE2" Residue "D ARG 136": "NH1" <-> "NH2" Residue "D GLU 146": "OE1" <-> "OE2" Residue "D GLU 168": "OE1" <-> "OE2" Residue "D GLU 199": "OE1" <-> "OE2" Residue "D ARG 203": "NH1" <-> "NH2" Residue "D ASP 214": "OD1" <-> "OD2" Residue "D ASP 216": "OD1" <-> "OD2" Residue "D GLU 217": "OE1" <-> "OE2" Residue "D ARG 231": "NH1" <-> "NH2" Residue "D ASP 232": "OD1" <-> "OD2" Residue "D TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 255": "OD1" <-> "OD2" Residue "D ASP 269": "OD1" <-> "OD2" Residue "D ASP 274": "OD1" <-> "OD2" Residue "D GLU 335": "OE1" <-> "OE2" Residue "D ARG 356": "NH1" <-> "NH2" Residue "D ASP 364": "OD1" <-> "OD2" Residue "D GLU 395": "OE1" <-> "OE2" Residue "D GLU 399": "OE1" <-> "OE2" Residue "D PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 407": "NH1" <-> "NH2" Residue "D TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 412": "NH1" <-> "NH2" Residue "D GLU 421": "OE1" <-> "OE2" Residue "D ASP 470": "OD1" <-> "OD2" Residue "D GLU 500": "OE1" <-> "OE2" Residue "D ARG 512": "NH1" <-> "NH2" Residue "D TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 15": "OE1" <-> "OE2" Residue "E TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 43": "OD1" <-> "OD2" Residue "E ASP 50": "OD1" <-> "OD2" Residue "E GLU 75": "OE1" <-> "OE2" Residue "E PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 132": "OE1" <-> "OE2" Residue "E ARG 136": "NH1" <-> "NH2" Residue "E GLU 146": "OE1" <-> "OE2" Residue "E GLU 168": "OE1" <-> "OE2" Residue "E GLU 199": "OE1" <-> "OE2" Residue "E ARG 203": "NH1" <-> "NH2" Residue "E GLU 217": "OE1" <-> "OE2" Residue "E ARG 231": "NH1" <-> "NH2" Residue "E ASP 232": "OD1" <-> "OD2" Residue "E TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 255": "OD1" <-> "OD2" Residue "E ASP 261": "OD1" <-> "OD2" Residue "E ASP 319": "OD1" <-> "OD2" Residue "E GLU 335": "OE1" <-> "OE2" Residue "E ARG 356": "NH1" <-> "NH2" Residue "E ASP 364": "OD1" <-> "OD2" Residue "E GLU 395": "OE1" <-> "OE2" Residue "E PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 407": "NH1" <-> "NH2" Residue "E TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 412": "NH1" <-> "NH2" Residue "E ASP 470": "OD1" <-> "OD2" Residue "E GLU 500": "OE1" <-> "OE2" Residue "E ARG 512": "NH1" <-> "NH2" Residue "E TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 43": "OD1" <-> "OD2" Residue "F ASP 50": "OD1" <-> "OD2" Residue "F GLU 75": "OE1" <-> "OE2" Residue "F PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 111": "OE1" <-> "OE2" Residue "F GLU 132": "OE1" <-> "OE2" Residue "F ARG 136": "NH1" <-> "NH2" Residue "F GLU 146": "OE1" <-> "OE2" Residue "F GLU 168": "OE1" <-> "OE2" Residue "F GLU 196": "OE1" <-> "OE2" Residue "F ARG 203": "NH1" <-> "NH2" Residue "F ASP 214": "OD1" <-> "OD2" Residue "F ASP 216": "OD1" <-> "OD2" Residue "F GLU 217": "OE1" <-> "OE2" Residue "F ARG 231": "NH1" <-> "NH2" Residue "F ASP 232": "OD1" <-> "OD2" Residue "F TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 239": "OD1" <-> "OD2" Residue "F ASP 255": "OD1" <-> "OD2" Residue "F ASP 269": "OD1" <-> "OD2" Residue "F GLU 335": "OE1" <-> "OE2" Residue "F ARG 356": "NH1" <-> "NH2" Residue "F ASP 364": "OD1" <-> "OD2" Residue "F GLU 395": "OE1" <-> "OE2" Residue "F PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 404": "OD1" <-> "OD2" Residue "F ARG 407": "NH1" <-> "NH2" Residue "F TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 412": "NH1" <-> "NH2" Residue "F GLU 421": "OE1" <-> "OE2" Residue "F ASP 470": "OD1" <-> "OD2" Residue "F GLU 500": "OE1" <-> "OE2" Residue "F ARG 512": "NH1" <-> "NH2" Residue "F TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 50": "OD1" <-> "OD2" Residue "G GLU 75": "OE1" <-> "OE2" Residue "G PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 111": "OE1" <-> "OE2" Residue "G GLU 132": "OE1" <-> "OE2" Residue "G ARG 136": "NH1" <-> "NH2" Residue "G GLU 146": "OE1" <-> "OE2" Residue "G GLU 168": "OE1" <-> "OE2" Residue "G GLU 196": "OE1" <-> "OE2" Residue "G GLU 199": "OE1" <-> "OE2" Residue "G ARG 203": "NH1" <-> "NH2" Residue "G ASP 214": "OD1" <-> "OD2" Residue "G ARG 231": "NH1" <-> "NH2" Residue "G ASP 232": "OD1" <-> "OD2" Residue "G TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 255": "OD1" <-> "OD2" Residue "G ASP 269": "OD1" <-> "OD2" Residue "G ASP 274": "OD1" <-> "OD2" Residue "G GLU 335": "OE1" <-> "OE2" Residue "G ARG 356": "NH1" <-> "NH2" Residue "G ASP 364": "OD1" <-> "OD2" Residue "G GLU 395": "OE1" <-> "OE2" Residue "G GLU 399": "OE1" <-> "OE2" Residue "G PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 407": "NH1" <-> "NH2" Residue "G TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 412": "NH1" <-> "NH2" Residue "G GLU 421": "OE1" <-> "OE2" Residue "G ASP 470": "OD1" <-> "OD2" Residue "G GLU 500": "OE1" <-> "OE2" Residue "G ARG 512": "NH1" <-> "NH2" Residue "G TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 15": "OE1" <-> "OE2" Residue "H TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 43": "OD1" <-> "OD2" Residue "H ASP 47": "OD1" <-> "OD2" Residue "H ASP 50": "OD1" <-> "OD2" Residue "H GLU 75": "OE1" <-> "OE2" Residue "H PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 111": "OE1" <-> "OE2" Residue "H GLU 132": "OE1" <-> "OE2" Residue "H ARG 136": "NH1" <-> "NH2" Residue "H GLU 146": "OE1" <-> "OE2" Residue "H GLU 168": "OE1" <-> "OE2" Residue "H GLU 196": "OE1" <-> "OE2" Residue "H GLU 199": "OE1" <-> "OE2" Residue "H ARG 203": "NH1" <-> "NH2" Residue "H ASP 214": "OD1" <-> "OD2" Residue "H ARG 231": "NH1" <-> "NH2" Residue "H ASP 232": "OD1" <-> "OD2" Residue "H TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 255": "OD1" <-> "OD2" Residue "H ASP 261": "OD1" <-> "OD2" Residue "H ASP 269": "OD1" <-> "OD2" Residue "H GLU 335": "OE1" <-> "OE2" Residue "H ARG 356": "NH1" <-> "NH2" Residue "H ASP 364": "OD1" <-> "OD2" Residue "H GLU 395": "OE1" <-> "OE2" Residue "H GLU 399": "OE1" <-> "OE2" Residue "H PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 407": "NH1" <-> "NH2" Residue "H TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 412": "NH1" <-> "NH2" Residue "H GLU 421": "OE1" <-> "OE2" Residue "H ASP 470": "OD1" <-> "OD2" Residue "H GLU 500": "OE1" <-> "OE2" Residue "H ARG 512": "NH1" <-> "NH2" Residue "H TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 30088 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3632 Classifications: {'peptide': 482} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 463} Chain breaks: 3 Chain: "B" Number of atoms: 3632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3632 Classifications: {'peptide': 482} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 463} Chain breaks: 3 Chain: "C" Number of atoms: 3632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3632 Classifications: {'peptide': 482} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 463} Chain breaks: 3 Chain: "D" Number of atoms: 3632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3632 Classifications: {'peptide': 482} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 463} Chain breaks: 3 Chain: "E" Number of atoms: 3632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3632 Classifications: {'peptide': 482} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 463} Chain breaks: 3 Chain: "F" Number of atoms: 3632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3632 Classifications: {'peptide': 482} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 463} Chain breaks: 3 Chain: "G" Number of atoms: 3632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3632 Classifications: {'peptide': 482} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 463} Chain breaks: 3 Chain: "H" Number of atoms: 3632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3632 Classifications: {'peptide': 482} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 463} Chain breaks: 3 Chain: "A" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "B" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "C" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "D" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "E" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "F" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "G" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "H" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Time building chain proxies: 14.96, per 1000 atoms: 0.50 Number of scatterers: 30088 At special positions: 0 Unit cell: (135.45, 136.5, 142.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 184 16.00 P 72 15.00 O 5912 8.00 N 5152 7.00 C 18768 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.97 Conformation dependent library (CDL) restraints added in 4.3 seconds 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6912 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 152 helices and 40 sheets defined 33.5% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.18 Creating SS restraints... Processing helix chain 'A' and resid 20 through 23 No H-bonds generated for 'chain 'A' and resid 20 through 23' Processing helix chain 'A' and resid 32 through 34 No H-bonds generated for 'chain 'A' and resid 32 through 34' Processing helix chain 'A' and resid 46 through 48 No H-bonds generated for 'chain 'A' and resid 46 through 48' Processing helix chain 'A' and resid 76 through 85 Processing helix chain 'A' and resid 97 through 108 Processing helix chain 'A' and resid 128 through 136 Processing helix chain 'A' and resid 160 through 162 No H-bonds generated for 'chain 'A' and resid 160 through 162' Processing helix chain 'A' and resid 194 through 204 Processing helix chain 'A' and resid 224 through 229 removed outlier: 3.525A pdb=" N LYS A 229 " --> pdb=" O THR A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 265 Processing helix chain 'A' and resid 281 through 293 Processing helix chain 'A' and resid 307 through 316 Processing helix chain 'A' and resid 334 through 337 No H-bonds generated for 'chain 'A' and resid 334 through 337' Processing helix chain 'A' and resid 343 through 357 removed outlier: 3.984A pdb=" N ARG A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N PHE A 357 " --> pdb=" O TYR A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 378 Processing helix chain 'A' and resid 417 through 420 No H-bonds generated for 'chain 'A' and resid 417 through 420' Processing helix chain 'A' and resid 453 through 471 Proline residue: A 458 - end of helix Processing helix chain 'A' and resid 476 through 484 Processing helix chain 'A' and resid 495 through 501 Processing helix chain 'B' and resid 20 through 23 No H-bonds generated for 'chain 'B' and resid 20 through 23' Processing helix chain 'B' and resid 32 through 34 No H-bonds generated for 'chain 'B' and resid 32 through 34' Processing helix chain 'B' and resid 46 through 48 No H-bonds generated for 'chain 'B' and resid 46 through 48' Processing helix chain 'B' and resid 76 through 85 Processing helix chain 'B' and resid 97 through 108 Processing helix chain 'B' and resid 128 through 136 Processing helix chain 'B' and resid 160 through 162 No H-bonds generated for 'chain 'B' and resid 160 through 162' Processing helix chain 'B' and resid 194 through 204 Processing helix chain 'B' and resid 224 through 227 No H-bonds generated for 'chain 'B' and resid 224 through 227' Processing helix chain 'B' and resid 254 through 265 removed outlier: 3.518A pdb=" N TYR B 258 " --> pdb=" O ASP B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 293 Processing helix chain 'B' and resid 307 through 316 Processing helix chain 'B' and resid 334 through 337 No H-bonds generated for 'chain 'B' and resid 334 through 337' Processing helix chain 'B' and resid 343 through 357 removed outlier: 3.969A pdb=" N ARG B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N PHE B 357 " --> pdb=" O TYR B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 378 Processing helix chain 'B' and resid 417 through 420 No H-bonds generated for 'chain 'B' and resid 417 through 420' Processing helix chain 'B' and resid 453 through 471 Proline residue: B 458 - end of helix Processing helix chain 'B' and resid 476 through 484 Processing helix chain 'B' and resid 495 through 501 Processing helix chain 'C' and resid 20 through 23 No H-bonds generated for 'chain 'C' and resid 20 through 23' Processing helix chain 'C' and resid 32 through 34 No H-bonds generated for 'chain 'C' and resid 32 through 34' Processing helix chain 'C' and resid 46 through 48 No H-bonds generated for 'chain 'C' and resid 46 through 48' Processing helix chain 'C' and resid 76 through 85 Processing helix chain 'C' and resid 97 through 108 Processing helix chain 'C' and resid 128 through 136 Processing helix chain 'C' and resid 160 through 162 No H-bonds generated for 'chain 'C' and resid 160 through 162' Processing helix chain 'C' and resid 194 through 204 Processing helix chain 'C' and resid 224 through 227 No H-bonds generated for 'chain 'C' and resid 224 through 227' Processing helix chain 'C' and resid 254 through 265 removed outlier: 3.544A pdb=" N TYR C 258 " --> pdb=" O ASP C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 293 Processing helix chain 'C' and resid 307 through 316 Processing helix chain 'C' and resid 334 through 337 No H-bonds generated for 'chain 'C' and resid 334 through 337' Processing helix chain 'C' and resid 343 through 357 removed outlier: 3.978A pdb=" N ARG C 356 " --> pdb=" O GLU C 352 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N PHE C 357 " --> pdb=" O TYR C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 378 Processing helix chain 'C' and resid 417 through 420 No H-bonds generated for 'chain 'C' and resid 417 through 420' Processing helix chain 'C' and resid 453 through 471 Proline residue: C 458 - end of helix Processing helix chain 'C' and resid 476 through 484 Processing helix chain 'C' and resid 495 through 501 Processing helix chain 'D' and resid 20 through 23 No H-bonds generated for 'chain 'D' and resid 20 through 23' Processing helix chain 'D' and resid 32 through 34 No H-bonds generated for 'chain 'D' and resid 32 through 34' Processing helix chain 'D' and resid 46 through 48 No H-bonds generated for 'chain 'D' and resid 46 through 48' Processing helix chain 'D' and resid 76 through 85 Processing helix chain 'D' and resid 97 through 108 Processing helix chain 'D' and resid 128 through 136 Processing helix chain 'D' and resid 160 through 162 No H-bonds generated for 'chain 'D' and resid 160 through 162' Processing helix chain 'D' and resid 194 through 204 Processing helix chain 'D' and resid 224 through 227 No H-bonds generated for 'chain 'D' and resid 224 through 227' Processing helix chain 'D' and resid 254 through 265 Processing helix chain 'D' and resid 281 through 293 Processing helix chain 'D' and resid 307 through 316 Processing helix chain 'D' and resid 334 through 337 No H-bonds generated for 'chain 'D' and resid 334 through 337' Processing helix chain 'D' and resid 343 through 357 removed outlier: 3.970A pdb=" N ARG D 356 " --> pdb=" O GLU D 352 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N PHE D 357 " --> pdb=" O TYR D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 378 Processing helix chain 'D' and resid 417 through 420 No H-bonds generated for 'chain 'D' and resid 417 through 420' Processing helix chain 'D' and resid 453 through 471 Proline residue: D 458 - end of helix Processing helix chain 'D' and resid 476 through 484 Processing helix chain 'D' and resid 495 through 501 Processing helix chain 'E' and resid 20 through 23 No H-bonds generated for 'chain 'E' and resid 20 through 23' Processing helix chain 'E' and resid 32 through 34 No H-bonds generated for 'chain 'E' and resid 32 through 34' Processing helix chain 'E' and resid 46 through 48 No H-bonds generated for 'chain 'E' and resid 46 through 48' Processing helix chain 'E' and resid 76 through 85 Processing helix chain 'E' and resid 97 through 108 Processing helix chain 'E' and resid 128 through 136 Processing helix chain 'E' and resid 160 through 162 No H-bonds generated for 'chain 'E' and resid 160 through 162' Processing helix chain 'E' and resid 194 through 204 Processing helix chain 'E' and resid 224 through 227 No H-bonds generated for 'chain 'E' and resid 224 through 227' Processing helix chain 'E' and resid 254 through 265 removed outlier: 3.549A pdb=" N TYR E 258 " --> pdb=" O ASP E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 293 Processing helix chain 'E' and resid 307 through 316 Processing helix chain 'E' and resid 334 through 337 No H-bonds generated for 'chain 'E' and resid 334 through 337' Processing helix chain 'E' and resid 343 through 357 removed outlier: 3.975A pdb=" N ARG E 356 " --> pdb=" O GLU E 352 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N PHE E 357 " --> pdb=" O TYR E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 378 Processing helix chain 'E' and resid 417 through 420 No H-bonds generated for 'chain 'E' and resid 417 through 420' Processing helix chain 'E' and resid 453 through 471 Proline residue: E 458 - end of helix Processing helix chain 'E' and resid 476 through 484 Processing helix chain 'E' and resid 495 through 501 Processing helix chain 'F' and resid 20 through 23 No H-bonds generated for 'chain 'F' and resid 20 through 23' Processing helix chain 'F' and resid 32 through 34 No H-bonds generated for 'chain 'F' and resid 32 through 34' Processing helix chain 'F' and resid 46 through 48 No H-bonds generated for 'chain 'F' and resid 46 through 48' Processing helix chain 'F' and resid 76 through 85 Processing helix chain 'F' and resid 97 through 108 Processing helix chain 'F' and resid 128 through 136 Processing helix chain 'F' and resid 160 through 162 No H-bonds generated for 'chain 'F' and resid 160 through 162' Processing helix chain 'F' and resid 194 through 204 Processing helix chain 'F' and resid 224 through 227 No H-bonds generated for 'chain 'F' and resid 224 through 227' Processing helix chain 'F' and resid 254 through 265 removed outlier: 3.559A pdb=" N TYR F 258 " --> pdb=" O ASP F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 293 Processing helix chain 'F' and resid 307 through 316 Processing helix chain 'F' and resid 334 through 337 No H-bonds generated for 'chain 'F' and resid 334 through 337' Processing helix chain 'F' and resid 343 through 357 removed outlier: 3.979A pdb=" N ARG F 356 " --> pdb=" O GLU F 352 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N PHE F 357 " --> pdb=" O TYR F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 370 through 378 Processing helix chain 'F' and resid 417 through 420 No H-bonds generated for 'chain 'F' and resid 417 through 420' Processing helix chain 'F' and resid 453 through 471 Proline residue: F 458 - end of helix Processing helix chain 'F' and resid 476 through 484 Processing helix chain 'F' and resid 495 through 501 Processing helix chain 'G' and resid 20 through 23 No H-bonds generated for 'chain 'G' and resid 20 through 23' Processing helix chain 'G' and resid 32 through 34 No H-bonds generated for 'chain 'G' and resid 32 through 34' Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'G' and resid 76 through 85 Processing helix chain 'G' and resid 97 through 108 Processing helix chain 'G' and resid 127 through 136 removed outlier: 3.816A pdb=" N LEU G 131 " --> pdb=" O VAL G 127 " (cutoff:3.500A) Processing helix chain 'G' and resid 160 through 162 No H-bonds generated for 'chain 'G' and resid 160 through 162' Processing helix chain 'G' and resid 194 through 204 Processing helix chain 'G' and resid 224 through 227 No H-bonds generated for 'chain 'G' and resid 224 through 227' Processing helix chain 'G' and resid 254 through 265 removed outlier: 3.531A pdb=" N TYR G 258 " --> pdb=" O ASP G 255 " (cutoff:3.500A) Processing helix chain 'G' and resid 281 through 293 Processing helix chain 'G' and resid 307 through 316 Processing helix chain 'G' and resid 334 through 337 No H-bonds generated for 'chain 'G' and resid 334 through 337' Processing helix chain 'G' and resid 343 through 357 removed outlier: 3.964A pdb=" N ARG G 356 " --> pdb=" O GLU G 352 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N PHE G 357 " --> pdb=" O TYR G 353 " (cutoff:3.500A) Processing helix chain 'G' and resid 370 through 378 Processing helix chain 'G' and resid 417 through 420 No H-bonds generated for 'chain 'G' and resid 417 through 420' Processing helix chain 'G' and resid 453 through 471 Proline residue: G 458 - end of helix Processing helix chain 'G' and resid 476 through 484 Processing helix chain 'G' and resid 495 through 501 Processing helix chain 'H' and resid 20 through 23 No H-bonds generated for 'chain 'H' and resid 20 through 23' Processing helix chain 'H' and resid 32 through 34 No H-bonds generated for 'chain 'H' and resid 32 through 34' Processing helix chain 'H' and resid 46 through 48 No H-bonds generated for 'chain 'H' and resid 46 through 48' Processing helix chain 'H' and resid 76 through 85 Processing helix chain 'H' and resid 97 through 108 Processing helix chain 'H' and resid 128 through 136 Processing helix chain 'H' and resid 160 through 162 No H-bonds generated for 'chain 'H' and resid 160 through 162' Processing helix chain 'H' and resid 194 through 204 Processing helix chain 'H' and resid 224 through 227 No H-bonds generated for 'chain 'H' and resid 224 through 227' Processing helix chain 'H' and resid 254 through 265 Processing helix chain 'H' and resid 281 through 293 Processing helix chain 'H' and resid 307 through 316 Processing helix chain 'H' and resid 334 through 337 No H-bonds generated for 'chain 'H' and resid 334 through 337' Processing helix chain 'H' and resid 343 through 357 removed outlier: 3.977A pdb=" N ARG H 356 " --> pdb=" O GLU H 352 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N PHE H 357 " --> pdb=" O TYR H 353 " (cutoff:3.500A) Processing helix chain 'H' and resid 370 through 378 Processing helix chain 'H' and resid 417 through 420 No H-bonds generated for 'chain 'H' and resid 417 through 420' Processing helix chain 'H' and resid 453 through 471 Proline residue: H 458 - end of helix Processing helix chain 'H' and resid 476 through 484 Processing helix chain 'H' and resid 495 through 501 Processing sheet with id= A, first strand: chain 'A' and resid 35 through 37 Processing sheet with id= B, first strand: chain 'A' and resid 65 through 67 removed outlier: 6.488A pdb=" N VAL A 384 " --> pdb=" O ILE A 66 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 208 through 211 removed outlier: 3.733A pdb=" N ALA A 220 " --> pdb=" O ILE A 211 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 247 through 250 removed outlier: 6.796A pdb=" N VAL A 270 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N VAL A 250 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N VAL A 272 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLN A 298 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N LEU A 273 " --> pdb=" O GLN A 298 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N ILE A 300 " --> pdb=" O LEU A 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 401 through 403 removed outlier: 3.661A pdb=" N SER A 403 " --> pdb=" O VAL A 406 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 35 through 37 Processing sheet with id= G, first strand: chain 'B' and resid 65 through 67 removed outlier: 6.476A pdb=" N VAL B 384 " --> pdb=" O ILE B 66 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 208 through 211 removed outlier: 3.794A pdb=" N ALA B 220 " --> pdb=" O ILE B 211 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 247 through 250 removed outlier: 6.788A pdb=" N VAL B 270 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N VAL B 250 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N VAL B 272 " --> pdb=" O VAL B 250 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLN B 298 " --> pdb=" O ILE B 271 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N LEU B 273 " --> pdb=" O GLN B 298 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N ILE B 300 " --> pdb=" O LEU B 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'B' and resid 401 through 403 removed outlier: 3.635A pdb=" N SER B 403 " --> pdb=" O VAL B 406 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 35 through 37 Processing sheet with id= L, first strand: chain 'C' and resid 65 through 67 removed outlier: 6.481A pdb=" N VAL C 384 " --> pdb=" O ILE C 66 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 208 through 211 removed outlier: 3.816A pdb=" N ALA C 220 " --> pdb=" O ILE C 211 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 247 through 250 removed outlier: 6.791A pdb=" N VAL C 270 " --> pdb=" O ALA C 248 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N VAL C 250 " --> pdb=" O VAL C 270 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N VAL C 272 " --> pdb=" O VAL C 250 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N GLN C 298 " --> pdb=" O ILE C 271 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N LEU C 273 " --> pdb=" O GLN C 298 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N ILE C 300 " --> pdb=" O LEU C 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'C' and resid 401 through 403 removed outlier: 3.574A pdb=" N SER C 403 " --> pdb=" O VAL C 406 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 35 through 37 Processing sheet with id= Q, first strand: chain 'D' and resid 65 through 67 removed outlier: 6.485A pdb=" N VAL D 384 " --> pdb=" O ILE D 66 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 208 through 211 removed outlier: 3.818A pdb=" N ALA D 220 " --> pdb=" O ILE D 211 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 247 through 250 removed outlier: 6.795A pdb=" N VAL D 270 " --> pdb=" O ALA D 248 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N VAL D 250 " --> pdb=" O VAL D 270 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N VAL D 272 " --> pdb=" O VAL D 250 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N GLN D 298 " --> pdb=" O ILE D 271 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N LEU D 273 " --> pdb=" O GLN D 298 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N ILE D 300 " --> pdb=" O LEU D 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'D' and resid 401 through 403 removed outlier: 3.590A pdb=" N SER D 403 " --> pdb=" O VAL D 406 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 35 through 37 Processing sheet with id= V, first strand: chain 'E' and resid 65 through 67 removed outlier: 6.475A pdb=" N VAL E 384 " --> pdb=" O ILE E 66 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 208 through 211 removed outlier: 3.699A pdb=" N ALA E 220 " --> pdb=" O ILE E 211 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 247 through 250 removed outlier: 6.797A pdb=" N VAL E 270 " --> pdb=" O ALA E 248 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N VAL E 250 " --> pdb=" O VAL E 270 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N VAL E 272 " --> pdb=" O VAL E 250 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N GLN E 298 " --> pdb=" O ILE E 271 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N LEU E 273 " --> pdb=" O GLN E 298 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N ILE E 300 " --> pdb=" O LEU E 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'E' and resid 401 through 403 removed outlier: 3.628A pdb=" N SER E 403 " --> pdb=" O VAL E 406 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'F' and resid 35 through 37 Processing sheet with id= AA, first strand: chain 'F' and resid 65 through 67 removed outlier: 6.484A pdb=" N VAL F 384 " --> pdb=" O ILE F 66 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'F' and resid 208 through 211 removed outlier: 3.829A pdb=" N ALA F 220 " --> pdb=" O ILE F 211 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'F' and resid 247 through 250 removed outlier: 6.793A pdb=" N VAL F 270 " --> pdb=" O ALA F 248 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N VAL F 250 " --> pdb=" O VAL F 270 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N VAL F 272 " --> pdb=" O VAL F 250 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLN F 298 " --> pdb=" O ILE F 271 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N LEU F 273 " --> pdb=" O GLN F 298 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N ILE F 300 " --> pdb=" O LEU F 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain 'F' and resid 401 through 403 removed outlier: 3.615A pdb=" N SER F 403 " --> pdb=" O VAL F 406 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'G' and resid 35 through 37 Processing sheet with id= AF, first strand: chain 'G' and resid 65 through 67 removed outlier: 6.482A pdb=" N VAL G 384 " --> pdb=" O ILE G 66 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'G' and resid 208 through 211 removed outlier: 3.813A pdb=" N ALA G 220 " --> pdb=" O ILE G 211 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'G' and resid 247 through 250 removed outlier: 6.804A pdb=" N VAL G 270 " --> pdb=" O ALA G 248 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N VAL G 250 " --> pdb=" O VAL G 270 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N VAL G 272 " --> pdb=" O VAL G 250 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N GLN G 298 " --> pdb=" O ILE G 271 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N LEU G 273 " --> pdb=" O GLN G 298 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ILE G 300 " --> pdb=" O LEU G 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AH Processing sheet with id= AI, first strand: chain 'G' and resid 401 through 403 removed outlier: 3.598A pdb=" N SER G 403 " --> pdb=" O VAL G 406 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'H' and resid 35 through 37 Processing sheet with id= AK, first strand: chain 'H' and resid 65 through 67 removed outlier: 6.484A pdb=" N VAL H 384 " --> pdb=" O ILE H 66 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'H' and resid 208 through 211 removed outlier: 3.698A pdb=" N ALA H 220 " --> pdb=" O ILE H 211 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'H' and resid 247 through 250 removed outlier: 6.798A pdb=" N VAL H 270 " --> pdb=" O ALA H 248 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N VAL H 250 " --> pdb=" O VAL H 270 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N VAL H 272 " --> pdb=" O VAL H 250 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N GLN H 298 " --> pdb=" O ILE H 271 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N LEU H 273 " --> pdb=" O GLN H 298 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ILE H 300 " --> pdb=" O LEU H 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AM Processing sheet with id= AN, first strand: chain 'H' and resid 401 through 403 removed outlier: 3.639A pdb=" N SER H 403 " --> pdb=" O VAL H 406 " (cutoff:3.500A) 820 hydrogen bonds defined for protein. 2187 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: 9.54 Time building geometry restraints manager: 13.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 4987 1.26 - 1.40: 6918 1.40 - 1.53: 17690 1.53 - 1.67: 669 1.67 - 1.81: 328 Bond restraints: 30592 Sorted by residual: bond pdb=" C2' ATP B 601 " pdb=" C3' ATP B 601 " ideal model delta sigma weight residual 1.531 1.241 0.290 1.20e-02 6.94e+03 5.84e+02 bond pdb=" C2' ATP E 601 " pdb=" C3' ATP E 601 " ideal model delta sigma weight residual 1.531 1.241 0.290 1.20e-02 6.94e+03 5.83e+02 bond pdb=" C2' ATP G 601 " pdb=" C3' ATP G 601 " ideal model delta sigma weight residual 1.531 1.242 0.289 1.20e-02 6.94e+03 5.81e+02 bond pdb=" C2' ATP H 601 " pdb=" C3' ATP H 601 " ideal model delta sigma weight residual 1.531 1.242 0.289 1.20e-02 6.94e+03 5.79e+02 bond pdb=" C2' ATP F 601 " pdb=" C3' ATP F 601 " ideal model delta sigma weight residual 1.531 1.242 0.289 1.20e-02 6.94e+03 5.79e+02 ... (remaining 30587 not shown) Histogram of bond angle deviations from ideal: 97.58 - 106.52: 896 106.52 - 115.46: 19601 115.46 - 124.40: 20572 124.40 - 133.34: 379 133.34 - 142.28: 48 Bond angle restraints: 41496 Sorted by residual: angle pdb=" PB ATP G 601 " pdb=" O3B ATP G 601 " pdb=" PG ATP G 601 " ideal model delta sigma weight residual 139.87 117.23 22.64 1.00e+00 1.00e+00 5.12e+02 angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 117.68 22.19 1.00e+00 1.00e+00 4.93e+02 angle pdb=" PB ATP C 602 " pdb=" O3B ATP C 602 " pdb=" PG ATP C 602 " ideal model delta sigma weight residual 139.87 117.81 22.06 1.00e+00 1.00e+00 4.87e+02 angle pdb=" PB ATP H 601 " pdb=" O3B ATP H 601 " pdb=" PG ATP H 601 " ideal model delta sigma weight residual 139.87 118.19 21.68 1.00e+00 1.00e+00 4.70e+02 angle pdb=" PB ATP F 601 " pdb=" O3B ATP F 601 " pdb=" PG ATP F 601 " ideal model delta sigma weight residual 139.87 118.27 21.60 1.00e+00 1.00e+00 4.66e+02 ... (remaining 41491 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.92: 17329 32.92 - 65.84: 556 65.84 - 98.76: 114 98.76 - 131.68: 0 131.68 - 164.60: 1 Dihedral angle restraints: 18000 sinusoidal: 7144 harmonic: 10856 Sorted by residual: dihedral pdb=" C5' IMP H 603 " pdb=" O5' IMP H 603 " pdb=" P IMP H 603 " pdb=" O2P IMP H 603 " ideal model delta sinusoidal sigma weight residual -168.07 -3.47 -164.60 1 2.00e+01 2.50e-03 4.71e+01 dihedral pdb=" N THR A 10 " pdb=" C THR A 10 " pdb=" CA THR A 10 " pdb=" CB THR A 10 " ideal model delta harmonic sigma weight residual 123.40 140.08 -16.68 0 2.50e+00 1.60e-01 4.45e+01 dihedral pdb=" C THR A 10 " pdb=" N THR A 10 " pdb=" CA THR A 10 " pdb=" CB THR A 10 " ideal model delta harmonic sigma weight residual -122.00 -136.36 14.36 0 2.50e+00 1.60e-01 3.30e+01 ... (remaining 17997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.136: 4730 0.136 - 0.273: 38 0.273 - 0.409: 30 0.409 - 0.545: 0 0.545 - 0.682: 2 Chirality restraints: 4800 Sorted by residual: chirality pdb=" CA THR A 10 " pdb=" N THR A 10 " pdb=" C THR A 10 " pdb=" CB THR A 10 " both_signs ideal model delta sigma weight residual False 2.53 1.84 0.68 2.00e-01 2.50e+01 1.16e+01 chirality pdb=" CA TYR E 12 " pdb=" N TYR E 12 " pdb=" C TYR E 12 " pdb=" CB TYR E 12 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.61 2.00e-01 2.50e+01 9.16e+00 chirality pdb=" C3B NAD H 604 " pdb=" C2B NAD H 604 " pdb=" C4B NAD H 604 " pdb=" O3B NAD H 604 " both_signs ideal model delta sigma weight residual False -2.71 -2.34 -0.37 2.00e-01 2.50e+01 3.44e+00 ... (remaining 4797 not shown) Planarity restraints: 5160 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR E 12 " 0.033 2.00e-02 2.50e+03 6.47e-02 4.19e+01 pdb=" C TYR E 12 " -0.112 2.00e-02 2.50e+03 pdb=" O TYR E 12 " 0.043 2.00e-02 2.50e+03 pdb=" N VAL E 13 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 12 " -0.010 2.00e-02 2.50e+03 3.27e-02 2.14e+01 pdb=" CG TYR E 12 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR E 12 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR E 12 " -0.050 2.00e-02 2.50e+03 pdb=" CE1 TYR E 12 " -0.051 2.00e-02 2.50e+03 pdb=" CE2 TYR E 12 " 0.022 2.00e-02 2.50e+03 pdb=" CZ TYR E 12 " 0.008 2.00e-02 2.50e+03 pdb=" OH TYR E 12 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 8 " -0.009 2.00e-02 2.50e+03 1.83e-02 3.35e+00 pdb=" C GLY A 8 " 0.032 2.00e-02 2.50e+03 pdb=" O GLY A 8 " -0.012 2.00e-02 2.50e+03 pdb=" N GLY A 9 " -0.011 2.00e-02 2.50e+03 ... (remaining 5157 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 1609 2.70 - 3.25: 31025 3.25 - 3.80: 51617 3.80 - 4.35: 68617 4.35 - 4.90: 110847 Nonbonded interactions: 263715 Sorted by model distance: nonbonded pdb=" OD1 ASP C 364 " pdb=" O3' IMP C 603 " model vdw 2.150 2.440 nonbonded pdb=" OD1 ASP F 226 " pdb=" O3' ATP F 602 " model vdw 2.188 2.440 nonbonded pdb=" O ALA D 396 " pdb=" NZ LYS D 409 " model vdw 2.188 2.520 nonbonded pdb=" O2' ATP C 601 " pdb=" O3' ATP C 601 " model vdw 2.188 2.432 nonbonded pdb=" O ALA A 396 " pdb=" NZ LYS A 409 " model vdw 2.189 2.520 ... (remaining 263710 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' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 3.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 9.890 Check model and map are aligned: 0.430 Set scattering table: 0.260 Process input model: 73.650 Find NCS groups from input model: 2.010 Set up NCS constraints: 0.200 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 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 : 0.017 0.290 30592 Z= 1.120 Angle : 1.397 22.637 41496 Z= 0.939 Chirality : 0.060 0.682 4800 Planarity : 0.004 0.065 5160 Dihedral : 16.615 164.597 11088 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.99 % Favored : 92.96 % Rotamer Outliers : 4.87 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.02 (0.12), residues: 3792 helix: -1.31 (0.12), residues: 1416 sheet: -1.25 (0.23), residues: 352 loop : -2.74 (0.12), residues: 2024 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 755 residues out of total 3120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 603 time to evaluate : 3.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 152 outliers final: 108 residues processed: 735 average time/residue: 0.4392 time to fit residues: 504.4585 Evaluate side-chains 671 residues out of total 3120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 563 time to evaluate : 3.612 Switching outliers to nearest non-outliers outliers start: 108 outliers final: 0 residues processed: 108 average time/residue: 0.3030 time to fit residues: 63.6465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 324 optimal weight: 0.6980 chunk 291 optimal weight: 1.9990 chunk 161 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 196 optimal weight: 0.6980 chunk 155 optimal weight: 5.9990 chunk 300 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 chunk 183 optimal weight: 0.9980 chunk 224 optimal weight: 0.6980 chunk 348 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN A 277 GLN A 303 ASN A 454 GLN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 GLN B 277 GLN B 303 ASN ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 GLN C 277 GLN C 303 ASN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 GLN D 277 GLN D 303 ASN D 454 GLN ** D 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 GLN E 277 GLN E 303 ASN E 469 GLN ** E 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 GLN ** F 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 GLN F 303 ASN F 454 GLN ** F 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 GLN G 277 GLN ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 303 ASN ** G 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 112 GLN ** H 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 277 GLN H 303 ASN H 454 GLN ** H 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 30592 Z= 0.218 Angle : 0.538 7.647 41496 Z= 0.281 Chirality : 0.043 0.156 4800 Planarity : 0.004 0.079 5160 Dihedral : 9.399 170.216 4272 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer Outliers : 1.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.13), residues: 3792 helix: -0.22 (0.13), residues: 1432 sheet: -0.89 (0.26), residues: 288 loop : -2.09 (0.13), residues: 2072 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 3120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 664 time to evaluate : 3.461 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 outliers start: 57 outliers final: 26 residues processed: 711 average time/residue: 0.4452 time to fit residues: 492.1136 Evaluate side-chains 660 residues out of total 3120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 634 time to evaluate : 3.309 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.2774 time to fit residues: 17.8572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 193 optimal weight: 1.9990 chunk 108 optimal weight: 8.9990 chunk 290 optimal weight: 0.5980 chunk 237 optimal weight: 0.5980 chunk 96 optimal weight: 4.9990 chunk 349 optimal weight: 0.8980 chunk 377 optimal weight: 7.9990 chunk 311 optimal weight: 2.9990 chunk 346 optimal weight: 5.9990 chunk 119 optimal weight: 0.6980 chunk 280 optimal weight: 0.0980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 GLN ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 GLN C 241 GLN ** C 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 GLN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 GLN ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 230 ASN ** E 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 334 GLN ** F 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 202 GLN ** G 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 334 GLN ** H 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 30592 Z= 0.169 Angle : 0.493 7.622 41496 Z= 0.255 Chirality : 0.041 0.143 4800 Planarity : 0.004 0.032 5160 Dihedral : 8.984 176.395 4272 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer Outliers : 1.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: -1.15 (0.14), residues: 3792 helix: 0.35 (0.14), residues: 1416 sheet: -0.50 (0.24), residues: 288 loop : -1.65 (0.14), residues: 2088 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 726 residues out of total 3120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 684 time to evaluate : 3.434 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 outliers start: 42 outliers final: 21 residues processed: 709 average time/residue: 0.4333 time to fit residues: 485.0998 Evaluate side-chains 666 residues out of total 3120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 645 time to evaluate : 3.475 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.2958 time to fit residues: 16.2251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 345 optimal weight: 2.9990 chunk 262 optimal weight: 0.3980 chunk 181 optimal weight: 3.9990 chunk 38 optimal weight: 0.3980 chunk 166 optimal weight: 3.9990 chunk 234 optimal weight: 1.9990 chunk 350 optimal weight: 5.9990 chunk 371 optimal weight: 0.8980 chunk 183 optimal weight: 0.0070 chunk 332 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 GLN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 GLN ** D 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 334 GLN E 469 GLN ** E 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 334 GLN ** G 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 30592 Z= 0.190 Angle : 0.494 7.038 41496 Z= 0.253 Chirality : 0.042 0.142 4800 Planarity : 0.004 0.034 5160 Dihedral : 8.729 168.923 4272 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer Outliers : 1.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: -0.96 (0.14), residues: 3792 helix: 0.53 (0.14), residues: 1416 sheet: -0.50 (0.25), residues: 280 loop : -1.53 (0.14), residues: 2096 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 699 residues out of total 3120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 658 time to evaluate : 3.805 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 outliers start: 41 outliers final: 27 residues processed: 678 average time/residue: 0.4349 time to fit residues: 464.2582 Evaluate side-chains 662 residues out of total 3120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 635 time to evaluate : 3.539 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.2896 time to fit residues: 19.2100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 309 optimal weight: 5.9990 chunk 210 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 276 optimal weight: 0.9990 chunk 153 optimal weight: 5.9990 chunk 316 optimal weight: 4.9990 chunk 256 optimal weight: 0.0770 chunk 0 optimal weight: 5.9990 chunk 189 optimal weight: 2.9990 chunk 333 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 overall best weight: 1.1544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 498 GLN ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN ** C 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN ** D 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 498 GLN ** E 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 498 GLN ** F 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 498 GLN ** G 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 498 GLN ** H 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 498 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.029 30592 Z= 0.251 Angle : 0.509 8.898 41496 Z= 0.261 Chirality : 0.042 0.142 4800 Planarity : 0.004 0.036 5160 Dihedral : 8.506 140.068 4272 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer Outliers : 2.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.14), residues: 3792 helix: 0.36 (0.14), residues: 1472 sheet: -0.50 (0.25), residues: 280 loop : -1.44 (0.14), residues: 2040 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 716 residues out of total 3120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 652 time to evaluate : 3.321 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 outliers start: 64 outliers final: 37 residues processed: 687 average time/residue: 0.4233 time to fit residues: 459.3771 Evaluate side-chains 674 residues out of total 3120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 637 time to evaluate : 3.454 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.2776 time to fit residues: 23.8847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 124 optimal weight: 4.9990 chunk 334 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 217 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 371 optimal weight: 3.9990 chunk 308 optimal weight: 0.4980 chunk 172 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 195 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 GLN C 230 ASN ** C 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 30592 Z= 0.176 Angle : 0.488 10.132 41496 Z= 0.250 Chirality : 0.042 0.173 4800 Planarity : 0.003 0.035 5160 Dihedral : 8.167 100.869 4272 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer Outliers : 0.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: -0.85 (0.14), residues: 3792 helix: 0.42 (0.14), residues: 1472 sheet: -0.48 (0.24), residues: 280 loop : -1.32 (0.14), residues: 2040 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 3120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 667 time to evaluate : 3.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 10 residues processed: 679 average time/residue: 0.4274 time to fit residues: 459.3692 Evaluate side-chains 654 residues out of total 3120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 644 time to evaluate : 3.413 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2755 time to fit residues: 9.6239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 358 optimal weight: 3.9990 chunk 41 optimal weight: 7.9990 chunk 211 optimal weight: 0.2980 chunk 271 optimal weight: 1.9990 chunk 210 optimal weight: 2.9990 chunk 312 optimal weight: 0.9990 chunk 207 optimal weight: 0.8980 chunk 370 optimal weight: 0.7980 chunk 231 optimal weight: 7.9990 chunk 225 optimal weight: 2.9990 chunk 170 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 GLN ** C 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 202 GLN ** E 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 230 ASN ** F 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 202 GLN ** H 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 30592 Z= 0.197 Angle : 0.490 9.090 41496 Z= 0.251 Chirality : 0.042 0.169 4800 Planarity : 0.003 0.035 5160 Dihedral : 8.001 86.988 4272 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer Outliers : 1.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: -0.78 (0.14), residues: 3792 helix: 0.43 (0.14), residues: 1480 sheet: -0.43 (0.24), residues: 280 loop : -1.26 (0.14), residues: 2032 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 699 residues out of total 3120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 657 time to evaluate : 3.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 28 residues processed: 682 average time/residue: 0.4321 time to fit residues: 466.4043 Evaluate side-chains 670 residues out of total 3120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 642 time to evaluate : 3.660 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.2800 time to fit residues: 19.7745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 228 optimal weight: 0.6980 chunk 147 optimal weight: 0.0060 chunk 221 optimal weight: 2.9990 chunk 111 optimal weight: 7.9990 chunk 72 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 235 optimal weight: 1.9990 chunk 252 optimal weight: 7.9990 chunk 182 optimal weight: 0.0870 chunk 34 optimal weight: 1.9990 chunk 290 optimal weight: 0.2980 overall best weight: 0.3774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 202 GLN ** E 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 202 GLN ** H 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 30592 Z= 0.139 Angle : 0.472 9.776 41496 Z= 0.240 Chirality : 0.041 0.173 4800 Planarity : 0.003 0.033 5160 Dihedral : 7.803 87.665 4272 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer Outliers : 0.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.14), residues: 3792 helix: 0.53 (0.14), residues: 1472 sheet: -0.30 (0.24), residues: 280 loop : -1.18 (0.14), residues: 2040 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 3120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 659 time to evaluate : 3.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 15 residues processed: 664 average time/residue: 0.4410 time to fit residues: 461.5706 Evaluate side-chains 657 residues out of total 3120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 642 time to evaluate : 3.429 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2789 time to fit residues: 12.5774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 336 optimal weight: 2.9990 chunk 354 optimal weight: 3.9990 chunk 323 optimal weight: 0.9980 chunk 344 optimal weight: 4.9990 chunk 207 optimal weight: 4.9990 chunk 150 optimal weight: 0.9990 chunk 270 optimal weight: 3.9990 chunk 105 optimal weight: 0.7980 chunk 311 optimal weight: 3.9990 chunk 326 optimal weight: 4.9990 chunk 343 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 ASN ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 230 ASN ** G 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.037 30592 Z= 0.322 Angle : 0.549 9.795 41496 Z= 0.280 Chirality : 0.044 0.181 4800 Planarity : 0.004 0.038 5160 Dihedral : 7.981 89.217 4272 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer Outliers : 0.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: -0.66 (0.14), residues: 3792 helix: 0.44 (0.14), residues: 1480 sheet: -0.19 (0.23), residues: 360 loop : -1.17 (0.14), residues: 1952 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 3120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 648 time to evaluate : 3.426 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 outliers start: 16 outliers final: 7 residues processed: 658 average time/residue: 0.4529 time to fit residues: 469.5565 Evaluate side-chains 643 residues out of total 3120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 636 time to evaluate : 3.623 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2954 time to fit residues: 9.1174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 226 optimal weight: 0.7980 chunk 364 optimal weight: 0.9980 chunk 222 optimal weight: 0.6980 chunk 173 optimal weight: 1.9990 chunk 253 optimal weight: 0.9980 chunk 382 optimal weight: 0.7980 chunk 352 optimal weight: 7.9990 chunk 304 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 235 optimal weight: 0.6980 chunk 186 optimal weight: 0.0980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 30592 Z= 0.175 Angle : 0.496 9.193 41496 Z= 0.253 Chirality : 0.042 0.178 4800 Planarity : 0.003 0.035 5160 Dihedral : 7.808 89.525 4272 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: -0.59 (0.14), residues: 3792 helix: 0.45 (0.14), residues: 1480 sheet: -0.13 (0.23), residues: 360 loop : -1.09 (0.14), residues: 1952 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 3120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 672 time to evaluate : 3.680 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 outliers start: 7 outliers final: 6 residues processed: 672 average time/residue: 0.4465 time to fit residues: 475.9874 Evaluate side-chains 660 residues out of total 3120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 654 time to evaluate : 3.862 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2963 time to fit residues: 8.5756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 241 optimal weight: 1.9990 chunk 324 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 chunk 280 optimal weight: 0.4980 chunk 44 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 305 optimal weight: 0.6980 chunk 127 optimal weight: 0.9990 chunk 313 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 56 optimal weight: 3.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 241 GLN ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 241 GLN ** E 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 202 GLN ** F 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.157883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.111431 restraints weight = 33599.476| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.02 r_work: 0.2912 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 30592 Z= 0.187 Angle : 0.499 8.394 41496 Z= 0.255 Chirality : 0.042 0.175 4800 Planarity : 0.003 0.035 5160 Dihedral : 7.728 88.751 4272 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: -0.49 (0.14), residues: 3792 helix: 0.53 (0.14), residues: 1472 sheet: 0.07 (0.23), residues: 344 loop : -1.05 (0.14), residues: 1976 =============================================================================== Job complete usr+sys time: 8433.60 seconds wall clock time: 152 minutes 40.96 seconds (9160.96 seconds total)