Starting phenix.real_space_refine on Mon Mar 11 09:36:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8et3_28585/03_2024/8et3_28585_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8et3_28585/03_2024/8et3_28585.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8et3_28585/03_2024/8et3_28585.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8et3_28585/03_2024/8et3_28585.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8et3_28585/03_2024/8et3_28585_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8et3_28585/03_2024/8et3_28585_trim_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 16 5.49 5 S 128 5.16 5 C 17844 2.51 5 N 4847 2.21 5 O 5477 1.98 5 H 28542 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 234": "OE1" <-> "OE2" Residue "B ASP 194": "OD1" <-> "OD2" Residue "B PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 201": "OD1" <-> "OD2" Residue "E PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 239": "OD1" <-> "OD2" Residue "F PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 279": "OD1" <-> "OD2" Residue "F PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 134": "OD1" <-> "OD2" Residue "H GLU 136": "OE1" <-> "OE2" Residue "H ASP 167": "OD1" <-> "OD2" Residue "H GLU 169": "OE1" <-> "OE2" Residue "H PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 14": "OE1" <-> "OE2" Residue "I TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ASP 134": "OD1" <-> "OD2" Residue "I GLU 162": "OE1" <-> "OE2" Residue "I GLU 169": "OE1" <-> "OE2" Residue "J TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ASP 134": "OD1" <-> "OD2" Residue "J GLU 141": "OE1" <-> "OE2" Residue "J GLU 169": "OE1" <-> "OE2" Residue "K TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K GLU 162": "OE1" <-> "OE2" Residue "K GLU 169": "OE1" <-> "OE2" Residue "K PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L GLU 14": "OE1" <-> "OE2" Residue "L PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ASP 134": "OD1" <-> "OD2" Residue "L GLU 136": "OE1" <-> "OE2" Residue "L GLU 141": "OE1" <-> "OE2" Residue "L GLU 151": "OE1" <-> "OE2" Residue "L GLU 162": "OE1" <-> "OE2" Residue "L GLU 165": "OE1" <-> "OE2" Residue "L ASP 171": "OD1" <-> "OD2" Residue "L GLU 178": "OE1" <-> "OE2" Residue "L GLU 181": "OE1" <-> "OE2" Residue "M PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ASP 134": "OD1" <-> "OD2" Residue "M GLU 141": "OE1" <-> "OE2" Residue "M GLU 162": "OE1" <-> "OE2" Residue "M GLU 169": "OE1" <-> "OE2" Residue "M ASP 171": "OD1" <-> "OD2" Residue "M PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M GLU 181": "OE1" <-> "OE2" Residue "N TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ASP 134": "OD1" <-> "OD2" Residue "N PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Y TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Y ASP 23": "OD1" <-> "OD2" Residue "Y TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Y ASP 48": "OD1" <-> "OD2" Residue "Y ASP 68": "OD1" <-> "OD2" Residue "Y PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Z TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Z ASP 23": "OD1" <-> "OD2" Residue "Z ASP 33": "OD1" <-> "OD2" Residue "Z TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Z GLU 64": "OE1" <-> "OE2" Residue "Z PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Z PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Z GLU 107": "OE1" <-> "OE2" Residue "Z TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 56854 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 5334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 5334 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 14, 'TRANS': 328} Chain breaks: 1 Chain: "B" Number of atoms: 5441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 5441 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 14, 'TRANS': 337} Chain: "C" Number of atoms: 5452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 5452 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 14, 'TRANS': 338} Chain: "D" Number of atoms: 5452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 5452 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 14, 'TRANS': 338} Chain: "E" Number of atoms: 5304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 5304 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 13, 'TRANS': 328} Chain breaks: 1 Chain: "F" Number of atoms: 5147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 5147 Classifications: {'peptide': 331} Link IDs: {'PTRANS': 12, 'TRANS': 318} Chain breaks: 3 Chain: "H" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "I" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "J" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "K" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "L" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "M" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "N" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "S" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 145 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "Y" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 1645 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 9, 'TRANS': 95} Chain: "Z" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 1644 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 9, 'TRANS': 95} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 18.00, per 1000 atoms: 0.32 Number of scatterers: 56854 At special positions: 0 Unit cell: (146.432, 144.768, 181.376, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 128 16.00 P 16 15.00 O 5477 8.00 N 4847 7.00 C 17844 6.00 H 28542 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 34.46 Conformation dependent library (CDL) restraints added in 4.4 seconds 7194 Ramachandran restraints generated. 3597 Oldfield, 0 Emsley, 3597 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6692 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 150 helices and 43 sheets defined 43.4% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.13 Creating SS restraints... Processing helix chain 'A' and resid 67 through 75 Processing helix chain 'A' and resid 83 through 100 Processing helix chain 'A' and resid 125 through 135 removed outlier: 3.647A pdb=" N ARG A 134 " --> pdb=" O GLU A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 168 Processing helix chain 'A' and resid 173 through 177 Processing helix chain 'A' and resid 205 through 216 removed outlier: 3.984A pdb=" N ALA A 210 " --> pdb=" O GLY A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 262 removed outlier: 3.558A pdb=" N HIS A 260 " --> pdb=" O LYS A 256 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG A 261 " --> pdb=" O VAL A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 289 removed outlier: 3.514A pdb=" N GLN A 289 " --> pdb=" O GLU A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 297 removed outlier: 3.644A pdb=" N LYS A 297 " --> pdb=" O GLU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 307 Processing helix chain 'A' and resid 319 through 327 removed outlier: 3.756A pdb=" N LYS A 327 " --> pdb=" O ILE A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 342 Processing helix chain 'A' and resid 352 through 365 Processing helix chain 'A' and resid 368 through 379 removed outlier: 4.007A pdb=" N GLU A 377 " --> pdb=" O SER A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 387 Processing helix chain 'A' and resid 400 through 404 Processing helix chain 'B' and resid 67 through 77 removed outlier: 3.930A pdb=" N TYR B 77 " --> pdb=" O HIS B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 100 Processing helix chain 'B' and resid 125 through 135 removed outlier: 3.598A pdb=" N ALA B 129 " --> pdb=" O LYS B 125 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG B 134 " --> pdb=" O GLU B 130 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU B 135 " --> pdb=" O THR B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 168 Processing helix chain 'B' and resid 173 through 177 Processing helix chain 'B' and resid 205 through 216 removed outlier: 4.433A pdb=" N LYS B 213 " --> pdb=" O GLN B 209 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU B 214 " --> pdb=" O ALA B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 229 No H-bonds generated for 'chain 'B' and resid 227 through 229' Processing helix chain 'B' and resid 254 through 262 Processing helix chain 'B' and resid 283 through 288 removed outlier: 3.630A pdb=" N ALA B 288 " --> pdb=" O GLY B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 298 Processing helix chain 'B' and resid 302 through 307 Processing helix chain 'B' and resid 319 through 326 Processing helix chain 'B' and resid 333 through 344 removed outlier: 3.651A pdb=" N GLU B 344 " --> pdb=" O LEU B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 365 Processing helix chain 'B' and resid 368 through 379 removed outlier: 3.838A pdb=" N VAL B 376 " --> pdb=" O ARG B 373 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU B 377 " --> pdb=" O SER B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 387 Processing helix chain 'B' and resid 400 through 404 Processing helix chain 'C' and resid 67 through 76 removed outlier: 3.644A pdb=" N ASP C 76 " --> pdb=" O ASN C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 100 Processing helix chain 'C' and resid 125 through 133 removed outlier: 3.615A pdb=" N ALA C 129 " --> pdb=" O LYS C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 168 Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 205 through 216 removed outlier: 4.777A pdb=" N LYS C 213 " --> pdb=" O GLN C 209 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU C 214 " --> pdb=" O ALA C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 263 Processing helix chain 'C' and resid 283 through 288 Processing helix chain 'C' and resid 292 through 298 Processing helix chain 'C' and resid 302 through 307 Processing helix chain 'C' and resid 319 through 326 removed outlier: 3.557A pdb=" N GLN C 324 " --> pdb=" O GLU C 320 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU C 326 " --> pdb=" O LEU C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 344 removed outlier: 4.273A pdb=" N GLU C 344 " --> pdb=" O LEU C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 365 removed outlier: 3.530A pdb=" N ALA C 364 " --> pdb=" O LYS C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 379 removed outlier: 3.689A pdb=" N VAL C 376 " --> pdb=" O ARG C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 386 removed outlier: 3.666A pdb=" N ASP C 386 " --> pdb=" O ASP C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 404 removed outlier: 3.535A pdb=" N ASP C 404 " --> pdb=" O GLU C 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 400 through 404' Processing helix chain 'D' and resid 67 through 77 removed outlier: 3.837A pdb=" N TYR D 77 " --> pdb=" O HIS D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 100 Processing helix chain 'D' and resid 125 through 134 removed outlier: 3.699A pdb=" N ALA D 129 " --> pdb=" O LYS D 125 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG D 134 " --> pdb=" O GLU D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 168 Processing helix chain 'D' and resid 173 through 178 removed outlier: 3.802A pdb=" N ARG D 178 " --> pdb=" O GLN D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 216 removed outlier: 4.502A pdb=" N LYS D 213 " --> pdb=" O GLN D 209 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU D 214 " --> pdb=" O ALA D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 262 Processing helix chain 'D' and resid 283 through 289 removed outlier: 3.630A pdb=" N GLN D 289 " --> pdb=" O GLU D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 297 Processing helix chain 'D' and resid 302 through 307 removed outlier: 3.577A pdb=" N ARG D 307 " --> pdb=" O GLU D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 327 removed outlier: 3.763A pdb=" N LYS D 327 " --> pdb=" O ILE D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 344 removed outlier: 4.363A pdb=" N GLU D 344 " --> pdb=" O LEU D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 365 Processing helix chain 'D' and resid 369 through 386 removed outlier: 3.917A pdb=" N GLU D 377 " --> pdb=" O SER D 374 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU D 381 " --> pdb=" O ALA D 378 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N ASP D 382 " --> pdb=" O ALA D 379 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASP D 386 " --> pdb=" O THR D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 404 Processing helix chain 'E' and resid 67 through 77 removed outlier: 3.670A pdb=" N TYR E 77 " --> pdb=" O HIS E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 100 Processing helix chain 'E' and resid 125 through 135 Processing helix chain 'E' and resid 158 through 168 Processing helix chain 'E' and resid 173 through 177 Processing helix chain 'E' and resid 204 through 216 removed outlier: 3.916A pdb=" N LYS E 213 " --> pdb=" O ALA E 210 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU E 216 " --> pdb=" O LYS E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 262 Processing helix chain 'E' and resid 280 through 289 Processing helix chain 'E' and resid 292 through 298 Processing helix chain 'E' and resid 302 through 307 Processing helix chain 'E' and resid 319 through 327 removed outlier: 3.783A pdb=" N LYS E 327 " --> pdb=" O ILE E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 344 removed outlier: 3.779A pdb=" N GLU E 344 " --> pdb=" O LEU E 340 " (cutoff:3.500A) Processing helix chain 'E' and resid 352 through 365 Processing helix chain 'E' and resid 371 through 387 removed outlier: 3.857A pdb=" N ALA E 379 " --> pdb=" O ILE E 375 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ASP E 382 " --> pdb=" O ALA E 378 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR E 383 " --> pdb=" O ALA E 379 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP E 386 " --> pdb=" O ASP E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 400 through 404 Processing helix chain 'F' and resid 67 through 77 removed outlier: 3.697A pdb=" N ASP F 76 " --> pdb=" O ASN F 72 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N TYR F 77 " --> pdb=" O HIS F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 100 Processing helix chain 'F' and resid 125 through 134 Processing helix chain 'F' and resid 145 through 148 No H-bonds generated for 'chain 'F' and resid 145 through 148' Processing helix chain 'F' and resid 158 through 168 Processing helix chain 'F' and resid 173 through 178 Processing helix chain 'F' and resid 186 through 189 No H-bonds generated for 'chain 'F' and resid 186 through 189' Processing helix chain 'F' and resid 204 through 216 Processing helix chain 'F' and resid 254 through 262 removed outlier: 3.833A pdb=" N ARG F 261 " --> pdb=" O VAL F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 283 through 288 Processing helix chain 'F' and resid 292 through 298 Processing helix chain 'F' and resid 302 through 307 Processing helix chain 'F' and resid 319 through 327 removed outlier: 3.555A pdb=" N LYS F 327 " --> pdb=" O ILE F 323 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 344 Processing helix chain 'F' and resid 352 through 365 Processing helix chain 'F' and resid 370 through 379 Processing helix chain 'F' and resid 381 through 387 removed outlier: 3.547A pdb=" N ASP F 386 " --> pdb=" O ASP F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 404 Processing helix chain 'H' and resid 19 through 25 removed outlier: 3.668A pdb=" N LEU H 23 " --> pdb=" O ILE H 19 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 53 Processing helix chain 'H' and resid 70 through 82 removed outlier: 3.563A pdb=" N SER H 75 " --> pdb=" O THR H 71 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE H 76 " --> pdb=" O ALA H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 104 Processing helix chain 'H' and resid 132 through 157 Processing helix chain 'H' and resid 161 through 168 Processing helix chain 'H' and resid 176 through 182 Processing helix chain 'I' and resid 19 through 24 removed outlier: 3.634A pdb=" N LEU I 23 " --> pdb=" O ILE I 19 " (cutoff:3.500A) Processing helix chain 'I' and resid 37 through 53 removed outlier: 3.626A pdb=" N GLU I 53 " --> pdb=" O PHE I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 82 removed outlier: 3.569A pdb=" N SER I 75 " --> pdb=" O THR I 71 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ILE I 76 " --> pdb=" O ALA I 72 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR I 79 " --> pdb=" O SER I 75 " (cutoff:3.500A) Processing helix chain 'I' and resid 97 through 104 Processing helix chain 'I' and resid 132 through 157 Processing helix chain 'I' and resid 161 through 168 Processing helix chain 'I' and resid 176 through 182 Processing helix chain 'J' and resid 19 through 26 removed outlier: 3.766A pdb=" N LEU J 23 " --> pdb=" O ILE J 19 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLU J 26 " --> pdb=" O ARG J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 53 Processing helix chain 'J' and resid 70 through 82 removed outlier: 3.799A pdb=" N ILE J 76 " --> pdb=" O ALA J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 97 through 104 Processing helix chain 'J' and resid 132 through 157 Processing helix chain 'J' and resid 161 through 167 Processing helix chain 'J' and resid 176 through 182 Processing helix chain 'K' and resid 19 through 26 removed outlier: 4.101A pdb=" N GLU K 26 " --> pdb=" O ARG K 22 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 53 Processing helix chain 'K' and resid 70 through 82 removed outlier: 3.506A pdb=" N ILE K 76 " --> pdb=" O ALA K 72 " (cutoff:3.500A) Processing helix chain 'K' and resid 97 through 104 Processing helix chain 'K' and resid 132 through 157 removed outlier: 3.511A pdb=" N ILE K 137 " --> pdb=" O THR K 133 " (cutoff:3.500A) Processing helix chain 'K' and resid 161 through 169 Processing helix chain 'K' and resid 176 through 182 Processing helix chain 'L' and resid 19 through 26 removed outlier: 3.605A pdb=" N LYS L 25 " --> pdb=" O SER L 21 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLU L 26 " --> pdb=" O ARG L 22 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 53 removed outlier: 3.565A pdb=" N ALA L 52 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing helix chain 'L' and resid 70 through 82 removed outlier: 3.703A pdb=" N ILE L 76 " --> pdb=" O ALA L 72 " (cutoff:3.500A) Processing helix chain 'L' and resid 97 through 104 Processing helix chain 'L' and resid 132 through 157 Processing helix chain 'L' and resid 161 through 169 Processing helix chain 'L' and resid 176 through 182 Processing helix chain 'M' and resid 19 through 26 removed outlier: 3.744A pdb=" N GLU M 26 " --> pdb=" O ARG M 22 " (cutoff:3.500A) Processing helix chain 'M' and resid 37 through 53 removed outlier: 3.567A pdb=" N LEU M 42 " --> pdb=" O HIS M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 70 through 82 Processing helix chain 'M' and resid 97 through 104 Processing helix chain 'M' and resid 132 through 157 removed outlier: 3.558A pdb=" N ILE M 137 " --> pdb=" O THR M 133 " (cutoff:3.500A) Processing helix chain 'M' and resid 161 through 168 Processing helix chain 'M' and resid 176 through 182 Processing helix chain 'N' and resid 19 through 26 removed outlier: 3.564A pdb=" N LYS N 25 " --> pdb=" O SER N 21 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLU N 26 " --> pdb=" O ARG N 22 " (cutoff:3.500A) Processing helix chain 'N' and resid 37 through 53 Processing helix chain 'N' and resid 70 through 82 removed outlier: 3.505A pdb=" N SER N 75 " --> pdb=" O THR N 71 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE N 76 " --> pdb=" O ALA N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 97 through 103 Processing helix chain 'N' and resid 132 through 157 Processing helix chain 'N' and resid 161 through 168 Processing helix chain 'N' and resid 176 through 182 Processing helix chain 'Y' and resid 10 through 23 Processing helix chain 'Z' and resid 10 through 23 removed outlier: 3.546A pdb=" N LEU Z 22 " --> pdb=" O TYR Z 18 " (cutoff:3.500A) Processing helix chain 'Z' and resid 43 through 45 No H-bonds generated for 'chain 'Z' and resid 43 through 45' Processing helix chain 'Z' and resid 87 through 89 No H-bonds generated for 'chain 'Z' and resid 87 through 89' Processing sheet with id= A, first strand: chain 'A' and resid 140 through 144 removed outlier: 7.321A pdb=" N ILE A 180 " --> pdb=" O THR A 141 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N ALA A 143 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N TYR A 182 " --> pdb=" O ALA A 143 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N LEU A 244 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ILE A 183 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ILE A 246 " --> pdb=" O ILE A 183 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 219 through 221 removed outlier: 3.812A pdb=" N ALA A 220 " --> pdb=" O VAL A 238 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL A 238 " --> pdb=" O ALA A 220 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 347 through 349 Processing sheet with id= D, first strand: chain 'B' and resid 310 through 314 removed outlier: 7.821A pdb=" N TYR B 182 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N THR B 141 " --> pdb=" O TYR B 182 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N ASP B 184 " --> pdb=" O THR B 141 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ALA B 143 " --> pdb=" O ASP B 184 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 220 through 222 removed outlier: 3.532A pdb=" N VAL B 238 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL B 222 " --> pdb=" O LEU B 236 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 347 through 349 removed outlier: 6.854A pdb=" N ILE B 412 " --> pdb=" O GLU B 394 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N VAL B 396 " --> pdb=" O LEU B 410 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N LEU B 410 " --> pdb=" O VAL B 396 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 310 through 313 removed outlier: 3.555A pdb=" N ILE C 115 " --> pdb=" O PHE C 245 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 219 through 222 Processing sheet with id= I, first strand: chain 'C' and resid 347 through 349 removed outlier: 6.999A pdb=" N ILE C 412 " --> pdb=" O GLU C 394 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N VAL C 396 " --> pdb=" O LEU C 410 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LEU C 410 " --> pdb=" O VAL C 396 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 310 through 313 removed outlier: 3.529A pdb=" N THR D 141 " --> pdb=" O ILE D 180 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 347 through 349 removed outlier: 6.857A pdb=" N ILE D 412 " --> pdb=" O GLU D 394 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N VAL D 396 " --> pdb=" O LEU D 410 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU D 410 " --> pdb=" O VAL D 396 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 310 through 314 removed outlier: 3.600A pdb=" N GLY E 119 " --> pdb=" O GLY E 249 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL E 181 " --> pdb=" O ILE E 246 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N GLY E 248 " --> pdb=" O VAL E 181 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N ILE E 183 " --> pdb=" O GLY E 248 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 219 through 222 Processing sheet with id= N, first strand: chain 'E' and resid 347 through 350 Processing sheet with id= O, first strand: chain 'F' and resid 310 through 313 removed outlier: 7.385A pdb=" N PHE F 245 " --> pdb=" O ILE F 115 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N LEU F 117 " --> pdb=" O PHE F 245 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N CYS F 247 " --> pdb=" O LEU F 117 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N THR F 141 " --> pdb=" O ILE F 180 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR F 182 " --> pdb=" O THR F 141 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA F 143 " --> pdb=" O TYR F 182 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 219 through 222 Processing sheet with id= Q, first strand: chain 'F' and resid 393 through 397 removed outlier: 7.021A pdb=" N ILE F 412 " --> pdb=" O GLU F 394 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N VAL F 396 " --> pdb=" O LEU F 410 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N LEU F 410 " --> pdb=" O VAL F 396 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'H' and resid 5 through 9 Processing sheet with id= S, first strand: chain 'H' and resid 28 through 32 removed outlier: 6.480A pdb=" N TYR H 60 " --> pdb=" O ILE H 29 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N LEU H 31 " --> pdb=" O TYR H 60 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N TYR H 62 " --> pdb=" O LEU H 31 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N SER H 187 " --> pdb=" O CYS H 113 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'H' and resid 118 through 121 Processing sheet with id= U, first strand: chain 'I' and resid 5 through 10 Processing sheet with id= V, first strand: chain 'I' and resid 28 through 32 removed outlier: 6.350A pdb=" N TYR I 60 " --> pdb=" O ILE I 29 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N LEU I 31 " --> pdb=" O TYR I 60 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N TYR I 62 " --> pdb=" O LEU I 31 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'I' and resid 118 through 121 Processing sheet with id= X, first strand: chain 'J' and resid 5 through 9 removed outlier: 3.745A pdb=" N ARG J 15 " --> pdb=" O GLU J 8 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'J' and resid 28 through 32 removed outlier: 6.602A pdb=" N TYR J 60 " --> pdb=" O ILE J 29 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N LEU J 31 " --> pdb=" O TYR J 60 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N TYR J 62 " --> pdb=" O LEU J 31 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N SER J 187 " --> pdb=" O CYS J 113 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'J' and resid 118 through 121 Processing sheet with id= AA, first strand: chain 'K' and resid 5 through 9 Processing sheet with id= AB, first strand: chain 'K' and resid 28 through 32 removed outlier: 6.596A pdb=" N TYR K 60 " --> pdb=" O ILE K 29 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N LEU K 31 " --> pdb=" O TYR K 60 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N TYR K 62 " --> pdb=" O LEU K 31 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'K' and resid 112 through 114 removed outlier: 6.818A pdb=" N SER K 187 " --> pdb=" O CYS K 113 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain 'K' and resid 119 through 121 removed outlier: 3.519A pdb=" N ARG K 172 " --> pdb=" O ILE K 121 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'L' and resid 5 through 7 Processing sheet with id= AF, first strand: chain 'L' and resid 28 through 32 removed outlier: 6.561A pdb=" N TYR L 60 " --> pdb=" O ILE L 29 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N LEU L 31 " --> pdb=" O TYR L 60 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N TYR L 62 " --> pdb=" O LEU L 31 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N SER L 187 " --> pdb=" O CYS L 113 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'L' and resid 118 through 121 Processing sheet with id= AH, first strand: chain 'M' and resid 5 through 8 Processing sheet with id= AI, first strand: chain 'M' and resid 28 through 32 removed outlier: 6.627A pdb=" N TYR M 60 " --> pdb=" O ILE M 29 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N LEU M 31 " --> pdb=" O TYR M 60 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N TYR M 62 " --> pdb=" O LEU M 31 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'M' and resid 119 through 121 Processing sheet with id= AK, first strand: chain 'N' and resid 5 through 9 Processing sheet with id= AL, first strand: chain 'N' and resid 28 through 32 removed outlier: 6.521A pdb=" N TYR N 60 " --> pdb=" O ILE N 29 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N LEU N 31 " --> pdb=" O TYR N 60 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N TYR N 62 " --> pdb=" O LEU N 31 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N SER N 187 " --> pdb=" O CYS N 113 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'N' and resid 118 through 121 Processing sheet with id= AN, first strand: chain 'Y' and resid 51 through 54 removed outlier: 3.921A pdb=" N ALA Y 92 " --> pdb=" O VAL Y 31 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'Y' and resid 70 through 75 removed outlier: 3.578A pdb=" N VAL Y 70 " --> pdb=" O VAL Y 85 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'Z' and resid 50 through 54 removed outlier: 3.669A pdb=" N ALA Z 92 " --> pdb=" O VAL Z 31 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ASP Z 33 " --> pdb=" O VAL Z 90 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N VAL Z 90 " --> pdb=" O ASP Z 33 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'Z' and resid 69 through 76 1133 hydrogen bonds defined for protein. 3003 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: 17.70 Time building geometry restraints manager: 36.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.06: 28516 1.06 - 1.28: 4970 1.28 - 1.50: 11320 1.50 - 1.73: 12250 1.73 - 1.95: 226 Bond restraints: 57282 Sorted by residual: bond pdb=" C ASN M 54 " pdb=" N PRO M 55 " ideal model delta sigma weight residual 1.334 1.349 -0.015 8.40e-03 1.42e+04 3.36e+00 bond pdb=" CB PHE F 235 " pdb=" CG PHE F 235 " ideal model delta sigma weight residual 1.502 1.534 -0.032 2.30e-02 1.89e+03 1.93e+00 bond pdb=" C ASN N 54 " pdb=" N PRO N 55 " ideal model delta sigma weight residual 1.339 1.379 -0.040 3.40e-02 8.65e+02 1.37e+00 bond pdb=" C SER N 65 " pdb=" N PRO N 66 " ideal model delta sigma weight residual 1.339 1.379 -0.039 3.40e-02 8.65e+02 1.34e+00 bond pdb=" CB PRO L 85 " pdb=" CG PRO L 85 " ideal model delta sigma weight residual 1.492 1.434 0.058 5.00e-02 4.00e+02 1.33e+00 ... (remaining 57277 not shown) Histogram of bond angle deviations from ideal: 99.66 - 106.99: 1494 106.99 - 114.32: 71480 114.32 - 121.64: 20692 121.64 - 128.97: 10143 128.97 - 136.30: 174 Bond angle restraints: 103983 Sorted by residual: angle pdb=" C ILE H 83 " pdb=" N LYS H 84 " pdb=" CA LYS H 84 " ideal model delta sigma weight residual 119.78 123.80 -4.02 1.24e+00 6.50e-01 1.05e+01 angle pdb=" N GLN F 233 " pdb=" CA GLN F 233 " pdb=" C GLN F 233 " ideal model delta sigma weight residual 112.72 116.48 -3.76 1.28e+00 6.10e-01 8.61e+00 angle pdb=" N GLU F 234 " pdb=" CA GLU F 234 " pdb=" C GLU F 234 " ideal model delta sigma weight residual 111.36 114.48 -3.12 1.09e+00 8.42e-01 8.19e+00 angle pdb=" N SER L 65 " pdb=" CA SER L 65 " pdb=" C SER L 65 " ideal model delta sigma weight residual 108.23 112.75 -4.52 1.62e+00 3.81e-01 7.78e+00 angle pdb=" C ASP D 103 " pdb=" N THR D 104 " pdb=" CA THR D 104 " ideal model delta sigma weight residual 122.41 128.18 -5.77 2.09e+00 2.29e-01 7.63e+00 ... (remaining 103978 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.09: 25740 30.09 - 60.17: 848 60.17 - 90.26: 54 90.26 - 120.34: 0 120.34 - 150.43: 2 Dihedral angle restraints: 26644 sinusoidal: 15036 harmonic: 11608 Sorted by residual: dihedral pdb=" O1B ADP F 501 " pdb=" O3A ADP F 501 " pdb=" PB ADP F 501 " pdb=" PA ADP F 501 " ideal model delta sinusoidal sigma weight residual 300.00 149.57 150.43 1 2.00e+01 2.50e-03 4.49e+01 dihedral pdb=" O1A AGS D 500 " pdb=" O3A AGS D 500 " pdb=" PA AGS D 500 " pdb=" PB AGS D 500 " ideal model delta sinusoidal sigma weight residual 292.27 150.71 141.56 1 3.00e+01 1.11e-03 1.90e+01 dihedral pdb=" CB GLU M 136 " pdb=" CG GLU M 136 " pdb=" CD GLU M 136 " pdb=" OE1 GLU M 136 " ideal model delta sinusoidal sigma weight residual 0.00 89.60 -89.60 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 26641 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 3267 0.037 - 0.075: 786 0.075 - 0.112: 305 0.112 - 0.149: 132 0.149 - 0.187: 6 Chirality restraints: 4496 Sorted by residual: chirality pdb=" CB THR D 104 " pdb=" CA THR D 104 " pdb=" OG1 THR D 104 " pdb=" CG2 THR D 104 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.19 2.00e-01 2.50e+01 8.70e-01 chirality pdb=" CA VAL A 222 " pdb=" N VAL A 222 " pdb=" C VAL A 222 " pdb=" CB VAL A 222 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.40e-01 chirality pdb=" CA PRO A 224 " pdb=" N PRO A 224 " pdb=" C PRO A 224 " pdb=" CB PRO A 224 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.50e-01 ... (remaining 4493 not shown) Planarity restraints: 8511 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 230 " -0.045 5.00e-02 4.00e+02 6.80e-02 7.39e+00 pdb=" N PRO A 231 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 231 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 231 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 222 " 0.043 5.00e-02 4.00e+02 6.42e-02 6.59e+00 pdb=" N PRO A 223 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 223 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 223 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 235 " 0.016 2.00e-02 2.50e+03 9.88e-03 2.93e+00 pdb=" CG PHE F 235 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE F 235 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE F 235 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE F 235 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE F 235 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE F 235 " 0.004 2.00e-02 2.50e+03 pdb=" HD1 PHE F 235 " 0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE F 235 " 0.000 2.00e-02 2.50e+03 pdb=" HE1 PHE F 235 " 0.004 2.00e-02 2.50e+03 pdb=" HE2 PHE F 235 " 0.002 2.00e-02 2.50e+03 pdb=" HZ PHE F 235 " 0.001 2.00e-02 2.50e+03 ... (remaining 8508 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.23: 4361 2.23 - 2.82: 127535 2.82 - 3.41: 150445 3.41 - 4.01: 205304 4.01 - 4.60: 315975 Nonbonded interactions: 803620 Sorted by model distance: nonbonded pdb=" O ALA L 96 " pdb=" H ALA L 100 " model vdw 1.633 1.850 nonbonded pdb=" O ALA K 96 " pdb=" H ALA K 100 " model vdw 1.649 1.850 nonbonded pdb=" O ALA M 96 " pdb=" H ALA M 100 " model vdw 1.658 1.850 nonbonded pdb=" O ALA J 96 " pdb=" H ALA J 100 " model vdw 1.661 1.850 nonbonded pdb=" O ALA N 96 " pdb=" H ALA N 100 " model vdw 1.664 1.850 ... (remaining 803615 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 65 through 151 or resid 157 through 191 or (resid 202 and \ (name N or name CA or name C or name O or name CB or name CG1 or name CG2 or nam \ e HA or name HB or name HG11 or name HG12 or name HG13 or name HG21 or name HG22 \ or name HG23)) or resid 203 through 413)) selection = (chain 'B' and (resid 65 through 101 or (resid 110 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2 or name HA or name H \ B2 or name HB3 or name HG or name HD11 or name HD12 or name HD13 or name HD21 or \ name HD22 or name HD23)) or resid 111 through 151 or resid 157 through 191 or ( \ resid 202 and (name N or name CA or name C or name O or name CB or name CG1 or n \ ame CG2 or name HA or name HB or name HG11 or name HG12 or name HG13 or name HG2 \ 1 or name HG22 or name HG23)) or resid 203 through 413)) selection = (chain 'C' and (resid 65 through 101 or (resid 110 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2 or name HA or name H \ B2 or name HB3 or name HG or name HD11 or name HD12 or name HD13 or name HD21 or \ name HD22 or name HD23)) or resid 111 through 151 or resid 157 through 191 or ( \ resid 202 and (name N or name CA or name C or name O or name CB or name CG1 or n \ ame CG2 or name HA or name HB or name HG11 or name HG12 or name HG13 or name HG2 \ 1 or name HG22 or name HG23)) or resid 203 through 413)) selection = (chain 'D' and (resid 65 through 101 or (resid 110 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2 or name HA or name H \ B2 or name HB3 or name HG or name HD11 or name HD12 or name HD13 or name HD21 or \ name HD22 or name HD23)) or resid 111 through 151 or resid 157 through 191 or ( \ resid 202 and (name N or name CA or name C or name O or name CB or name CG1 or n \ ame CG2 or name HA or name HB or name HG11 or name HG12 or name HG13 or name HG2 \ 1 or name HG22 or name HG23)) or resid 203 through 413)) selection = (chain 'E' and (resid 65 through 101 or (resid 110 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2 or name HA or name H \ B2 or name HB3 or name HG or name HD11 or name HD12 or name HD13 or name HD21 or \ name HD22 or name HD23)) or resid 111 through 151 or resid 157 through 191 or ( \ resid 202 and (name N or name CA or name C or name O or name CB or name CG1 or n \ ame CG2 or name HA or name HB or name HG11 or name HG12 or name HG13 or name HG2 \ 1 or name HG22 or name HG23)) or resid 203 through 413)) selection = (chain 'F' and (resid 65 through 101 or (resid 110 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2 or name HA or name H \ B2 or name HB3 or name HG or name HD11 or name HD12 or name HD13 or name HD21 or \ name HD22 or name HD23)) or resid 111 through 413)) } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } ncs_group { reference = (chain 'Y' and ((resid 7 and (name N or name CA or name C or name O or name CB o \ r name OG1 or name CG2 or name HA or name HB or name HG1 or name HG21 or name HG \ 22 or name HG23)) or resid 8 through 111)) selection = chain 'Z' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.760 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: 0.610 Extract box with map and model: 5.640 Check model and map are aligned: 0.610 Set scattering table: 0.380 Process input model: 134.810 Find NCS groups from input model: 2.160 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 147.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 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 : 0.003 0.058 28740 Z= 0.215 Angle : 0.615 6.807 38873 Z= 0.325 Chirality : 0.042 0.187 4496 Planarity : 0.004 0.068 5041 Dihedral : 12.769 150.429 10918 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.13), residues: 3597 helix: 0.51 (0.12), residues: 1663 sheet: 0.32 (0.20), residues: 540 loop : -0.69 (0.15), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Z 20 HIS 0.007 0.001 HIS H 122 PHE 0.029 0.001 PHE F 235 TYR 0.007 0.001 TYR B 153 ARG 0.010 0.001 ARG L 140 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7194 Ramachandran restraints generated. 3597 Oldfield, 0 Emsley, 3597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7194 Ramachandran restraints generated. 3597 Oldfield, 0 Emsley, 3597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 3034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 373 time to evaluate : 3.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 256 LYS cc_start: 0.9388 (mmmm) cc_final: 0.9148 (mmmm) REVERT: B 384 MET cc_start: 0.8947 (mtp) cc_final: 0.8745 (mtp) REVERT: E 142 MET cc_start: 0.7655 (tmm) cc_final: 0.7150 (tmm) REVERT: F 245 PHE cc_start: 0.8695 (m-80) cc_final: 0.8446 (m-80) REVERT: F 384 MET cc_start: 0.9230 (mpp) cc_final: 0.8895 (mpp) REVERT: H 17 PHE cc_start: 0.7975 (m-80) cc_final: 0.7546 (m-80) REVERT: H 171 ASP cc_start: 0.7935 (m-30) cc_final: 0.7339 (t0) REVERT: I 5 MET cc_start: 0.8787 (mmm) cc_final: 0.8414 (mmm) REVERT: I 120 MET cc_start: 0.8646 (ttp) cc_final: 0.8054 (tmm) REVERT: I 171 ASP cc_start: 0.8461 (m-30) cc_final: 0.7580 (t0) REVERT: J 125 LEU cc_start: 0.8847 (mp) cc_final: 0.8627 (mp) REVERT: J 172 ARG cc_start: 0.8383 (ttt90) cc_final: 0.8169 (mmm160) REVERT: K 8 GLU cc_start: 0.8165 (tt0) cc_final: 0.7846 (tt0) REVERT: K 11 SER cc_start: 0.5234 (p) cc_final: 0.5014 (p) REVERT: L 63 ILE cc_start: 0.9366 (mt) cc_final: 0.9132 (tt) REVERT: L 92 MET cc_start: 0.8662 (mtm) cc_final: 0.8182 (mtt) REVERT: L 94 GLN cc_start: 0.8722 (pt0) cc_final: 0.7835 (pm20) REVERT: L 113 CYS cc_start: 0.8529 (t) cc_final: 0.8100 (t) REVERT: M 8 GLU cc_start: 0.7834 (tp30) cc_final: 0.7470 (tp30) REVERT: M 17 PHE cc_start: 0.8172 (m-80) cc_final: 0.7873 (m-80) REVERT: M 113 CYS cc_start: 0.8780 (t) cc_final: 0.8506 (t) REVERT: N 34 GLN cc_start: 0.8961 (mm110) cc_final: 0.8567 (mm-40) REVERT: N 153 MET cc_start: 0.9620 (mtp) cc_final: 0.9401 (ttm) REVERT: Y 43 MET cc_start: 0.7951 (mpp) cc_final: 0.7569 (mmt) REVERT: Y 81 ARG cc_start: 0.5881 (mtp-110) cc_final: 0.5148 (ttt180) outliers start: 0 outliers final: 0 residues processed: 373 average time/residue: 0.8893 time to fit residues: 499.8255 Evaluate side-chains 241 residues out of total 3034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 241 time to evaluate : 3.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 303 optimal weight: 8.9990 chunk 272 optimal weight: 0.0670 chunk 151 optimal weight: 9.9990 chunk 93 optimal weight: 0.9980 chunk 184 optimal weight: 40.0000 chunk 145 optimal weight: 9.9990 chunk 282 optimal weight: 7.9990 chunk 109 optimal weight: 6.9990 chunk 171 optimal weight: 20.0000 chunk 210 optimal weight: 7.9990 chunk 326 optimal weight: 8.9990 overall best weight: 4.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 HIS B 260 HIS C 94 ASN D 163 GLN E 260 HIS F 83 GLN F 324 GLN I 163 GLN J 41 ASN K 81 GLN K 156 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 28740 Z= 0.247 Angle : 0.527 7.271 38873 Z= 0.272 Chirality : 0.040 0.150 4496 Planarity : 0.004 0.050 5041 Dihedral : 6.876 144.109 4011 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.66 % Allowed : 5.08 % Favored : 94.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.13), residues: 3597 helix: 1.19 (0.12), residues: 1700 sheet: 0.65 (0.20), residues: 553 loop : -0.45 (0.16), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP Z 20 HIS 0.007 0.001 HIS E 260 PHE 0.013 0.001 PHE C 298 TYR 0.015 0.001 TYR D 171 ARG 0.007 0.000 ARG K 12 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7194 Ramachandran restraints generated. 3597 Oldfield, 0 Emsley, 3597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7194 Ramachandran restraints generated. 3597 Oldfield, 0 Emsley, 3597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 3034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 243 time to evaluate : 3.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 256 LYS cc_start: 0.9422 (mmmm) cc_final: 0.9155 (mmmm) REVERT: E 142 MET cc_start: 0.7807 (tmm) cc_final: 0.7347 (tmm) REVERT: H 17 PHE cc_start: 0.8105 (m-80) cc_final: 0.7686 (m-80) REVERT: H 86 ASP cc_start: 0.8540 (m-30) cc_final: 0.7963 (t0) REVERT: H 120 MET cc_start: 0.8553 (ttp) cc_final: 0.8344 (ttp) REVERT: H 171 ASP cc_start: 0.8048 (m-30) cc_final: 0.7735 (t0) REVERT: I 5 MET cc_start: 0.8941 (mmm) cc_final: 0.8575 (mmp) REVERT: J 34 GLN cc_start: 0.8568 (mm-40) cc_final: 0.8187 (mm-40) REVERT: J 120 MET cc_start: 0.8394 (ttp) cc_final: 0.8183 (ttt) REVERT: J 172 ARG cc_start: 0.7986 (ttt90) cc_final: 0.7724 (mmm160) REVERT: K 149 MET cc_start: 0.8812 (mmm) cc_final: 0.8514 (mmm) REVERT: L 120 MET cc_start: 0.6334 (mmt) cc_final: 0.6097 (mmt) REVERT: M 8 GLU cc_start: 0.8053 (tp30) cc_final: 0.7690 (tp30) REVERT: N 34 GLN cc_start: 0.8893 (mm110) cc_final: 0.8655 (mm-40) REVERT: Y 43 MET cc_start: 0.7951 (mpp) cc_final: 0.7583 (mmt) REVERT: Y 81 ARG cc_start: 0.5749 (mtp-110) cc_final: 0.5040 (ttt180) outliers start: 20 outliers final: 17 residues processed: 250 average time/residue: 0.9018 time to fit residues: 342.3029 Evaluate side-chains 238 residues out of total 3034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 221 time to evaluate : 3.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 256 LYS Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 324 GLN Chi-restraints excluded: chain J residue 18 ASP Chi-restraints excluded: chain J residue 113 CYS Chi-restraints excluded: chain K residue 18 ASP Chi-restraints excluded: chain L residue 37 ASP Chi-restraints excluded: chain L residue 58 ASP Chi-restraints excluded: chain L residue 80 MET Chi-restraints excluded: chain M residue 18 ASP Chi-restraints excluded: chain M residue 86 ASP Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain N residue 80 MET Chi-restraints excluded: chain N residue 113 CYS Chi-restraints excluded: chain Y residue 18 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 181 optimal weight: 20.0000 chunk 101 optimal weight: 10.0000 chunk 272 optimal weight: 20.0000 chunk 222 optimal weight: 20.0000 chunk 90 optimal weight: 9.9990 chunk 327 optimal weight: 10.0000 chunk 353 optimal weight: 3.9990 chunk 291 optimal weight: 20.0000 chunk 324 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 chunk 262 optimal weight: 0.3980 overall best weight: 5.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 83 GLN E 260 HIS ** F 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 28740 Z= 0.242 Angle : 0.493 9.065 38873 Z= 0.250 Chirality : 0.040 0.141 4496 Planarity : 0.003 0.042 5041 Dihedral : 6.606 135.633 4011 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.66 % Allowed : 5.93 % Favored : 93.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.14), residues: 3597 helix: 1.38 (0.12), residues: 1693 sheet: 0.56 (0.19), residues: 652 loop : -0.24 (0.17), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP Y 20 HIS 0.010 0.001 HIS E 260 PHE 0.016 0.001 PHE N 101 TYR 0.010 0.001 TYR E 96 ARG 0.006 0.000 ARG K 15 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7194 Ramachandran restraints generated. 3597 Oldfield, 0 Emsley, 3597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7194 Ramachandran restraints generated. 3597 Oldfield, 0 Emsley, 3597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 3034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 229 time to evaluate : 3.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 142 MET cc_start: 0.7881 (tmm) cc_final: 0.7441 (tmm) REVERT: H 17 PHE cc_start: 0.8353 (m-80) cc_final: 0.7874 (m-80) REVERT: H 120 MET cc_start: 0.8579 (ttp) cc_final: 0.8341 (ttp) REVERT: H 171 ASP cc_start: 0.8233 (m-30) cc_final: 0.7790 (t0) REVERT: I 5 MET cc_start: 0.8961 (mmm) cc_final: 0.8550 (mmp) REVERT: I 171 ASP cc_start: 0.8664 (m-30) cc_final: 0.7819 (t0) REVERT: J 34 GLN cc_start: 0.8648 (mm-40) cc_final: 0.7899 (mm-40) REVERT: J 36 GLU cc_start: 0.8764 (pt0) cc_final: 0.8440 (pm20) REVERT: J 172 ARG cc_start: 0.8019 (ttt90) cc_final: 0.7778 (mmm160) REVERT: K 34 GLN cc_start: 0.8297 (tm-30) cc_final: 0.8077 (tm-30) REVERT: K 149 MET cc_start: 0.8810 (mmm) cc_final: 0.8423 (mmm) REVERT: L 120 MET cc_start: 0.6441 (mmt) cc_final: 0.6066 (mmt) REVERT: M 8 GLU cc_start: 0.8200 (tp30) cc_final: 0.7751 (tp30) REVERT: N 34 GLN cc_start: 0.8945 (mm110) cc_final: 0.8706 (mm-40) REVERT: N 150 ASN cc_start: 0.8610 (m110) cc_final: 0.8192 (m110) REVERT: Y 43 MET cc_start: 0.7966 (mpp) cc_final: 0.7529 (mmt) outliers start: 20 outliers final: 18 residues processed: 237 average time/residue: 0.8243 time to fit residues: 301.6315 Evaluate side-chains 229 residues out of total 3034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 211 time to evaluate : 3.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain J residue 18 ASP Chi-restraints excluded: chain J residue 113 CYS Chi-restraints excluded: chain K residue 18 ASP Chi-restraints excluded: chain L residue 53 GLU Chi-restraints excluded: chain L residue 58 ASP Chi-restraints excluded: chain L residue 80 MET Chi-restraints excluded: chain L residue 113 CYS Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain M residue 18 ASP Chi-restraints excluded: chain M residue 80 MET Chi-restraints excluded: chain M residue 86 ASP Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain N residue 80 MET Chi-restraints excluded: chain N residue 113 CYS Chi-restraints excluded: chain Y residue 18 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 323 optimal weight: 5.9990 chunk 246 optimal weight: 8.9990 chunk 169 optimal weight: 9.9990 chunk 36 optimal weight: 6.9990 chunk 156 optimal weight: 6.9990 chunk 219 optimal weight: 3.9990 chunk 328 optimal weight: 1.9990 chunk 347 optimal weight: 40.0000 chunk 171 optimal weight: 9.9990 chunk 311 optimal weight: 9.9990 chunk 93 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 331 ASN F 94 ASN F 324 GLN L 41 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 28740 Z= 0.217 Angle : 0.469 9.060 38873 Z= 0.235 Chirality : 0.039 0.140 4496 Planarity : 0.003 0.039 5041 Dihedral : 6.497 135.455 4011 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.82 % Allowed : 6.00 % Favored : 93.18 % 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: 1.09 (0.14), residues: 3597 helix: 1.50 (0.13), residues: 1694 sheet: 0.65 (0.19), residues: 650 loop : -0.20 (0.17), residues: 1253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP Z 20 HIS 0.008 0.001 HIS E 260 PHE 0.012 0.001 PHE L 17 TYR 0.008 0.001 TYR A 337 ARG 0.004 0.000 ARG J 118 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7194 Ramachandran restraints generated. 3597 Oldfield, 0 Emsley, 3597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7194 Ramachandran restraints generated. 3597 Oldfield, 0 Emsley, 3597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 3034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 209 time to evaluate : 3.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 384 MET cc_start: 0.9107 (mtp) cc_final: 0.8873 (mtp) REVERT: E 142 MET cc_start: 0.7866 (tmm) cc_final: 0.7446 (tmm) REVERT: H 120 MET cc_start: 0.8562 (ttp) cc_final: 0.8355 (ttp) REVERT: H 162 GLU cc_start: 0.9402 (mp0) cc_final: 0.9131 (pp20) REVERT: H 171 ASP cc_start: 0.8304 (m-30) cc_final: 0.7803 (t0) REVERT: I 171 ASP cc_start: 0.8716 (m-30) cc_final: 0.7892 (t0) REVERT: J 34 GLN cc_start: 0.8581 (mm-40) cc_final: 0.8089 (mm-40) REVERT: J 172 ARG cc_start: 0.7954 (ttt90) cc_final: 0.7727 (mmm160) REVERT: K 12 ARG cc_start: 0.5841 (mmm160) cc_final: 0.5595 (mmm160) REVERT: M 8 GLU cc_start: 0.8225 (tp30) cc_final: 0.7794 (tp30) REVERT: M 98 MET cc_start: 0.9182 (mmm) cc_final: 0.8834 (mmm) REVERT: N 34 GLN cc_start: 0.8946 (mm110) cc_final: 0.8706 (tm-30) REVERT: Y 43 MET cc_start: 0.7975 (mpp) cc_final: 0.7487 (mmt) outliers start: 25 outliers final: 21 residues processed: 219 average time/residue: 0.8732 time to fit residues: 295.4547 Evaluate side-chains 221 residues out of total 3034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 200 time to evaluate : 3.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 283 GLU Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 324 GLN Chi-restraints excluded: chain J residue 18 ASP Chi-restraints excluded: chain J residue 113 CYS Chi-restraints excluded: chain K residue 18 ASP Chi-restraints excluded: chain K residue 80 MET Chi-restraints excluded: chain L residue 8 GLU Chi-restraints excluded: chain L residue 53 GLU Chi-restraints excluded: chain L residue 58 ASP Chi-restraints excluded: chain L residue 113 CYS Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain M residue 18 ASP Chi-restraints excluded: chain M residue 80 MET Chi-restraints excluded: chain M residue 86 ASP Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain N residue 80 MET Chi-restraints excluded: chain N residue 113 CYS Chi-restraints excluded: chain Y residue 18 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 289 optimal weight: 9.9990 chunk 197 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 259 optimal weight: 8.9990 chunk 143 optimal weight: 20.0000 chunk 296 optimal weight: 30.0000 chunk 240 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 177 optimal weight: 4.9990 chunk 312 optimal weight: 10.0000 chunk 87 optimal weight: 4.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 HIS ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 GLN E 260 HIS F 342 ASN L 41 ASN ** N 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 28740 Z= 0.300 Angle : 0.513 8.344 38873 Z= 0.258 Chirality : 0.040 0.163 4496 Planarity : 0.003 0.044 5041 Dihedral : 6.506 136.331 4011 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.86 % Allowed : 6.62 % Favored : 92.52 % 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: 0.98 (0.14), residues: 3597 helix: 1.38 (0.12), residues: 1708 sheet: 0.58 (0.20), residues: 649 loop : -0.23 (0.17), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP Y 20 HIS 0.017 0.001 HIS N 122 PHE 0.010 0.001 PHE A 270 TYR 0.013 0.001 TYR D 182 ARG 0.015 0.000 ARG I 166 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7194 Ramachandran restraints generated. 3597 Oldfield, 0 Emsley, 3597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7194 Ramachandran restraints generated. 3597 Oldfield, 0 Emsley, 3597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 3034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 203 time to evaluate : 3.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 142 MET cc_start: 0.7865 (tmm) cc_final: 0.7473 (tmm) REVERT: H 120 MET cc_start: 0.8644 (ttp) cc_final: 0.8397 (ttp) REVERT: H 171 ASP cc_start: 0.8410 (m-30) cc_final: 0.7859 (t0) REVERT: I 171 ASP cc_start: 0.8798 (m-30) cc_final: 0.7907 (t0) REVERT: J 172 ARG cc_start: 0.8028 (ttt90) cc_final: 0.7794 (mmm160) REVERT: K 12 ARG cc_start: 0.5950 (mmm160) cc_final: 0.5720 (mmm160) REVERT: L 120 MET cc_start: 0.6073 (mmt) cc_final: 0.5638 (mmt) REVERT: M 8 GLU cc_start: 0.8236 (tp30) cc_final: 0.7778 (tp30) REVERT: M 9 GLN cc_start: 0.8783 (tp40) cc_final: 0.8155 (tp-100) REVERT: M 74 MET cc_start: 0.9508 (mmm) cc_final: 0.9292 (mmm) REVERT: M 98 MET cc_start: 0.9192 (mmm) cc_final: 0.8781 (mmm) REVERT: M 149 MET cc_start: 0.3864 (mmm) cc_final: 0.3612 (tpt) REVERT: N 34 GLN cc_start: 0.8929 (mm110) cc_final: 0.8688 (mm-40) REVERT: Y 43 MET cc_start: 0.7996 (mpp) cc_final: 0.7513 (mmt) outliers start: 26 outliers final: 21 residues processed: 215 average time/residue: 0.8807 time to fit residues: 291.2351 Evaluate side-chains 217 residues out of total 3034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 196 time to evaluate : 3.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 283 GLU Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain I residue 18 ASP Chi-restraints excluded: chain J residue 18 ASP Chi-restraints excluded: chain J residue 113 CYS Chi-restraints excluded: chain K residue 18 ASP Chi-restraints excluded: chain K residue 80 MET Chi-restraints excluded: chain L residue 53 GLU Chi-restraints excluded: chain L residue 58 ASP Chi-restraints excluded: chain L residue 113 CYS Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain M residue 18 ASP Chi-restraints excluded: chain M residue 80 MET Chi-restraints excluded: chain M residue 86 ASP Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain N residue 80 MET Chi-restraints excluded: chain N residue 113 CYS Chi-restraints excluded: chain Y residue 18 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 117 optimal weight: 5.9990 chunk 313 optimal weight: 20.0000 chunk 68 optimal weight: 0.0670 chunk 204 optimal weight: 10.0000 chunk 85 optimal weight: 20.0000 chunk 348 optimal weight: 50.0000 chunk 289 optimal weight: 9.9990 chunk 161 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 115 optimal weight: 9.9990 chunk 182 optimal weight: 10.0000 overall best weight: 7.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 GLN L 41 ASN M 46 GLN ** M 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 28740 Z= 0.316 Angle : 0.520 8.279 38873 Z= 0.265 Chirality : 0.040 0.147 4496 Planarity : 0.003 0.036 5041 Dihedral : 6.577 137.847 4011 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.96 % Allowed : 7.22 % Favored : 91.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.14), residues: 3597 helix: 1.27 (0.13), residues: 1714 sheet: 0.52 (0.20), residues: 659 loop : -0.32 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP Z 20 HIS 0.004 0.001 HIS M 156 PHE 0.021 0.001 PHE J 173 TYR 0.011 0.001 TYR A 337 ARG 0.006 0.000 ARG I 12 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7194 Ramachandran restraints generated. 3597 Oldfield, 0 Emsley, 3597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7194 Ramachandran restraints generated. 3597 Oldfield, 0 Emsley, 3597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 3034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 199 time to evaluate : 3.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 142 MET cc_start: 0.7848 (tmm) cc_final: 0.7485 (tmm) REVERT: H 120 MET cc_start: 0.8658 (ttp) cc_final: 0.8380 (ttp) REVERT: H 162 GLU cc_start: 0.9418 (mp0) cc_final: 0.9130 (pp20) REVERT: H 171 ASP cc_start: 0.8413 (m-30) cc_final: 0.7827 (t0) REVERT: J 34 GLN cc_start: 0.8334 (mm-40) cc_final: 0.8044 (tp-100) REVERT: M 8 GLU cc_start: 0.8245 (tp30) cc_final: 0.7850 (tp30) REVERT: M 9 GLN cc_start: 0.8822 (tp40) cc_final: 0.8200 (tp40) REVERT: M 60 TYR cc_start: 0.8882 (m-80) cc_final: 0.8277 (m-80) REVERT: N 34 GLN cc_start: 0.8921 (mm110) cc_final: 0.8673 (mm-40) REVERT: Y 43 MET cc_start: 0.8019 (mpp) cc_final: 0.7532 (mmt) outliers start: 29 outliers final: 26 residues processed: 215 average time/residue: 0.9314 time to fit residues: 309.3368 Evaluate side-chains 216 residues out of total 3034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 190 time to evaluate : 3.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 96 TYR Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 283 GLU Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 170 ASP Chi-restraints excluded: chain F residue 304 PHE Chi-restraints excluded: chain I residue 18 ASP Chi-restraints excluded: chain I residue 134 ASP Chi-restraints excluded: chain J residue 18 ASP Chi-restraints excluded: chain J residue 113 CYS Chi-restraints excluded: chain K residue 18 ASP Chi-restraints excluded: chain K residue 80 MET Chi-restraints excluded: chain L residue 58 ASP Chi-restraints excluded: chain L residue 113 CYS Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain M residue 18 ASP Chi-restraints excluded: chain M residue 80 MET Chi-restraints excluded: chain M residue 86 ASP Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain N residue 80 MET Chi-restraints excluded: chain N residue 113 CYS Chi-restraints excluded: chain Y residue 18 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 335 optimal weight: 20.0000 chunk 39 optimal weight: 5.9990 chunk 198 optimal weight: 10.0000 chunk 254 optimal weight: 6.9990 chunk 197 optimal weight: 6.9990 chunk 293 optimal weight: 20.0000 chunk 194 optimal weight: 2.9990 chunk 346 optimal weight: 50.0000 chunk 217 optimal weight: 8.9990 chunk 211 optimal weight: 8.9990 chunk 160 optimal weight: 0.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 9 GLN L 41 ASN ** N 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 28740 Z= 0.222 Angle : 0.474 10.471 38873 Z= 0.238 Chirality : 0.040 0.138 4496 Planarity : 0.003 0.036 5041 Dihedral : 6.486 138.193 4011 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.82 % Allowed : 7.81 % Favored : 91.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.14), residues: 3597 helix: 1.47 (0.13), residues: 1711 sheet: 0.47 (0.21), residues: 589 loop : -0.22 (0.17), residues: 1297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP Y 20 HIS 0.005 0.001 HIS N 122 PHE 0.010 0.001 PHE M 49 TYR 0.010 0.001 TYR A 337 ARG 0.005 0.000 ARG I 118 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7194 Ramachandran restraints generated. 3597 Oldfield, 0 Emsley, 3597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7194 Ramachandran restraints generated. 3597 Oldfield, 0 Emsley, 3597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 3034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 193 time to evaluate : 3.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 142 MET cc_start: 0.7787 (tmm) cc_final: 0.7409 (tmm) REVERT: H 86 ASP cc_start: 0.8503 (m-30) cc_final: 0.8031 (t0) REVERT: H 120 MET cc_start: 0.8632 (ttp) cc_final: 0.8224 (ttp) REVERT: I 171 ASP cc_start: 0.8772 (m-30) cc_final: 0.7712 (t0) REVERT: J 34 GLN cc_start: 0.8337 (mm-40) cc_final: 0.8049 (tp-100) REVERT: M 8 GLU cc_start: 0.8217 (tp30) cc_final: 0.7863 (tp30) REVERT: M 74 MET cc_start: 0.9465 (mmm) cc_final: 0.9039 (mmm) REVERT: M 149 MET cc_start: 0.3882 (mmm) cc_final: 0.3646 (tpt) REVERT: N 34 GLN cc_start: 0.8936 (mm110) cc_final: 0.8669 (mm-40) REVERT: Y 43 MET cc_start: 0.7996 (mpp) cc_final: 0.7568 (mmt) outliers start: 25 outliers final: 22 residues processed: 206 average time/residue: 0.8752 time to fit residues: 277.9486 Evaluate side-chains 212 residues out of total 3034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 190 time to evaluate : 3.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 96 TYR Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 260 HIS Chi-restraints excluded: chain E residue 283 GLU Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 170 ASP Chi-restraints excluded: chain F residue 393 VAL Chi-restraints excluded: chain J residue 18 ASP Chi-restraints excluded: chain J residue 113 CYS Chi-restraints excluded: chain K residue 18 ASP Chi-restraints excluded: chain K residue 80 MET Chi-restraints excluded: chain L residue 113 CYS Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain M residue 18 ASP Chi-restraints excluded: chain M residue 47 MET Chi-restraints excluded: chain M residue 80 MET Chi-restraints excluded: chain M residue 86 ASP Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain N residue 80 MET Chi-restraints excluded: chain Y residue 18 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 214 optimal weight: 9.9990 chunk 138 optimal weight: 8.9990 chunk 207 optimal weight: 10.0000 chunk 104 optimal weight: 0.8980 chunk 68 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 chunk 220 optimal weight: 5.9990 chunk 236 optimal weight: 8.9990 chunk 171 optimal weight: 8.9990 chunk 32 optimal weight: 10.0000 chunk 272 optimal weight: 6.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 167 GLN ** J 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 41 ASN L 94 GLN ** N 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 28740 Z= 0.255 Angle : 0.488 10.373 38873 Z= 0.245 Chirality : 0.039 0.140 4496 Planarity : 0.003 0.038 5041 Dihedral : 6.491 138.813 4011 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.96 % Allowed : 7.88 % Favored : 91.17 % 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: 1.00 (0.14), residues: 3597 helix: 1.46 (0.13), residues: 1713 sheet: 0.48 (0.21), residues: 591 loop : -0.23 (0.17), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP Y 20 HIS 0.004 0.001 HIS N 122 PHE 0.010 0.001 PHE A 270 TYR 0.010 0.001 TYR A 337 ARG 0.005 0.000 ARG I 12 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7194 Ramachandran restraints generated. 3597 Oldfield, 0 Emsley, 3597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7194 Ramachandran restraints generated. 3597 Oldfield, 0 Emsley, 3597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 3034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 194 time to evaluate : 3.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 142 MET cc_start: 0.7803 (tmm) cc_final: 0.7401 (tmm) REVERT: H 86 ASP cc_start: 0.8519 (m-30) cc_final: 0.8024 (t0) REVERT: H 162 GLU cc_start: 0.9408 (mp0) cc_final: 0.9143 (pp20) REVERT: H 171 ASP cc_start: 0.8459 (m-30) cc_final: 0.7688 (t0) REVERT: I 171 ASP cc_start: 0.8792 (m-30) cc_final: 0.7693 (t0) REVERT: J 34 GLN cc_start: 0.8397 (mm-40) cc_final: 0.8081 (tp-100) REVERT: M 8 GLU cc_start: 0.8236 (tp30) cc_final: 0.7883 (tp30) REVERT: M 53 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7623 (mp0) REVERT: M 60 TYR cc_start: 0.8919 (m-80) cc_final: 0.8227 (m-80) REVERT: N 34 GLN cc_start: 0.8966 (mm110) cc_final: 0.8681 (mm-40) REVERT: Y 43 MET cc_start: 0.8045 (mpp) cc_final: 0.7624 (mmt) outliers start: 29 outliers final: 26 residues processed: 208 average time/residue: 0.9132 time to fit residues: 289.8008 Evaluate side-chains 217 residues out of total 3034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 191 time to evaluate : 3.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 96 TYR Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 283 GLU Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 170 ASP Chi-restraints excluded: chain F residue 393 VAL Chi-restraints excluded: chain I residue 18 ASP Chi-restraints excluded: chain I residue 113 CYS Chi-restraints excluded: chain J residue 18 ASP Chi-restraints excluded: chain J residue 113 CYS Chi-restraints excluded: chain K residue 18 ASP Chi-restraints excluded: chain K residue 80 MET Chi-restraints excluded: chain L residue 113 CYS Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain M residue 18 ASP Chi-restraints excluded: chain M residue 47 MET Chi-restraints excluded: chain M residue 80 MET Chi-restraints excluded: chain M residue 86 ASP Chi-restraints excluded: chain M residue 174 LEU Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain N residue 80 MET Chi-restraints excluded: chain N residue 113 CYS Chi-restraints excluded: chain Y residue 18 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 315 optimal weight: 7.9990 chunk 332 optimal weight: 7.9990 chunk 303 optimal weight: 8.9990 chunk 323 optimal weight: 9.9990 chunk 194 optimal weight: 0.6980 chunk 140 optimal weight: 9.9990 chunk 253 optimal weight: 9.9990 chunk 99 optimal weight: 10.0000 chunk 292 optimal weight: 10.0000 chunk 305 optimal weight: 5.9990 chunk 322 optimal weight: 3.9990 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 41 ASN ** N 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 24 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 28740 Z= 0.243 Angle : 0.485 9.821 38873 Z= 0.244 Chirality : 0.040 0.140 4496 Planarity : 0.003 0.045 5041 Dihedral : 6.493 139.468 4011 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.86 % Allowed : 8.04 % Favored : 91.10 % 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: 1.04 (0.14), residues: 3597 helix: 1.51 (0.13), residues: 1713 sheet: 0.48 (0.21), residues: 591 loop : -0.22 (0.17), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP Y 20 HIS 0.004 0.001 HIS N 122 PHE 0.010 0.001 PHE A 270 TYR 0.010 0.001 TYR A 337 ARG 0.007 0.000 ARG I 12 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7194 Ramachandran restraints generated. 3597 Oldfield, 0 Emsley, 3597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7194 Ramachandran restraints generated. 3597 Oldfield, 0 Emsley, 3597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 3034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 190 time to evaluate : 3.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 142 MET cc_start: 0.7788 (tmm) cc_final: 0.7397 (tmm) REVERT: H 86 ASP cc_start: 0.8514 (m-30) cc_final: 0.8014 (t0) REVERT: H 162 GLU cc_start: 0.9408 (mp0) cc_final: 0.9097 (pp20) REVERT: H 171 ASP cc_start: 0.8412 (m-30) cc_final: 0.7663 (t0) REVERT: I 171 ASP cc_start: 0.8798 (m-30) cc_final: 0.7692 (t0) REVERT: J 34 GLN cc_start: 0.8446 (mm-40) cc_final: 0.8126 (tp-100) REVERT: M 8 GLU cc_start: 0.8215 (tp30) cc_final: 0.7761 (tp30) REVERT: M 60 TYR cc_start: 0.8949 (m-80) cc_final: 0.8156 (m-80) REVERT: N 34 GLN cc_start: 0.8973 (mm110) cc_final: 0.8697 (mm-40) REVERT: Y 25 GLN cc_start: 0.8336 (tp-100) cc_final: 0.7704 (tm-30) REVERT: Y 43 MET cc_start: 0.8027 (mpp) cc_final: 0.7583 (mmt) outliers start: 26 outliers final: 23 residues processed: 202 average time/residue: 0.8998 time to fit residues: 279.5110 Evaluate side-chains 211 residues out of total 3034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 188 time to evaluate : 3.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 96 TYR Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 283 GLU Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 170 ASP Chi-restraints excluded: chain F residue 393 VAL Chi-restraints excluded: chain I residue 113 CYS Chi-restraints excluded: chain J residue 18 ASP Chi-restraints excluded: chain J residue 113 CYS Chi-restraints excluded: chain K residue 18 ASP Chi-restraints excluded: chain K residue 80 MET Chi-restraints excluded: chain L residue 113 CYS Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain M residue 18 ASP Chi-restraints excluded: chain M residue 47 MET Chi-restraints excluded: chain M residue 80 MET Chi-restraints excluded: chain M residue 86 ASP Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain N residue 80 MET Chi-restraints excluded: chain Y residue 18 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 212 optimal weight: 5.9990 chunk 341 optimal weight: 30.0000 chunk 208 optimal weight: 5.9990 chunk 162 optimal weight: 0.8980 chunk 237 optimal weight: 4.9990 chunk 358 optimal weight: 9.9990 chunk 330 optimal weight: 10.0000 chunk 285 optimal weight: 6.9990 chunk 29 optimal weight: 9.9990 chunk 220 optimal weight: 1.9990 chunk 175 optimal weight: 9.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 9 GLN L 41 ASN ** N 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 28740 Z= 0.199 Angle : 0.468 9.966 38873 Z= 0.234 Chirality : 0.039 0.139 4496 Planarity : 0.003 0.036 5041 Dihedral : 6.425 139.587 4011 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.69 % Allowed : 8.27 % Favored : 91.03 % 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: 1.18 (0.14), residues: 3597 helix: 1.63 (0.13), residues: 1712 sheet: 0.55 (0.21), residues: 591 loop : -0.16 (0.17), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP Y 20 HIS 0.003 0.001 HIS N 122 PHE 0.011 0.001 PHE M 101 TYR 0.010 0.001 TYR A 337 ARG 0.005 0.000 ARG I 12 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7194 Ramachandran restraints generated. 3597 Oldfield, 0 Emsley, 3597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7194 Ramachandran restraints generated. 3597 Oldfield, 0 Emsley, 3597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 3034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 189 time to evaluate : 3.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 142 MET cc_start: 0.7757 (tmm) cc_final: 0.7366 (tmm) REVERT: H 86 ASP cc_start: 0.8518 (m-30) cc_final: 0.8023 (t0) REVERT: H 171 ASP cc_start: 0.8439 (m-30) cc_final: 0.7664 (t0) REVERT: I 149 MET cc_start: 0.9240 (mmm) cc_final: 0.8968 (mmm) REVERT: I 171 ASP cc_start: 0.8819 (m-30) cc_final: 0.7714 (t0) REVERT: J 34 GLN cc_start: 0.8481 (mm-40) cc_final: 0.8018 (mm-40) REVERT: J 144 LYS cc_start: 0.9166 (tmtt) cc_final: 0.8861 (tmmt) REVERT: K 178 GLU cc_start: 0.9242 (mp0) cc_final: 0.8890 (mp0) REVERT: M 8 GLU cc_start: 0.8199 (tp30) cc_final: 0.7743 (tp30) REVERT: M 60 TYR cc_start: 0.8941 (m-80) cc_final: 0.8142 (m-80) REVERT: N 34 GLN cc_start: 0.8985 (mm110) cc_final: 0.8701 (mm-40) REVERT: Y 25 GLN cc_start: 0.8193 (tp-100) cc_final: 0.7450 (tm-30) REVERT: Y 43 MET cc_start: 0.7992 (mpp) cc_final: 0.7539 (mmt) outliers start: 21 outliers final: 20 residues processed: 198 average time/residue: 0.8574 time to fit residues: 260.3462 Evaluate side-chains 207 residues out of total 3034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 187 time to evaluate : 3.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 96 TYR Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 170 ASP Chi-restraints excluded: chain F residue 393 VAL Chi-restraints excluded: chain I residue 113 CYS Chi-restraints excluded: chain I residue 134 ASP Chi-restraints excluded: chain J residue 18 ASP Chi-restraints excluded: chain J residue 113 CYS Chi-restraints excluded: chain K residue 18 ASP Chi-restraints excluded: chain K residue 80 MET Chi-restraints excluded: chain L residue 113 CYS Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain M residue 18 ASP Chi-restraints excluded: chain M residue 47 MET Chi-restraints excluded: chain M residue 80 MET Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain N residue 80 MET Chi-restraints excluded: chain Y residue 18 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 226 optimal weight: 6.9990 chunk 304 optimal weight: 5.9990 chunk 87 optimal weight: 8.9990 chunk 263 optimal weight: 10.0000 chunk 42 optimal weight: 0.0070 chunk 79 optimal weight: 3.9990 chunk 286 optimal weight: 0.8980 chunk 119 optimal weight: 0.6980 chunk 293 optimal weight: 9.9990 chunk 36 optimal weight: 7.9990 chunk 52 optimal weight: 8.9990 overall best weight: 2.3202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 41 ASN ** N 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.078058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.053681 restraints weight = 366836.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.056165 restraints weight = 167287.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.057641 restraints weight = 111003.800| |-----------------------------------------------------------------------------| r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 28740 Z= 0.142 Angle : 0.451 9.437 38873 Z= 0.224 Chirality : 0.040 0.139 4496 Planarity : 0.003 0.038 5041 Dihedral : 6.321 139.419 4011 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.69 % Allowed : 8.21 % Favored : 91.10 % 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: 1.36 (0.14), residues: 3597 helix: 1.79 (0.13), residues: 1713 sheet: 0.63 (0.21), residues: 591 loop : -0.09 (0.17), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP Y 20 HIS 0.003 0.001 HIS N 122 PHE 0.008 0.001 PHE A 270 TYR 0.009 0.001 TYR A 337 ARG 0.007 0.000 ARG I 166 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7819.20 seconds wall clock time: 137 minutes 19.95 seconds (8239.95 seconds total)