Starting phenix.real_space_refine on Fri Mar 22 04:48:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihp_35451/03_2024/8ihp_35451.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihp_35451/03_2024/8ihp_35451.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihp_35451/03_2024/8ihp_35451.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihp_35451/03_2024/8ihp_35451.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihp_35451/03_2024/8ihp_35451.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihp_35451/03_2024/8ihp_35451.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 3 9.91 5 S 254 5.16 5 C 20354 2.51 5 N 5604 2.21 5 O 6122 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 13": "NH1" <-> "NH2" Residue "A ASP 21": "OD1" <-> "OD2" Residue "A GLU 35": "OE1" <-> "OE2" Residue "A ARG 38": "NH1" <-> "NH2" Residue "A ASP 43": "OD1" <-> "OD2" Residue "A ASP 63": "OD1" <-> "OD2" Residue "A ARG 80": "NH1" <-> "NH2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 109": "OE1" <-> "OE2" Residue "A PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 117": "OD1" <-> "OD2" Residue "A ARG 119": "NH1" <-> "NH2" Residue "A ARG 123": "NH1" <-> "NH2" Residue "A TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 139": "OE1" <-> "OE2" Residue "A ARG 144": "NH1" <-> "NH2" Residue "A TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 178": "NH1" <-> "NH2" Residue "A PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 244": "NH1" <-> "NH2" Residue "A ARG 250": "NH1" <-> "NH2" Residue "A ASP 261": "OD1" <-> "OD2" Residue "A ARG 271": "NH1" <-> "NH2" Residue "A PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 20": "OE1" <-> "OE2" Residue "B TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 109": "OD1" <-> "OD2" Residue "B ASP 112": "OD1" <-> "OD2" Residue "B ASP 117": "OD1" <-> "OD2" Residue "B TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 188": "OD1" <-> "OD2" Residue "B TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 202": "OD1" <-> "OD2" Residue "B TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 341": "OE1" <-> "OE2" Residue "B PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 373": "NH1" <-> "NH2" Residue "B TYR 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 437": "NH1" <-> "NH2" Residue "C PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 138": "OD1" <-> "OD2" Residue "C TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 243": "NH1" <-> "NH2" Residue "C ARG 258": "NH1" <-> "NH2" Residue "D PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 13": "NH1" <-> "NH2" Residue "D TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 35": "OE1" <-> "OE2" Residue "D ARG 38": "NH1" <-> "NH2" Residue "D ASP 57": "OD1" <-> "OD2" Residue "D ASP 63": "OD1" <-> "OD2" Residue "D TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 80": "NH1" <-> "NH2" Residue "D PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 117": "OD1" <-> "OD2" Residue "D ARG 119": "NH1" <-> "NH2" Residue "D ARG 123": "NH1" <-> "NH2" Residue "D TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 132": "OD1" <-> "OD2" Residue "D GLU 139": "OE1" <-> "OE2" Residue "D ARG 144": "NH1" <-> "NH2" Residue "D TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 165": "OE1" <-> "OE2" Residue "D ARG 178": "NH1" <-> "NH2" Residue "D PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 244": "NH1" <-> "NH2" Residue "D ARG 250": "NH1" <-> "NH2" Residue "D ASP 261": "OD1" <-> "OD2" Residue "D ARG 271": "NH1" <-> "NH2" Residue "D PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 326": "OE1" <-> "OE2" Residue "D TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 344": "OE1" <-> "OE2" Residue "D TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 45": "OE1" <-> "OE2" Residue "E TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 109": "OD1" <-> "OD2" Residue "E ASP 112": "OD1" <-> "OD2" Residue "E ASP 117": "OD1" <-> "OD2" Residue "E TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 188": "OD1" <-> "OD2" Residue "E TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 209": "OE1" <-> "OE2" Residue "E TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 381": "OE1" <-> "OE2" Residue "E PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 169": "OE1" <-> "OE2" Residue "F TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 258": "NH1" <-> "NH2" Residue "G PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 13": "NH1" <-> "NH2" Residue "G TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 38": "NH1" <-> "NH2" Residue "G ASP 63": "OD1" <-> "OD2" Residue "G TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 76": "OE1" <-> "OE2" Residue "G ARG 80": "NH1" <-> "NH2" Residue "G GLU 109": "OE1" <-> "OE2" Residue "G PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 117": "OD1" <-> "OD2" Residue "G ARG 119": "NH1" <-> "NH2" Residue "G ARG 123": "NH1" <-> "NH2" Residue "G GLU 139": "OE1" <-> "OE2" Residue "G ARG 144": "NH1" <-> "NH2" Residue "G TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 150": "OE1" <-> "OE2" Residue "G ARG 178": "NH1" <-> "NH2" Residue "G PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 244": "NH1" <-> "NH2" Residue "G ASP 261": "OD1" <-> "OD2" Residue "G ARG 271": "NH1" <-> "NH2" Residue "G GLU 281": "OE1" <-> "OE2" Residue "G TYR 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 301": "OE1" <-> "OE2" Residue "G TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 1": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 35": "OE1" <-> "OE2" Residue "H TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 67": "OE1" <-> "OE2" Residue "H GLU 72": "OE1" <-> "OE2" Residue "H TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 105": "OE1" <-> "OE2" Residue "H ASP 109": "OD1" <-> "OD2" Residue "H ASP 112": "OD1" <-> "OD2" Residue "H ASP 117": "OD1" <-> "OD2" Residue "H TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 174": "OD1" <-> "OD2" Residue "H TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 209": "OE1" <-> "OE2" Residue "H PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 292": "OE1" <-> "OE2" Residue "H ASP 298": "OD1" <-> "OD2" Residue "H PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 341": "OE1" <-> "OE2" Residue "H PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 381": "OE1" <-> "OE2" Residue "H TYR 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 118": "OD1" <-> "OD2" Residue "I ASP 138": "OD1" <-> "OD2" Residue "I GLU 169": "OE1" <-> "OE2" Residue "I TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 258": "NH1" <-> "NH2" Residue "J ARG 13": "NH1" <-> "NH2" Residue "J TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 35": "OE1" <-> "OE2" Residue "J ARG 38": "NH1" <-> "NH2" Residue "J ASP 63": "OD1" <-> "OD2" Residue "J ARG 80": "NH1" <-> "NH2" Residue "J PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 109": "OE1" <-> "OE2" Residue "J PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 117": "OD1" <-> "OD2" Residue "J ARG 119": "NH1" <-> "NH2" Residue "J ARG 123": "NH1" <-> "NH2" Residue "J ASP 132": "OD1" <-> "OD2" Residue "J GLU 139": "OE1" <-> "OE2" Residue "J ARG 144": "NH1" <-> "NH2" Residue "J TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 178": "NH1" <-> "NH2" Residue "J ASP 231": "OD1" <-> "OD2" Residue "J PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 244": "NH1" <-> "NH2" Residue "J GLU 247": "OE1" <-> "OE2" Residue "J ASP 261": "OD1" <-> "OD2" Residue "J ARG 271": "NH1" <-> "NH2" Residue "J GLU 281": "OE1" <-> "OE2" Residue "J PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 1": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 39": "OE1" <-> "OE2" Residue "K TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 97": "OD1" <-> "OD2" Residue "K TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 109": "OD1" <-> "OD2" Residue "K TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 182": "OD1" <-> "OD2" Residue "K ASP 202": "OD1" <-> "OD2" Residue "K GLU 209": "OE1" <-> "OE2" Residue "K PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 323": "OD1" <-> "OD2" Residue "K PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 381": "OE1" <-> "OE2" Residue "K TYR 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 437": "NH1" <-> "NH2" Residue "L TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 138": "OD1" <-> "OD2" Residue "L PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 187": "OE1" <-> "OE2" Residue "L TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 258": "NH1" <-> "NH2" Residue "M ARG 111": "NH1" <-> "NH2" Residue "M ARG 114": "NH1" <-> "NH2" Residue "M GLU 117": "OE1" <-> "OE2" Residue "M ARG 133": "NH1" <-> "NH2" Residue "N ARG 111": "NH1" <-> "NH2" Residue "N ARG 133": "NH1" <-> "NH2" Residue "O ARG 111": "NH1" <-> "NH2" Residue "O ARG 133": "NH1" <-> "NH2" Residue "O GLU 137": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 32337 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 3250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3250 Classifications: {'peptide': 417} Link IDs: {'PTRANS': 31, 'TRANS': 385} Chain: "B" Number of atoms: 3318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3318 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 28, 'TRANS': 408} Chain: "C" Number of atoms: 1250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1250 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 154} Chain: "D" Number of atoms: 3250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3250 Classifications: {'peptide': 417} Link IDs: {'PTRANS': 31, 'TRANS': 385} Chain: "E" Number of atoms: 3318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3318 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 28, 'TRANS': 408} Chain: "F" Number of atoms: 1250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1250 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 154} Chain: "G" Number of atoms: 3250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3250 Classifications: {'peptide': 417} Link IDs: {'PTRANS': 31, 'TRANS': 385} Chain: "H" Number of atoms: 3318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3318 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 28, 'TRANS': 408} Chain: "I" Number of atoms: 1250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1250 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 154} Chain: "J" Number of atoms: 3250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3250 Classifications: {'peptide': 417} Link IDs: {'PTRANS': 31, 'TRANS': 385} Chain: "K" Number of atoms: 3318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3318 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 28, 'TRANS': 408} Chain: "L" Number of atoms: 1250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1250 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 154} Chain: "M" Number of atoms: 298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 298 Classifications: {'peptide': 39} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "N" Number of atoms: 298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 298 Classifications: {'peptide': 39} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "O" Number of atoms: 298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 298 Classifications: {'peptide': 39} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 15.81, per 1000 atoms: 0.49 Number of scatterers: 32337 At special positions: 0 Unit cell: (201.4, 204.58, 163.24, 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) Ca 3 19.99 S 254 16.00 O 6122 8.00 N 5604 7.00 C 20354 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=61, symmetry=0 Simple disulfide: pdb=" SG CYS A 19 " - pdb=" SG CYS A 125 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 28 " distance=2.03 Simple disulfide: pdb=" SG CYS A 91 " - pdb=" SG CYS A 105 " distance=2.02 Simple disulfide: pdb=" SG CYS A 153 " - pdb=" SG CYS A 265 " distance=1.79 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 225 " distance=2.03 Simple disulfide: pdb=" SG CYS A 203 " - pdb=" SG CYS A 220 " distance=2.03 Simple disulfide: pdb=" SG CYS B 49 " - pdb=" SG CYS B 114 " distance=2.04 Simple disulfide: pdb=" SG CYS B 62 " - pdb=" SG CYS B 94 " distance=2.04 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 96 " distance=2.04 Simple disulfide: pdb=" SG CYS B 259 " - pdb=" SG CYS B 271 " distance=2.03 Simple disulfide: pdb=" SG CYS B 301 " - pdb=" SG CYS B 376 " distance=2.03 Simple disulfide: pdb=" SG CYS B 306 " - pdb=" SG CYS B 380 " distance=2.03 Simple disulfide: pdb=" SG CYS B 328 " - pdb=" SG CYS B 370 " distance=2.93 Simple disulfide: pdb=" SG CYS D 19 " - pdb=" SG CYS D 125 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 28 " distance=2.03 Simple disulfide: pdb=" SG CYS D 91 " - pdb=" SG CYS D 105 " distance=2.02 Simple disulfide: pdb=" SG CYS D 153 " - pdb=" SG CYS D 265 " distance=2.10 Simple disulfide: pdb=" SG CYS D 201 " - pdb=" SG CYS D 225 " distance=2.03 Simple disulfide: pdb=" SG CYS D 203 " - pdb=" SG CYS D 220 " distance=2.03 Simple disulfide: pdb=" SG CYS E 49 " - pdb=" SG CYS E 114 " distance=2.03 Simple disulfide: pdb=" SG CYS E 62 " - pdb=" SG CYS E 94 " distance=2.04 Simple disulfide: pdb=" SG CYS E 63 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 259 " - pdb=" SG CYS E 271 " distance=2.03 Simple disulfide: pdb=" SG CYS E 301 " - pdb=" SG CYS E 376 " distance=2.03 Simple disulfide: pdb=" SG CYS E 306 " - pdb=" SG CYS E 380 " distance=2.02 Simple disulfide: pdb=" SG CYS E 328 " - pdb=" SG CYS E 370 " distance=2.03 Simple disulfide: pdb=" SG CYS G 19 " - pdb=" SG CYS G 125 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 28 " distance=2.03 Simple disulfide: pdb=" SG CYS G 91 " - pdb=" SG CYS G 105 " distance=2.02 Simple disulfide: pdb=" SG CYS G 153 " - pdb=" SG CYS G 265 " distance=2.04 Simple disulfide: pdb=" SG CYS G 201 " - pdb=" SG CYS G 225 " distance=2.03 Simple disulfide: pdb=" SG CYS G 203 " - pdb=" SG CYS G 220 " distance=2.03 Simple disulfide: pdb=" SG CYS H 49 " - pdb=" SG CYS H 114 " distance=2.03 Simple disulfide: pdb=" SG CYS H 62 " - pdb=" SG CYS H 94 " distance=2.04 Simple disulfide: pdb=" SG CYS H 63 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 259 " - pdb=" SG CYS H 271 " distance=2.03 Simple disulfide: pdb=" SG CYS H 301 " - pdb=" SG CYS H 376 " distance=2.03 Simple disulfide: pdb=" SG CYS H 306 " - pdb=" SG CYS H 380 " distance=2.03 Simple disulfide: pdb=" SG CYS H 328 " - pdb=" SG CYS H 370 " distance=2.02 Simple disulfide: pdb=" SG CYS J 19 " - pdb=" SG CYS J 125 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 28 " distance=2.03 Simple disulfide: pdb=" SG CYS J 91 " - pdb=" SG CYS J 105 " distance=2.03 Simple disulfide: pdb=" SG CYS J 153 " - pdb=" SG CYS J 265 " distance=1.58 Simple disulfide: pdb=" SG CYS J 201 " - pdb=" SG CYS J 225 " distance=2.03 Simple disulfide: pdb=" SG CYS J 203 " - pdb=" SG CYS J 220 " distance=2.02 Simple disulfide: pdb=" SG CYS K 49 " - pdb=" SG CYS K 114 " distance=2.04 Simple disulfide: pdb=" SG CYS K 62 " - pdb=" SG CYS K 94 " distance=2.03 Simple disulfide: pdb=" SG CYS K 63 " - pdb=" SG CYS K 96 " distance=2.03 Simple disulfide: pdb=" SG CYS K 259 " - pdb=" SG CYS K 271 " distance=2.03 Simple disulfide: pdb=" SG CYS K 301 " - pdb=" SG CYS K 376 " distance=2.03 Simple disulfide: pdb=" SG CYS K 306 " - pdb=" SG CYS K 380 " distance=2.02 Simple disulfide: pdb=" SG CYS K 328 " - pdb=" SG CYS K 370 " distance=2.03 Simple disulfide: pdb=" SG CYS M 113 " - pdb=" SG CYS M 127 " distance=2.03 Simple disulfide: pdb=" SG CYS M 120 " - pdb=" SG CYS M 140 " distance=2.03 Simple disulfide: pdb=" SG CYS M 134 " - pdb=" SG CYS M 149 " distance=2.03 Simple disulfide: pdb=" SG CYS N 113 " - pdb=" SG CYS N 127 " distance=2.04 Simple disulfide: pdb=" SG CYS N 120 " - pdb=" SG CYS N 140 " distance=2.03 Simple disulfide: pdb=" SG CYS N 134 " - pdb=" SG CYS N 149 " distance=2.03 Simple disulfide: pdb=" SG CYS O 113 " - pdb=" SG CYS O 127 " distance=2.03 Simple disulfide: pdb=" SG CYS O 120 " - pdb=" SG CYS O 140 " distance=2.03 Simple disulfide: pdb=" SG CYS O 134 " - pdb=" SG CYS O 149 " distance=2.03 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 Links applied NAG-ASN " NAG A 500 " - " ASN A 200 " " NAG A 501 " - " ASN A 262 " " NAG B 500 " - " ASN B 141 " " NAG D 500 " - " ASN D 200 " " NAG D 501 " - " ASN D 262 " " NAG E 500 " - " ASN E 141 " " NAG G 500 " - " ASN G 200 " " NAG G 501 " - " ASN G 262 " " NAG H 500 " - " ASN H 141 " " NAG J 500 " - " ASN J 200 " " NAG J 501 " - " ASN J 262 " " NAG K 500 " - " ASN K 141 " Time building additional restraints: 10.66 Conformation dependent library (CDL) restraints added in 6.2 seconds 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7736 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 86 sheets defined 14.3% alpha, 26.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.68 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 removed outlier: 4.142A pdb=" N PHE A 6 " --> pdb=" O VAL A 2 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA A 11 " --> pdb=" O ASN A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 221 through 223 No H-bonds generated for 'chain 'A' and resid 221 through 223' Processing helix chain 'A' and resid 350 through 362 Processing helix chain 'A' and resid 362 through 402 Proline residue: A 398 - end of helix removed outlier: 3.518A pdb=" N LEU A 401 " --> pdb=" O THR A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 416 Processing helix chain 'B' and resid 238 through 247 removed outlier: 3.883A pdb=" N LYS B 245 " --> pdb=" O LYS B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 259 removed outlier: 3.615A pdb=" N GLY B 258 " --> pdb=" O ALA B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 287 removed outlier: 3.630A pdb=" N ALA B 286 " --> pdb=" O PRO B 283 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE B 287 " --> pdb=" O ASP B 284 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 283 through 287' Processing helix chain 'B' and resid 291 through 293 No H-bonds generated for 'chain 'B' and resid 291 through 293' Processing helix chain 'B' and resid 404 through 437 removed outlier: 3.661A pdb=" N TRP B 409 " --> pdb=" O THR B 405 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL B 410 " --> pdb=" O ALA B 406 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG B 437 " --> pdb=" O CYS B 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 116 Processing helix chain 'C' and resid 152 through 157 Processing helix chain 'D' and resid 3 through 8 Processing helix chain 'D' and resid 9 through 12 removed outlier: 3.531A pdb=" N THR D 12 " --> pdb=" O TYR D 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 9 through 12' Processing helix chain 'D' and resid 81 through 83 No H-bonds generated for 'chain 'D' and resid 81 through 83' Processing helix chain 'D' and resid 177 through 181 removed outlier: 3.856A pdb=" N LEU D 180 " --> pdb=" O ASP D 177 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU D 181 " --> pdb=" O ARG D 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 177 through 181' Processing helix chain 'D' and resid 350 through 360 removed outlier: 3.595A pdb=" N VAL D 355 " --> pdb=" O PRO D 351 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLN D 356 " --> pdb=" O HIS D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 397 Processing helix chain 'D' and resid 398 through 401 Processing helix chain 'D' and resid 408 through 415 removed outlier: 3.780A pdb=" N LEU D 414 " --> pdb=" O THR D 410 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N CYS D 415 " --> pdb=" O LEU D 411 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 247 removed outlier: 3.562A pdb=" N LYS E 245 " --> pdb=" O LYS E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 259 removed outlier: 3.688A pdb=" N GLY E 258 " --> pdb=" O ALA E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 287 Processing helix chain 'E' and resid 404 through 436 Processing helix chain 'F' and resid 107 through 119 removed outlier: 3.767A pdb=" N MET F 113 " --> pdb=" O GLU F 109 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS F 114 " --> pdb=" O ARG F 110 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ASP F 118 " --> pdb=" O LYS F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 181 removed outlier: 3.643A pdb=" N MET F 177 " --> pdb=" O PRO F 174 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N SER F 179 " --> pdb=" O HIS F 176 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 83 No H-bonds generated for 'chain 'G' and resid 81 through 83' Processing helix chain 'G' and resid 221 through 223 No H-bonds generated for 'chain 'G' and resid 221 through 223' Processing helix chain 'G' and resid 350 through 360 removed outlier: 3.522A pdb=" N GLN G 356 " --> pdb=" O HIS G 352 " (cutoff:3.500A) Processing helix chain 'G' and resid 362 through 401 Proline residue: G 398 - end of helix Processing helix chain 'G' and resid 411 through 416 removed outlier: 3.993A pdb=" N CYS G 415 " --> pdb=" O LEU G 411 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N CYS G 416 " --> pdb=" O GLY G 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 411 through 416' Processing helix chain 'H' and resid 238 through 246 removed outlier: 3.568A pdb=" N LYS H 245 " --> pdb=" O LYS H 241 " (cutoff:3.500A) Processing helix chain 'H' and resid 255 through 259 removed outlier: 3.778A pdb=" N GLY H 258 " --> pdb=" O ALA H 255 " (cutoff:3.500A) Processing helix chain 'H' and resid 283 through 287 removed outlier: 3.525A pdb=" N ALA H 286 " --> pdb=" O PRO H 283 " (cutoff:3.500A) Processing helix chain 'H' and resid 404 through 435 removed outlier: 3.819A pdb=" N TRP H 409 " --> pdb=" O THR H 405 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N VAL H 410 " --> pdb=" O ALA H 406 " (cutoff:3.500A) Processing helix chain 'I' and resid 107 through 120 removed outlier: 3.794A pdb=" N MET I 113 " --> pdb=" O GLU I 109 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYS I 114 " --> pdb=" O ARG I 110 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ILE I 115 " --> pdb=" O MET I 111 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ASP I 118 " --> pdb=" O LYS I 114 " (cutoff:3.500A) Processing helix chain 'I' and resid 152 through 156 Processing helix chain 'I' and resid 174 through 179 removed outlier: 4.112A pdb=" N SER I 179 " --> pdb=" O VAL I 175 " (cutoff:3.500A) Processing helix chain 'J' and resid 6 through 11 removed outlier: 3.868A pdb=" N ALA J 11 " --> pdb=" O ASN J 7 " (cutoff:3.500A) Processing helix chain 'J' and resid 81 through 83 No H-bonds generated for 'chain 'J' and resid 81 through 83' Processing helix chain 'J' and resid 350 through 360 removed outlier: 3.581A pdb=" N GLN J 356 " --> pdb=" O HIS J 352 " (cutoff:3.500A) Processing helix chain 'J' and resid 362 through 397 Processing helix chain 'J' and resid 398 through 400 No H-bonds generated for 'chain 'J' and resid 398 through 400' Processing helix chain 'J' and resid 408 through 415 Processing helix chain 'K' and resid 238 through 247 removed outlier: 3.641A pdb=" N LYS K 245 " --> pdb=" O LYS K 241 " (cutoff:3.500A) Processing helix chain 'K' and resid 255 through 259 removed outlier: 3.618A pdb=" N GLY K 258 " --> pdb=" O ALA K 255 " (cutoff:3.500A) Processing helix chain 'K' and resid 283 through 287 Processing helix chain 'K' and resid 289 through 293 Processing helix chain 'K' and resid 404 through 436 removed outlier: 3.573A pdb=" N TRP K 409 " --> pdb=" O THR K 405 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL K 410 " --> pdb=" O ALA K 406 " (cutoff:3.500A) Processing helix chain 'L' and resid 107 through 111 Processing helix chain 'L' and resid 112 through 117 removed outlier: 4.312A pdb=" N GLU L 116 " --> pdb=" O CYS L 112 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ASN L 117 " --> pdb=" O MET L 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 112 through 117' Processing helix chain 'L' and resid 153 through 157 removed outlier: 3.873A pdb=" N LYS L 157 " --> pdb=" O ASP L 154 " (cutoff:3.500A) Processing helix chain 'M' and resid 131 through 133 No H-bonds generated for 'chain 'M' and resid 131 through 133' Processing helix chain 'M' and resid 143 through 147 removed outlier: 3.753A pdb=" N GLU M 146 " --> pdb=" O GLY M 143 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU M 147 " --> pdb=" O GLU M 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 143 through 147' Processing helix chain 'N' and resid 131 through 133 No H-bonds generated for 'chain 'N' and resid 131 through 133' Processing helix chain 'O' and resid 131 through 133 No H-bonds generated for 'chain 'O' and resid 131 through 133' Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 19 Processing sheet with id=AA2, first strand: chain 'A' and resid 37 through 38 removed outlier: 6.234A pdb=" N LYS A 66 " --> pdb=" O GLY A 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 86 Processing sheet with id=AA4, first strand: chain 'A' and resid 149 through 156 Processing sheet with id=AA5, first strand: chain 'A' and resid 236 through 237 Processing sheet with id=AA6, first strand: chain 'A' and resid 175 through 176 removed outlier: 3.600A pdb=" N VAL A 208 " --> pdb=" O TYR A 199 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N CYS A 201 " --> pdb=" O GLY A 206 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N GLY A 206 " --> pdb=" O CYS A 201 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA8, first strand: chain 'A' and resid 274 through 277 Processing sheet with id=AA9, first strand: chain 'A' and resid 306 through 310 Processing sheet with id=AB1, first strand: chain 'B' and resid 2 through 8 removed outlier: 3.657A pdb=" N GLN B 160 " --> pdb=" O ASN B 281 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 16 through 19 removed outlier: 6.950A pdb=" N LYS B 132 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N THR B 36 " --> pdb=" O LYS B 130 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LYS B 130 " --> pdb=" O THR B 36 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LEU B 38 " --> pdb=" O SER B 128 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N SER B 128 " --> pdb=" O LEU B 38 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 24 through 25 removed outlier: 4.630A pdb=" N THR B 288 " --> pdb=" O SER B 25 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 42 through 48 removed outlier: 7.013A pdb=" N ALA B 121 " --> pdb=" O GLU B 45 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ILE B 47 " --> pdb=" O ALA B 119 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ALA B 119 " --> pdb=" O ILE B 47 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 51 through 54 current: chain 'B' and resid 100 through 110 No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 203 through 204 Processing sheet with id=AB7, first strand: chain 'B' and resid 220 through 221 Processing sheet with id=AB8, first strand: chain 'B' and resid 260 through 261 Processing sheet with id=AB9, first strand: chain 'B' and resid 297 through 306 removed outlier: 5.476A pdb=" N ASP B 298 " --> pdb=" O LYS B 321 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N LYS B 321 " --> pdb=" O ASP B 298 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL B 315 " --> pdb=" O ALA B 304 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 326 through 328 Processing sheet with id=AC2, first strand: chain 'B' and resid 331 through 332 Processing sheet with id=AC3, first strand: chain 'C' and resid 149 through 150 removed outlier: 6.380A pdb=" N PHE C 121 " --> pdb=" O TYR C 132 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N TYR C 132 " --> pdb=" O PHE C 121 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL C 123 " --> pdb=" O THR C 130 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR C 130 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N TYR C 132 " --> pdb=" O PRO C 143 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 191 through 194 removed outlier: 4.067A pdb=" N GLY C 191 " --> pdb=" O TYR C 202 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR C 202 " --> pdb=" O GLY C 191 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N ALA C 199 " --> pdb=" O PRO C 210 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 207 through 210 current: chain 'C' and resid 232 through 238 removed outlier: 7.153A pdb=" N ALA C 232 " --> pdb=" O TRP C 251 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N TRP C 251 " --> pdb=" O ALA C 232 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N VAL C 234 " --> pdb=" O VAL C 249 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N VAL C 249 " --> pdb=" O VAL C 234 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 17 through 19 Processing sheet with id=AC6, first strand: chain 'D' and resid 34 through 38 removed outlier: 8.328A pdb=" N ILE D 34 " --> pdb=" O SER D 51 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N SER D 51 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA D 36 " --> pdb=" O GLN D 49 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 84 through 86 Processing sheet with id=AC8, first strand: chain 'D' and resid 149 through 156 Processing sheet with id=AC9, first strand: chain 'D' and resid 236 through 237 Processing sheet with id=AD1, first strand: chain 'D' and resid 182 through 183 removed outlier: 3.790A pdb=" N MET D 215 " --> pdb=" O ILE D 190 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 197 through 201 Processing sheet with id=AD3, first strand: chain 'D' and resid 274 through 277 Processing sheet with id=AD4, first strand: chain 'D' and resid 306 through 310 removed outlier: 3.504A pdb=" N TYR D 296 " --> pdb=" O HIS D 306 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 2 through 8 removed outlier: 3.668A pdb=" N GLN E 160 " --> pdb=" O ASN E 281 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 15 through 19 removed outlier: 3.582A pdb=" N TYR E 15 " --> pdb=" O MET E 31 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 27 through 33 current: chain 'E' and resid 119 through 137 removed outlier: 3.767A pdb=" N TYR E 137 " --> pdb=" O VAL E 140 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 140 through 147 current: chain 'E' and resid 184 through 185 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 184 through 185 current: chain 'E' and resid 268 through 269 Processing sheet with id=AD7, first strand: chain 'E' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 51 through 54 current: chain 'E' and resid 100 through 110 No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'E' and resid 203 through 204 Processing sheet with id=AD9, first strand: chain 'E' and resid 220 through 221 Processing sheet with id=AE1, first strand: chain 'E' and resid 296 through 306 removed outlier: 5.980A pdb=" N ASP E 298 " --> pdb=" O LYS E 321 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N LYS E 321 " --> pdb=" O ASP E 298 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL E 315 " --> pdb=" O ALA E 304 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 326 through 329 Processing sheet with id=AE3, first strand: chain 'E' and resid 364 through 367 Processing sheet with id=AE4, first strand: chain 'F' and resid 149 through 150 removed outlier: 6.352A pdb=" N PHE F 121 " --> pdb=" O TYR F 132 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N TYR F 132 " --> pdb=" O PHE F 121 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL F 123 " --> pdb=" O THR F 130 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N TYR F 132 " --> pdb=" O PRO F 143 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 183 through 184 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 183 through 184 current: chain 'F' and resid 198 through 203 removed outlier: 9.162A pdb=" N ALA F 199 " --> pdb=" O PRO F 210 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN F 201 " --> pdb=" O THR F 208 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 206 through 210 current: chain 'F' and resid 229 through 240 removed outlier: 7.901A pdb=" N ALA F 232 " --> pdb=" O TRP F 251 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N TRP F 251 " --> pdb=" O ALA F 232 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N VAL F 234 " --> pdb=" O VAL F 249 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N VAL F 249 " --> pdb=" O VAL F 234 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 17 through 19 Processing sheet with id=AE7, first strand: chain 'G' and resid 36 through 38 removed outlier: 9.619A pdb=" N SER G 51 " --> pdb=" O ALA G 70 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ALA G 70 " --> pdb=" O SER G 51 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LYS G 66 " --> pdb=" O GLY G 55 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR G 69 " --> pdb=" O GLU G 76 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 84 through 86 Processing sheet with id=AE9, first strand: chain 'G' and resid 149 through 156 Processing sheet with id=AF1, first strand: chain 'G' and resid 236 through 237 Processing sheet with id=AF2, first strand: chain 'G' and resid 175 through 177 removed outlier: 4.612A pdb=" N VAL G 227 " --> pdb=" O ASP G 177 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 181 through 182 Processing sheet with id=AF4, first strand: chain 'G' and resid 274 through 277 Processing sheet with id=AF5, first strand: chain 'G' and resid 306 through 310 Processing sheet with id=AF6, first strand: chain 'H' and resid 2 through 8 removed outlier: 3.536A pdb=" N GLN H 160 " --> pdb=" O ASN H 281 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR H 159 " --> pdb=" O ILE H 156 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 15 through 19 removed outlier: 3.716A pdb=" N TYR H 15 " --> pdb=" O MET H 31 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N LEU H 29 " --> pdb=" O TYR H 137 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N TYR H 137 " --> pdb=" O LEU H 29 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N MET H 31 " --> pdb=" O VAL H 135 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL H 135 " --> pdb=" O MET H 31 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL H 33 " --> pdb=" O VAL H 133 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL H 133 " --> pdb=" O VAL H 33 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N GLU H 35 " --> pdb=" O ALA H 131 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ALA H 131 " --> pdb=" O GLU H 35 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N SER H 37 " --> pdb=" O LEU H 129 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU H 129 " --> pdb=" O SER H 37 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N GLU H 39 " --> pdb=" O ALA H 127 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ALA H 127 " --> pdb=" O GLU H 39 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR H 41 " --> pdb=" O HIS H 125 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ALA H 121 " --> pdb=" O GLU H 45 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ILE H 47 " --> pdb=" O ALA H 119 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ALA H 119 " --> pdb=" O ILE H 47 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR H 137 " --> pdb=" O VAL H 140 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 140 through 147 current: chain 'H' and resid 184 through 185 Processing sheet with id=AF8, first strand: chain 'H' and resid 24 through 25 removed outlier: 4.678A pdb=" N THR H 288 " --> pdb=" O SER H 25 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 51 through 54 current: chain 'H' and resid 100 through 110 No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'H' and resid 203 through 204 Processing sheet with id=AG2, first strand: chain 'H' and resid 220 through 221 Processing sheet with id=AG3, first strand: chain 'H' and resid 260 through 262 removed outlier: 4.142A pdb=" N ARG H 267 " --> pdb=" O LYS H 262 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'H' and resid 297 through 306 removed outlier: 4.175A pdb=" N LEU H 299 " --> pdb=" O THR H 319 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N THR H 319 " --> pdb=" O LEU H 299 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N CYS H 301 " --> pdb=" O THR H 317 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N THR H 317 " --> pdb=" O CYS H 301 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N VAL H 303 " --> pdb=" O VAL H 315 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N VAL H 315 " --> pdb=" O VAL H 303 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'H' and resid 331 through 332 Processing sheet with id=AG6, first strand: chain 'I' and resid 128 through 129 removed outlier: 3.559A pdb=" N LYS I 124 " --> pdb=" O VAL I 149 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL I 149 " --> pdb=" O LYS I 124 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'I' and resid 134 through 135 Processing sheet with id=AG8, first strand: chain 'I' and resid 239 through 240 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 239 through 240 current: chain 'I' and resid 199 through 203 removed outlier: 4.144A pdb=" N GLY I 191 " --> pdb=" O TYR I 202 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ILE I 223 " --> pdb=" O VAL I 231 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N ALA I 232 " --> pdb=" O TRP I 251 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N TRP I 251 " --> pdb=" O ALA I 232 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N VAL I 234 " --> pdb=" O VAL I 249 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N VAL I 249 " --> pdb=" O VAL I 234 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'J' and resid 17 through 19 Processing sheet with id=AH1, first strand: chain 'J' and resid 37 through 38 removed outlier: 7.167A pdb=" N PHE J 100 " --> pdb=" O THR J 96 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N THR J 96 " --> pdb=" O PHE J 100 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU J 102 " --> pdb=" O HIS J 94 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'J' and resid 53 through 56 removed outlier: 6.346A pdb=" N LYS J 66 " --> pdb=" O GLY J 55 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'J' and resid 84 through 86 Processing sheet with id=AH4, first strand: chain 'J' and resid 149 through 156 Processing sheet with id=AH5, first strand: chain 'J' and resid 236 through 237 Processing sheet with id=AH6, first strand: chain 'J' and resid 175 through 176 Processing sheet with id=AH7, first strand: chain 'J' and resid 181 through 182 Processing sheet with id=AH8, first strand: chain 'J' and resid 274 through 278 removed outlier: 4.085A pdb=" N GLU J 281 " --> pdb=" O GLY J 278 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'J' and resid 306 through 310 Processing sheet with id=AI1, first strand: chain 'K' and resid 2 through 8 Processing sheet with id=AI2, first strand: chain 'K' and resid 15 through 19 removed outlier: 3.509A pdb=" N TYR K 15 " --> pdb=" O MET K 31 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LYS K 132 " --> pdb=" O VAL K 34 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N THR K 36 " --> pdb=" O LYS K 130 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LYS K 130 " --> pdb=" O THR K 36 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N LEU K 38 " --> pdb=" O SER K 128 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N SER K 128 " --> pdb=" O LEU K 38 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N THR K 126 " --> pdb=" O PRO K 40 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N LEU K 42 " --> pdb=" O ALA K 124 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ALA K 124 " --> pdb=" O LEU K 42 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LEU K 44 " --> pdb=" O TYR K 122 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N TYR K 122 " --> pdb=" O LEU K 44 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N TYR K 46 " --> pdb=" O SER K 120 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N SER K 120 " --> pdb=" O TYR K 46 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 140 through 147 current: chain 'K' and resid 184 through 185 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 184 through 185 current: chain 'K' and resid 268 through 269 Processing sheet with id=AI3, first strand: chain 'K' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 51 through 54 current: chain 'K' and resid 101 through 110 No H-bonds generated for sheet with id=AI3 Processing sheet with id=AI4, first strand: chain 'K' and resid 203 through 204 Processing sheet with id=AI5, first strand: chain 'K' and resid 220 through 221 Processing sheet with id=AI6, first strand: chain 'K' and resid 297 through 306 removed outlier: 5.590A pdb=" N ASP K 298 " --> pdb=" O LYS K 321 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LYS K 321 " --> pdb=" O ASP K 298 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL K 315 " --> pdb=" O ALA K 304 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'K' and resid 326 through 329 Processing sheet with id=AI8, first strand: chain 'K' and resid 331 through 332 Processing sheet with id=AI9, first strand: chain 'L' and resid 139 through 141 removed outlier: 3.501A pdb=" N VAL L 136 " --> pdb=" O LYS L 139 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N VAL L 123 " --> pdb=" O THR L 130 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N TYR L 132 " --> pdb=" O PHE L 121 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N PHE L 121 " --> pdb=" O TYR L 132 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'L' and resid 192 through 194 removed outlier: 8.836A pdb=" N ALA L 199 " --> pdb=" O PRO L 210 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG L 243 " --> pdb=" O GLU L 240 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY L 237 " --> pdb=" O GLU L 265 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'L' and resid 222 through 223 removed outlier: 3.885A pdb=" N ALA L 232 " --> pdb=" O ILE L 223 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'M' and resid 117 through 119 Processing sheet with id=AJ4, first strand: chain 'N' and resid 117 through 119 Processing sheet with id=AJ5, first strand: chain 'O' and resid 117 through 118 968 hydrogen bonds defined for protein. 2472 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: 11.26 Time building geometry restraints manager: 11.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 10382 1.34 - 1.46: 7122 1.46 - 1.58: 15327 1.58 - 1.70: 1 1.70 - 1.83: 342 Bond restraints: 33174 Sorted by residual: bond pdb=" CG1 ILE G 143 " pdb=" CD1 ILE G 143 " ideal model delta sigma weight residual 1.513 1.425 0.088 3.90e-02 6.57e+02 5.12e+00 bond pdb=" CA ASN K 211 " pdb=" C ASN K 211 " ideal model delta sigma weight residual 1.521 1.549 -0.028 1.38e-02 5.25e+03 4.16e+00 bond pdb=" CA LEU B 369 " pdb=" C LEU B 369 " ideal model delta sigma weight residual 1.530 1.553 -0.022 1.12e-02 7.97e+03 4.00e+00 bond pdb=" CB PRO F 174 " pdb=" CG PRO F 174 " ideal model delta sigma weight residual 1.492 1.589 -0.097 5.00e-02 4.00e+02 3.75e+00 bond pdb=" C1 NAG D 501 " pdb=" O5 NAG D 501 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.70e+00 ... (remaining 33169 not shown) Histogram of bond angle deviations from ideal: 98.90 - 105.94: 939 105.94 - 112.99: 18327 112.99 - 120.03: 10564 120.03 - 127.07: 14813 127.07 - 134.11: 518 Bond angle restraints: 45161 Sorted by residual: angle pdb=" N LEU K 213 " pdb=" CA LEU K 213 " pdb=" C LEU K 213 " ideal model delta sigma weight residual 111.39 118.47 -7.08 1.38e+00 5.25e-01 2.63e+01 angle pdb=" N ASP K 212 " pdb=" CA ASP K 212 " pdb=" C ASP K 212 " ideal model delta sigma weight residual 111.07 116.29 -5.22 1.07e+00 8.73e-01 2.38e+01 angle pdb=" N GLU M 117 " pdb=" CA GLU M 117 " pdb=" C GLU M 117 " ideal model delta sigma weight residual 109.07 116.86 -7.79 1.61e+00 3.86e-01 2.34e+01 angle pdb=" CA PRO F 174 " pdb=" N PRO F 174 " pdb=" CD PRO F 174 " ideal model delta sigma weight residual 112.00 105.64 6.36 1.40e+00 5.10e-01 2.06e+01 angle pdb=" N ALA B 372 " pdb=" CA ALA B 372 " pdb=" C ALA B 372 " ideal model delta sigma weight residual 109.72 116.66 -6.94 1.60e+00 3.91e-01 1.88e+01 ... (remaining 45156 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 18207 17.86 - 35.72: 1555 35.72 - 53.58: 267 53.58 - 71.44: 40 71.44 - 89.30: 23 Dihedral angle restraints: 20092 sinusoidal: 8014 harmonic: 12078 Sorted by residual: dihedral pdb=" CB CYS A 153 " pdb=" SG CYS A 153 " pdb=" SG CYS A 265 " pdb=" CB CYS A 265 " ideal model delta sinusoidal sigma weight residual -86.00 0.86 -86.86 1 1.00e+01 1.00e-02 9.07e+01 dihedral pdb=" CB CYS D 153 " pdb=" SG CYS D 153 " pdb=" SG CYS D 265 " pdb=" CB CYS D 265 " ideal model delta sinusoidal sigma weight residual -86.00 -7.55 -78.45 1 1.00e+01 1.00e-02 7.68e+01 dihedral pdb=" CB CYS K 328 " pdb=" SG CYS K 328 " pdb=" SG CYS K 370 " pdb=" CB CYS K 370 " ideal model delta sinusoidal sigma weight residual 93.00 20.85 72.15 1 1.00e+01 1.00e-02 6.66e+01 ... (remaining 20089 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 4519 0.083 - 0.165: 510 0.165 - 0.248: 15 0.248 - 0.330: 0 0.330 - 0.413: 2 Chirality restraints: 5046 Sorted by residual: chirality pdb=" C1 NAG H 500 " pdb=" ND2 ASN H 141 " pdb=" C2 NAG H 500 " pdb=" O5 NAG H 500 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.26e+00 chirality pdb=" C1 NAG E 500 " pdb=" ND2 ASN E 141 " pdb=" C2 NAG E 500 " pdb=" O5 NAG E 500 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" CA LEU K 213 " pdb=" N LEU K 213 " pdb=" C LEU K 213 " pdb=" CB LEU K 213 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 5043 not shown) Planarity restraints: 5839 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE F 173 " -0.075 5.00e-02 4.00e+02 1.10e-01 1.95e+01 pdb=" N PRO F 174 " 0.191 5.00e-02 4.00e+02 pdb=" CA PRO F 174 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO F 174 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE G 50 " -0.016 2.00e-02 2.50e+03 2.02e-02 7.17e+00 pdb=" CG PHE G 50 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE G 50 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE G 50 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE G 50 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE G 50 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE G 50 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 322 " 0.013 2.00e-02 2.50e+03 2.59e-02 6.72e+00 pdb=" C THR B 322 " -0.045 2.00e-02 2.50e+03 pdb=" O THR B 322 " 0.017 2.00e-02 2.50e+03 pdb=" N ASP B 323 " 0.015 2.00e-02 2.50e+03 ... (remaining 5836 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2745 2.74 - 3.28: 29997 3.28 - 3.82: 50536 3.82 - 4.36: 60061 4.36 - 4.90: 108317 Nonbonded interactions: 251656 Sorted by model distance: nonbonded pdb=" O SER D 239 " pdb=" OG SER E 57 " model vdw 2.197 2.440 nonbonded pdb=" OD1 ASN K 43 " pdb=" NE2 HIS K 125 " model vdw 2.200 2.520 nonbonded pdb=" OD1 ASN E 325 " pdb=" OG1 THR E 348 " model vdw 2.201 2.440 nonbonded pdb=" OG1 THR G 298 " pdb=" O PRO G 303 " model vdw 2.203 2.440 nonbonded pdb=" ND1 HIS L 145 " pdb=" OE2 GLU L 266 " model vdw 2.210 2.520 ... (remaining 251651 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' selection = chain 'J' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' selection = chain 'K' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 14.740 Check model and map are aligned: 0.070 Set scattering table: 0.220 Process input model: 77.660 Find NCS groups from input model: 2.370 Set up NCS constraints: 0.320 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 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 : 0.006 0.097 33174 Z= 0.385 Angle : 0.694 10.180 45161 Z= 0.379 Chirality : 0.050 0.413 5046 Planarity : 0.005 0.110 5827 Dihedral : 13.201 89.305 12173 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.13), residues: 4151 helix: 1.11 (0.25), residues: 500 sheet: -0.99 (0.14), residues: 1396 loop : -1.84 (0.12), residues: 2255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 89 HIS 0.013 0.001 HIS J 285 PHE 0.045 0.002 PHE G 50 TYR 0.020 0.002 TYR G 64 ARG 0.008 0.001 ARG F 229 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 3545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 451 time to evaluate : 3.328 Fit side-chains revert: symmetry clash REVERT: A 325 MET cc_start: 0.8933 (tmm) cc_final: 0.8359 (tmt) REVERT: E 31 MET cc_start: 0.8827 (ptt) cc_final: 0.8413 (ptt) REVERT: G 325 MET cc_start: 0.8825 (tmm) cc_final: 0.8567 (tmt) outliers start: 0 outliers final: 0 residues processed: 451 average time/residue: 1.3576 time to fit residues: 728.6334 Evaluate side-chains 357 residues out of total 3545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 357 time to evaluate : 3.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 345 optimal weight: 6.9990 chunk 310 optimal weight: 0.9980 chunk 172 optimal weight: 10.0000 chunk 105 optimal weight: 9.9990 chunk 209 optimal weight: 2.9990 chunk 165 optimal weight: 3.9990 chunk 320 optimal weight: 0.0870 chunk 124 optimal weight: 4.9990 chunk 194 optimal weight: 20.0000 chunk 238 optimal weight: 5.9990 chunk 371 optimal weight: 0.0870 overall best weight: 1.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 ASN ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 197 HIS G 120 ASN G 170 HIS ** G 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 175 ASN H 325 ASN H 333 HIS J 116 GLN J 170 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.0922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 33174 Z= 0.181 Angle : 0.589 14.369 45161 Z= 0.309 Chirality : 0.045 0.348 5046 Planarity : 0.005 0.066 5827 Dihedral : 5.852 58.497 4759 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.44 % Allowed : 9.34 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.13), residues: 4151 helix: 1.42 (0.25), residues: 500 sheet: -0.77 (0.14), residues: 1316 loop : -1.70 (0.12), residues: 2335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 251 HIS 0.007 0.001 HIS J 285 PHE 0.024 0.001 PHE D 50 TYR 0.024 0.001 TYR A 199 ARG 0.006 0.000 ARG D 119 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 3545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 384 time to evaluate : 3.789 Fit side-chains REVERT: A 199 TYR cc_start: 0.5343 (OUTLIER) cc_final: 0.4533 (t80) REVERT: A 281 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7625 (pp20) REVERT: A 317 THR cc_start: 0.9258 (t) cc_final: 0.8955 (t) REVERT: A 325 MET cc_start: 0.8974 (tmm) cc_final: 0.8293 (tmt) REVERT: E 31 MET cc_start: 0.8901 (ptt) cc_final: 0.8444 (ptt) REVERT: F 113 MET cc_start: 0.7125 (mpm) cc_final: 0.6688 (mpm) REVERT: G 222 ILE cc_start: 0.7807 (OUTLIER) cc_final: 0.7553 (pp) REVERT: G 325 MET cc_start: 0.8784 (tmm) cc_final: 0.8575 (tmt) REVERT: J 158 GLN cc_start: 0.7223 (OUTLIER) cc_final: 0.6852 (mt0) REVERT: J 302 ASP cc_start: 0.6912 (OUTLIER) cc_final: 0.6674 (t0) REVERT: L 113 MET cc_start: 0.6620 (mpm) cc_final: 0.6401 (mpp) REVERT: L 255 MET cc_start: 0.6786 (OUTLIER) cc_final: 0.6378 (mtp) outliers start: 51 outliers final: 22 residues processed: 404 average time/residue: 1.2395 time to fit residues: 604.8131 Evaluate side-chains 380 residues out of total 3545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 352 time to evaluate : 3.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 CYS Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 433 CYS Chi-restraints excluded: chain C residue 251 TRP Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 323 ASP Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 300 THR Chi-restraints excluded: chain F residue 182 SER Chi-restraints excluded: chain G residue 170 HIS Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain H residue 305 THR Chi-restraints excluded: chain J residue 158 GLN Chi-restraints excluded: chain J residue 301 GLU Chi-restraints excluded: chain J residue 302 ASP Chi-restraints excluded: chain K residue 285 SER Chi-restraints excluded: chain L residue 255 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 206 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 309 optimal weight: 9.9990 chunk 252 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 372 optimal weight: 9.9990 chunk 401 optimal weight: 20.0000 chunk 331 optimal weight: 9.9990 chunk 368 optimal weight: 10.0000 chunk 126 optimal weight: 4.9990 chunk 298 optimal weight: 30.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 HIS C 252 ASN D 157 GLN G 120 ASN G 170 HIS ** G 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 226 HIS I 192 HIS J 170 HIS K 230 HIS N 138 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.0991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 33174 Z= 0.325 Angle : 0.627 11.701 45161 Z= 0.327 Chirality : 0.047 0.362 5046 Planarity : 0.005 0.050 5827 Dihedral : 5.870 56.789 4759 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 2.99 % Allowed : 12.19 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.13), residues: 4151 helix: 1.45 (0.25), residues: 500 sheet: -0.69 (0.14), residues: 1288 loop : -1.77 (0.12), residues: 2363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 251 HIS 0.010 0.001 HIS J 285 PHE 0.032 0.002 PHE G 50 TYR 0.017 0.002 TYR J 327 ARG 0.008 0.000 ARG D 119 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 3545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 369 time to evaluate : 3.722 Fit side-chains revert: symmetry clash REVERT: A 134 GLN cc_start: 0.7961 (OUTLIER) cc_final: 0.7652 (mp10) REVERT: A 151 ILE cc_start: 0.8777 (mm) cc_final: 0.8501 (mt) REVERT: A 199 TYR cc_start: 0.5222 (OUTLIER) cc_final: 0.3981 (t80) REVERT: A 325 MET cc_start: 0.8957 (tmm) cc_final: 0.8434 (tmt) REVERT: D 45 MET cc_start: 0.8612 (OUTLIER) cc_final: 0.8188 (tpp) REVERT: D 158 GLN cc_start: 0.7224 (OUTLIER) cc_final: 0.6440 (mt0) REVERT: E 31 MET cc_start: 0.9002 (ptt) cc_final: 0.8530 (ptt) REVERT: F 113 MET cc_start: 0.7295 (OUTLIER) cc_final: 0.6873 (mpm) REVERT: G 222 ILE cc_start: 0.7834 (OUTLIER) cc_final: 0.7554 (pp) REVERT: G 256 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8508 (pt) REVERT: G 325 MET cc_start: 0.8802 (tmm) cc_final: 0.8534 (tmt) REVERT: I 223 ILE cc_start: 0.6844 (mp) cc_final: 0.6602 (mp) REVERT: I 255 MET cc_start: 0.6081 (OUTLIER) cc_final: 0.5650 (tmm) REVERT: J 158 GLN cc_start: 0.7285 (OUTLIER) cc_final: 0.6890 (mt0) REVERT: L 255 MET cc_start: 0.6826 (OUTLIER) cc_final: 0.6332 (mtp) outliers start: 106 outliers final: 53 residues processed: 420 average time/residue: 1.2761 time to fit residues: 644.7291 Evaluate side-chains 407 residues out of total 3545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 344 time to evaluate : 3.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 433 CYS Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 251 TRP Chi-restraints excluded: chain D residue 45 MET Chi-restraints excluded: chain D residue 76 GLU Chi-restraints excluded: chain D residue 158 GLN Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 323 ASP Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 300 THR Chi-restraints excluded: chain F residue 113 MET Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 182 SER Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 256 ILE Chi-restraints excluded: chain G residue 333 ASP Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain H residue 305 THR Chi-restraints excluded: chain H residue 343 THR Chi-restraints excluded: chain H residue 405 THR Chi-restraints excluded: chain I residue 113 MET Chi-restraints excluded: chain I residue 255 MET Chi-restraints excluded: chain J residue 158 GLN Chi-restraints excluded: chain J residue 301 GLU Chi-restraints excluded: chain J residue 376 LEU Chi-restraints excluded: chain J residue 394 LYS Chi-restraints excluded: chain K residue 31 MET Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 140 VAL Chi-restraints excluded: chain K residue 213 LEU Chi-restraints excluded: chain K residue 231 VAL Chi-restraints excluded: chain K residue 269 MET Chi-restraints excluded: chain K residue 285 SER Chi-restraints excluded: chain K residue 288 THR Chi-restraints excluded: chain L residue 255 MET Chi-restraints excluded: chain O residue 139 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 367 optimal weight: 3.9990 chunk 279 optimal weight: 20.0000 chunk 193 optimal weight: 8.9990 chunk 41 optimal weight: 3.9990 chunk 177 optimal weight: 4.9990 chunk 249 optimal weight: 10.0000 chunk 373 optimal weight: 20.0000 chunk 395 optimal weight: 9.9990 chunk 195 optimal weight: 6.9990 chunk 353 optimal weight: 10.0000 chunk 106 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 HIS D 157 GLN E 142 GLN E 411 GLN G 120 ASN ** G 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 226 HIS H 325 ASN J 170 HIS J 184 GLN J 232 HIS ** M 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 138 ASN O 126 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 33174 Z= 0.423 Angle : 0.681 9.965 45161 Z= 0.354 Chirality : 0.050 0.402 5046 Planarity : 0.005 0.055 5827 Dihedral : 5.997 57.130 4759 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 3.78 % Allowed : 14.58 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.13), residues: 4151 helix: 1.00 (0.25), residues: 528 sheet: -0.77 (0.14), residues: 1232 loop : -1.84 (0.12), residues: 2391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP L 251 HIS 0.012 0.002 HIS J 285 PHE 0.032 0.002 PHE G 50 TYR 0.018 0.002 TYR J 327 ARG 0.007 0.001 ARG D 119 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 3545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 372 time to evaluate : 3.392 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7549 (mp10) REVERT: A 151 ILE cc_start: 0.8855 (mm) cc_final: 0.8590 (mt) REVERT: A 325 MET cc_start: 0.8935 (tmm) cc_final: 0.8467 (tmt) REVERT: A 326 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8345 (tt0) REVERT: B 2 GLU cc_start: 0.8224 (mm-30) cc_final: 0.8022 (mm-30) REVERT: D 45 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.8361 (tpp) REVERT: D 158 GLN cc_start: 0.7234 (OUTLIER) cc_final: 0.6507 (mt0) REVERT: E 31 MET cc_start: 0.9009 (ptt) cc_final: 0.8509 (ptt) REVERT: E 289 ARG cc_start: 0.7222 (OUTLIER) cc_final: 0.6410 (mtp85) REVERT: F 113 MET cc_start: 0.7266 (OUTLIER) cc_final: 0.6866 (mpm) REVERT: G 222 ILE cc_start: 0.7838 (OUTLIER) cc_final: 0.7543 (pp) REVERT: G 256 ILE cc_start: 0.8706 (OUTLIER) cc_final: 0.8491 (pt) REVERT: G 325 MET cc_start: 0.8808 (tmm) cc_final: 0.8508 (tmt) REVERT: I 223 ILE cc_start: 0.6951 (mp) cc_final: 0.6739 (mp) REVERT: I 255 MET cc_start: 0.6225 (OUTLIER) cc_final: 0.5695 (tmm) REVERT: L 111 MET cc_start: 0.4347 (tmm) cc_final: 0.4135 (tmm) REVERT: L 113 MET cc_start: 0.6639 (mpm) cc_final: 0.6420 (mpm) REVERT: L 240 GLU cc_start: 0.5577 (tp30) cc_final: 0.4830 (tm-30) REVERT: L 255 MET cc_start: 0.7130 (OUTLIER) cc_final: 0.6601 (mtp) outliers start: 134 outliers final: 75 residues processed: 449 average time/residue: 1.2669 time to fit residues: 688.0868 Evaluate side-chains 444 residues out of total 3545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 359 time to evaluate : 4.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 433 CYS Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain D residue 45 MET Chi-restraints excluded: chain D residue 76 GLU Chi-restraints excluded: chain D residue 158 GLN Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 323 ASP Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 289 ARG Chi-restraints excluded: chain E residue 300 THR Chi-restraints excluded: chain F residue 113 MET Chi-restraints excluded: chain F residue 182 SER Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 45 MET Chi-restraints excluded: chain G residue 61 ASN Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain G residue 199 TYR Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 256 ILE Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain H residue 305 THR Chi-restraints excluded: chain H residue 343 THR Chi-restraints excluded: chain H residue 351 LYS Chi-restraints excluded: chain H residue 405 THR Chi-restraints excluded: chain I residue 113 MET Chi-restraints excluded: chain I residue 255 MET Chi-restraints excluded: chain J residue 215 MET Chi-restraints excluded: chain J residue 227 VAL Chi-restraints excluded: chain J residue 301 GLU Chi-restraints excluded: chain J residue 376 LEU Chi-restraints excluded: chain J residue 394 LYS Chi-restraints excluded: chain K residue 31 MET Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 140 VAL Chi-restraints excluded: chain K residue 174 ASP Chi-restraints excluded: chain K residue 183 GLU Chi-restraints excluded: chain K residue 231 VAL Chi-restraints excluded: chain K residue 269 MET Chi-restraints excluded: chain K residue 285 SER Chi-restraints excluded: chain K residue 288 THR Chi-restraints excluded: chain L residue 248 VAL Chi-restraints excluded: chain L residue 255 MET Chi-restraints excluded: chain O residue 128 ILE Chi-restraints excluded: chain O residue 139 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 329 optimal weight: 1.9990 chunk 224 optimal weight: 7.9990 chunk 5 optimal weight: 8.9990 chunk 294 optimal weight: 20.0000 chunk 163 optimal weight: 5.9990 chunk 337 optimal weight: 10.0000 chunk 273 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 201 optimal weight: 0.9980 chunk 354 optimal weight: 10.0000 chunk 99 optimal weight: 8.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 HIS A 290 HIS ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 GLN ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 411 GLN G 120 ASN ** G 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 170 HIS J 232 HIS M 116 HIS ** M 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 33174 Z= 0.345 Angle : 0.640 10.339 45161 Z= 0.334 Chirality : 0.048 0.383 5046 Planarity : 0.005 0.052 5827 Dihedral : 5.880 56.833 4759 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 4.26 % Allowed : 15.71 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.13), residues: 4151 helix: 1.02 (0.25), residues: 528 sheet: -0.82 (0.14), residues: 1260 loop : -1.80 (0.12), residues: 2363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP K 89 HIS 0.010 0.001 HIS J 99 PHE 0.024 0.002 PHE D 50 TYR 0.017 0.002 TYR A 199 ARG 0.008 0.000 ARG D 119 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 3545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 366 time to evaluate : 3.880 Fit side-chains revert: symmetry clash REVERT: A 134 GLN cc_start: 0.8078 (OUTLIER) cc_final: 0.7509 (mp10) REVERT: A 151 ILE cc_start: 0.8844 (mm) cc_final: 0.8594 (mt) REVERT: A 325 MET cc_start: 0.8877 (tmm) cc_final: 0.8434 (tmt) REVERT: A 326 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8325 (tt0) REVERT: C 223 ILE cc_start: 0.8325 (OUTLIER) cc_final: 0.7922 (mp) REVERT: D 45 MET cc_start: 0.8560 (OUTLIER) cc_final: 0.8354 (tpp) REVERT: E 289 ARG cc_start: 0.7205 (OUTLIER) cc_final: 0.6352 (mtp85) REVERT: F 113 MET cc_start: 0.7238 (OUTLIER) cc_final: 0.6796 (mpm) REVERT: G 222 ILE cc_start: 0.7819 (OUTLIER) cc_final: 0.7532 (pp) REVERT: G 256 ILE cc_start: 0.8728 (OUTLIER) cc_final: 0.8511 (pt) REVERT: G 325 MET cc_start: 0.8815 (tmm) cc_final: 0.8500 (tmt) REVERT: I 185 THR cc_start: 0.7919 (OUTLIER) cc_final: 0.7571 (t) REVERT: I 223 ILE cc_start: 0.6968 (mp) cc_final: 0.6738 (mp) REVERT: I 255 MET cc_start: 0.6175 (OUTLIER) cc_final: 0.5831 (tmm) REVERT: L 113 MET cc_start: 0.6742 (OUTLIER) cc_final: 0.6456 (mpm) REVERT: L 240 GLU cc_start: 0.5573 (tp30) cc_final: 0.4840 (tm-30) REVERT: L 255 MET cc_start: 0.7203 (OUTLIER) cc_final: 0.6617 (mtp) REVERT: M 115 ILE cc_start: 0.7504 (OUTLIER) cc_final: 0.7261 (pp) outliers start: 151 outliers final: 92 residues processed: 458 average time/residue: 1.2052 time to fit residues: 673.3236 Evaluate side-chains 458 residues out of total 3545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 353 time to evaluate : 3.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 62 HIS Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 433 CYS Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 251 TRP Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain D residue 45 MET Chi-restraints excluded: chain D residue 62 HIS Chi-restraints excluded: chain D residue 76 GLU Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 323 ASP Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 289 ARG Chi-restraints excluded: chain E residue 300 THR Chi-restraints excluded: chain F residue 113 MET Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 182 SER Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 45 MET Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain G residue 199 TYR Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 256 ILE Chi-restraints excluded: chain G residue 333 ASP Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain H residue 305 THR Chi-restraints excluded: chain H residue 343 THR Chi-restraints excluded: chain H residue 351 LYS Chi-restraints excluded: chain H residue 352 VAL Chi-restraints excluded: chain H residue 405 THR Chi-restraints excluded: chain H residue 425 ILE Chi-restraints excluded: chain I residue 113 MET Chi-restraints excluded: chain I residue 185 THR Chi-restraints excluded: chain I residue 255 MET Chi-restraints excluded: chain J residue 50 PHE Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 218 ASN Chi-restraints excluded: chain J residue 227 VAL Chi-restraints excluded: chain J residue 290 HIS Chi-restraints excluded: chain J residue 301 GLU Chi-restraints excluded: chain J residue 376 LEU Chi-restraints excluded: chain J residue 394 LYS Chi-restraints excluded: chain K residue 31 MET Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 140 VAL Chi-restraints excluded: chain K residue 174 ASP Chi-restraints excluded: chain K residue 183 GLU Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain K residue 231 VAL Chi-restraints excluded: chain K residue 269 MET Chi-restraints excluded: chain K residue 285 SER Chi-restraints excluded: chain K residue 288 THR Chi-restraints excluded: chain K residue 433 CYS Chi-restraints excluded: chain L residue 113 MET Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain L residue 248 VAL Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 255 MET Chi-restraints excluded: chain M residue 115 ILE Chi-restraints excluded: chain O residue 139 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 133 optimal weight: 7.9990 chunk 356 optimal weight: 0.5980 chunk 78 optimal weight: 6.9990 chunk 232 optimal weight: 6.9990 chunk 97 optimal weight: 9.9990 chunk 395 optimal weight: 0.0040 chunk 328 optimal weight: 0.9990 chunk 183 optimal weight: 20.0000 chunk 32 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 207 optimal weight: 0.5980 overall best weight: 1.2396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 HIS A 290 HIS C 252 ASN D 157 GLN ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 411 GLN G 120 ASN G 187 ASN G 290 HIS J 170 HIS J 232 HIS K 142 GLN M 148 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 33174 Z= 0.151 Angle : 0.540 9.362 45161 Z= 0.282 Chirality : 0.044 0.300 5046 Planarity : 0.004 0.051 5827 Dihedral : 5.342 59.683 4759 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.05 % Allowed : 17.46 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.13), residues: 4151 helix: 1.56 (0.25), residues: 504 sheet: -0.53 (0.14), residues: 1268 loop : -1.61 (0.12), residues: 2379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP L 251 HIS 0.004 0.001 HIS J 170 PHE 0.012 0.001 PHE A 50 TYR 0.014 0.001 TYR G 199 ARG 0.009 0.000 ARG D 119 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 3545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 370 time to evaluate : 3.556 Fit side-chains REVERT: A 134 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.7489 (mp10) REVERT: A 151 ILE cc_start: 0.8812 (mm) cc_final: 0.8520 (mt) REVERT: A 166 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7664 (pm20) REVERT: A 280 ARG cc_start: 0.8882 (OUTLIER) cc_final: 0.7738 (mpt180) REVERT: A 325 MET cc_start: 0.8854 (tmm) cc_final: 0.8172 (tmt) REVERT: B 136 MET cc_start: 0.8854 (mtm) cc_final: 0.8250 (mtm) REVERT: B 183 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8211 (mp0) REVERT: E 289 ARG cc_start: 0.7200 (OUTLIER) cc_final: 0.6385 (mtp85) REVERT: F 113 MET cc_start: 0.7192 (OUTLIER) cc_final: 0.6987 (mpm) REVERT: F 169 GLU cc_start: 0.6995 (tt0) cc_final: 0.6726 (tt0) REVERT: G 325 MET cc_start: 0.8764 (tmm) cc_final: 0.8468 (tmt) REVERT: I 113 MET cc_start: 0.4884 (OUTLIER) cc_final: 0.4446 (mmt) REVERT: I 255 MET cc_start: 0.5804 (OUTLIER) cc_final: 0.5522 (tmm) REVERT: L 113 MET cc_start: 0.6767 (OUTLIER) cc_final: 0.6517 (mpm) REVERT: L 240 GLU cc_start: 0.5557 (tp30) cc_final: 0.4850 (tm-30) REVERT: L 255 MET cc_start: 0.7120 (OUTLIER) cc_final: 0.6431 (mtp) REVERT: M 115 ILE cc_start: 0.7422 (OUTLIER) cc_final: 0.7077 (pp) outliers start: 108 outliers final: 54 residues processed: 437 average time/residue: 1.1770 time to fit residues: 624.0850 Evaluate side-chains 417 residues out of total 3545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 352 time to evaluate : 3.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 62 HIS Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 280 ARG Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 323 ASP Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 160 GLN Chi-restraints excluded: chain E residue 281 ASN Chi-restraints excluded: chain E residue 289 ARG Chi-restraints excluded: chain F residue 113 MET Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 250 THR Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain G residue 43 ASP Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 199 TYR Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 333 ASP Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain H residue 351 LYS Chi-restraints excluded: chain H residue 352 VAL Chi-restraints excluded: chain H residue 425 ILE Chi-restraints excluded: chain I residue 113 MET Chi-restraints excluded: chain I residue 255 MET Chi-restraints excluded: chain J residue 50 PHE Chi-restraints excluded: chain J residue 210 THR Chi-restraints excluded: chain J residue 227 VAL Chi-restraints excluded: chain J residue 301 GLU Chi-restraints excluded: chain J residue 376 LEU Chi-restraints excluded: chain J residue 394 LYS Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 140 VAL Chi-restraints excluded: chain K residue 174 ASP Chi-restraints excluded: chain K residue 183 GLU Chi-restraints excluded: chain K residue 231 VAL Chi-restraints excluded: chain K residue 252 ASN Chi-restraints excluded: chain K residue 402 MET Chi-restraints excluded: chain L residue 113 MET Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain L residue 208 THR Chi-restraints excluded: chain L residue 255 MET Chi-restraints excluded: chain M residue 115 ILE Chi-restraints excluded: chain M residue 125 THR Chi-restraints excluded: chain M residue 145 ASP Chi-restraints excluded: chain O residue 145 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 381 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 225 optimal weight: 0.9990 chunk 288 optimal weight: 7.9990 chunk 223 optimal weight: 7.9990 chunk 333 optimal weight: 8.9990 chunk 220 optimal weight: 20.0000 chunk 394 optimal weight: 20.0000 chunk 246 optimal weight: 3.9990 chunk 240 optimal weight: 5.9990 chunk 182 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 HIS A 290 HIS D 157 GLN E 411 GLN G 120 ASN G 187 ASN J 170 HIS M 148 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 33174 Z= 0.256 Angle : 0.592 11.932 45161 Z= 0.308 Chirality : 0.046 0.321 5046 Planarity : 0.005 0.051 5827 Dihedral : 5.425 57.324 4759 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.61 % Allowed : 18.59 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.13), residues: 4151 helix: 1.59 (0.25), residues: 504 sheet: -0.56 (0.14), residues: 1316 loop : -1.66 (0.12), residues: 2331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 89 HIS 0.007 0.001 HIS J 99 PHE 0.019 0.001 PHE G 50 TYR 0.015 0.002 TYR G 199 ARG 0.008 0.000 ARG D 119 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 3545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 352 time to evaluate : 3.528 Fit side-chains REVERT: A 134 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7565 (mp10) REVERT: A 151 ILE cc_start: 0.8833 (mm) cc_final: 0.8546 (mt) REVERT: A 280 ARG cc_start: 0.8922 (OUTLIER) cc_final: 0.7846 (mpt180) REVERT: A 281 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7519 (pp20) REVERT: A 325 MET cc_start: 0.8857 (tmm) cc_final: 0.8404 (tmt) REVERT: A 326 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8298 (tt0) REVERT: B 183 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8200 (mp0) REVERT: C 223 ILE cc_start: 0.8179 (OUTLIER) cc_final: 0.7799 (mp) REVERT: E 289 ARG cc_start: 0.7191 (OUTLIER) cc_final: 0.6378 (mtp85) REVERT: F 113 MET cc_start: 0.7177 (OUTLIER) cc_final: 0.6965 (mpm) REVERT: G 325 MET cc_start: 0.8797 (tmm) cc_final: 0.8460 (tmt) REVERT: H 269 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.8170 (mtm) REVERT: I 113 MET cc_start: 0.4912 (OUTLIER) cc_final: 0.4557 (mmt) REVERT: L 113 MET cc_start: 0.6744 (OUTLIER) cc_final: 0.6540 (mpt) REVERT: L 240 GLU cc_start: 0.5468 (tp30) cc_final: 0.4782 (tm-30) REVERT: L 255 MET cc_start: 0.7187 (OUTLIER) cc_final: 0.6586 (mtp) REVERT: M 115 ILE cc_start: 0.7410 (OUTLIER) cc_final: 0.7125 (pp) outliers start: 128 outliers final: 74 residues processed: 435 average time/residue: 1.1885 time to fit residues: 629.9887 Evaluate side-chains 430 residues out of total 3545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 343 time to evaluate : 3.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 62 HIS Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 280 ARG Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 323 ASP Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 160 GLN Chi-restraints excluded: chain E residue 289 ARG Chi-restraints excluded: chain E residue 300 THR Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain F residue 113 MET Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 182 SER Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 250 THR Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain G residue 45 MET Chi-restraints excluded: chain G residue 199 TYR Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 290 HIS Chi-restraints excluded: chain G residue 333 ASP Chi-restraints excluded: chain G residue 387 MET Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain H residue 305 THR Chi-restraints excluded: chain H residue 343 THR Chi-restraints excluded: chain H residue 351 LYS Chi-restraints excluded: chain H residue 352 VAL Chi-restraints excluded: chain H residue 425 ILE Chi-restraints excluded: chain I residue 113 MET Chi-restraints excluded: chain I residue 250 THR Chi-restraints excluded: chain J residue 50 PHE Chi-restraints excluded: chain J residue 154 THR Chi-restraints excluded: chain J residue 210 THR Chi-restraints excluded: chain J residue 227 VAL Chi-restraints excluded: chain J residue 301 GLU Chi-restraints excluded: chain J residue 376 LEU Chi-restraints excluded: chain J residue 394 LYS Chi-restraints excluded: chain K residue 31 MET Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 140 VAL Chi-restraints excluded: chain K residue 174 ASP Chi-restraints excluded: chain K residue 183 GLU Chi-restraints excluded: chain K residue 231 VAL Chi-restraints excluded: chain K residue 339 LEU Chi-restraints excluded: chain K residue 433 CYS Chi-restraints excluded: chain L residue 113 MET Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain L residue 208 THR Chi-restraints excluded: chain L residue 248 VAL Chi-restraints excluded: chain L residue 255 MET Chi-restraints excluded: chain L residue 257 THR Chi-restraints excluded: chain M residue 115 ILE Chi-restraints excluded: chain M residue 125 THR Chi-restraints excluded: chain M residue 145 ASP Chi-restraints excluded: chain O residue 145 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 243 optimal weight: 10.0000 chunk 157 optimal weight: 9.9990 chunk 235 optimal weight: 9.9990 chunk 118 optimal weight: 40.0000 chunk 77 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 250 optimal weight: 9.9990 chunk 268 optimal weight: 0.8980 chunk 194 optimal weight: 20.0000 chunk 36 optimal weight: 1.9990 chunk 309 optimal weight: 0.0270 overall best weight: 3.1844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 HIS A 290 HIS B 100 ASN E 411 GLN G 120 ASN G 187 ASN J 170 HIS J 232 HIS J 290 HIS M 148 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 33174 Z= 0.253 Angle : 0.592 10.747 45161 Z= 0.308 Chirality : 0.046 0.326 5046 Planarity : 0.005 0.050 5827 Dihedral : 5.435 56.825 4759 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 3.67 % Allowed : 18.82 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.13), residues: 4151 helix: 1.61 (0.25), residues: 504 sheet: -0.57 (0.14), residues: 1324 loop : -1.67 (0.12), residues: 2323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 89 HIS 0.007 0.001 HIS J 99 PHE 0.019 0.001 PHE D 50 TYR 0.015 0.002 TYR G 199 ARG 0.009 0.000 ARG D 119 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 3545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 349 time to evaluate : 3.680 Fit side-chains REVERT: A 134 GLN cc_start: 0.8166 (OUTLIER) cc_final: 0.7578 (mp10) REVERT: A 151 ILE cc_start: 0.8867 (mm) cc_final: 0.8590 (mt) REVERT: A 280 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.7840 (mpt180) REVERT: A 281 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7488 (pp20) REVERT: A 325 MET cc_start: 0.8834 (tmm) cc_final: 0.8414 (tmt) REVERT: B 136 MET cc_start: 0.8859 (mtm) cc_final: 0.8278 (mtm) REVERT: B 183 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.8194 (mp0) REVERT: E 289 ARG cc_start: 0.7189 (OUTLIER) cc_final: 0.6381 (mtp85) REVERT: F 113 MET cc_start: 0.7097 (OUTLIER) cc_final: 0.6884 (mpm) REVERT: G 325 MET cc_start: 0.8803 (tmm) cc_final: 0.8459 (tmt) REVERT: H 269 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.8187 (mtm) REVERT: I 113 MET cc_start: 0.4917 (OUTLIER) cc_final: 0.4461 (mmt) REVERT: L 240 GLU cc_start: 0.5466 (tp30) cc_final: 0.4799 (tm-30) REVERT: L 255 MET cc_start: 0.7274 (OUTLIER) cc_final: 0.6578 (mtp) REVERT: M 115 ILE cc_start: 0.7413 (OUTLIER) cc_final: 0.7080 (pp) outliers start: 130 outliers final: 93 residues processed: 436 average time/residue: 1.1593 time to fit residues: 615.3580 Evaluate side-chains 446 residues out of total 3545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 343 time to evaluate : 3.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 62 HIS Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 280 ARG Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 323 ASP Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 281 ASN Chi-restraints excluded: chain E residue 289 ARG Chi-restraints excluded: chain E residue 300 THR Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain F residue 113 MET Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 182 SER Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 250 THR Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 43 ASP Chi-restraints excluded: chain G residue 50 PHE Chi-restraints excluded: chain G residue 199 TYR Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 290 HIS Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain H residue 302 THR Chi-restraints excluded: chain H residue 305 THR Chi-restraints excluded: chain H residue 343 THR Chi-restraints excluded: chain H residue 351 LYS Chi-restraints excluded: chain H residue 352 VAL Chi-restraints excluded: chain H residue 405 THR Chi-restraints excluded: chain H residue 425 ILE Chi-restraints excluded: chain I residue 113 MET Chi-restraints excluded: chain I residue 250 THR Chi-restraints excluded: chain J residue 50 PHE Chi-restraints excluded: chain J residue 154 THR Chi-restraints excluded: chain J residue 210 THR Chi-restraints excluded: chain J residue 227 VAL Chi-restraints excluded: chain J residue 301 GLU Chi-restraints excluded: chain J residue 376 LEU Chi-restraints excluded: chain J residue 394 LYS Chi-restraints excluded: chain J residue 411 LEU Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 140 VAL Chi-restraints excluded: chain K residue 174 ASP Chi-restraints excluded: chain K residue 183 GLU Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain K residue 213 LEU Chi-restraints excluded: chain K residue 231 VAL Chi-restraints excluded: chain K residue 285 SER Chi-restraints excluded: chain K residue 288 THR Chi-restraints excluded: chain K residue 339 LEU Chi-restraints excluded: chain K residue 433 CYS Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain L residue 208 THR Chi-restraints excluded: chain L residue 248 VAL Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 255 MET Chi-restraints excluded: chain L residue 257 THR Chi-restraints excluded: chain M residue 115 ILE Chi-restraints excluded: chain M residue 125 THR Chi-restraints excluded: chain M residue 145 ASP Chi-restraints excluded: chain O residue 145 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 358 optimal weight: 2.9990 chunk 377 optimal weight: 9.9990 chunk 344 optimal weight: 0.3980 chunk 367 optimal weight: 0.5980 chunk 221 optimal weight: 0.7980 chunk 160 optimal weight: 0.8980 chunk 288 optimal weight: 5.9990 chunk 112 optimal weight: 4.9990 chunk 331 optimal weight: 6.9990 chunk 347 optimal weight: 30.0000 chunk 366 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 HIS A 290 HIS E 411 GLN G 120 ASN G 187 ASN J 170 HIS J 232 HIS M 148 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 33174 Z= 0.147 Angle : 0.542 9.781 45161 Z= 0.283 Chirality : 0.044 0.291 5046 Planarity : 0.004 0.050 5827 Dihedral : 5.152 57.748 4759 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.79 % Allowed : 19.92 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.13), residues: 4151 helix: 1.69 (0.25), residues: 504 sheet: -0.36 (0.14), residues: 1272 loop : -1.55 (0.12), residues: 2375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 251 HIS 0.005 0.001 HIS J 170 PHE 0.012 0.001 PHE D 50 TYR 0.014 0.001 TYR G 199 ARG 0.009 0.000 ARG D 119 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 3545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 349 time to evaluate : 3.871 Fit side-chains REVERT: A 134 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.7523 (mp10) REVERT: A 151 ILE cc_start: 0.8815 (mm) cc_final: 0.8532 (mt) REVERT: A 166 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7713 (pm20) REVERT: A 280 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.7721 (mpt180) REVERT: A 325 MET cc_start: 0.8825 (tmm) cc_final: 0.8194 (tmt) REVERT: B 136 MET cc_start: 0.8854 (mtm) cc_final: 0.8255 (mtm) REVERT: E 289 ARG cc_start: 0.7182 (OUTLIER) cc_final: 0.6369 (mtp85) REVERT: F 122 GLU cc_start: 0.6521 (pm20) cc_final: 0.6320 (pm20) REVERT: F 169 GLU cc_start: 0.7016 (tt0) cc_final: 0.6760 (tt0) REVERT: G 325 MET cc_start: 0.8778 (tmm) cc_final: 0.8443 (tmt) REVERT: I 113 MET cc_start: 0.4760 (OUTLIER) cc_final: 0.4413 (mmt) REVERT: K 20 GLU cc_start: 0.7425 (mt-10) cc_final: 0.7167 (mt-10) REVERT: L 240 GLU cc_start: 0.5423 (tp30) cc_final: 0.4878 (tm-30) REVERT: L 255 MET cc_start: 0.7162 (OUTLIER) cc_final: 0.6447 (mtp) REVERT: M 115 ILE cc_start: 0.7386 (OUTLIER) cc_final: 0.7021 (pp) outliers start: 99 outliers final: 72 residues processed: 417 average time/residue: 1.2385 time to fit residues: 627.3347 Evaluate side-chains 419 residues out of total 3545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 340 time to evaluate : 3.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 62 HIS Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 280 ARG Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 433 CYS Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain D residue 323 ASP Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 281 ASN Chi-restraints excluded: chain E residue 289 ARG Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 182 SER Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 199 TYR Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain H residue 302 THR Chi-restraints excluded: chain H residue 343 THR Chi-restraints excluded: chain H residue 352 VAL Chi-restraints excluded: chain H residue 425 ILE Chi-restraints excluded: chain I residue 113 MET Chi-restraints excluded: chain J residue 50 PHE Chi-restraints excluded: chain J residue 210 THR Chi-restraints excluded: chain J residue 227 VAL Chi-restraints excluded: chain J residue 301 GLU Chi-restraints excluded: chain J residue 376 LEU Chi-restraints excluded: chain J residue 394 LYS Chi-restraints excluded: chain J residue 411 LEU Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 140 VAL Chi-restraints excluded: chain K residue 183 GLU Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain K residue 231 VAL Chi-restraints excluded: chain K residue 252 ASN Chi-restraints excluded: chain K residue 285 SER Chi-restraints excluded: chain K residue 402 MET Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain L residue 208 THR Chi-restraints excluded: chain L residue 248 VAL Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 255 MET Chi-restraints excluded: chain L residue 257 THR Chi-restraints excluded: chain M residue 115 ILE Chi-restraints excluded: chain M residue 125 THR Chi-restraints excluded: chain M residue 145 ASP Chi-restraints excluded: chain O residue 145 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 241 optimal weight: 0.7980 chunk 388 optimal weight: 8.9990 chunk 237 optimal weight: 8.9990 chunk 184 optimal weight: 20.0000 chunk 270 optimal weight: 5.9990 chunk 407 optimal weight: 30.0000 chunk 375 optimal weight: 9.9990 chunk 324 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 250 optimal weight: 10.0000 chunk 198 optimal weight: 10.0000 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 HIS A 290 HIS D 157 GLN E 411 GLN G 187 ASN G 290 HIS J 120 ASN J 170 HIS J 232 HIS J 290 HIS ** L 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 148 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 33174 Z= 0.354 Angle : 0.647 10.947 45161 Z= 0.336 Chirality : 0.048 0.354 5046 Planarity : 0.005 0.050 5827 Dihedral : 5.606 57.283 4759 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 2.96 % Allowed : 19.86 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.13), residues: 4151 helix: 1.56 (0.25), residues: 504 sheet: -0.52 (0.14), residues: 1292 loop : -1.65 (0.12), residues: 2355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 89 HIS 0.009 0.001 HIS B 308 PHE 0.020 0.002 PHE D 50 TYR 0.019 0.002 TYR E 51 ARG 0.009 0.001 ARG D 119 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 3545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 355 time to evaluate : 3.639 Fit side-chains revert: symmetry clash REVERT: A 134 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7564 (mp10) REVERT: A 151 ILE cc_start: 0.8905 (mm) cc_final: 0.8619 (mt) REVERT: A 280 ARG cc_start: 0.8921 (OUTLIER) cc_final: 0.7868 (mpt180) REVERT: A 281 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7432 (pp20) REVERT: A 325 MET cc_start: 0.8828 (tmm) cc_final: 0.8449 (tmt) REVERT: E 289 ARG cc_start: 0.7149 (OUTLIER) cc_final: 0.6339 (mtp85) REVERT: G 325 MET cc_start: 0.8819 (tmm) cc_final: 0.8462 (tmt) REVERT: L 240 GLU cc_start: 0.5472 (tp30) cc_final: 0.4954 (tm-30) REVERT: L 255 MET cc_start: 0.7353 (OUTLIER) cc_final: 0.6702 (mtp) REVERT: M 115 ILE cc_start: 0.7378 (OUTLIER) cc_final: 0.7010 (pp) REVERT: N 145 ASP cc_start: 0.7251 (m-30) cc_final: 0.7030 (m-30) outliers start: 105 outliers final: 82 residues processed: 431 average time/residue: 1.2029 time to fit residues: 630.7344 Evaluate side-chains 435 residues out of total 3545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 347 time to evaluate : 3.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 62 HIS Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 280 ARG Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 433 CYS Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain D residue 246 ASP Chi-restraints excluded: chain D residue 318 ILE Chi-restraints excluded: chain D residue 323 ASP Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 289 ARG Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 182 SER Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 43 ASP Chi-restraints excluded: chain G residue 45 MET Chi-restraints excluded: chain G residue 50 PHE Chi-restraints excluded: chain G residue 199 TYR Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 290 HIS Chi-restraints excluded: chain G residue 387 MET Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain H residue 302 THR Chi-restraints excluded: chain H residue 343 THR Chi-restraints excluded: chain H residue 352 VAL Chi-restraints excluded: chain H residue 425 ILE Chi-restraints excluded: chain I residue 113 MET Chi-restraints excluded: chain J residue 50 PHE Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 210 THR Chi-restraints excluded: chain J residue 227 VAL Chi-restraints excluded: chain J residue 301 GLU Chi-restraints excluded: chain J residue 376 LEU Chi-restraints excluded: chain J residue 394 LYS Chi-restraints excluded: chain J residue 411 LEU Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 140 VAL Chi-restraints excluded: chain K residue 174 ASP Chi-restraints excluded: chain K residue 183 GLU Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain K residue 231 VAL Chi-restraints excluded: chain K residue 285 SER Chi-restraints excluded: chain K residue 339 LEU Chi-restraints excluded: chain K residue 433 CYS Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain L residue 208 THR Chi-restraints excluded: chain L residue 248 VAL Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 252 ASN Chi-restraints excluded: chain L residue 255 MET Chi-restraints excluded: chain M residue 115 ILE Chi-restraints excluded: chain M residue 125 THR Chi-restraints excluded: chain M residue 145 ASP Chi-restraints excluded: chain O residue 145 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 257 optimal weight: 7.9990 chunk 345 optimal weight: 5.9990 chunk 99 optimal weight: 8.9990 chunk 299 optimal weight: 10.0000 chunk 47 optimal weight: 20.0000 chunk 90 optimal weight: 20.0000 chunk 324 optimal weight: 1.9990 chunk 136 optimal weight: 0.4980 chunk 333 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 HIS A 290 HIS D 157 GLN E 411 GLN G 120 ASN G 187 ASN G 290 HIS J 120 ASN J 170 HIS J 232 HIS ** L 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 148 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.159099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.122594 restraints weight = 40740.256| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 3.71 r_work: 0.2912 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 33174 Z= 0.155 Angle : 0.563 12.187 45161 Z= 0.292 Chirality : 0.045 0.296 5046 Planarity : 0.004 0.053 5827 Dihedral : 5.228 58.673 4759 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.68 % Allowed : 20.31 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.13), residues: 4151 helix: 1.68 (0.25), residues: 504 sheet: -0.36 (0.14), residues: 1280 loop : -1.55 (0.12), residues: 2367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP L 251 HIS 0.010 0.001 HIS G 290 PHE 0.014 0.001 PHE H 95 TYR 0.015 0.001 TYR G 199 ARG 0.009 0.000 ARG D 119 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10562.34 seconds wall clock time: 188 minutes 32.54 seconds (11312.54 seconds total)