Starting phenix.real_space_refine (version: 1.21rc1) on Wed Jul 12 23:37:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l9p_23244/07_2023/7l9p_23244_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l9p_23244/07_2023/7l9p_23244.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l9p_23244/07_2023/7l9p_23244.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l9p_23244/07_2023/7l9p_23244.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l9p_23244/07_2023/7l9p_23244_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l9p_23244/07_2023/7l9p_23244_updated.pdb" } resolution = 3.6 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= 0.002 sd= 1.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5328 atoms to isotropic. 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 15 5.49 5 S 76 5.16 5 C 14015 2.51 5 N 3699 2.21 5 O 4103 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 137": "OD1" <-> "OD2" Residue "A ASP 142": "OD1" <-> "OD2" Residue "A GLU 144": "OE1" <-> "OE2" Residue "A PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 241": "OD1" <-> "OD2" Residue "A ASP 244": "OD1" <-> "OD2" Residue "A PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 285": "OD1" <-> "OD2" Residue "A GLU 337": "OE1" <-> "OE2" Residue "A PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 419": "OD1" <-> "OD2" Residue "B GLU 24": "OE1" <-> "OE2" Residue "B ASP 37": "OD1" <-> "OD2" Residue "B GLU 60": "OE1" <-> "OE2" Residue "B ASP 62": "OD1" <-> "OD2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 104": "OE1" <-> "OE2" Residue "B PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 142": "OD1" <-> "OD2" Residue "B ASP 161": "OD1" <-> "OD2" Residue "B TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 241": "OD1" <-> "OD2" Residue "B ASP 242": "OD1" <-> "OD2" Residue "B ASP 244": "OD1" <-> "OD2" Residue "B PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 269": "OE1" <-> "OE2" Residue "B ASP 311": "OD1" <-> "OD2" Residue "B TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 355": "OE1" <-> "OE2" Residue "B PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 375": "OD1" <-> "OD2" Residue "B GLU 381": "OE1" <-> "OE2" Residue "B ARG 386": "NH1" <-> "NH2" Residue "B GLU 408": "OE1" <-> "OE2" Residue "B GLU 424": "OE1" <-> "OE2" Residue "C ASP 37": "OD1" <-> "OD2" Residue "C PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 104": "OE1" <-> "OE2" Residue "C ASP 105": "OD1" <-> "OD2" Residue "C GLU 114": "OE1" <-> "OE2" Residue "C GLU 131": "OE1" <-> "OE2" Residue "C ASP 137": "OD1" <-> "OD2" Residue "C ASP 142": "OD1" <-> "OD2" Residue "C GLU 144": "OE1" <-> "OE2" Residue "C TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 224": "OE1" <-> "OE2" Residue "C PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 252": "OD1" <-> "OD2" Residue "C ASP 306": "OD1" <-> "OD2" Residue "C PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 311": "OD1" <-> "OD2" Residue "C TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 336": "OE1" <-> "OE2" Residue "C GLU 337": "OE1" <-> "OE2" Residue "C PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 375": "OD1" <-> "OD2" Residue "C GLU 381": "OE1" <-> "OE2" Residue "C TYR 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 36": "OE1" <-> "OE2" Residue "D ASP 37": "OD1" <-> "OD2" Residue "D TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 77": "OD1" <-> "OD2" Residue "D PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 113": "OE1" <-> "OE2" Residue "D TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 211": "OE1" <-> "OE2" Residue "D PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 238": "OD1" <-> "OD2" Residue "D ASP 242": "OD1" <-> "OD2" Residue "D ASP 244": "OD1" <-> "OD2" Residue "D ASP 306": "OD1" <-> "OD2" Residue "D PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 311": "OD1" <-> "OD2" Residue "D GLU 336": "OE1" <-> "OE2" Residue "D GLU 337": "OE1" <-> "OE2" Residue "D TYR 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 381": "OE1" <-> "OE2" Residue "D PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 423": "OE1" <-> "OE2" Residue "E GLU 24": "OE1" <-> "OE2" Residue "E GLU 36": "OE1" <-> "OE2" Residue "E ASP 77": "OD1" <-> "OD2" Residue "E ASP 89": "OD1" <-> "OD2" Residue "E PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 161": "OD1" <-> "OD2" Residue "E TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 224": "OE1" <-> "OE2" Residue "E PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 238": "OD1" <-> "OD2" Residue "E ASP 244": "OD1" <-> "OD2" Residue "E PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 252": "OD1" <-> "OD2" Residue "E GLU 255": "OE1" <-> "OE2" Residue "E ARG 289": "NH1" <-> "NH2" Residue "E ASP 306": "OD1" <-> "OD2" Residue "E PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 312": "NH1" <-> "NH2" Residue "E TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 381": "OE1" <-> "OE2" Residue "E PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 419": "OD1" <-> "OD2" Residue "E GLU 424": "OE1" <-> "OE2" Residue "F TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 142": "OD1" <-> "OD2" Residue "F GLU 144": "OE1" <-> "OE2" Residue "F ASP 151": "OD1" <-> "OD2" Residue "F TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 161": "OD1" <-> "OD2" Residue "F TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 211": "OE1" <-> "OE2" Residue "F PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 238": "OD1" <-> "OD2" Residue "F ASP 241": "OD1" <-> "OD2" Residue "F ASP 244": "OD1" <-> "OD2" Residue "F PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 252": "OD1" <-> "OD2" Residue "F ASP 285": "OD1" <-> "OD2" Residue "F GLU 303": "OE1" <-> "OE2" Residue "F ASP 311": "OD1" <-> "OD2" Residue "F TYR 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 355": "OE1" <-> "OE2" Residue "F GLU 363": "OE1" <-> "OE2" Residue "F PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 408": "OE1" <-> "OE2" Residue "F PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 419": "OD1" <-> "OD2" Residue "F PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 17": "OD1" <-> "OD2" Residue "G ARG 45": "NH1" <-> "NH2" Residue "G TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 66": "OD1" <-> "OD2" Residue "G GLU 76": "OE1" <-> "OE2" Residue "G ASP 79": "OD1" <-> "OD2" Residue "G PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 101": "OE1" <-> "OE2" Residue "G GLU 120": "OE1" <-> "OE2" Residue "G GLU 154": "OE1" <-> "OE2" Residue "G PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 176": "OE1" <-> "OE2" Residue "G GLU 204": "OE1" <-> "OE2" Residue "I ASP 8": "OD1" <-> "OD2" Residue "I PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 35": "OE1" <-> "OE2" Residue "I ASP 66": "OD1" <-> "OD2" Residue "I ASP 79": "OD1" <-> "OD2" Residue "I ASP 89": "OD1" <-> "OD2" Residue "I GLU 91": "OE1" <-> "OE2" Residue "I GLU 96": "OE1" <-> "OE2" Residue "I PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 101": "OE1" <-> "OE2" Residue "I GLU 120": "OE1" <-> "OE2" Residue "I PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 138": "OD1" <-> "OD2" Residue "I GLU 154": "OE1" <-> "OE2" Residue "I ASP 175": "OD1" <-> "OD2" Residue "I ARG 185": "NH1" <-> "NH2" Residue "I ASP 195": "OD1" <-> "OD2" Residue "I TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 204": "OE1" <-> "OE2" Residue "J TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 89": "OD1" <-> "OD2" Residue "J GLU 91": "OE1" <-> "OE2" Residue "J ARG 93": "NH1" <-> "NH2" Residue "J GLU 96": "OE1" <-> "OE2" Residue "J PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 134": "OD1" <-> "OD2" Residue "J ASP 138": "OD1" <-> "OD2" Residue "J TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 204": "OE1" <-> "OE2" Residue "J GLU 205": "OE1" <-> "OE2" Residue "K ASP 17": "OD1" <-> "OD2" Residue "K PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 81": "OE1" <-> "OE2" Residue "K PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 120": "OE1" <-> "OE2" Residue "K GLU 205": "OE1" <-> "OE2" Residue "Y PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 46": "OD1" <-> "OD2" Residue "Y ASP 60": "OD1" <-> "OD2" Residue "Y PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 76": "OD1" <-> "OD2" Residue "X PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 60": "OD1" <-> "OD2" Residue "X PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 21908 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 2301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2301 Classifications: {'peptide': 308} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 9, 'TRANS': 298} Unresolved non-hydrogen bonds: 143 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 8, 'ASN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 83 Chain: "B" Number of atoms: 3037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3037 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 11, 'TRANS': 386} Chain breaks: 2 Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 152 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 3, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 77 Chain: "C" Number of atoms: 2995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 2995 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 386} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 167 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 132 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 5, 'GLU:plan': 12, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 107 Chain: "D" Number of atoms: 3043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3043 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 11, 'TRANS': 386} Chain breaks: 2 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 5, 'ASN:plan1': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 74 Chain: "E" Number of atoms: 2982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 2982 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 386} Chain breaks: 2 Unresolved non-hydrogen bonds: 179 Unresolved non-hydrogen angles: 215 Unresolved non-hydrogen dihedrals: 145 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 4, 'ASN:plan1': 4, 'HIS:plan': 1, 'GLU:plan': 11, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 121 Chain: "F" Number of atoms: 2007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2007 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 264} Chain breaks: 3 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 195 Unresolved non-hydrogen dihedrals: 133 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 7, 'PHE:plan': 2, 'ARG:plan': 4, 'ASN:plan1': 3, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 77 Chain: "G" Number of atoms: 1199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1199 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 9, 'TRANS': 162} Chain breaks: 2 Unresolved non-hydrogen bonds: 234 Unresolved non-hydrogen angles: 289 Unresolved non-hydrogen dihedrals: 211 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 1, 'TYR:plan': 3, 'TRP:plan': 1, 'HIS:plan': 4, 'PHE:plan': 4, 'GLU:plan': 5, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 148 Chain: "I" Number of atoms: 1325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1325 Classifications: {'peptide': 189} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 11, 'TRANS': 177} Chain breaks: 2 Unresolved non-hydrogen bonds: 234 Unresolved non-hydrogen angles: 288 Unresolved non-hydrogen dihedrals: 202 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 3, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 143 Chain: "J" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 945 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain breaks: 3 Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 67 Chain: "K" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 929 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 7, 'TRANS': 119} Chain breaks: 3 Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 64 Chain: "Y" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 522 Classifications: {'peptide': 69} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 12, 'TRANS': 56} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 23 Chain: "X" Number of atoms: 468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 468 Classifications: {'peptide': 63} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 11, 'TRANS': 51} Chain breaks: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 2, 'PHE:plan': 1, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.77, per 1000 atoms: 0.49 Number of scatterers: 21908 At special positions: 0 Unit cell: (147.896, 134.064, 192.584, 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 76 16.00 P 15 15.00 O 4103 8.00 N 3699 7.00 C 14015 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.04 Conformation dependent library (CDL) restraints added in 3.7 seconds 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5654 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 104 helices and 19 sheets defined 39.6% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.98 Creating SS restraints... Processing helix chain 'A' and resid 145 through 162 Processing helix chain 'A' and resid 185 through 199 Processing helix chain 'A' and resid 215 through 217 No H-bonds generated for 'chain 'A' and resid 215 through 217' Processing helix chain 'A' and resid 222 through 241 removed outlier: 4.551A pdb=" N LYS A 227 " --> pdb=" O SER A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 262 removed outlier: 4.594A pdb=" N ALA A 260 " --> pdb=" O SER A 256 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ARG A 261 " --> pdb=" O LEU A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 289 removed outlier: 4.434A pdb=" N ARG A 275 " --> pdb=" O SER A 271 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N VAL A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN A 283 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP A 285 " --> pdb=" O LEU A 281 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG A 289 " --> pdb=" O ASP A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 340 removed outlier: 4.074A pdb=" N PHE A 328 " --> pdb=" O ALA A 324 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LYS A 329 " --> pdb=" O ALA A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 359 Processing helix chain 'A' and resid 369 through 379 Processing helix chain 'A' and resid 387 through 399 Proline residue: A 392 - end of helix Processing helix chain 'A' and resid 407 through 427 removed outlier: 3.797A pdb=" N GLN A 412 " --> pdb=" O GLU A 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 49 Processing helix chain 'B' and resid 64 through 69 Processing helix chain 'B' and resid 130 through 132 No H-bonds generated for 'chain 'B' and resid 130 through 132' Processing helix chain 'B' and resid 135 through 138 No H-bonds generated for 'chain 'B' and resid 135 through 138' Processing helix chain 'B' and resid 146 through 161 Processing helix chain 'B' and resid 185 through 202 removed outlier: 4.113A pdb=" N CYS B 189 " --> pdb=" O LYS B 185 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N LYS B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA B 191 " --> pdb=" O SER B 187 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER B 201 " --> pdb=" O THR B 197 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N SER B 202 " --> pdb=" O ILE B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 216 No H-bonds generated for 'chain 'B' and resid 214 through 216' Processing helix chain 'B' and resid 224 through 240 Processing helix chain 'B' and resid 254 through 256 No H-bonds generated for 'chain 'B' and resid 254 through 256' Processing helix chain 'B' and resid 263 through 265 No H-bonds generated for 'chain 'B' and resid 263 through 265' Processing helix chain 'B' and resid 271 through 273 No H-bonds generated for 'chain 'B' and resid 271 through 273' Processing helix chain 'B' and resid 277 through 289 removed outlier: 3.590A pdb=" N LYS B 288 " --> pdb=" O ILE B 284 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N ARG B 289 " --> pdb=" O ASP B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 341 Processing helix chain 'B' and resid 353 through 358 removed outlier: 3.900A pdb=" N MET B 358 " --> pdb=" O ARG B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 379 Processing helix chain 'B' and resid 387 through 400 Proline residue: B 392 - end of helix Processing helix chain 'B' and resid 407 through 427 Processing helix chain 'C' and resid 35 through 49 Processing helix chain 'C' and resid 64 through 69 Processing helix chain 'C' and resid 135 through 138 No H-bonds generated for 'chain 'C' and resid 135 through 138' Processing helix chain 'C' and resid 145 through 161 removed outlier: 4.509A pdb=" N VAL C 153 " --> pdb=" O LEU C 149 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET C 154 " --> pdb=" O LEU C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 199 removed outlier: 3.541A pdb=" N LEU C 192 " --> pdb=" O LEU C 188 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ALA C 193 " --> pdb=" O CYS C 189 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN C 194 " --> pdb=" O LYS C 190 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N THR C 197 " --> pdb=" O ALA C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 217 No H-bonds generated for 'chain 'C' and resid 214 through 217' Processing helix chain 'C' and resid 229 through 240 Processing helix chain 'C' and resid 254 through 256 No H-bonds generated for 'chain 'C' and resid 254 through 256' Processing helix chain 'C' and resid 271 through 274 Processing helix chain 'C' and resid 277 through 280 No H-bonds generated for 'chain 'C' and resid 277 through 280' Processing helix chain 'C' and resid 302 through 304 No H-bonds generated for 'chain 'C' and resid 302 through 304' Processing helix chain 'C' and resid 324 through 341 Processing helix chain 'C' and resid 353 through 359 Processing helix chain 'C' and resid 367 through 379 Processing helix chain 'C' and resid 385 through 397 Proline residue: C 392 - end of helix Processing helix chain 'C' and resid 407 through 426 removed outlier: 5.166A pdb=" N GLN C 412 " --> pdb=" O GLU C 408 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ALA C 417 " --> pdb=" O ALA C 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 49 Processing helix chain 'D' and resid 64 through 69 Processing helix chain 'D' and resid 135 through 138 No H-bonds generated for 'chain 'D' and resid 135 through 138' Processing helix chain 'D' and resid 143 through 162 removed outlier: 3.619A pdb=" N LYS D 146 " --> pdb=" O VAL D 143 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N SER D 147 " --> pdb=" O GLU D 144 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N HIS D 148 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N TYR D 152 " --> pdb=" O LEU D 149 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP D 161 " --> pdb=" O LEU D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 199 Processing helix chain 'D' and resid 226 through 240 Processing helix chain 'D' and resid 254 through 256 No H-bonds generated for 'chain 'D' and resid 254 through 256' Processing helix chain 'D' and resid 271 through 286 removed outlier: 3.751A pdb=" N ARG D 275 " --> pdb=" O ASP D 272 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N VAL D 276 " --> pdb=" O ALA D 273 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN D 278 " --> pdb=" O ARG D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 310 No H-bonds generated for 'chain 'D' and resid 307 through 310' Processing helix chain 'D' and resid 324 through 341 Processing helix chain 'D' and resid 353 through 358 Processing helix chain 'D' and resid 365 through 380 removed outlier: 4.522A pdb=" N LEU D 369 " --> pdb=" O ASN D 365 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N SER D 370 " --> pdb=" O VAL D 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 388 No H-bonds generated for 'chain 'D' and resid 385 through 388' Processing helix chain 'D' and resid 391 through 394 No H-bonds generated for 'chain 'D' and resid 391 through 394' Processing helix chain 'D' and resid 411 through 427 Processing helix chain 'E' and resid 35 through 49 Processing helix chain 'E' and resid 64 through 69 Processing helix chain 'E' and resid 130 through 132 No H-bonds generated for 'chain 'E' and resid 130 through 132' Processing helix chain 'E' and resid 135 through 138 No H-bonds generated for 'chain 'E' and resid 135 through 138' Processing helix chain 'E' and resid 145 through 161 removed outlier: 4.485A pdb=" N VAL E 153 " --> pdb=" O LEU E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 199 Processing helix chain 'E' and resid 225 through 241 removed outlier: 4.687A pdb=" N THR E 230 " --> pdb=" O GLY E 226 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS E 231 " --> pdb=" O LYS E 227 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET E 232 " --> pdb=" O LEU E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 257 No H-bonds generated for 'chain 'E' and resid 254 through 257' Processing helix chain 'E' and resid 272 through 275 No H-bonds generated for 'chain 'E' and resid 272 through 275' Processing helix chain 'E' and resid 283 through 287 removed outlier: 3.539A pdb=" N ILE E 287 " --> pdb=" O GLN E 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 283 through 287' Processing helix chain 'E' and resid 324 through 340 Processing helix chain 'E' and resid 353 through 359 Processing helix chain 'E' and resid 367 through 379 Processing helix chain 'E' and resid 385 through 395 Proline residue: E 392 - end of helix Processing helix chain 'E' and resid 410 through 427 removed outlier: 4.194A pdb=" N ASP E 419 " --> pdb=" O SER E 415 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 138 No H-bonds generated for 'chain 'F' and resid 135 through 138' Processing helix chain 'F' and resid 148 through 162 removed outlier: 4.245A pdb=" N VAL F 153 " --> pdb=" O LEU F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 200 Processing helix chain 'F' and resid 231 through 239 Processing helix chain 'F' and resid 281 through 289 removed outlier: 4.064A pdb=" N ARG F 289 " --> pdb=" O ASP F 285 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 310 No H-bonds generated for 'chain 'F' and resid 307 through 310' Processing helix chain 'F' and resid 324 through 341 removed outlier: 3.805A pdb=" N CYS F 341 " --> pdb=" O GLU F 337 " (cutoff:3.500A) Processing helix chain 'F' and resid 353 through 359 Processing helix chain 'F' and resid 367 through 375 removed outlier: 3.994A pdb=" N LEU F 371 " --> pdb=" O LYS F 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 382 No H-bonds generated for 'chain 'F' and resid 380 through 382' Processing helix chain 'F' and resid 385 through 398 Proline residue: F 392 - end of helix Processing helix chain 'F' and resid 407 through 423 Processing helix chain 'G' and resid 16 through 33 Processing helix chain 'G' and resid 39 through 41 No H-bonds generated for 'chain 'G' and resid 39 through 41' Processing helix chain 'G' and resid 58 through 77 Proline residue: G 73 - end of helix Processing helix chain 'G' and resid 119 through 132 Processing helix chain 'G' and resid 157 through 163 Processing helix chain 'I' and resid 15 through 33 removed outlier: 4.327A pdb=" N LEU I 19 " --> pdb=" O VAL I 15 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N CYS I 20 " --> pdb=" O ALA I 16 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU I 21 " --> pdb=" O ASP I 17 " (cutoff:3.500A) Processing helix chain 'I' and resid 58 through 67 Processing helix chain 'I' and resid 118 through 135 removed outlier: 4.270A pdb=" N ALA I 125 " --> pdb=" O GLN I 121 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASP I 134 " --> pdb=" O ILE I 130 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N ALA I 135 " --> pdb=" O SER I 131 " (cutoff:3.500A) Processing helix chain 'I' and resid 160 through 163 No H-bonds generated for 'chain 'I' and resid 160 through 163' Processing helix chain 'J' and resid 16 through 34 removed outlier: 4.663A pdb=" N GLU J 21 " --> pdb=" O ASP J 17 " (cutoff:3.500A) Processing helix chain 'J' and resid 58 through 72 Processing helix chain 'J' and resid 121 through 136 removed outlier: 3.940A pdb=" N VAL J 136 " --> pdb=" O VAL J 132 " (cutoff:3.500A) Processing helix chain 'K' and resid 16 through 32 Processing helix chain 'K' and resid 58 through 76 Proline residue: K 73 - end of helix Processing helix chain 'K' and resid 121 through 136 removed outlier: 4.766A pdb=" N ILE K 127 " --> pdb=" O LEU K 123 " (cutoff:3.500A) Processing helix chain 'Y' and resid 51 through 58 Processing helix chain 'X' and resid 42 through 44 No H-bonds generated for 'chain 'X' and resid 42 through 44' Processing helix chain 'X' and resid 51 through 58 removed outlier: 3.597A pdb=" N LYS X 56 " --> pdb=" O LYS X 52 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA X 57 " --> pdb=" O ILE X 53 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE X 58 " --> pdb=" O ALA X 54 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 123 through 125 removed outlier: 6.501A pdb=" N LEU A 246 " --> pdb=" O GLN A 208 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ILE A 210 " --> pdb=" O LEU A 246 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N PHE A 248 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR A 298 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLN A 253 " --> pdb=" O THR A 298 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ILE A 315 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N HIS A 178 " --> pdb=" O ILE A 315 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLN A 317 " --> pdb=" O HIS A 178 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 95 through 100 removed outlier: 6.933A pdb=" N VAL B 21 " --> pdb=" O ALA B 96 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N HIS B 98 " --> pdb=" O VAL B 21 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL B 23 " --> pdb=" O HIS B 98 " (cutoff:3.500A) removed outlier: 8.607A pdb=" N PHE B 100 " --> pdb=" O VAL B 23 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N VAL B 25 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N HIS B 22 " --> pdb=" O ILE B 76 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 316 through 318 removed outlier: 6.481A pdb=" N LEU B 176 " --> pdb=" O GLN B 317 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR B 298 " --> pdb=" O ILE B 251 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ILE B 210 " --> pdb=" O LEU B 250 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 98 through 100 removed outlier: 3.837A pdb=" N HIS C 22 " --> pdb=" O ILE C 76 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER C 72 " --> pdb=" O HIS C 26 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 122 through 125 Processing sheet with id= F, first strand: chain 'C' and resid 175 through 178 Processing sheet with id= G, first strand: chain 'D' and resid 95 through 101 removed outlier: 6.512A pdb=" N VAL D 21 " --> pdb=" O ALA D 96 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N HIS D 98 " --> pdb=" O VAL D 21 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL D 23 " --> pdb=" O HIS D 98 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N PHE D 100 " --> pdb=" O VAL D 23 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N VAL D 25 " --> pdb=" O PHE D 100 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N HIS D 22 " --> pdb=" O ILE D 76 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N SER D 72 " --> pdb=" O HIS D 26 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 123 through 125 removed outlier: 3.792A pdb=" N GLY D 179 " --> pdb=" O SER D 299 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ILE D 315 " --> pdb=" O LEU D 176 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N HIS D 178 " --> pdb=" O ILE D 315 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N GLN D 317 " --> pdb=" O HIS D 178 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 95 through 100 removed outlier: 6.947A pdb=" N VAL E 21 " --> pdb=" O ALA E 96 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N HIS E 98 " --> pdb=" O VAL E 21 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N VAL E 23 " --> pdb=" O HIS E 98 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N PHE E 100 " --> pdb=" O VAL E 23 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL E 25 " --> pdb=" O PHE E 100 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N HIS E 22 " --> pdb=" O ILE E 76 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER E 72 " --> pdb=" O HIS E 26 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 108 through 110 removed outlier: 3.516A pdb=" N GLY E 207 " --> pdb=" O LEU E 127 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LEU E 246 " --> pdb=" O GLN E 208 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N ILE E 210 " --> pdb=" O LEU E 246 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N PHE E 248 " --> pdb=" O ILE E 210 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N ILE E 212 " --> pdb=" O PHE E 248 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LEU E 250 " --> pdb=" O ILE E 212 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N ILE E 315 " --> pdb=" O LEU E 176 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N HIS E 178 " --> pdb=" O ILE E 315 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N GLN E 317 " --> pdb=" O HIS E 178 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 315 through 319 removed outlier: 4.371A pdb=" N ILE F 315 " --> pdb=" O VAL F 174 " (cutoff:3.500A) removed outlier: 9.092A pdb=" N VAL F 175 " --> pdb=" O VAL F 293 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ILE F 295 " --> pdb=" O VAL F 175 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N LEU F 177 " --> pdb=" O ILE F 295 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N THR F 297 " --> pdb=" O LEU F 177 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N GLY F 179 " --> pdb=" O THR F 297 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N VAL F 294 " --> pdb=" O ALA F 245 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL F 247 " --> pdb=" O VAL F 294 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N LEU F 296 " --> pdb=" O VAL F 247 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N VAL F 249 " --> pdb=" O LEU F 296 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N THR F 298 " --> pdb=" O VAL F 249 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE F 251 " --> pdb=" O THR F 298 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N TYR F 206 " --> pdb=" O LEU F 246 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N PHE F 248 " --> pdb=" O TYR F 206 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N GLN F 208 " --> pdb=" O PHE F 248 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LEU F 250 " --> pdb=" O GLN F 208 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N ILE F 210 " --> pdb=" O LEU F 250 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ASP F 252 " --> pdb=" O ILE F 210 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N ILE F 212 " --> pdb=" O ASP F 252 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 43 through 47 Processing sheet with id= M, first strand: chain 'G' and resid 190 through 194 removed outlier: 4.229A pdb=" N GLU G 96 " --> pdb=" O ILE G 87 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE G 102 " --> pdb=" O GLU G 81 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N GLU G 81 " --> pdb=" O ILE G 102 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N HIS G 151 " --> pdb=" O GLU G 81 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N VAL G 83 " --> pdb=" O LEU G 149 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LEU G 149 " --> pdb=" O VAL G 83 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N VAL G 85 " --> pdb=" O THR G 147 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N THR G 147 " --> pdb=" O VAL G 85 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'I' and resid 42 through 44 Processing sheet with id= O, first strand: chain 'I' and resid 145 through 151 removed outlier: 4.074A pdb=" N VAL I 203 " --> pdb=" O ILE I 187 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE I 187 " --> pdb=" O VAL I 203 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'J' and resid 146 through 151 removed outlier: 3.831A pdb=" N GLU J 96 " --> pdb=" O ILE J 87 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'K' and resid 42 through 47 Processing sheet with id= R, first strand: chain 'K' and resid 82 through 86 removed outlier: 3.935A pdb=" N VAL K 86 " --> pdb=" O THR K 147 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'X' and resid 5 through 7 removed outlier: 8.306A pdb=" N ILE X 37 " --> pdb=" O ILE X 6 " (cutoff:3.500A) No H-bonds generated for sheet with id= S 851 hydrogen bonds defined for protein. 2406 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: 7.21 Time building geometry restraints manager: 10.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.36: 7310 1.36 - 1.54: 14690 1.54 - 1.72: 207 1.72 - 1.90: 100 1.90 - 2.07: 5 Bond restraints: 22312 Sorted by residual: bond pdb=" C3' AGS A 901 " pdb=" C4' AGS A 901 " ideal model delta sigma weight residual 1.526 1.318 0.208 1.10e-02 8.26e+03 3.56e+02 bond pdb=" C4 AGS D 901 " pdb=" N9 AGS D 901 " ideal model delta sigma weight residual 1.374 1.186 0.188 1.00e-02 1.00e+04 3.52e+02 bond pdb=" C5 AGS D 901 " pdb=" N7 AGS D 901 " ideal model delta sigma weight residual 1.387 1.201 0.186 1.00e-02 1.00e+04 3.47e+02 bond pdb=" C4' AGS A 901 " pdb=" O4' AGS A 901 " ideal model delta sigma weight residual 1.444 1.626 -0.182 1.20e-02 6.94e+03 2.29e+02 bond pdb=" C5 AGS E 901 " pdb=" N7 AGS E 901 " ideal model delta sigma weight residual 1.387 1.236 0.151 1.00e-02 1.00e+04 2.27e+02 ... (remaining 22307 not shown) Histogram of bond angle deviations from ideal: 84.40 - 95.45: 11 95.45 - 106.50: 696 106.50 - 117.55: 16291 117.55 - 128.60: 13311 128.60 - 139.65: 193 Bond angle restraints: 30502 Sorted by residual: angle pdb=" C5 AGS E 901 " pdb=" C4 AGS E 901 " pdb=" N3 AGS E 901 " ideal model delta sigma weight residual 126.80 114.99 11.81 7.41e-01 1.82e+00 2.54e+02 angle pdb=" C4 AGS D 901 " pdb=" C5 AGS D 901 " pdb=" N7 AGS D 901 " ideal model delta sigma weight residual 110.73 103.84 6.89 4.52e-01 4.89e+00 2.32e+02 angle pdb=" C5 AGS D 901 " pdb=" C4 AGS D 901 " pdb=" N9 AGS D 901 " ideal model delta sigma weight residual 105.77 112.17 -6.40 4.43e-01 5.10e+00 2.09e+02 angle pdb=" C5 AGS A 901 " pdb=" C6 AGS A 901 " pdb=" N6 AGS A 901 " ideal model delta sigma weight residual 123.61 138.16 -14.55 1.03e+00 9.46e-01 2.00e+02 angle pdb=" N1 AGS A 901 " pdb=" C6 AGS A 901 " pdb=" N6 AGS A 901 " ideal model delta sigma weight residual 118.30 101.59 16.71 1.19e+00 7.01e-01 1.96e+02 ... (remaining 30497 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.07: 12595 27.07 - 54.13: 678 54.13 - 81.20: 56 81.20 - 108.26: 13 108.26 - 135.33: 5 Dihedral angle restraints: 13347 sinusoidal: 4747 harmonic: 8600 Sorted by residual: dihedral pdb=" CA LEU I 197 " pdb=" C LEU I 197 " pdb=" N LYS I 198 " pdb=" CA LYS I 198 " ideal model delta harmonic sigma weight residual 180.00 150.19 29.81 0 5.00e+00 4.00e-02 3.56e+01 dihedral pdb=" CA PRO I 94 " pdb=" C PRO I 94 " pdb=" N VAL I 95 " pdb=" CA VAL I 95 " ideal model delta harmonic sigma weight residual 180.00 151.10 28.90 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" C LYS D 316 " pdb=" N LYS D 316 " pdb=" CA LYS D 316 " pdb=" CB LYS D 316 " ideal model delta harmonic sigma weight residual -122.60 -108.61 -13.99 0 2.50e+00 1.60e-01 3.13e+01 ... (remaining 13344 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.192: 3738 0.192 - 0.385: 35 0.385 - 0.577: 3 0.577 - 0.770: 0 0.770 - 0.962: 3 Chirality restraints: 3779 Sorted by residual: chirality pdb=" PA AGS D 901 " pdb=" O2A AGS D 901 " pdb=" O3A AGS D 901 " pdb=" O5' AGS D 901 " both_signs ideal model delta sigma weight residual True 3.18 2.22 0.96 2.00e-01 2.50e+01 2.31e+01 chirality pdb=" PB AGS C 901 " pdb=" O2B AGS C 901 " pdb=" O3A AGS C 901 " pdb=" O3B AGS C 901 " both_signs ideal model delta sigma weight residual True 3.18 -2.29 0.89 2.00e-01 2.50e+01 1.99e+01 chirality pdb=" PA AGS C 901 " pdb=" O2A AGS C 901 " pdb=" O3A AGS C 901 " pdb=" O5' AGS C 901 " both_signs ideal model delta sigma weight residual True 3.18 2.33 0.85 2.00e-01 2.50e+01 1.82e+01 ... (remaining 3776 not shown) Planarity restraints: 3833 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN I 7 " 0.027 2.00e-02 2.50e+03 5.22e-02 2.73e+01 pdb=" C GLN I 7 " -0.090 2.00e-02 2.50e+03 pdb=" O GLN I 7 " 0.034 2.00e-02 2.50e+03 pdb=" N ASP I 8 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 125 " -0.018 2.00e-02 2.50e+03 2.09e-02 1.09e+01 pdb=" CG TRP B 125 " 0.056 2.00e-02 2.50e+03 pdb=" CD1 TRP B 125 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP B 125 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 125 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 125 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 125 " -0.013 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 125 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 125 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 125 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA K 26 " 0.016 2.00e-02 2.50e+03 3.20e-02 1.02e+01 pdb=" C ALA K 26 " -0.055 2.00e-02 2.50e+03 pdb=" O ALA K 26 " 0.021 2.00e-02 2.50e+03 pdb=" N VAL K 27 " 0.019 2.00e-02 2.50e+03 ... (remaining 3830 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 370 2.61 - 3.18: 21115 3.18 - 3.76: 33378 3.76 - 4.33: 44142 4.33 - 4.90: 71008 Nonbonded interactions: 170013 Sorted by model distance: nonbonded pdb=" O2B AGS C 901 " pdb=" O2G AGS C 901 " model vdw 2.041 2.440 nonbonded pdb=" O1B AGS D 901 " pdb=" O2G AGS D 901 " model vdw 2.046 2.440 nonbonded pdb=" O PRO B 181 " pdb=" OG SER B 384 " model vdw 2.161 2.440 nonbonded pdb=" O1B AGS E 901 " pdb=" O2G AGS E 901 " model vdw 2.192 2.440 nonbonded pdb=" O GLN D 253 " pdb=" OG SER D 256 " model vdw 2.207 2.440 ... (remaining 170008 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' and (resid 122 through 145 or (resid 146 and (name N or name CA or na \ me C or name O or name CB )) or resid 147 through 184 or (resid 185 and (name N \ or name CA or name C or name O or name CB )) or resid 186 or (resid 187 and (nam \ e N or name CA or name C or name O or name CB )) or resid 188 through 194 or (re \ sid 195 and (name N or name CA or name C or name O or name CB )) or resid 196 th \ rough 216 or resid 229 through 236 or (resid 237 and (name N or name CA or name \ C or name O or name CB )) or resid 238 through 245 or (resid 246 and (name N or \ name CA or name C or name O or name CB )) or resid 247 through 254 or (resid 273 \ through 277 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 78 through 280 or (resid 281 and (name N or name CA or name C or name O or name \ CB )) or resid 282 through 285 or (resid 286 and (name N or name CA or name C or \ name O or name CB )) or resid 287 through 291 or (resid 292 through 293 and (na \ me N or name CA or name C or name O or name CB )) or resid 294 through 304 or (r \ esid 305 through 308 and (name N or name CA or name C or name O or name CB )) or \ resid 309 through 327 or (resid 328 through 329 and (name N or name CA or name \ C or name O or name CB )) or resid 330 through 335 or (resid 336 through 337 and \ (name N or name CA or name C or name O or name CB )) or resid 338 or (resid 339 \ through 340 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 41 or (resid 342 through 343 and (name N or name CA or name C or name O or name \ CB )) or resid 344 through 345 or resid 347 or (resid 348 and (name N or name CA \ or name C or name O or name CB )) or resid 349 through 360 or (resid 361 and (n \ ame N or name CA or name C or name O or name CB )) or resid 362 through 367 or ( \ resid 368 through 369 and (name N or name CA or name C or name O or name CB )) o \ r resid 370 or (resid 371 and (name N or name CA or name C or name O or name CB \ )) or resid 372 through 373 or (resid 374 and (name N or name CA or name C or na \ me O or name CB )) or resid 375 or (resid 376 and (name N or name CA or name C o \ r name O or name CB )) or resid 377 through 382 or (resid 383 and (name N or nam \ e CA or name C or name O or name CB )) or resid 384 through 385 or (resid 386 an \ d (name N or name CA or name C or name O or name CB )) or resid 387 through 388 \ or (resid 389 through 390 and (name N or name CA or name C or name O or name CB \ )) or resid 391 through 400 or (resid 401 through 402 and (name N or name CA or \ name C or name O or name CB )) or resid 403 through 419 or (resid 420 through 42 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 422 through \ 424)) selection = (chain 'F' and (resid 122 through 167 or (resid 168 and (name N or name CA or na \ me C or name O or name CB )) or resid 169 through 172 or (resid 173 and (name N \ or name CA or name C or name O or name CB )) or resid 174 through 193 or (resid \ 194 through 195 and (name N or name CA or name C or name O or name CB )) or resi \ d 196 through 204 or (resid 205 and (name N or name CA or name C or name O or na \ me CB )) or resid 206 through 230 or (resid 231 and (name N or name CA or name C \ or name O or name CB )) or resid 232 through 234 or (resid 235 and (name N or n \ ame CA or name C or name O or name CB )) or resid 236 through 251 or (resid 252 \ and (name N or name CA or name C or name O or name CB )) or resid 253 through 30 \ 5 or (resid 306 through 308 and (name N or name CA or name C or name O or name C \ B )) or resid 309 through 311 or (resid 312 through 313 and (name N or name CA o \ r name C or name O or name CB )) or resid 314 through 326 or (resid 327 through \ 329 and (name N or name CA or name C or name O or name CB )) or resid 330 throug \ h 356 or (resid 357 through 359 and (name N or name CA or name C or name O or na \ me CB )) or resid 360 through 377 or (resid 378 and (name N or name CA or name C \ or name O or name CB )) or resid 379 through 380 or (resid 381 and (name N or n \ ame CA or name C or name O or name CB )) or resid 382 through 407 or (resid 408 \ and (name N or name CA or name C or name O or name CB )) or resid 409 through 42 \ 4)) } ncs_group { reference = (chain 'B' and (resid 19 through 23 or (resid 24 and (name N or name CA or name \ C or name O or name CB )) or resid 25 through 27 or (resid 28 and (name N or nam \ e CA or name C or name O or name CB )) or resid 29 through 30 or (resid 31 and ( \ name N or name CA or name C or name O or name CB )) or resid 32 through 33 or (r \ esid 34 through 36 and (name N or name CA or name C or name O or name CB )) or r \ esid 37 through 42 or (resid 43 through 45 and (name N or name CA or name C or n \ ame O or name CB )) or resid 46 or (resid 47 through 48 and (name N or name CA o \ r name C or name O or name CB )) or resid 49 or (resid 50 and (name N or name CA \ or name C or name O or name CB )) or resid 51 through 59 or (resid 60 and (name \ N or name CA or name C or name O or name CB )) or resid 61 or (resid 62 through \ 63 and (name N or name CA or name C or name O or name CB )) or resid 64 through \ 70 or (resid 71 and (name N or name CA or name C or name O or name CB )) or res \ id 72 through 104 or (resid 105 and (name N or name CA or name C or name O or na \ me CB )) or resid 106 or (resid 107 through 122 and (name N or name CA or name C \ or name O or name CB )) or resid 123 through 130 or (resid 131 and (name N or n \ ame CA or name C or name O or name CB )) or resid 132 through 160 or (resid 161 \ and (name N or name CA or name C or name O or name CB )) or resid 162 through 17 \ 1 or (resid 172 through 173 and (name N or name CA or name C or name O or name C \ B )) or resid 174 through 210 or (resid 211 and (name N or name CA or name C or \ name O or name CB )) or resid 212 through 214 or (resid 215 and (name N or name \ CA or name C or name O or name CB )) or resid 216 through 219 or (resid 220 and \ (name N or name CA or name C or name O or name CB )) or resid 221 through 240 or \ (resid 241 through 243 and (name N or name CA or name C or name O or name CB )) \ or resid 244 through 261 or (resid 262 through 266 and (name N or name CA or na \ me C or name O or name CB )) or resid 267 or (resid 268 through 269 and (name N \ or name CA or name C or name O or name CB )) or resid 270 through 271 or (resid \ 272 through 273 and (name N or name CA or name C or name O or name CB )) or resi \ d 274 or (resid 275 and (name N or name CA or name C or name O or name CB )) or \ resid 276 through 287 or (resid 288 and (name N or name CA or name C or name O o \ r name CB )) or resid 289 through 300 or (resid 301 and (name N or name CA or na \ me C or name O or name CB )) or resid 302 or (resid 303 through 304 and (name N \ or name CA or name C or name O or name CB )) or resid 305 through 313 or (resid \ 314 and (name N or name CA or name C or name O or name CB )) or resid 315 throug \ h 326 or (resid 327 and (name N or name CA or name C or name O or name CB )) or \ resid 328 through 340 or (resid 341 through 342 and (name N or name CA or name C \ or name O or name CB )) or resid 343 through 346 or (resid 347 and (name N or n \ ame CA or name C or name O or name CB )) or resid 348 or (resid 349 and (name N \ or name CA or name C or name O or name CB )) or resid 350 through 356 or (resid \ 357 through 358 and (name N or name CA or name C or name O or name CB )) or resi \ d 359 through 362 or (resid 363 through 365 and (name N or name CA or name C or \ name O or name CB )) or resid 366 through 367 or (resid 368 and (name N or name \ CA or name C or name O or name CB )) or resid 369 through 371 or (resid 372 and \ (name N or name CA or name C or name O or name CB )) or resid 373 through 376 or \ (resid 377 through 379 and (name N or name CA or name C or name O or name CB )) \ or resid 380 through 389 or (resid 390 and (name N or name CA or name C or name \ O or name CB )) or resid 391 through 400 or (resid 401 through 402 and (name N \ or name CA or name C or name O or name CB )) or resid 403 through 407 or (resid \ 408 and (name N or name CA or name C or name O or name CB )) or resid 409 throug \ h 411 or (resid 412 through 413 and (name N or name CA or name C or name O or na \ me CB )) or resid 414 through 423 or (resid 424 through 429 and (name N or name \ CA or name C or name O or name CB )) or resid 901)) selection = (chain 'C' and (resid 19 through 27 or (resid 28 and (name N or name CA or name \ C or name O or name CB )) or resid 29 through 30 or (resid 31 and (name N or nam \ e CA or name C or name O or name CB )) or resid 32 through 42 or (resid 43 throu \ gh 45 and (name N or name CA or name C or name O or name CB )) or resid 46 or (r \ esid 47 through 48 and (name N or name CA or name C or name O or name CB )) or r \ esid 49 or (resid 50 and (name N or name CA or name C or name O or name CB )) or \ resid 51 through 70 or (resid 71 and (name N or name CA or name C or name O or \ name CB )) or resid 72 through 100 or (resid 101 and (name N or name CA or name \ C or name O or name CB )) or resid 102 through 104 or (resid 105 and (name N or \ name CA or name C or name O or name CB )) or (resid 106 through 122 and (name N \ or name CA or name C or name O or name CB )) or resid 123 through 130 or (resid \ 131 and (name N or name CA or name C or name O or name CB )) or resid 132 throug \ h 171 or (resid 172 through 173 and (name N or name CA or name C or name O or na \ me CB )) or resid 174 through 204 or (resid 205 and (name N or name CA or name C \ or name O or name CB )) or resid 206 through 210 or (resid 211 and (name N or n \ ame CA or name C or name O or name CB )) or resid 212 through 214 or (resid 215 \ and (name N or name CA or name C or name O or name CB )) or resid 216 through 21 \ 9 or (resid 220 and (name N or name CA or name C or name O or name CB )) or resi \ d 221 through 240 or (resid 241 through 243 and (name N or name CA or name C or \ name O or name CB )) or resid 244 through 251 or (resid 252 and (name N or name \ CA or name C or name O or name CB )) or resid 253 through 254 or (resid 255 and \ (name N or name CA or name C or name O or name CB )) or resid 256 through 261 or \ (resid 262 through 266 and (name N or name CA or name C or name O or name CB )) \ or resid 267 or (resid 268 through 269 and (name N or name CA or name C or name \ O or name CB )) or resid 270 through 271 or (resid 272 through 273 and (name N \ or name CA or name C or name O or name CB )) or resid 274 or (resid 275 and (nam \ e N or name CA or name C or name O or name CB )) or resid 276 through 284 or (re \ sid 285 and (name N or name CA or name C or name O or name CB )) or resid 286 th \ rough 287 or (resid 288 and (name N or name CA or name C or name O or name CB )) \ or resid 289 through 300 or (resid 301 and (name N or name CA or name C or name \ O or name CB )) or resid 302 or (resid 303 through 304 and (name N or name CA o \ r name C or name O or name CB )) or resid 305 through 328 or (resid 329 and (nam \ e N or name CA or name C or name O or name CB )) or resid 330 through 340 or (re \ sid 341 through 342 and (name N or name CA or name C or name O or name CB )) or \ resid 343 through 346 or (resid 347 and (name N or name CA or name C or name O o \ r name CB )) or resid 348 or (resid 349 and (name N or name CA or name C or name \ O or name CB )) or resid 350 or (resid 351 and (name N or name CA or name C or \ name O or name CB )) or resid 352 through 357 or (resid 358 and (name N or name \ CA or name C or name O or name CB )) or resid 359 through 361 or (resid 362 thro \ ugh 365 and (name N or name CA or name C or name O or name CB )) or resid 366 th \ rough 367 or (resid 368 and (name N or name CA or name C or name O or name CB )) \ or resid 369 through 371 or (resid 372 and (name N or name CA or name C or name \ O or name CB )) or resid 373 through 376 or (resid 377 through 379 and (name N \ or name CA or name C or name O or name CB )) or resid 380 through 389 or (resid \ 390 and (name N or name CA or name C or name O or name CB )) or resid 391 throug \ h 400 or (resid 401 through 402 and (name N or name CA or name C or name O or na \ me CB )) or resid 403 through 419 or (resid 420 and (name N or name CA or name C \ or name O or name CB )) or resid 421 through 424 or (resid 425 through 429 and \ (name N or name CA or name C or name O or name CB )) or resid 901)) selection = (chain 'D' and (resid 19 through 26 or (resid 27 through 28 and (name N or name \ CA or name C or name O or name CB )) or resid 29 through 30 or (resid 31 and (na \ me N or name CA or name C or name O or name CB )) or resid 32 through 34 or (res \ id 35 through 36 and (name N or name CA or name C or name O or name CB )) or res \ id 37 through 44 or (resid 45 and (name N or name CA or name C or name O or name \ CB )) or resid 46 or (resid 47 through 48 and (name N or name CA or name C or n \ ame O or name CB )) or resid 49 or (resid 50 and (name N or name CA or name C or \ name O or name CB )) or resid 51 through 59 or (resid 60 and (name N or name CA \ or name C or name O or name CB )) or resid 61 through 67 or (resid 68 and (name \ N or name CA or name C or name O or name CB )) or resid 69 through 70 or (resid \ 71 and (name N or name CA or name C or name O or name CB )) or resid 72 through \ 100 or (resid 101 and (name N or name CA or name C or name O or name CB )) or r \ esid 102 through 106 or (resid 107 through 122 and (name N or name CA or name C \ or name O or name CB )) or resid 123 through 130 or (resid 131 and (name N or na \ me CA or name C or name O or name CB )) or resid 132 through 160 or (resid 161 a \ nd (name N or name CA or name C or name O or name CB )) or resid 162 through 210 \ or (resid 211 and (name N or name CA or name C or name O or name CB )) or resid \ 212 through 214 or (resid 215 and (name N or name CA or name C or name O or nam \ e CB )) or resid 216 through 219 or (resid 220 and (name N or name CA or name C \ or name O or name CB )) or resid 221 through 241 or (resid 242 through 243 and ( \ name N or name CA or name C or name O or name CB )) or resid 244 through 251 or \ (resid 252 and (name N or name CA or name C or name O or name CB )) or resid 253 \ through 254 or (resid 255 and (name N or name CA or name C or name O or name CB \ )) or resid 256 through 261 or (resid 262 through 266 and (name N or name CA or \ name C or name O or name CB )) or resid 267 through 271 or (resid 272 through 2 \ 73 and (name N or name CA or name C or name O or name CB )) or resid 274 through \ 284 or (resid 285 and (name N or name CA or name C or name O or name CB )) or r \ esid 286 through 303 or (resid 304 and (name N or name CA or name C or name O or \ name CB )) or resid 305 through 313 or (resid 314 and (name N or name CA or nam \ e C or name O or name CB )) or resid 315 through 326 or (resid 327 and (name N o \ r name CA or name C or name O or name CB )) or resid 328 or (resid 329 and (name \ N or name CA or name C or name O or name CB )) or resid 330 through 341 or (res \ id 342 and (name N or name CA or name C or name O or name CB )) or resid 343 thr \ ough 344 or (resid 345 and (name N or name CA or name C or name O or name CB )) \ or resid 346 or (resid 347 and (name N or name CA or name C or name O or name CB \ )) or resid 348 or (resid 349 and (name N or name CA or name C or name O or nam \ e CB )) or resid 350 or (resid 351 and (name N or name CA or name C or name O or \ name CB )) or resid 352 through 356 or (resid 357 through 358 and (name N or na \ me CA or name C or name O or name CB )) or resid 359 through 361 or (resid 362 t \ hrough 365 and (name N or name CA or name C or name O or name CB )) or resid 366 \ through 371 or (resid 372 and (name N or name CA or name C or name O or name CB \ )) or resid 373 through 376 or (resid 377 through 379 and (name N or name CA or \ name C or name O or name CB )) or resid 380 through 389 or (resid 390 and (name \ N or name CA or name C or name O or name CB )) or resid 391 through 407 or (res \ id 408 and (name N or name CA or name C or name O or name CB )) or resid 409 thr \ ough 411 or (resid 412 through 413 and (name N or name CA or name C or name O or \ name CB )) or resid 414 through 419 or (resid 420 and (name N or name CA or nam \ e C or name O or name CB )) or resid 421 through 423 or (resid 424 through 429 a \ nd (name N or name CA or name C or name O or name CB )) or resid 901)) selection = (chain 'E' and (resid 19 through 23 or (resid 24 and (name N or name CA or name \ C or name O or name CB )) or resid 25 through 26 or (resid 27 through 28 and (na \ me N or name CA or name C or name O or name CB )) or resid 29 through 33 or (res \ id 34 through 36 and (name N or name CA or name C or name O or name CB )) or res \ id 37 through 42 or (resid 43 through 45 and (name N or name CA or name C or nam \ e O or name CB )) or resid 46 through 47 or (resid 48 and (name N or name CA or \ name C or name O or name CB )) or resid 49 through 100 or (resid 101 and (name N \ or name CA or name C or name O or name CB )) or resid 102 through 106 or (resid \ 107 through 122 and (name N or name CA or name C or name O or name CB )) or res \ id 123 through 126 or (resid 127 and (name N or name CA or name C or name O or n \ ame CB )) or resid 128 through 160 or (resid 161 and (name N or name CA or name \ C or name O or name CB )) or resid 162 through 171 or (resid 172 through 173 and \ (name N or name CA or name C or name O or name CB )) or resid 174 through 240 o \ r (resid 241 through 243 and (name N or name CA or name C or name O or name CB ) \ ) or resid 244 through 251 or (resid 252 and (name N or name CA or name C or nam \ e O or name CB )) or resid 253 through 254 or (resid 255 and (name N or name CA \ or name C or name O or name CB )) or resid 256 through 267 or (resid 268 through \ 269 and (name N or name CA or name C or name O or name CB )) or resid 270 or (r \ esid 271 through 273 and (name N or name CA or name C or name O or name CB )) or \ resid 274 through 284 or (resid 285 and (name N or name CA or name C or name O \ or name CB )) or resid 286 through 287 or (resid 288 and (name N or name CA or n \ ame C or name O or name CB )) or resid 289 through 300 or (resid 301 and (name N \ or name CA or name C or name O or name CB )) or resid 302 through 309 or (resid \ 310 and (name N or name CA or name C or name O or name CB )) or resid 311 throu \ gh 313 or (resid 314 and (name N or name CA or name C or name O or name CB )) or \ resid 315 through 326 or (resid 327 and (name N or name CA or name C or name O \ or name CB )) or resid 328 or (resid 329 and (name N or name CA or name C or nam \ e O or name CB )) or resid 330 through 340 or (resid 341 through 342 and (name N \ or name CA or name C or name O or name CB )) or resid 343 through 344 or (resid \ 345 and (name N or name CA or name C or name O or name CB )) or resid 346 throu \ gh 350 or (resid 351 and (name N or name CA or name C or name O or name CB )) or \ resid 352 through 356 or (resid 357 through 358 and (name N or name CA or name \ C or name O or name CB )) or resid 359 through 362 or (resid 363 through 365 and \ (name N or name CA or name C or name O or name CB )) or resid 366 through 367 o \ r (resid 368 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 69 through 378 or (resid 379 and (name N or name CA or name C or name O or name \ CB )) or resid 380 through 400 or (resid 401 through 402 and (name N or name CA \ or name C or name O or name CB )) or resid 403 through 411 or (resid 412 through \ 413 and (name N or name CA or name C or name O or name CB )) or resid 414 throu \ gh 419 or (resid 420 and (name N or name CA or name C or name O or name CB )) or \ resid 421 through 423 or (resid 424 through 429 and (name N or name CA or name \ C or name O or name CB )) or resid 901)) } ncs_group { reference = (chain 'G' and (resid 15 through 16 or (resid 17 and (name N or name CA or name \ C or name O or name CB )) or resid 18 through 20 or (resid 21 through 22 and (na \ me N or name CA or name C or name O or name CB )) or resid 23 through 26 or (res \ id 27 through 29 and (name N or name CA or name C or name O or name CB )) or res \ id 30 through 37 or resid 40 through 41 or (resid 42 and (name N or name CA or n \ ame C or name O or name CB )) or resid 43 through 44 or (resid 45 and (name N or \ name CA or name C or name O or name CB )) or resid 46 or (resid 47 through 48 a \ nd (name N or name CA or name C or name O or name CB )) or resid 49 through 73 o \ r (resid 74 and (name N or name CA or name C or name O or name CB )) or resid 75 \ or (resid 76 through 77 and (name N or name CA or name C or name O or name CB ) \ ) or resid 78 through 80 or (resid 81 through 82 and (name N or name CA or name \ C or name O or name CB )) or resid 83 through 87 or (resid 88 through 93 and (na \ me N or name CA or name C or name O or name CB )) or resid 94 through 120 or (re \ sid 121 and (name N or name CA or name C or name O or name CB )) or resid 122 th \ rough 126 or (resid 127 and (name N or name CA or name C or name O or name CB )) \ or resid 128 through 156 or (resid 157 through 158 and (name N or name CA or na \ me C or name O or name CB )) or resid 159 through 165 or (resid 166 through 168 \ and (name N or name CA or name C or name O or name CB )) or resid 169 through 17 \ 2 or (resid 173 through 174 and (name N or name CA or name C or name O or name C \ B )) or resid 175 or (resid 176 through 177 and (name N or name CA or name C or \ name O or name CB )) or resid 178 through 180 or (resid 181 and (name N or name \ CA or name C or name O or name CB )) or resid 182 or (resid 183 and (name N or n \ ame CA or name C or name O or name CB )) or resid 184 through 200 or (resid 201 \ and (name N or name CA or name C or name O or name CB )) or resid 202 through 20 \ 6)) selection = (chain 'I' and (resid 15 through 27 or (resid 28 through 29 and (name N or name \ CA or name C or name O or name CB )) or resid 30 through 64 or (resid 65 and (na \ me N or name CA or name C or name O or name CB )) or resid 66 through 68 or (res \ id 69 and (name N or name CA or name C or name O or name CB )) or resid 70 throu \ gh 81 or (resid 82 and (name N or name CA or name C or name O or name CB )) or r \ esid 83 through 85 or (resid 86 through 93 and (name N or name CA or name C or n \ ame O or name CB )) or resid 94 through 95 or (resid 96 through 98 and (name N o \ r name CA or name C or name O or name CB )) or resid 99 through 105 or resid 117 \ through 122 or (resid 123 through 127 and (name N or name CA or name C or name \ O or name CB )) or resid 128 through 133 or resid 145 or (resid 146 and (name N \ or name CA or name C or name O or name CB )) or resid 147 through 159 or (resid \ 160 through 162 and (name N or name CA or name C or name O or name CB )) or resi \ d 163 through 164 or (resid 165 through 168 and (name N or name CA or name C or \ name O or name CB )) or resid 169 through 179 or (resid 180 through 181 and (nam \ e N or name CA or name C or name O or name CB )) or resid 182 through 184 or (re \ sid 185 and (name N or name CA or name C or name O or name CB )) or resid 186 th \ rough 188 or (resid 189 through 190 and (name N or name CA or name C or name O o \ r name CB )) or resid 191 through 198 or (resid 199 through 201 and (name N or n \ ame CA or name C or name O or name CB )) or resid 202 through 206)) } ncs_group { reference = (chain 'J' and (resid 15 through 29 or (resid 30 and (name N or name CA or name \ C or name O or name CB )) or resid 31 or (resid 32 and (name N or name CA or nam \ e C or name O or name CB )) or resid 33 or resid 39 through 51 or (resid 52 thro \ ugh 54 and (name N or name CA or name C or name O or name CB )) or resid 55 thro \ ugh 63 or (resid 64 and (name N or name CA or name C or name O or name CB )) or \ resid 65 through 73 or (resid 74 and (name N or name CA or name C or name O or n \ ame CB )) or resid 75 or (resid 76 and (name N or name CA or name C or name O or \ name CB )) or resid 77 through 87 or (resid 88 and (name N or name CA or name C \ or name O or name CB )) or resid 89 or (resid 90 through 93 and (name N or name \ CA or name C or name O or name CB )) or resid 94 through 97 or (resid 98 and (n \ ame N or name CA or name C or name O or name CB )) or resid 99 through 137 or (r \ esid 138 and (name N or name CA or name C or name O or name CB )) or resid 145 t \ hrough 151 or resid 199 through 203 or (resid 204 and (name N or name CA or name \ C or name O or name CB )) or resid 205)) selection = (chain 'K' and (resid 15 through 16 or (resid 17 and (name N or name CA or name \ C or name O or name CB )) or resid 18 through 40 or (resid 41 and (name N or nam \ e CA or name C or name O or name CB )) or resid 42 through 47 or (resid 48 throu \ gh 50 and (name N or name CA or name C or name O or name CB )) or resid 51 throu \ gh 53 or (resid 54 and (name N or name CA or name C or name O or name CB )) or r \ esid 55 through 80 or (resid 81 through 82 and (name N or name CA or name C or n \ ame O or name CB )) or resid 83 through 91 or (resid 92 through 93 and (name N o \ r name CA or name C or name O or name CB )) or resid 94 through 104 or resid 119 \ or (resid 120 and (name N or name CA or name C or name O or name CB )) or resid \ 121 through 125 or (resid 126 and (name N or name CA or name C or name O or nam \ e CB )) or resid 127 through 128 or (resid 129 and (name N or name CA or name C \ or name O or name CB )) or resid 130 through 135 or (resid 136 and (name N or na \ me CA or name C or name O or name CB )) or resid 137 through 138 or resid 145 th \ rough 151 or resid 199 through 205)) } ncs_group { reference = (chain 'X' and ((resid 3 through 4 and (name N or name CA or name C or name O or \ name CB )) or resid 5 through 48 or (resid 49 through 50 and (name N or name CA \ or name C or name O or name CB )) or resid 51 through 67 or (resid 68 through 7 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 71 through 7 \ 8 or (resid 79 through 80 and (name N or name CA or name C or name O or name CB \ )) or resid 81 or (resid 82 through 83 and (name N or name CA or name C or name \ O or name CB )) or resid 84 through 89)) selection = (chain 'Y' and (resid 3 through 8 or resid 34 through 35 or (resid 36 and (name \ N or name CA or name C or name O or name CB )) or resid 37 through 39 or (resid \ 40 through 41 and (name N or name CA or name C or name O or name CB )) or resid \ 42 through 45 or (resid 46 and (name N or name CA or name C or name O or name CB \ )) or resid 47 or (resid 48 through 50 and (name N or name CA or name C or name \ O or name CB )) or resid 51 or (resid 52 through 54 and (name N or name CA or n \ ame C or name O or name CB )) or resid 55 or (resid 56 through 57 and (name N or \ name CA or name C or name O or name CB )) or resid 58 through 63 or (resid 64 a \ nd (name N or name CA or name C or name O or name CB )) or resid 65 through 68 o \ r (resid 69 through 70 and (name N or name CA or name C or name O or name CB )) \ or resid 71 through 74 or (resid 75 and (name N or name CA or name C or name O o \ r name CB )) or resid 76 through 85 or (resid 86 and (name N or name CA or name \ C or name O or name CB )) or resid 87 through 89)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.170 Construct map_model_manager: 0.020 Extract box with map and model: 5.130 Check model and map are aligned: 0.320 Set scattering table: 0.190 Process input model: 56.190 Find NCS groups from input model: 1.520 Set up NCS constraints: 0.130 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:3.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 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 : 0.008 0.208 22312 Z= 0.539 Angle : 1.240 26.899 30502 Z= 0.728 Chirality : 0.066 0.962 3779 Planarity : 0.006 0.059 3833 Dihedral : 16.881 135.327 7693 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 20.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.44 % Favored : 90.49 % Rotamer Outliers : 0.54 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 2.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.15), residues: 2849 helix: -1.24 (0.14), residues: 1201 sheet: -0.98 (0.28), residues: 330 loop : -2.74 (0.16), residues: 1318 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 331 time to evaluate : 2.635 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 340 average time/residue: 0.3365 time to fit residues: 177.4685 Evaluate side-chains 265 residues out of total 2649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 260 time to evaluate : 2.413 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.4309 time to fit residues: 6.2890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 239 optimal weight: 10.0000 chunk 215 optimal weight: 9.9990 chunk 119 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 145 optimal weight: 0.3980 chunk 115 optimal weight: 4.9990 chunk 222 optimal weight: 30.0000 chunk 86 optimal weight: 0.8980 chunk 135 optimal weight: 0.9990 chunk 165 optimal weight: 10.0000 chunk 257 optimal weight: 4.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 ASN ** B 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 GLN ** C 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 HIS ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 163 ASN E 292 ASN ** E 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 22312 Z= 0.215 Angle : 0.725 11.736 30502 Z= 0.371 Chirality : 0.047 0.369 3779 Planarity : 0.005 0.051 3833 Dihedral : 8.319 113.114 3070 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.83 % Favored : 92.14 % Rotamer Outliers : 1.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.15), residues: 2849 helix: -0.68 (0.14), residues: 1216 sheet: -0.80 (0.28), residues: 370 loop : -2.47 (0.17), residues: 1263 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 305 time to evaluate : 2.714 Fit side-chains outliers start: 41 outliers final: 27 residues processed: 323 average time/residue: 0.3339 time to fit residues: 171.7999 Evaluate side-chains 290 residues out of total 2649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 263 time to evaluate : 2.550 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.2106 time to fit residues: 13.8475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 143 optimal weight: 6.9990 chunk 80 optimal weight: 7.9990 chunk 214 optimal weight: 5.9990 chunk 175 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 258 optimal weight: 4.9990 chunk 279 optimal weight: 0.2980 chunk 230 optimal weight: 9.9990 chunk 256 optimal weight: 2.9990 chunk 88 optimal weight: 8.9990 chunk 207 optimal weight: 9.9990 overall best weight: 3.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 ASN B 300 ASN D 49 HIS D 283 GLN D 348 GLN E 163 ASN E 348 GLN ** G 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 28 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.054 22312 Z= 0.313 Angle : 0.708 9.938 30502 Z= 0.364 Chirality : 0.048 0.312 3779 Planarity : 0.005 0.048 3833 Dihedral : 8.026 118.520 3070 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.41 % Favored : 90.56 % Rotamer Outliers : 2.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.15), residues: 2849 helix: -0.55 (0.15), residues: 1224 sheet: -0.57 (0.28), residues: 351 loop : -2.46 (0.17), residues: 1274 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 280 time to evaluate : 2.469 Fit side-chains revert: symmetry clash outliers start: 62 outliers final: 37 residues processed: 323 average time/residue: 0.3123 time to fit residues: 160.9067 Evaluate side-chains 281 residues out of total 2649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 244 time to evaluate : 2.766 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.1932 time to fit residues: 17.1406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 255 optimal weight: 0.4980 chunk 194 optimal weight: 30.0000 chunk 134 optimal weight: 0.8980 chunk 28 optimal weight: 6.9990 chunk 123 optimal weight: 0.5980 chunk 173 optimal weight: 8.9990 chunk 259 optimal weight: 2.9990 chunk 274 optimal weight: 8.9990 chunk 135 optimal weight: 0.7980 chunk 245 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 ASN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 GLN E 163 ASN ** G 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 28 HIS J 151 HIS X 5 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 22312 Z= 0.180 Angle : 0.639 10.707 30502 Z= 0.323 Chirality : 0.045 0.220 3779 Planarity : 0.004 0.041 3833 Dihedral : 7.529 108.639 3070 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.81 % Favored : 93.16 % Rotamer Outliers : 2.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.16), residues: 2849 helix: -0.23 (0.15), residues: 1218 sheet: -0.40 (0.28), residues: 361 loop : -2.28 (0.17), residues: 1270 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 296 time to evaluate : 2.676 Fit side-chains revert: symmetry clash outliers start: 60 outliers final: 32 residues processed: 335 average time/residue: 0.3118 time to fit residues: 168.1083 Evaluate side-chains 285 residues out of total 2649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 253 time to evaluate : 2.772 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.2090 time to fit residues: 15.9244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 228 optimal weight: 5.9990 chunk 155 optimal weight: 30.0000 chunk 3 optimal weight: 4.9990 chunk 204 optimal weight: 20.0000 chunk 113 optimal weight: 0.0370 chunk 234 optimal weight: 0.9980 chunk 189 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 140 optimal weight: 0.8980 chunk 246 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 overall best weight: 2.5862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 ASN B 69 ASN B 194 GLN B 283 GLN ** C 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 HIS D 283 GLN ** G 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 28 HIS X 5 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 22312 Z= 0.251 Angle : 0.650 11.381 30502 Z= 0.330 Chirality : 0.046 0.204 3779 Planarity : 0.004 0.038 3833 Dihedral : 7.425 113.615 3070 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.49 % Favored : 91.47 % Rotamer Outliers : 2.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.16), residues: 2849 helix: -0.23 (0.15), residues: 1226 sheet: -0.28 (0.29), residues: 343 loop : -2.25 (0.17), residues: 1280 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 277 time to evaluate : 2.666 Fit side-chains revert: symmetry clash outliers start: 53 outliers final: 23 residues processed: 312 average time/residue: 0.3163 time to fit residues: 157.8170 Evaluate side-chains 276 residues out of total 2649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 253 time to evaluate : 2.380 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.2004 time to fit residues: 11.7360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 92 optimal weight: 3.9990 chunk 247 optimal weight: 9.9990 chunk 54 optimal weight: 0.8980 chunk 161 optimal weight: 1.9990 chunk 67 optimal weight: 0.0270 chunk 274 optimal weight: 8.9990 chunk 228 optimal weight: 40.0000 chunk 127 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 144 optimal weight: 1.9990 overall best weight: 1.3844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 ASN ** C 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 GLN G 43 GLN I 28 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 22312 Z= 0.186 Angle : 0.626 11.734 30502 Z= 0.315 Chirality : 0.045 0.264 3779 Planarity : 0.004 0.037 3833 Dihedral : 7.174 108.699 3070 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.74 % Favored : 93.23 % Rotamer Outliers : 2.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.16), residues: 2849 helix: -0.05 (0.15), residues: 1222 sheet: -0.57 (0.28), residues: 375 loop : -2.12 (0.17), residues: 1252 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 283 time to evaluate : 2.537 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 26 residues processed: 313 average time/residue: 0.3156 time to fit residues: 158.3681 Evaluate side-chains 281 residues out of total 2649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 255 time to evaluate : 2.554 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.1982 time to fit residues: 13.1651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 264 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 156 optimal weight: 1.9990 chunk 200 optimal weight: 6.9990 chunk 155 optimal weight: 2.9990 chunk 231 optimal weight: 10.0000 chunk 153 optimal weight: 0.0570 chunk 273 optimal weight: 9.9990 chunk 171 optimal weight: 7.9990 chunk 166 optimal weight: 3.9990 chunk 126 optimal weight: 0.8980 overall best weight: 1.9904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 HIS D 283 GLN E 163 ASN ** G 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 22312 Z= 0.216 Angle : 0.632 11.758 30502 Z= 0.317 Chirality : 0.046 0.329 3779 Planarity : 0.004 0.059 3833 Dihedral : 7.127 109.769 3070 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.79 % Favored : 92.17 % Rotamer Outliers : 2.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.16), residues: 2849 helix: 0.05 (0.15), residues: 1220 sheet: -0.46 (0.28), residues: 377 loop : -2.12 (0.17), residues: 1252 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 256 time to evaluate : 2.649 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 19 residues processed: 286 average time/residue: 0.3184 time to fit residues: 147.1735 Evaluate side-chains 265 residues out of total 2649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 246 time to evaluate : 2.835 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2813 time to fit residues: 12.6197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 169 optimal weight: 7.9990 chunk 109 optimal weight: 9.9990 chunk 163 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 174 optimal weight: 0.0060 chunk 186 optimal weight: 30.0000 chunk 135 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 215 optimal weight: 4.9990 chunk 249 optimal weight: 1.9990 overall best weight: 3.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 283 GLN E 163 ASN F 124 HIS F 290 HIS ** G 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 28 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.064 22312 Z= 0.327 Angle : 0.696 11.317 30502 Z= 0.352 Chirality : 0.048 0.303 3779 Planarity : 0.004 0.046 3833 Dihedral : 7.347 112.022 3070 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.06 % Favored : 90.91 % Rotamer Outliers : 2.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.16), residues: 2849 helix: -0.09 (0.15), residues: 1213 sheet: -0.39 (0.29), residues: 352 loop : -2.22 (0.17), residues: 1284 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 249 time to evaluate : 2.598 Fit side-chains revert: symmetry clash outliers start: 46 outliers final: 23 residues processed: 281 average time/residue: 0.3108 time to fit residues: 140.8648 Evaluate side-chains 255 residues out of total 2649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 232 time to evaluate : 2.853 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1941 time to fit residues: 12.0772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 262 optimal weight: 4.9990 chunk 239 optimal weight: 0.6980 chunk 255 optimal weight: 0.8980 chunk 153 optimal weight: 9.9990 chunk 111 optimal weight: 0.4980 chunk 200 optimal weight: 8.9990 chunk 78 optimal weight: 2.9990 chunk 230 optimal weight: 5.9990 chunk 241 optimal weight: 8.9990 chunk 254 optimal weight: 3.9990 chunk 167 optimal weight: 0.9980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 ASN ** C 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 HIS D 283 GLN E 124 HIS E 163 ASN ** G 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 159 ASN I 28 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 22312 Z= 0.186 Angle : 0.638 12.368 30502 Z= 0.318 Chirality : 0.045 0.262 3779 Planarity : 0.004 0.040 3833 Dihedral : 7.030 106.119 3070 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.49 % Favored : 93.47 % Rotamer Outliers : 1.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.16), residues: 2849 helix: 0.11 (0.15), residues: 1217 sheet: -0.40 (0.28), residues: 362 loop : -2.09 (0.17), residues: 1270 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 262 time to evaluate : 2.596 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 17 residues processed: 276 average time/residue: 0.3064 time to fit residues: 136.5769 Evaluate side-chains 261 residues out of total 2649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 244 time to evaluate : 2.480 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1988 time to fit residues: 10.0247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 269 optimal weight: 3.9990 chunk 164 optimal weight: 8.9990 chunk 127 optimal weight: 6.9990 chunk 187 optimal weight: 0.7980 chunk 282 optimal weight: 10.0000 chunk 260 optimal weight: 6.9990 chunk 225 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 chunk 174 optimal weight: 3.9990 chunk 138 optimal weight: 7.9990 chunk 178 optimal weight: 10.0000 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 50 ASN D 27 GLN D 283 GLN E 163 ASN ** G 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 28 HIS J 104 GLN X 5 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.067 22312 Z= 0.356 Angle : 0.726 11.493 30502 Z= 0.365 Chirality : 0.049 0.284 3779 Planarity : 0.005 0.064 3833 Dihedral : 7.354 112.637 3070 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.37 % Favored : 90.59 % Rotamer Outliers : 0.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.16), residues: 2849 helix: -0.09 (0.15), residues: 1213 sheet: -0.54 (0.28), residues: 357 loop : -2.20 (0.17), residues: 1279 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 248 time to evaluate : 2.674 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 7 residues processed: 256 average time/residue: 0.3253 time to fit residues: 132.8729 Evaluate side-chains 242 residues out of total 2649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 235 time to evaluate : 2.342 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1850 time to fit residues: 5.6250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 240 optimal weight: 0.6980 chunk 69 optimal weight: 10.0000 chunk 207 optimal weight: 8.9990 chunk 33 optimal weight: 4.9990 chunk 62 optimal weight: 8.9990 chunk 225 optimal weight: 0.7980 chunk 94 optimal weight: 0.5980 chunk 231 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 198 optimal weight: 30.0000 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 ASN D 283 GLN E 163 ASN E 178 HIS ** G 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 28 HIS X 5 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.149301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.117628 restraints weight = 45475.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.117108 restraints weight = 32046.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.118031 restraints weight = 28719.820| |-----------------------------------------------------------------------------| r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 22312 Z= 0.219 Angle : 0.659 12.264 30502 Z= 0.327 Chirality : 0.046 0.240 3779 Planarity : 0.004 0.044 3833 Dihedral : 7.095 107.134 3070 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.77 % Favored : 93.19 % Rotamer Outliers : 0.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.16), residues: 2849 helix: 0.10 (0.15), residues: 1213 sheet: -0.54 (0.28), residues: 367 loop : -2.14 (0.17), residues: 1269 =============================================================================== Job complete usr+sys time: 4179.58 seconds wall clock time: 77 minutes 13.95 seconds (4633.95 seconds total)