Starting phenix.real_space_refine on Sat Mar 16 21:24:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e8q_27946/03_2024/8e8q_27946_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e8q_27946/03_2024/8e8q_27946.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e8q_27946/03_2024/8e8q_27946.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e8q_27946/03_2024/8e8q_27946.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e8q_27946/03_2024/8e8q_27946_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e8q_27946/03_2024/8e8q_27946_trim_updated.pdb" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 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: 7 Type Number sf(0) Gaussians P 16 5.49 5 Mg 3 5.21 5 S 198 5.16 5 C 23457 2.51 5 N 6394 2.21 5 O 7190 1.98 5 H 37561 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 216": "OE1" <-> "OE2" Residue "A GLU 293": "OE1" <-> "OE2" Residue "A GLU 316": "OE1" <-> "OE2" Residue "B GLU 283": "OE1" <-> "OE2" Residue "B GLU 408": "OE1" <-> "OE2" Residue "C GLU 159": "OE1" <-> "OE2" Residue "C PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 391": "OE1" <-> "OE2" Residue "D GLU 109": "OE1" <-> "OE2" Residue "D GLU 159": "OE1" <-> "OE2" Residue "D GLU 216": "OE1" <-> "OE2" Residue "E GLU 130": "OE1" <-> "OE2" Residue "E GLU 150": "OE1" <-> "OE2" Residue "E GLU 283": "OE1" <-> "OE2" Residue "E GLU 285": "OE1" <-> "OE2" Residue "F ARG 100": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 109": "OE1" <-> "OE2" Residue "F GLU 185": "OE1" <-> "OE2" Residue "h ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "h ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "h ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "h ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "h ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "i ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "i ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "i ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "i ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "i ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "j ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "j ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "j ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "j ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "j ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "k ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "k ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "k ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "k ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "k ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "l ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "l ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "l ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "l ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "l ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "m ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "m ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "m ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "m ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "m ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "n GLU 8": "OE1" <-> "OE2" Residue "n GLU 14": "OE1" <-> "OE2" Residue "n ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "n ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "n ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "n ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "n ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 74819 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 5424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 5424 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 14, 'TRANS': 335} Chain: "B" Number of atoms: 5445 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 351, 5433 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 14, 'TRANS': 336} Conformer: "B" Number of residues, atoms: 351, 5433 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 14, 'TRANS': 336} bond proxies already assigned to first conformer: 5456 Chain: "C" 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: "D" 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: "E" Number of atoms: 5442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 5442 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 14, 'TRANS': 337} Chain: "F" Number of atoms: 5244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 5244 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 13, 'TRANS': 324} Chain breaks: 1 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: 3002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 3002 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 7, 'TRANS': 183} 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: 3045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 3045 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 7, 'TRANS': 186} 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: 2978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 2978 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 7, 'TRANS': 182} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ASER B 197 " occ=0.50 ... (20 atoms not shown) pdb=" HG BSER B 197 " occ=0.50 Time building chain proxies: 24.85, per 1000 atoms: 0.33 Number of scatterers: 74819 At special positions: 0 Unit cell: (136.038, 147.098, 194.656, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 198 16.00 P 16 15.00 Mg 3 11.99 O 7190 8.00 N 6394 7.00 C 23457 6.00 H 37561 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: 46.67 Conformation dependent library (CDL) restraints added in 6.4 seconds 9486 Ramachandran restraints generated. 4743 Oldfield, 0 Emsley, 4743 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8792 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 201 helices and 65 sheets defined 45.4% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.05 Creating SS restraints... Processing helix chain 'A' and resid 67 through 77 removed outlier: 3.779A pdb=" N TYR A 77 " --> pdb=" O HIS A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 100 Processing helix chain 'A' and resid 103 through 105 No H-bonds generated for 'chain 'A' and resid 103 through 105' Processing helix chain 'A' and resid 125 through 135 removed outlier: 3.875A pdb=" N ARG A 134 " --> pdb=" O GLU A 130 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU A 135 " --> pdb=" O THR A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 168 Processing helix chain 'A' and resid 173 through 178 removed outlier: 3.979A pdb=" N ARG A 178 " --> pdb=" O GLN A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 189 Processing helix chain 'A' and resid 205 through 216 removed outlier: 3.658A pdb=" N ALA A 210 " --> pdb=" O GLY A 206 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A 214 " --> pdb=" O ALA A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 262 Processing helix chain 'A' and resid 277 through 279 No H-bonds generated for 'chain 'A' and resid 277 through 279' Processing helix chain 'A' and resid 287 through 289 No H-bonds generated for 'chain 'A' and resid 287 through 289' Processing helix chain 'A' and resid 292 through 298 Processing helix chain 'A' and resid 302 through 306 Processing helix chain 'A' and resid 319 through 327 removed outlier: 3.759A pdb=" N LYS A 327 " --> pdb=" O ILE A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 344 removed outlier: 3.675A pdb=" N GLU A 344 " --> pdb=" O LEU A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 365 removed outlier: 3.661A pdb=" N ASP A 356 " --> pdb=" O ASP A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 379 removed outlier: 3.521A 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 removed outlier: 3.528A pdb=" N ASP A 404 " --> pdb=" O GLU A 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 400 through 404' Processing helix chain 'B' and resid 67 through 77 removed outlier: 3.586A 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: 3.632A pdb=" N ARG B 134 " --> pdb=" O GLU B 130 " (cutoff:3.500A) removed outlier: 3.838A 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 186 through 189 removed outlier: 3.516A pdb=" N ILE B 189 " --> pdb=" O ILE B 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 186 through 189' Processing helix chain 'B' and resid 205 through 216 removed outlier: 4.691A pdb=" N LYS B 213 " --> pdb=" O GLN B 209 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU B 214 " --> pdb=" O ALA B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 234 Processing helix chain 'B' and resid 254 through 262 removed outlier: 3.799A pdb=" N ARG B 261 " --> pdb=" O VAL B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 289 removed outlier: 3.630A pdb=" N GLN B 289 " --> pdb=" O GLU B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 298 removed outlier: 3.656A pdb=" N LYS B 297 " --> pdb=" O GLU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 307 Processing helix chain 'B' and resid 319 through 325 Processing helix chain 'B' and resid 333 through 342 Processing helix chain 'B' and resid 352 through 365 Processing helix chain 'B' and resid 368 through 379 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 77 removed outlier: 3.879A pdb=" N TYR C 77 " --> pdb=" O HIS C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 100 Processing helix chain 'C' and resid 125 through 135 removed outlier: 3.500A pdb=" N ALA C 129 " --> pdb=" O LYS C 125 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG C 134 " --> pdb=" O GLU C 130 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU C 135 " --> pdb=" O THR C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 168 Processing helix chain 'C' and resid 173 through 178 removed outlier: 3.690A pdb=" N ARG C 178 " --> pdb=" O GLN C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 188 No H-bonds generated for 'chain 'C' and resid 186 through 188' Processing helix chain 'C' and resid 205 through 216 removed outlier: 4.648A pdb=" N LYS C 213 " --> pdb=" O GLN C 209 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU C 214 " --> pdb=" O ALA C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 263 removed outlier: 3.634A pdb=" N ARG C 261 " --> pdb=" O VAL C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 289 removed outlier: 3.697A pdb=" N GLN C 289 " --> pdb=" O GLU C 285 " (cutoff:3.500A) 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 327 removed outlier: 3.790A pdb=" N LYS C 327 " --> pdb=" O ILE C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 344 Processing helix chain 'C' and resid 352 through 365 Processing helix chain 'C' and resid 368 through 379 removed outlier: 3.770A pdb=" N VAL C 376 " --> pdb=" O ARG C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 387 Processing helix chain 'C' and resid 400 through 404 removed outlier: 3.548A 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: 4.054A 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: 3.603A pdb=" N ALA D 129 " --> pdb=" O LYS D 125 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG D 134 " --> pdb=" O GLU D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 168 removed outlier: 3.539A pdb=" N LYS D 168 " --> pdb=" O LEU D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 177 Processing helix chain 'D' and resid 186 through 188 No H-bonds generated for 'chain 'D' and resid 186 through 188' Processing helix chain 'D' and resid 205 through 216 removed outlier: 4.446A pdb=" N LYS D 213 " --> pdb=" O GLN D 209 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU D 214 " --> pdb=" O ALA D 210 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLU D 216 " --> pdb=" O LEU D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 262 removed outlier: 3.507A pdb=" N ARG D 261 " --> pdb=" O VAL D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 289 removed outlier: 3.717A pdb=" N GLN D 289 " --> pdb=" O GLU D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 298 removed outlier: 3.540A pdb=" N LYS D 297 " --> pdb=" O GLU D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 307 removed outlier: 3.717A pdb=" N ARG D 307 " --> pdb=" O GLU D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 327 removed outlier: 3.844A pdb=" N LYS D 327 " --> pdb=" O ILE D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 342 Processing helix chain 'D' and resid 352 through 365 removed outlier: 3.540A pdb=" N ALA D 364 " --> pdb=" O LYS D 360 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG D 365 " --> pdb=" O LYS D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 379 removed outlier: 3.521A pdb=" N GLU D 377 " --> pdb=" O SER D 374 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA D 378 " --> pdb=" O ILE D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 387 Processing helix chain 'D' and resid 400 through 404 removed outlier: 3.668A pdb=" N ASP D 404 " --> pdb=" O GLU D 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 400 through 404' Processing helix chain 'E' and resid 67 through 77 removed outlier: 3.585A 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 130 removed outlier: 3.681A pdb=" N ALA E 129 " --> pdb=" O LYS E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 168 removed outlier: 3.728A pdb=" N LYS E 168 " --> pdb=" O LEU E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 178 removed outlier: 4.289A pdb=" N ARG E 178 " --> pdb=" O GLN E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 189 Processing helix chain 'E' and resid 205 through 216 removed outlier: 4.711A pdb=" N LYS E 213 " --> pdb=" O GLN E 209 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU E 214 " --> pdb=" O ALA E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 262 Processing helix chain 'E' and resid 283 through 289 removed outlier: 3.530A pdb=" N ALA E 288 " --> pdb=" O GLY E 284 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLN E 289 " --> pdb=" O GLU E 285 " (cutoff:3.500A) Processing helix chain 'E' and resid 292 through 298 removed outlier: 3.543A pdb=" N LYS E 297 " --> pdb=" O GLU E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 307 removed outlier: 3.780A pdb=" N ARG E 307 " --> pdb=" O GLU E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 327 removed outlier: 3.752A pdb=" N LYS E 327 " --> pdb=" O ILE E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 342 Processing helix chain 'E' and resid 352 through 365 Processing helix chain 'E' and resid 370 through 379 Processing helix chain 'E' and resid 381 through 387 Processing helix chain 'E' and resid 400 through 404 removed outlier: 3.576A pdb=" N ASP E 404 " --> pdb=" O GLU E 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 400 through 404' Processing helix chain 'F' and resid 67 through 77 removed outlier: 3.787A 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 135 removed outlier: 3.558A pdb=" N ALA F 129 " --> pdb=" O LYS F 125 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU F 130 " --> pdb=" O THR F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 154 through 168 removed outlier: 3.852A pdb=" N ILE F 162 " --> pdb=" O VAL F 158 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS F 168 " --> pdb=" O LYS F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 177 Processing helix chain 'F' and resid 205 through 216 removed outlier: 3.501A pdb=" N GLN F 209 " --> pdb=" O GLU F 205 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA F 210 " --> pdb=" O GLY F 206 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LYS F 213 " --> pdb=" O GLN F 209 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU F 214 " --> pdb=" O ALA F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 262 Processing helix chain 'F' and resid 281 through 289 removed outlier: 4.094A pdb=" N GLU F 285 " --> pdb=" O ALA F 281 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN F 289 " --> pdb=" O GLU F 285 " (cutoff:3.500A) Processing helix chain 'F' and resid 292 through 298 Processing helix chain 'F' and resid 302 through 306 Processing helix chain 'F' and resid 319 through 327 removed outlier: 3.753A pdb=" N LYS F 327 " --> pdb=" O ILE F 323 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 344 removed outlier: 3.623A pdb=" N GLU F 344 " --> pdb=" O LEU F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 352 through 365 removed outlier: 3.547A pdb=" N ALA F 357 " --> pdb=" O GLU F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 370 through 387 removed outlier: 3.546A pdb=" N VAL F 376 " --> pdb=" O ARG F 373 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA F 378 " --> pdb=" O ILE F 375 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ASP F 382 " --> pdb=" O ALA F 379 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR F 383 " --> pdb=" O LEU F 380 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LEU F 387 " --> pdb=" O MET F 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 404 Processing helix chain 'H' and resid 19 through 26 removed outlier: 3.744A pdb=" N GLU H 26 " --> pdb=" O ARG H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 53 Processing helix chain 'H' and resid 70 through 82 removed outlier: 3.807A 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 169 Processing helix chain 'H' and resid 176 through 182 removed outlier: 3.626A pdb=" N VAL H 180 " --> pdb=" O ALA H 176 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU H 181 " --> pdb=" O PRO H 177 " (cutoff:3.500A) Processing helix chain 'I' and resid 19 through 26 removed outlier: 3.762A pdb=" N GLU I 26 " --> pdb=" O ARG I 22 " (cutoff:3.500A) Processing helix chain 'I' and resid 37 through 53 Processing helix chain 'I' and resid 70 through 82 removed outlier: 3.598A pdb=" N ILE I 76 " --> pdb=" O ALA I 72 " (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: 3.821A 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: 3.598A 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 removed outlier: 3.509A pdb=" N GLU J 141 " --> pdb=" O ILE J 137 " (cutoff:3.500A) Processing helix chain 'J' and resid 161 through 168 Processing helix chain 'J' and resid 176 through 182 Processing helix chain 'K' and resid 19 through 26 removed outlier: 3.729A 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: 3.568A 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 Processing helix chain 'K' and resid 161 through 168 Processing helix chain 'K' and resid 176 through 182 Processing helix chain 'L' and resid 19 through 26 removed outlier: 3.746A pdb=" N GLU L 26 " --> pdb=" O ARG L 22 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 53 removed outlier: 3.630A pdb=" N ALA L 52 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU L 53 " --> pdb=" O PHE L 49 " (cutoff:3.500A) Processing helix chain 'L' and resid 70 through 82 removed outlier: 3.640A 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 167 Processing helix chain 'L' and resid 176 through 182 Processing helix chain 'M' and resid 19 through 26 removed outlier: 3.868A pdb=" N GLU M 26 " --> pdb=" O ARG M 22 " (cutoff:3.500A) Processing helix chain 'M' and resid 37 through 53 Processing helix chain 'M' and resid 70 through 82 removed outlier: 3.598A pdb=" N ILE M 76 " --> pdb=" O ALA M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 104 Processing helix chain 'M' and resid 132 through 157 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: 3.514A pdb=" N LYS N 25 " --> pdb=" O SER N 21 " (cutoff:3.500A) removed outlier: 4.084A 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: 3.533A pdb=" N SER N 75 " --> pdb=" O THR N 71 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE N 76 " --> pdb=" O ALA N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 97 through 104 Processing helix chain 'N' and resid 132 through 157 Processing helix chain 'N' and resid 161 through 167 Processing helix chain 'N' and resid 176 through 182 Processing helix chain 'h' and resid 19 through 26 removed outlier: 3.807A pdb=" N GLU h 26 " --> pdb=" O ARG h 22 " (cutoff:3.500A) Processing helix chain 'h' and resid 37 through 53 Processing helix chain 'h' and resid 70 through 82 removed outlier: 3.691A 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 26 removed outlier: 3.948A pdb=" N GLU i 26 " --> pdb=" O ARG i 22 " (cutoff:3.500A) Processing helix chain 'i' and resid 37 through 53 Processing helix chain 'i' and resid 70 through 82 removed outlier: 3.572A pdb=" N ILE i 76 " --> pdb=" O ALA i 72 " (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 181 Processing helix chain 'j' and resid 19 through 26 removed outlier: 3.834A 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: 3.622A 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 168 Processing helix chain 'j' and resid 176 through 182 Processing helix chain 'k' and resid 19 through 26 removed outlier: 3.503A pdb=" N LYS k 25 " --> pdb=" O SER k 21 " (cutoff:3.500A) removed outlier: 3.989A 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: 3.673A 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 Processing helix chain 'k' and resid 161 through 168 Processing helix chain 'k' and resid 176 through 181 Processing helix chain 'l' and resid 19 through 26 removed outlier: 3.841A pdb=" N GLU l 26 " --> pdb=" O ARG l 22 " (cutoff:3.500A) Processing helix chain 'l' and resid 37 through 53 Processing helix chain 'l' and resid 70 through 82 removed outlier: 3.528A 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 168 Processing helix chain 'l' and resid 176 through 182 Processing helix chain 'm' and resid 19 through 26 removed outlier: 3.897A pdb=" N GLU m 26 " --> pdb=" O ARG m 22 " (cutoff:3.500A) Processing helix chain 'm' and resid 37 through 53 Processing helix chain 'm' and resid 70 through 82 removed outlier: 3.555A pdb=" N ILE m 76 " --> pdb=" O ALA m 72 " (cutoff:3.500A) Processing helix chain 'm' and resid 97 through 104 Processing helix chain 'm' and resid 132 through 157 Processing helix chain 'm' and resid 161 through 169 Processing helix chain 'm' and resid 176 through 182 Processing helix chain 'n' and resid 19 through 26 removed outlier: 3.566A pdb=" N LEU n 23 " --> pdb=" O ILE n 19 " (cutoff:3.500A) removed outlier: 3.693A 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: 3.598A pdb=" N ILE n 76 " --> pdb=" O ALA n 72 " (cutoff:3.500A) Processing helix chain 'n' and resid 97 through 104 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 sheet with id= A, first strand: chain 'A' and resid 115 through 118 removed outlier: 3.719A pdb=" N ILE A 115 " --> pdb=" O PHE A 245 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 220 through 222 Processing sheet with id= C, first strand: chain 'A' and resid 347 through 350 removed outlier: 3.796A pdb=" N LYS A 395 " --> pdb=" O ILE A 412 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 310 through 313 removed outlier: 3.823A pdb=" N THR B 141 " --> pdb=" O ILE B 180 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 347 through 350 removed outlier: 3.967A pdb=" N LYS B 395 " --> pdb=" O ILE B 412 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 310 through 314 removed outlier: 7.061A pdb=" N CYS C 247 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N GLY C 119 " --> pdb=" O CYS C 247 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N GLY C 249 " --> pdb=" O GLY C 119 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 140 through 144 removed outlier: 6.694A pdb=" N ILE C 180 " --> pdb=" O THR C 141 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N ALA C 143 " --> pdb=" O ILE C 180 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N TYR C 182 " --> pdb=" O ALA C 143 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'C' and resid 347 through 350 removed outlier: 3.764A pdb=" N GLU C 349 " --> pdb=" O VAL C 396 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE C 398 " --> pdb=" O GLU C 349 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ILE C 412 " --> pdb=" O GLU C 394 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N VAL C 396 " --> pdb=" O LEU C 410 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU C 410 " --> pdb=" O VAL C 396 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 310 through 314 removed outlier: 3.696A pdb=" N GLY D 119 " --> pdb=" O GLY D 249 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR D 141 " --> pdb=" O ILE D 180 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 219 through 222 Processing sheet with id= K, first strand: chain 'D' and resid 347 through 350 removed outlier: 7.277A pdb=" N ILE D 412 " --> pdb=" O GLU D 394 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N VAL D 396 " --> pdb=" O LEU D 410 " (cutoff:3.500A) removed outlier: 7.092A 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: 3.628A pdb=" N THR E 141 " --> pdb=" O ILE E 180 " (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 removed outlier: 6.957A pdb=" N ILE E 412 " --> pdb=" O GLU E 394 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N VAL E 396 " --> pdb=" O LEU E 410 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N LEU E 410 " --> pdb=" O VAL E 396 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'F' and resid 115 through 118 removed outlier: 6.909A pdb=" N VAL F 310 " --> pdb=" O LEU F 116 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N ILE F 118 " --> pdb=" O VAL F 310 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ALA F 312 " --> pdb=" O ILE F 118 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'F' and resid 140 through 144 removed outlier: 6.629A pdb=" N ILE F 180 " --> pdb=" O THR F 141 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N ALA F 143 " --> pdb=" O ILE F 180 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N TYR F 182 " --> pdb=" O ALA F 143 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU F 244 " --> pdb=" O VAL F 181 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ILE F 183 " --> pdb=" O LEU F 244 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ILE F 246 " --> pdb=" O ILE F 183 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'F' and resid 219 through 222 Processing sheet with id= R, first strand: chain 'F' and resid 347 through 350 Processing sheet with id= S, first strand: chain 'H' and resid 6 through 9 Processing sheet with id= T, first strand: chain 'H' and resid 28 through 32 removed outlier: 6.504A pdb=" N TYR H 60 " --> pdb=" O ILE H 29 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N LEU H 31 " --> pdb=" O TYR H 60 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N TYR H 62 " --> pdb=" O LEU H 31 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'H' and resid 118 through 121 Processing sheet with id= V, first strand: chain 'I' and resid 5 through 9 Processing sheet with id= W, first strand: chain 'I' and resid 28 through 32 removed outlier: 6.465A pdb=" N TYR I 60 " --> pdb=" O ILE I 29 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N LEU I 31 " --> pdb=" O TYR I 60 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N TYR I 62 " --> pdb=" O LEU I 31 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'I' and resid 118 through 121 Processing sheet with id= Y, first strand: chain 'J' and resid 5 through 9 Processing sheet with id= Z, first strand: chain 'J' and resid 28 through 32 removed outlier: 6.434A pdb=" N TYR J 60 " --> pdb=" O ILE J 29 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N LEU J 31 " --> pdb=" O TYR J 60 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N TYR J 62 " --> pdb=" O LEU J 31 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'J' and resid 112 through 114 removed outlier: 6.754A pdb=" N SER J 187 " --> pdb=" O CYS J 113 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'J' and resid 118 through 121 Processing sheet with id= AC, first strand: chain 'K' and resid 5 through 9 Processing sheet with id= AD, first strand: chain 'K' and resid 28 through 32 removed outlier: 6.508A pdb=" N TYR K 60 " --> pdb=" O ILE K 29 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N LEU K 31 " --> pdb=" O TYR K 60 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N TYR K 62 " --> pdb=" O LEU K 31 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'K' and resid 118 through 121 Processing sheet with id= AF, first strand: chain 'L' and resid 5 through 8 removed outlier: 3.702A pdb=" N ARG L 15 " --> pdb=" O GLU L 8 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'L' and resid 28 through 32 removed outlier: 6.509A pdb=" N TYR L 60 " --> pdb=" O ILE L 29 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N LEU L 31 " --> pdb=" O TYR L 60 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N TYR L 62 " --> pdb=" O LEU L 31 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N SER L 187 " --> pdb=" O CYS L 113 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'L' and resid 118 through 121 Processing sheet with id= AI, first strand: chain 'M' and resid 6 through 8 Processing sheet with id= AJ, first strand: chain 'M' and resid 28 through 32 removed outlier: 6.390A pdb=" N TYR M 60 " --> pdb=" O ILE M 29 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N LEU M 31 " --> pdb=" O TYR M 60 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N TYR M 62 " --> pdb=" O LEU M 31 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'M' and resid 118 through 121 Processing sheet with id= AL, first strand: chain 'N' and resid 5 through 9 Processing sheet with id= AM, first strand: chain 'N' and resid 28 through 32 removed outlier: 6.567A pdb=" N TYR N 60 " --> pdb=" O ILE N 29 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N LEU N 31 " --> pdb=" O TYR N 60 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N TYR N 62 " --> pdb=" O LEU N 31 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'N' and resid 118 through 121 removed outlier: 3.575A pdb=" N ILE N 121 " --> pdb=" O ARG N 172 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'h' and resid 5 through 9 Processing sheet with id= AP, first strand: chain 'h' and resid 28 through 32 removed outlier: 6.511A pdb=" N TYR h 60 " --> pdb=" O ILE h 29 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N LEU h 31 " --> pdb=" O TYR h 60 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N TYR h 62 " --> pdb=" O LEU h 31 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'h' and resid 112 through 114 removed outlier: 7.069A pdb=" N SER h 187 " --> pdb=" O CYS h 113 " (cutoff:3.500A) No H-bonds generated for sheet with id= AQ Processing sheet with id= AR, first strand: chain 'h' and resid 118 through 121 Processing sheet with id= AS, first strand: chain 'i' and resid 5 through 9 Processing sheet with id= AT, first strand: chain 'i' and resid 28 through 32 removed outlier: 6.546A pdb=" N TYR i 60 " --> pdb=" O ILE i 29 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N LEU i 31 " --> pdb=" O TYR i 60 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N TYR i 62 " --> pdb=" O LEU i 31 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'i' and resid 119 through 121 Processing sheet with id= AV, first strand: chain 'j' and resid 5 through 9 Processing sheet with id= AW, first strand: chain 'j' and resid 28 through 32 removed outlier: 6.627A pdb=" N TYR j 60 " --> pdb=" O ILE j 29 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N LEU j 31 " --> pdb=" O TYR j 60 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N TYR j 62 " --> pdb=" O LEU j 31 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'j' and resid 112 through 114 removed outlier: 6.797A pdb=" N SER j 187 " --> pdb=" O CYS j 113 " (cutoff:3.500A) No H-bonds generated for sheet with id= AX Processing sheet with id= AY, first strand: chain 'j' and resid 119 through 121 Processing sheet with id= AZ, first strand: chain 'k' and resid 5 through 9 Processing sheet with id= BA, first strand: chain 'k' and resid 28 through 32 removed outlier: 6.590A pdb=" N TYR k 60 " --> pdb=" O ILE k 29 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N LEU k 31 " --> pdb=" O TYR k 60 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N TYR k 62 " --> pdb=" O LEU k 31 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'k' and resid 118 through 121 Processing sheet with id= BC, first strand: chain 'l' and resid 5 through 9 Processing sheet with id= BD, first strand: chain 'l' and resid 28 through 32 removed outlier: 6.520A pdb=" N TYR l 60 " --> pdb=" O ILE l 29 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N LEU l 31 " --> pdb=" O TYR l 60 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N TYR l 62 " --> pdb=" O LEU l 31 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'l' and resid 112 through 114 removed outlier: 6.758A pdb=" N SER l 187 " --> pdb=" O CYS l 113 " (cutoff:3.500A) No H-bonds generated for sheet with id= BE Processing sheet with id= BF, first strand: chain 'l' and resid 118 through 121 Processing sheet with id= BG, first strand: chain 'm' and resid 5 through 8 removed outlier: 3.503A pdb=" N ARG m 15 " --> pdb=" O GLU m 8 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'm' and resid 28 through 32 removed outlier: 6.572A pdb=" N TYR m 60 " --> pdb=" O ILE m 29 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N LEU m 31 " --> pdb=" O TYR m 60 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TYR m 62 " --> pdb=" O LEU m 31 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'm' and resid 118 through 121 Processing sheet with id= BJ, first strand: chain 'n' and resid 5 through 9 Processing sheet with id= BK, first strand: chain 'n' and resid 28 through 32 removed outlier: 6.472A pdb=" N TYR n 60 " --> pdb=" O ILE n 29 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N LEU n 31 " --> pdb=" O TYR n 60 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N TYR n 62 " --> pdb=" O LEU n 31 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'n' and resid 112 through 114 removed outlier: 6.786A pdb=" N SER n 187 " --> pdb=" O CYS n 113 " (cutoff:3.500A) No H-bonds generated for sheet with id= BL Processing sheet with id= BM, first strand: chain 'n' and resid 118 through 121 1550 hydrogen bonds defined for protein. 4278 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: 29.87 Time building geometry restraints manager: 49.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 37527 1.03 - 1.23: 42 1.23 - 1.42: 15084 1.42 - 1.62: 22364 1.62 - 1.81: 362 Bond restraints: 75379 Sorted by residual: bond pdb=" C4 ADP F 600 " pdb=" C5 ADP F 600 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" C4 ADP E 601 " pdb=" C5 ADP E 601 " ideal model delta sigma weight residual 1.490 1.382 0.108 2.00e-02 2.50e+03 2.90e+01 bond pdb=" C5 ADP F 600 " pdb=" C6 ADP F 600 " ideal model delta sigma weight residual 1.490 1.407 0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" C5 ADP E 601 " pdb=" C6 ADP E 601 " ideal model delta sigma weight residual 1.490 1.407 0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" O5' ATP B 501 " pdb=" PA ATP B 501 " ideal model delta sigma weight residual 1.579 1.605 -0.026 1.10e-02 8.26e+03 5.56e+00 ... (remaining 75374 not shown) Histogram of bond angle deviations from ideal: 98.87 - 105.65: 818 105.65 - 112.43: 89375 112.43 - 119.21: 16936 119.21 - 125.98: 29057 125.98 - 132.76: 541 Bond angle restraints: 136727 Sorted by residual: angle pdb=" PB ATP D 501 " pdb=" O3B ATP D 501 " pdb=" PG ATP D 501 " ideal model delta sigma weight residual 139.87 129.03 10.84 1.00e+00 1.00e+00 1.18e+02 angle pdb=" PA ATP B 501 " pdb=" O3A ATP B 501 " pdb=" PB ATP B 501 " ideal model delta sigma weight residual 136.83 126.65 10.18 1.00e+00 1.00e+00 1.04e+02 angle pdb=" PB ATP C 501 " pdb=" O3B ATP C 501 " pdb=" PG ATP C 501 " ideal model delta sigma weight residual 139.87 129.80 10.07 1.00e+00 1.00e+00 1.01e+02 angle pdb=" PB ATP B 501 " pdb=" O3B ATP B 501 " pdb=" PG ATP B 501 " ideal model delta sigma weight residual 139.87 130.22 9.65 1.00e+00 1.00e+00 9.31e+01 angle pdb=" PA ATP C 501 " pdb=" O3A ATP C 501 " pdb=" PB ATP C 501 " ideal model delta sigma weight residual 136.83 127.51 9.32 1.00e+00 1.00e+00 8.68e+01 ... (remaining 136722 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.54: 33420 25.54 - 51.08: 1393 51.08 - 76.61: 285 76.61 - 102.15: 28 102.15 - 127.69: 5 Dihedral angle restraints: 35131 sinusoidal: 19826 harmonic: 15305 Sorted by residual: dihedral pdb=" O1B ADP F 600 " pdb=" O3A ADP F 600 " pdb=" PB ADP F 600 " pdb=" PA ADP F 600 " ideal model delta sinusoidal sigma weight residual 300.00 172.31 127.69 1 2.00e+01 2.50e-03 3.87e+01 dihedral pdb=" O1B ADP E 601 " pdb=" O3A ADP E 601 " pdb=" PB ADP E 601 " pdb=" PA ADP E 601 " ideal model delta sinusoidal sigma weight residual -60.00 64.02 -124.02 1 2.00e+01 2.50e-03 3.74e+01 dihedral pdb=" O2A ADP E 601 " pdb=" O3A ADP E 601 " pdb=" PA ADP E 601 " pdb=" PB ADP E 601 " ideal model delta sinusoidal sigma weight residual -60.00 57.07 -117.07 1 2.00e+01 2.50e-03 3.49e+01 ... (remaining 35128 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 4393 0.043 - 0.086: 1098 0.086 - 0.130: 341 0.130 - 0.173: 39 0.173 - 0.216: 2 Chirality restraints: 5873 Sorted by residual: chirality pdb=" C3' ADP E 601 " pdb=" C2' ADP E 601 " pdb=" C4' ADP E 601 " pdb=" O3' ADP E 601 " both_signs ideal model delta sigma weight residual False -2.51 -2.73 0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA ASP A 392 " pdb=" N ASP A 392 " pdb=" C ASP A 392 " pdb=" CB ASP A 392 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA VAL F 222 " pdb=" N VAL F 222 " pdb=" C VAL F 222 " pdb=" CB VAL F 222 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.40e-01 ... (remaining 5870 not shown) Planarity restraints: 11209 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B 230 " -0.040 5.00e-02 4.00e+02 6.08e-02 5.91e+00 pdb=" N PRO B 231 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO B 231 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 231 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS E 230 " -0.035 5.00e-02 4.00e+02 5.28e-02 4.46e+00 pdb=" N PRO E 231 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO E 231 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO E 231 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN D 195 " -0.034 5.00e-02 4.00e+02 5.07e-02 4.11e+00 pdb=" N PRO D 196 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO D 196 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 196 " -0.029 5.00e-02 4.00e+02 ... (remaining 11206 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 6719 2.23 - 2.83: 171197 2.83 - 3.42: 195525 3.42 - 4.01: 276202 4.01 - 4.60: 428284 Nonbonded interactions: 1077927 Sorted by model distance: nonbonded pdb=" O ALA l 96 " pdb=" H ALA l 100 " model vdw 1.643 1.850 nonbonded pdb=" O ALA L 96 " pdb=" H ALA L 100 " model vdw 1.656 1.850 nonbonded pdb=" O ALA M 96 " pdb=" H ALA M 100 " model vdw 1.657 1.850 nonbonded pdb=" O ALA j 96 " pdb=" H ALA j 100 " model vdw 1.659 1.850 nonbonded pdb=" O ALA J 96 " pdb=" H ALA J 100 " model vdw 1.660 1.850 ... (remaining 1077922 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 64 through 125 or (resid 126 and (name N or name CA or nam \ e C or name O or name CB or name OG1 or name CG2 or name H or name HA or name HB \ or name HG21 or name HG22 or name HG23)) or resid 127 through 191 or (resid 204 \ and (name N or name CA or name C or name O or name HA2 or name HA3)) or resid 2 \ 05 through 413)) selection = (chain 'B' and ((resid 64 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name HA or name HB2 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 65 through 191 or (resid 204 and (name N or name CA or name C or name \ O or name HA2 or name HA3)) or resid 205 through 413)) selection = (chain 'C' and ((resid 64 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name HA or name HB2 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 65 through 191 or (resid 204 and (name N or name CA or name C or name \ O or name HA2 or name HA3)) or resid 205 through 413)) selection = (chain 'D' and ((resid 64 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name HA or name HB2 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 65 through 191 or (resid 204 and (name N or name CA or name C or name \ O or name HA2 or name HA3)) or resid 205 through 413)) selection = (chain 'E' and ((resid 64 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name HA or name HB2 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 65 through 125 or (resid 126 and (name N or name CA or name C or name \ O or name CB or name OG1 or name CG2 or name H or name HA or name HB or name HG2 \ 1 or name HG22 or name HG23)) or resid 127 through 191 or (resid 204 and (name N \ or name CA or name C or name O or name HA2 or name HA3)) or resid 205 through 4 \ 13)) selection = (chain 'F' and ((resid 64 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name HA or name HB2 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 65 through 125 or (resid 126 and (name N or name CA or name C or name \ O or name CB or name OG1 or name CG2 or name H or name HA or name HB or name HG2 \ 1 or name HG22 or name HG23)) or resid 127 through 413)) } ncs_group { reference = (chain 'H' and resid 2 through 191) selection = (chain 'I' and resid 2 through 191) selection = (chain 'J' and resid 2 through 191) selection = (chain 'K' and resid 2 through 191) selection = (chain 'L' and resid 2 through 191) selection = (chain 'M' and resid 2 through 191) selection = (chain 'N' and resid 2 through 191) selection = (chain 'h' and resid 2 through 191) selection = (chain 'i' and resid 2 through 191) selection = (chain 'j' and resid 2 through 191) selection = (chain 'k' and resid 2 through 191) selection = (chain 'l' and resid 2 through 191) selection = (chain 'm' and resid 2 through 191) selection = chain 'n' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.840 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: 0.830 Extract box with map and model: 6.510 Check model and map are aligned: 0.820 Set scattering table: 0.520 Process input model: 188.330 Find NCS groups from input model: 3.370 Set up NCS constraints: 0.230 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:2.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 203.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 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 : 0.004 0.109 37818 Z= 0.261 Angle : 0.655 12.221 51085 Z= 0.365 Chirality : 0.043 0.216 5873 Planarity : 0.004 0.061 6627 Dihedral : 13.072 127.688 14451 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % 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: -0.37 (0.11), residues: 4743 helix: 0.45 (0.10), residues: 2278 sheet: -0.73 (0.16), residues: 779 loop : -0.78 (0.14), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS N 122 PHE 0.016 0.001 PHE L 17 TYR 0.011 0.001 TYR C 153 ARG 0.006 0.000 ARG D 228 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9486 Ramachandran restraints generated. 4743 Oldfield, 0 Emsley, 4743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9486 Ramachandran restraints generated. 4743 Oldfield, 0 Emsley, 4743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Evaluate side-chains 855 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 855 time to evaluate : 4.480 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 GLU cc_start: 0.8584 (tt0) cc_final: 0.8255 (tm-30) REVERT: A 205 GLU cc_start: 0.8204 (pm20) cc_final: 0.7902 (pt0) REVERT: A 237 GLN cc_start: 0.8828 (mp10) cc_final: 0.8616 (mp10) REVERT: A 393 VAL cc_start: 0.7942 (p) cc_final: 0.7219 (p) REVERT: A 404 ASP cc_start: 0.8253 (m-30) cc_final: 0.7464 (m-30) REVERT: C 101 ASN cc_start: 0.7522 (t0) cc_final: 0.7085 (t0) REVERT: C 144 ASP cc_start: 0.7533 (p0) cc_final: 0.7206 (p0) REVERT: C 182 TYR cc_start: 0.8857 (t80) cc_final: 0.8585 (t80) REVERT: D 171 TYR cc_start: 0.8784 (m-80) cc_final: 0.8339 (m-80) REVERT: E 187 ASP cc_start: 0.8170 (p0) cc_final: 0.7920 (p0) REVERT: F 96 TYR cc_start: 0.7684 (m-80) cc_final: 0.7467 (m-80) REVERT: F 160 ASN cc_start: 0.9045 (t0) cc_final: 0.8705 (t0) REVERT: F 185 GLU cc_start: 0.7446 (mp0) cc_final: 0.7034 (mp0) REVERT: F 297 LYS cc_start: 0.9338 (mmmm) cc_final: 0.9137 (mtpt) REVERT: F 323 ILE cc_start: 0.9659 (mt) cc_final: 0.9436 (mm) REVERT: H 70 ILE cc_start: 0.8746 (mp) cc_final: 0.8533 (mm) REVERT: I 18 ASP cc_start: 0.7417 (p0) cc_final: 0.7138 (p0) REVERT: I 34 GLN cc_start: 0.8017 (tp-100) cc_final: 0.7787 (mm-40) REVERT: J 129 GLN cc_start: 0.8328 (mm-40) cc_final: 0.7880 (mm-40) REVERT: K 10 THR cc_start: 0.8857 (p) cc_final: 0.8620 (p) REVERT: K 129 GLN cc_start: 0.8608 (mm-40) cc_final: 0.7628 (mm110) REVERT: K 143 LEU cc_start: 0.9316 (mm) cc_final: 0.8978 (tt) REVERT: L 9 GLN cc_start: 0.7236 (mm-40) cc_final: 0.6975 (mm-40) REVERT: L 125 LEU cc_start: 0.8834 (pp) cc_final: 0.8545 (pp) REVERT: M 26 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7855 (tm-30) REVERT: M 129 GLN cc_start: 0.8591 (mm110) cc_final: 0.7991 (mm110) REVERT: h 86 ASP cc_start: 0.8039 (m-30) cc_final: 0.7659 (m-30) REVERT: h 116 ASN cc_start: 0.9451 (m-40) cc_final: 0.9232 (m110) REVERT: h 163 GLN cc_start: 0.8404 (tp40) cc_final: 0.7909 (tp-100) REVERT: h 182 TYR cc_start: 0.8229 (t80) cc_final: 0.7731 (t80) REVERT: i 34 GLN cc_start: 0.8346 (tp40) cc_final: 0.7720 (tp40) REVERT: i 49 PHE cc_start: 0.7762 (t80) cc_final: 0.7527 (t80) REVERT: i 77 TYR cc_start: 0.8306 (t80) cc_final: 0.8105 (t80) REVERT: i 86 ASP cc_start: 0.7787 (m-30) cc_final: 0.7331 (m-30) REVERT: i 150 ASN cc_start: 0.8850 (m-40) cc_final: 0.8476 (m-40) REVERT: j 77 TYR cc_start: 0.7823 (t80) cc_final: 0.7030 (t80) REVERT: k 58 ASP cc_start: 0.7917 (m-30) cc_final: 0.7694 (m-30) REVERT: l 110 LYS cc_start: 0.9004 (mttt) cc_final: 0.8746 (mttt) REVERT: m 77 TYR cc_start: 0.8774 (t80) cc_final: 0.8511 (t80) REVERT: m 101 PHE cc_start: 0.8143 (t80) cc_final: 0.7553 (t80) REVERT: n 34 GLN cc_start: 0.8232 (pp30) cc_final: 0.7780 (pp30) REVERT: n 86 ASP cc_start: 0.8928 (m-30) cc_final: 0.8662 (m-30) REVERT: n 163 GLN cc_start: 0.8929 (tp40) cc_final: 0.8352 (tp-100) REVERT: n 166 ARG cc_start: 0.8697 (mtm-85) cc_final: 0.8465 (mtm-85) outliers start: 0 outliers final: 0 residues processed: 855 average time/residue: 1.1263 time to fit residues: 1495.5139 Evaluate side-chains 557 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 557 time to evaluate : 4.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 400 optimal weight: 10.0000 chunk 359 optimal weight: 9.9990 chunk 199 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 242 optimal weight: 0.2980 chunk 191 optimal weight: 7.9990 chunk 371 optimal weight: 10.0000 chunk 143 optimal weight: 4.9990 chunk 225 optimal weight: 2.9990 chunk 276 optimal weight: 4.9990 chunk 430 optimal weight: 6.9990 overall best weight: 3.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 ASN E 195 ASN E 406 GLN H 41 ASN ** K 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 94 GLN i 41 ASN j 41 ASN j 150 ASN l 41 ASN m 41 ASN m 191 HIS n 41 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 37818 Z= 0.340 Angle : 0.558 6.016 51085 Z= 0.297 Chirality : 0.042 0.184 5873 Planarity : 0.004 0.051 6627 Dihedral : 7.114 120.999 5309 Min Nonbonded Distance : 1.732 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.82 % Allowed : 6.37 % Favored : 92.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.11), residues: 4743 helix: 1.22 (0.10), residues: 2277 sheet: -0.33 (0.14), residues: 939 loop : -0.88 (0.15), residues: 1527 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS D 73 PHE 0.021 0.002 PHE i 173 TYR 0.017 0.001 TYR j 128 ARG 0.005 0.000 ARG n 172 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9486 Ramachandran restraints generated. 4743 Oldfield, 0 Emsley, 4743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9486 Ramachandran restraints generated. 4743 Oldfield, 0 Emsley, 4743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Evaluate side-chains 568 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 535 time to evaluate : 4.563 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: A 130 GLU cc_start: 0.8608 (tt0) cc_final: 0.8296 (tm-30) REVERT: C 144 ASP cc_start: 0.7981 (p0) cc_final: 0.7594 (p0) REVERT: H 5 MET cc_start: 0.7963 (mmm) cc_final: 0.7652 (mmm) REVERT: H 70 ILE cc_start: 0.8771 (mp) cc_final: 0.8543 (mm) REVERT: I 18 ASP cc_start: 0.7836 (p0) cc_final: 0.7460 (p0) REVERT: J 18 ASP cc_start: 0.7578 (p0) cc_final: 0.7324 (p0) REVERT: J 114 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.8056 (mp) REVERT: J 129 GLN cc_start: 0.8176 (mm-40) cc_final: 0.7893 (mm-40) REVERT: K 17 PHE cc_start: 0.8510 (m-80) cc_final: 0.8291 (m-80) REVERT: K 143 LEU cc_start: 0.9370 (mm) cc_final: 0.9016 (tt) REVERT: L 9 GLN cc_start: 0.7667 (mm-40) cc_final: 0.7219 (mm-40) REVERT: L 125 LEU cc_start: 0.8976 (pp) cc_final: 0.8664 (pp) REVERT: M 8 GLU cc_start: 0.7689 (pt0) cc_final: 0.7025 (pt0) REVERT: M 25 LYS cc_start: 0.9166 (mtpp) cc_final: 0.8943 (ttmt) REVERT: M 26 GLU cc_start: 0.8482 (mm-30) cc_final: 0.7953 (tm-30) REVERT: h 84 LYS cc_start: 0.8308 (mmtt) cc_final: 0.8090 (mmtt) REVERT: h 86 ASP cc_start: 0.8232 (m-30) cc_final: 0.7021 (p0) REVERT: h 163 GLN cc_start: 0.8385 (tp40) cc_final: 0.8092 (tp40) REVERT: i 34 GLN cc_start: 0.8378 (tp40) cc_final: 0.7766 (tp40) REVERT: i 49 PHE cc_start: 0.7919 (t80) cc_final: 0.7615 (t80) REVERT: i 150 ASN cc_start: 0.9065 (m-40) cc_final: 0.8659 (m110) REVERT: j 120 MET cc_start: 0.8826 (ttt) cc_final: 0.8390 (tmm) REVERT: k 25 LYS cc_start: 0.9007 (mtpp) cc_final: 0.8675 (mmmt) REVERT: k 97 SER cc_start: 0.7245 (p) cc_final: 0.6906 (t) REVERT: m 101 PHE cc_start: 0.8342 (t80) cc_final: 0.7863 (t80) REVERT: n 41 ASN cc_start: 0.7785 (t0) cc_final: 0.7566 (t0) REVERT: n 84 LYS cc_start: 0.8871 (mtpt) cc_final: 0.8571 (tppt) REVERT: n 163 GLN cc_start: 0.9030 (tp40) cc_final: 0.8739 (tp-100) outliers start: 33 outliers final: 18 residues processed: 554 average time/residue: 1.0264 time to fit residues: 896.5000 Evaluate side-chains 516 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 497 time to evaluate : 4.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain E residue 277 LYS Chi-restraints excluded: chain F residue 68 HIS Chi-restraints excluded: chain F residue 294 ASP Chi-restraints excluded: chain H residue 17 PHE Chi-restraints excluded: chain I residue 91 CYS Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 181 GLU Chi-restraints excluded: chain h residue 92 MET Chi-restraints excluded: chain h residue 188 ILE Chi-restraints excluded: chain j residue 81 GLN Chi-restraints excluded: chain k residue 23 LEU Chi-restraints excluded: chain k residue 89 THR Chi-restraints excluded: chain k residue 91 CYS Chi-restraints excluded: chain k residue 92 MET Chi-restraints excluded: chain m residue 191 HIS Chi-restraints excluded: chain n residue 91 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 239 optimal weight: 5.9990 chunk 133 optimal weight: 5.9990 chunk 358 optimal weight: 6.9990 chunk 293 optimal weight: 6.9990 chunk 118 optimal weight: 10.0000 chunk 431 optimal weight: 9.9990 chunk 465 optimal weight: 9.9990 chunk 384 optimal weight: 7.9990 chunk 427 optimal weight: 9.9990 chunk 147 optimal weight: 2.9990 chunk 345 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 174 GLN D 230 HIS F 101 ASN H 131 GLN i 41 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 37818 Z= 0.436 Angle : 0.567 8.467 51085 Z= 0.305 Chirality : 0.043 0.316 5873 Planarity : 0.004 0.051 6627 Dihedral : 7.307 129.196 5309 Min Nonbonded Distance : 1.651 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.10 % Allowed : 7.84 % Favored : 91.06 % 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: 0.30 (0.12), residues: 4743 helix: 1.29 (0.11), residues: 2296 sheet: -0.24 (0.15), residues: 929 loop : -1.13 (0.15), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS L 156 PHE 0.018 0.001 PHE h 173 TYR 0.021 0.002 TYR j 128 ARG 0.004 0.000 ARG M 192 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9486 Ramachandran restraints generated. 4743 Oldfield, 0 Emsley, 4743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9486 Ramachandran restraints generated. 4743 Oldfield, 0 Emsley, 4743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Evaluate side-chains 523 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 479 time to evaluate : 4.605 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: A 130 GLU cc_start: 0.8688 (tt0) cc_final: 0.8361 (tm-30) REVERT: A 144 ASP cc_start: 0.7929 (p0) cc_final: 0.7391 (p0) REVERT: A 205 GLU cc_start: 0.8463 (pm20) cc_final: 0.7876 (pt0) REVERT: C 263 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7305 (mp0) REVERT: C 283 GLU cc_start: 0.7978 (tm-30) cc_final: 0.7486 (tm-30) REVERT: F 363 MET cc_start: 0.8877 (mtp) cc_final: 0.8255 (mtp) REVERT: H 70 ILE cc_start: 0.8828 (mp) cc_final: 0.8612 (mm) REVERT: J 129 GLN cc_start: 0.8141 (mm-40) cc_final: 0.7784 (mm-40) REVERT: K 17 PHE cc_start: 0.9042 (m-80) cc_final: 0.8788 (m-80) REVERT: K 18 ASP cc_start: 0.8511 (p0) cc_final: 0.8287 (p0) REVERT: K 129 GLN cc_start: 0.8596 (mm-40) cc_final: 0.8336 (mm-40) REVERT: K 143 LEU cc_start: 0.9415 (mm) cc_final: 0.9020 (tt) REVERT: L 125 LEU cc_start: 0.9142 (pp) cc_final: 0.8860 (pp) REVERT: M 26 GLU cc_start: 0.8585 (mm-30) cc_final: 0.8127 (tm-30) REVERT: M 98 MET cc_start: 0.8950 (tpp) cc_final: 0.8640 (tpp) REVERT: h 86 ASP cc_start: 0.8224 (m-30) cc_final: 0.7148 (p0) REVERT: i 49 PHE cc_start: 0.7876 (t80) cc_final: 0.7544 (t80) REVERT: i 150 ASN cc_start: 0.9001 (m-40) cc_final: 0.8626 (m110) REVERT: j 129 GLN cc_start: 0.8396 (mp10) cc_final: 0.8110 (mp10) REVERT: j 191 HIS cc_start: 0.8573 (m-70) cc_final: 0.8317 (t-170) REVERT: k 25 LYS cc_start: 0.9031 (mtpp) cc_final: 0.8740 (mmmt) REVERT: k 97 SER cc_start: 0.7377 (p) cc_final: 0.7101 (t) REVERT: l 120 MET cc_start: 0.9195 (ttp) cc_final: 0.8811 (tmm) REVERT: m 47 MET cc_start: 0.7804 (mtt) cc_final: 0.7455 (mtp) REVERT: m 101 PHE cc_start: 0.8359 (t80) cc_final: 0.7818 (t80) outliers start: 44 outliers final: 28 residues processed: 508 average time/residue: 1.0198 time to fit residues: 818.5174 Evaluate side-chains 490 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 461 time to evaluate : 4.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain D residue 230 HIS Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain E residue 277 LYS Chi-restraints excluded: chain F residue 68 HIS Chi-restraints excluded: chain F residue 294 ASP Chi-restraints excluded: chain H residue 17 PHE Chi-restraints excluded: chain I residue 91 CYS Chi-restraints excluded: chain I residue 134 ASP Chi-restraints excluded: chain J residue 91 CYS Chi-restraints excluded: chain J residue 181 GLU Chi-restraints excluded: chain K residue 141 GLU Chi-restraints excluded: chain L residue 91 CYS Chi-restraints excluded: chain M residue 91 CYS Chi-restraints excluded: chain N residue 41 ASN Chi-restraints excluded: chain N residue 91 CYS Chi-restraints excluded: chain N residue 143 LEU Chi-restraints excluded: chain h residue 91 CYS Chi-restraints excluded: chain h residue 188 ILE Chi-restraints excluded: chain i residue 92 MET Chi-restraints excluded: chain j residue 81 GLN Chi-restraints excluded: chain k residue 92 MET Chi-restraints excluded: chain m residue 92 MET Chi-restraints excluded: chain n residue 91 CYS Chi-restraints excluded: chain n residue 167 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 426 optimal weight: 3.9990 chunk 324 optimal weight: 1.9990 chunk 223 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 205 optimal weight: 6.9990 chunk 289 optimal weight: 2.9990 chunk 432 optimal weight: 9.9990 chunk 458 optimal weight: 9.9990 chunk 226 optimal weight: 3.9990 chunk 410 optimal weight: 1.9990 chunk 123 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 230 HIS F 114 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 37818 Z= 0.206 Angle : 0.461 6.072 51085 Z= 0.239 Chirality : 0.040 0.145 5873 Planarity : 0.003 0.045 6627 Dihedral : 6.913 122.653 5309 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.62 % Allowed : 8.39 % Favored : 90.99 % 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: 0.67 (0.12), residues: 4743 helix: 1.56 (0.11), residues: 2298 sheet: -0.03 (0.16), residues: 871 loop : -0.90 (0.15), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.021 0.001 HIS D 230 PHE 0.014 0.001 PHE h 173 TYR 0.013 0.001 TYR j 128 ARG 0.003 0.000 ARG B 100 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9486 Ramachandran restraints generated. 4743 Oldfield, 0 Emsley, 4743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9486 Ramachandran restraints generated. 4743 Oldfield, 0 Emsley, 4743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Evaluate side-chains 517 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 492 time to evaluate : 4.639 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: A 94 ASN cc_start: 0.9005 (m-40) cc_final: 0.8654 (m-40) REVERT: A 130 GLU cc_start: 0.8681 (tt0) cc_final: 0.8311 (tm-30) REVERT: A 144 ASP cc_start: 0.7775 (p0) cc_final: 0.7233 (p0) REVERT: A 205 GLU cc_start: 0.8457 (pm20) cc_final: 0.7935 (pt0) REVERT: B 101 ASN cc_start: 0.8116 (t0) cc_final: 0.7882 (t0) REVERT: H 41 ASN cc_start: 0.8356 (m110) cc_final: 0.7951 (m110) REVERT: H 70 ILE cc_start: 0.8795 (mp) cc_final: 0.8587 (mm) REVERT: J 129 GLN cc_start: 0.8160 (mm-40) cc_final: 0.7838 (mm-40) REVERT: K 129 GLN cc_start: 0.8589 (mm-40) cc_final: 0.8340 (mm-40) REVERT: K 143 LEU cc_start: 0.9419 (mm) cc_final: 0.9035 (tt) REVERT: L 125 LEU cc_start: 0.9089 (pp) cc_final: 0.8808 (pp) REVERT: M 25 LYS cc_start: 0.9230 (mtpp) cc_final: 0.8909 (ttmm) REVERT: M 26 GLU cc_start: 0.8561 (mm-30) cc_final: 0.8155 (tm-30) REVERT: N 120 MET cc_start: 0.8534 (tmm) cc_final: 0.8242 (tmm) REVERT: h 84 LYS cc_start: 0.8242 (mmtt) cc_final: 0.7897 (mmtt) REVERT: h 86 ASP cc_start: 0.8165 (m-30) cc_final: 0.7036 (p0) REVERT: h 120 MET cc_start: 0.8293 (ttp) cc_final: 0.7952 (ttm) REVERT: i 49 PHE cc_start: 0.7843 (t80) cc_final: 0.7502 (t80) REVERT: i 150 ASN cc_start: 0.8957 (m-40) cc_final: 0.8396 (m110) REVERT: j 108 LYS cc_start: 0.9193 (tptt) cc_final: 0.8926 (tptp) REVERT: j 129 GLN cc_start: 0.8426 (mp10) cc_final: 0.8203 (mp10) REVERT: j 191 HIS cc_start: 0.8566 (m-70) cc_final: 0.8329 (t-170) REVERT: k 25 LYS cc_start: 0.9034 (mtpp) cc_final: 0.8752 (mmmt) REVERT: k 97 SER cc_start: 0.7353 (p) cc_final: 0.7061 (t) REVERT: k 171 ASP cc_start: 0.8801 (m-30) cc_final: 0.8560 (m-30) REVERT: l 94 GLN cc_start: 0.8679 (pt0) cc_final: 0.8182 (pp30) REVERT: m 47 MET cc_start: 0.7796 (mtt) cc_final: 0.7518 (mtp) REVERT: m 101 PHE cc_start: 0.8285 (t80) cc_final: 0.7761 (t80) outliers start: 25 outliers final: 20 residues processed: 503 average time/residue: 1.0383 time to fit residues: 827.1423 Evaluate side-chains 485 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 465 time to evaluate : 4.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain E residue 277 LYS Chi-restraints excluded: chain F residue 294 ASP Chi-restraints excluded: chain H residue 17 PHE Chi-restraints excluded: chain I residue 134 ASP Chi-restraints excluded: chain J residue 34 GLN Chi-restraints excluded: chain J residue 181 GLU Chi-restraints excluded: chain L residue 53 GLU Chi-restraints excluded: chain N residue 41 ASN Chi-restraints excluded: chain N residue 143 LEU Chi-restraints excluded: chain h residue 91 CYS Chi-restraints excluded: chain h residue 103 LEU Chi-restraints excluded: chain h residue 188 ILE Chi-restraints excluded: chain i residue 70 ILE Chi-restraints excluded: chain i residue 92 MET Chi-restraints excluded: chain j residue 81 GLN Chi-restraints excluded: chain k residue 23 LEU Chi-restraints excluded: chain m residue 92 MET Chi-restraints excluded: chain n residue 91 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 381 optimal weight: 9.9990 chunk 260 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 341 optimal weight: 20.0000 chunk 189 optimal weight: 0.5980 chunk 390 optimal weight: 9.9990 chunk 316 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 233 optimal weight: 3.9990 chunk 411 optimal weight: 6.9990 chunk 115 optimal weight: 5.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 233 GLN E 289 GLN N 150 ASN i 41 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 37818 Z= 0.318 Angle : 0.493 6.027 51085 Z= 0.258 Chirality : 0.041 0.153 5873 Planarity : 0.003 0.045 6627 Dihedral : 6.876 119.893 5309 Min Nonbonded Distance : 1.711 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.82 % Allowed : 8.79 % Favored : 90.39 % 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: 0.63 (0.12), residues: 4743 helix: 1.56 (0.11), residues: 2309 sheet: 0.01 (0.16), residues: 892 loop : -1.03 (0.15), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 73 PHE 0.015 0.001 PHE h 173 TYR 0.016 0.001 TYR A 96 ARG 0.004 0.000 ARG M 15 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9486 Ramachandran restraints generated. 4743 Oldfield, 0 Emsley, 4743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9486 Ramachandran restraints generated. 4743 Oldfield, 0 Emsley, 4743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Evaluate side-chains 508 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 475 time to evaluate : 4.521 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: A 94 ASN cc_start: 0.8997 (m-40) cc_final: 0.8588 (m-40) REVERT: A 130 GLU cc_start: 0.8724 (tt0) cc_final: 0.8350 (tm-30) REVERT: A 144 ASP cc_start: 0.7943 (p0) cc_final: 0.7388 (p0) REVERT: A 205 GLU cc_start: 0.8471 (pm20) cc_final: 0.8018 (pt0) REVERT: B 101 ASN cc_start: 0.8061 (t0) cc_final: 0.7812 (t0) REVERT: C 256 LYS cc_start: 0.8989 (mttp) cc_final: 0.8736 (tptt) REVERT: C 263 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7392 (mp0) REVERT: C 283 GLU cc_start: 0.7929 (tm-30) cc_final: 0.7432 (tm-30) REVERT: F 363 MET cc_start: 0.8711 (mtp) cc_final: 0.8181 (mtp) REVERT: H 70 ILE cc_start: 0.8869 (mp) cc_final: 0.8655 (mm) REVERT: K 129 GLN cc_start: 0.8510 (mm-40) cc_final: 0.8283 (mm-40) REVERT: K 143 LEU cc_start: 0.9442 (mm) cc_final: 0.9029 (tt) REVERT: M 26 GLU cc_start: 0.8585 (mm-30) cc_final: 0.8158 (tm-30) REVERT: M 98 MET cc_start: 0.8990 (tpp) cc_final: 0.8681 (tpp) REVERT: N 120 MET cc_start: 0.8628 (tmm) cc_final: 0.8324 (tmm) REVERT: h 84 LYS cc_start: 0.8271 (mmtt) cc_final: 0.8002 (mmtt) REVERT: i 49 PHE cc_start: 0.7861 (t80) cc_final: 0.7514 (t80) REVERT: i 150 ASN cc_start: 0.8946 (m-40) cc_final: 0.8385 (m110) REVERT: j 25 LYS cc_start: 0.9031 (mmmt) cc_final: 0.8708 (mmtm) REVERT: j 108 LYS cc_start: 0.9206 (tptt) cc_final: 0.8940 (tptp) REVERT: j 129 GLN cc_start: 0.8438 (mp10) cc_final: 0.8194 (mp10) REVERT: j 191 HIS cc_start: 0.8559 (m-70) cc_final: 0.8318 (t-170) REVERT: k 25 LYS cc_start: 0.9056 (mtpp) cc_final: 0.8761 (mmmt) REVERT: k 171 ASP cc_start: 0.8826 (m-30) cc_final: 0.8592 (m-30) REVERT: m 5 MET cc_start: 0.4565 (mmm) cc_final: 0.4106 (mmt) REVERT: m 47 MET cc_start: 0.7837 (mtt) cc_final: 0.7589 (mtp) REVERT: m 101 PHE cc_start: 0.8265 (t80) cc_final: 0.7705 (t80) outliers start: 33 outliers final: 24 residues processed: 498 average time/residue: 1.0178 time to fit residues: 799.4557 Evaluate side-chains 482 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 457 time to evaluate : 4.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain E residue 277 LYS Chi-restraints excluded: chain F residue 211 LEU Chi-restraints excluded: chain F residue 294 ASP Chi-restraints excluded: chain H residue 17 PHE Chi-restraints excluded: chain I residue 91 CYS Chi-restraints excluded: chain I residue 134 ASP Chi-restraints excluded: chain J residue 181 GLU Chi-restraints excluded: chain L residue 53 GLU Chi-restraints excluded: chain N residue 91 CYS Chi-restraints excluded: chain h residue 91 CYS Chi-restraints excluded: chain h residue 103 LEU Chi-restraints excluded: chain h residue 188 ILE Chi-restraints excluded: chain i residue 70 ILE Chi-restraints excluded: chain i residue 92 MET Chi-restraints excluded: chain i residue 190 THR Chi-restraints excluded: chain j residue 81 GLN Chi-restraints excluded: chain k residue 23 LEU Chi-restraints excluded: chain m residue 92 MET Chi-restraints excluded: chain n residue 91 CYS Chi-restraints excluded: chain n residue 167 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 154 optimal weight: 5.9990 chunk 412 optimal weight: 8.9990 chunk 90 optimal weight: 1.9990 chunk 269 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 458 optimal weight: 9.9990 chunk 380 optimal weight: 20.0000 chunk 212 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 151 optimal weight: 3.9990 chunk 240 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 101 ASN i 41 ASN n 41 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 37818 Z= 0.217 Angle : 0.454 5.774 51085 Z= 0.234 Chirality : 0.040 0.158 5873 Planarity : 0.003 0.045 6627 Dihedral : 6.716 110.915 5309 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.80 % Allowed : 9.21 % Favored : 89.99 % 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: 0.81 (0.12), residues: 4743 helix: 1.67 (0.11), residues: 2320 sheet: 0.07 (0.16), residues: 888 loop : -0.87 (0.15), residues: 1535 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 73 PHE 0.017 0.001 PHE K 17 TYR 0.015 0.001 TYR j 128 ARG 0.005 0.000 ARG M 15 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9486 Ramachandran restraints generated. 4743 Oldfield, 0 Emsley, 4743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9486 Ramachandran restraints generated. 4743 Oldfield, 0 Emsley, 4743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Evaluate side-chains 503 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 471 time to evaluate : 4.636 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: A 130 GLU cc_start: 0.8726 (tt0) cc_final: 0.8355 (tm-30) REVERT: A 144 ASP cc_start: 0.7909 (p0) cc_final: 0.7363 (p0) REVERT: A 205 GLU cc_start: 0.8434 (pm20) cc_final: 0.8063 (pt0) REVERT: A 237 GLN cc_start: 0.9053 (mp10) cc_final: 0.8790 (mp10) REVERT: C 263 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7201 (mp0) REVERT: C 283 GLU cc_start: 0.7881 (tm-30) cc_final: 0.7385 (tm-30) REVERT: D 390 MET cc_start: 0.8890 (mtt) cc_final: 0.8654 (mtt) REVERT: F 363 MET cc_start: 0.8721 (mtp) cc_final: 0.8252 (mtp) REVERT: H 41 ASN cc_start: 0.8384 (m110) cc_final: 0.7996 (m110) REVERT: H 70 ILE cc_start: 0.8847 (mp) cc_final: 0.8621 (mm) REVERT: J 129 GLN cc_start: 0.8138 (mm-40) cc_final: 0.7791 (mm-40) REVERT: K 143 LEU cc_start: 0.9445 (mm) cc_final: 0.9030 (tt) REVERT: M 26 GLU cc_start: 0.8573 (mm-30) cc_final: 0.8127 (tm-30) REVERT: h 84 LYS cc_start: 0.8255 (mmtt) cc_final: 0.7987 (mmtt) REVERT: h 153 MET cc_start: 0.9123 (mmm) cc_final: 0.8818 (tpp) REVERT: i 49 PHE cc_start: 0.7855 (t80) cc_final: 0.7503 (t80) REVERT: j 17 PHE cc_start: 0.7021 (m-80) cc_final: 0.6782 (m-80) REVERT: j 41 ASN cc_start: 0.7627 (t0) cc_final: 0.7321 (t0) REVERT: j 108 LYS cc_start: 0.9208 (tptt) cc_final: 0.8948 (tptp) REVERT: j 191 HIS cc_start: 0.8555 (m-70) cc_final: 0.8313 (t-170) REVERT: k 25 LYS cc_start: 0.9058 (mtpp) cc_final: 0.8772 (mmmt) REVERT: k 171 ASP cc_start: 0.8876 (m-30) cc_final: 0.8640 (m-30) REVERT: m 5 MET cc_start: 0.4604 (mmm) cc_final: 0.4215 (mmt) REVERT: m 47 MET cc_start: 0.7908 (mtt) cc_final: 0.7641 (mtp) REVERT: m 101 PHE cc_start: 0.8228 (t80) cc_final: 0.7660 (t80) outliers start: 32 outliers final: 22 residues processed: 490 average time/residue: 1.0184 time to fit residues: 787.2005 Evaluate side-chains 481 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 458 time to evaluate : 4.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain E residue 277 LYS Chi-restraints excluded: chain F residue 294 ASP Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain H residue 17 PHE Chi-restraints excluded: chain I residue 91 CYS Chi-restraints excluded: chain J residue 91 CYS Chi-restraints excluded: chain J residue 181 GLU Chi-restraints excluded: chain L residue 53 GLU Chi-restraints excluded: chain h residue 91 CYS Chi-restraints excluded: chain h residue 103 LEU Chi-restraints excluded: chain h residue 120 MET Chi-restraints excluded: chain h residue 188 ILE Chi-restraints excluded: chain i residue 70 ILE Chi-restraints excluded: chain i residue 92 MET Chi-restraints excluded: chain i residue 190 THR Chi-restraints excluded: chain j residue 81 GLN Chi-restraints excluded: chain j residue 91 CYS Chi-restraints excluded: chain m residue 92 MET Chi-restraints excluded: chain n residue 91 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 442 optimal weight: 9.9990 chunk 51 optimal weight: 8.9990 chunk 261 optimal weight: 6.9990 chunk 334 optimal weight: 2.9990 chunk 259 optimal weight: 7.9990 chunk 386 optimal weight: 10.0000 chunk 256 optimal weight: 2.9990 chunk 456 optimal weight: 20.0000 chunk 285 optimal weight: 4.9990 chunk 278 optimal weight: 5.9990 chunk 210 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN B 101 ASN ** F 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 41 ASN ** n 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 37818 Z= 0.325 Angle : 0.489 6.086 51085 Z= 0.255 Chirality : 0.041 0.142 5873 Planarity : 0.003 0.046 6627 Dihedral : 6.731 105.977 5309 Min Nonbonded Distance : 1.709 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.00 % Allowed : 9.36 % Favored : 89.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.12), residues: 4743 helix: 1.57 (0.11), residues: 2335 sheet: 0.17 (0.16), residues: 881 loop : -0.99 (0.15), residues: 1527 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS j 138 PHE 0.014 0.001 PHE K 17 TYR 0.016 0.001 TYR A 96 ARG 0.005 0.000 ARG M 15 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9486 Ramachandran restraints generated. 4743 Oldfield, 0 Emsley, 4743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9486 Ramachandran restraints generated. 4743 Oldfield, 0 Emsley, 4743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Evaluate side-chains 499 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 459 time to evaluate : 4.636 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: A 130 GLU cc_start: 0.8733 (tt0) cc_final: 0.8368 (tm-30) REVERT: A 144 ASP cc_start: 0.8100 (p0) cc_final: 0.7523 (p0) REVERT: A 205 GLU cc_start: 0.8390 (pm20) cc_final: 0.8163 (pt0) REVERT: A 237 GLN cc_start: 0.9028 (mp10) cc_final: 0.8815 (mp10) REVERT: C 256 LYS cc_start: 0.8957 (mttp) cc_final: 0.8742 (tptt) REVERT: C 263 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7342 (mp0) REVERT: C 283 GLU cc_start: 0.7949 (tm-30) cc_final: 0.7462 (tm-30) REVERT: D 390 MET cc_start: 0.8910 (mtt) cc_final: 0.8685 (mtt) REVERT: F 363 MET cc_start: 0.8724 (mtp) cc_final: 0.8253 (mtp) REVERT: H 70 ILE cc_start: 0.8864 (mp) cc_final: 0.8634 (mm) REVERT: J 129 GLN cc_start: 0.8124 (mm-40) cc_final: 0.7758 (mm-40) REVERT: K 143 LEU cc_start: 0.9466 (mm) cc_final: 0.9032 (tt) REVERT: M 26 GLU cc_start: 0.8555 (mm-30) cc_final: 0.8110 (tm-30) REVERT: M 98 MET cc_start: 0.9039 (tpp) cc_final: 0.8795 (tpp) REVERT: h 84 LYS cc_start: 0.8271 (mmtt) cc_final: 0.8017 (mmtt) REVERT: h 153 MET cc_start: 0.9126 (mmm) cc_final: 0.8819 (tpp) REVERT: i 49 PHE cc_start: 0.7854 (t80) cc_final: 0.7509 (t80) REVERT: j 25 LYS cc_start: 0.8994 (mmmt) cc_final: 0.8660 (mmtm) REVERT: j 108 LYS cc_start: 0.9205 (tptt) cc_final: 0.8956 (tptp) REVERT: j 191 HIS cc_start: 0.8550 (m-70) cc_final: 0.8290 (t-170) REVERT: k 25 LYS cc_start: 0.9078 (mtpp) cc_final: 0.8791 (mmmt) REVERT: k 171 ASP cc_start: 0.8929 (m-30) cc_final: 0.8703 (m-30) REVERT: m 5 MET cc_start: 0.4517 (mmm) cc_final: 0.4130 (mmt) REVERT: m 47 MET cc_start: 0.7897 (mtt) cc_final: 0.7637 (mtp) REVERT: m 101 PHE cc_start: 0.8273 (t80) cc_final: 0.8071 (t80) REVERT: n 74 MET cc_start: 0.6709 (mmp) cc_final: 0.6389 (mmp) outliers start: 40 outliers final: 34 residues processed: 487 average time/residue: 1.0427 time to fit residues: 807.5279 Evaluate side-chains 485 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 450 time to evaluate : 4.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 406 GLN Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain E residue 277 LYS Chi-restraints excluded: chain F residue 294 ASP Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain H residue 17 PHE Chi-restraints excluded: chain I residue 91 CYS Chi-restraints excluded: chain I residue 134 ASP Chi-restraints excluded: chain J residue 91 CYS Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 181 GLU Chi-restraints excluded: chain L residue 53 GLU Chi-restraints excluded: chain N residue 91 CYS Chi-restraints excluded: chain N residue 157 THR Chi-restraints excluded: chain h residue 91 CYS Chi-restraints excluded: chain h residue 120 MET Chi-restraints excluded: chain h residue 188 ILE Chi-restraints excluded: chain i residue 70 ILE Chi-restraints excluded: chain i residue 92 MET Chi-restraints excluded: chain i residue 190 THR Chi-restraints excluded: chain j residue 81 GLN Chi-restraints excluded: chain j residue 91 CYS Chi-restraints excluded: chain k residue 23 LEU Chi-restraints excluded: chain k residue 41 ASN Chi-restraints excluded: chain l residue 16 SER Chi-restraints excluded: chain l residue 17 PHE Chi-restraints excluded: chain m residue 92 MET Chi-restraints excluded: chain n residue 91 CYS Chi-restraints excluded: chain n residue 167 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 282 optimal weight: 0.8980 chunk 182 optimal weight: 4.9990 chunk 272 optimal weight: 3.9990 chunk 137 optimal weight: 5.9990 chunk 89 optimal weight: 0.7980 chunk 88 optimal weight: 3.9990 chunk 290 optimal weight: 1.9990 chunk 311 optimal weight: 3.9990 chunk 225 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 359 optimal weight: 10.0000 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 ASN n 41 ASN ** n 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 37818 Z= 0.252 Angle : 0.585 59.200 51085 Z= 0.324 Chirality : 0.040 0.450 5873 Planarity : 0.003 0.045 6627 Dihedral : 6.736 105.939 5309 Min Nonbonded Distance : 1.719 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.00 % Allowed : 9.51 % Favored : 89.49 % Cbeta Deviations : 0.02 % 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: 0.74 (0.12), residues: 4743 helix: 1.65 (0.11), residues: 2313 sheet: 0.08 (0.16), residues: 892 loop : -1.02 (0.15), residues: 1538 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS j 138 PHE 0.013 0.001 PHE K 17 TYR 0.016 0.001 TYR A 96 ARG 0.020 0.000 ARG m 172 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9486 Ramachandran restraints generated. 4743 Oldfield, 0 Emsley, 4743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9486 Ramachandran restraints generated. 4743 Oldfield, 0 Emsley, 4743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Evaluate side-chains 491 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 451 time to evaluate : 4.690 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: A 130 GLU cc_start: 0.8728 (tt0) cc_final: 0.8362 (tm-30) REVERT: A 144 ASP cc_start: 0.8090 (p0) cc_final: 0.7515 (p0) REVERT: A 205 GLU cc_start: 0.8457 (pm20) cc_final: 0.8153 (pt0) REVERT: A 237 GLN cc_start: 0.9027 (mp10) cc_final: 0.8814 (mp10) REVERT: B 101 ASN cc_start: 0.8259 (OUTLIER) cc_final: 0.7905 (t0) REVERT: C 256 LYS cc_start: 0.8954 (mttp) cc_final: 0.8739 (tptt) REVERT: C 263 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7332 (mp0) REVERT: C 283 GLU cc_start: 0.7937 (tm-30) cc_final: 0.7448 (tm-30) REVERT: D 390 MET cc_start: 0.8907 (mtt) cc_final: 0.8680 (mtt) REVERT: F 363 MET cc_start: 0.8722 (mtp) cc_final: 0.8250 (mtp) REVERT: H 70 ILE cc_start: 0.8855 (mp) cc_final: 0.8625 (mm) REVERT: J 129 GLN cc_start: 0.8116 (mm-40) cc_final: 0.7755 (mm-40) REVERT: K 143 LEU cc_start: 0.9462 (mm) cc_final: 0.9025 (tt) REVERT: M 26 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8104 (tm-30) REVERT: M 98 MET cc_start: 0.9044 (tpp) cc_final: 0.8802 (tpp) REVERT: h 84 LYS cc_start: 0.8259 (mmtt) cc_final: 0.8012 (mmtt) REVERT: h 153 MET cc_start: 0.9126 (mmm) cc_final: 0.8816 (tpp) REVERT: i 49 PHE cc_start: 0.7852 (t80) cc_final: 0.7507 (t80) REVERT: j 108 LYS cc_start: 0.9202 (tptt) cc_final: 0.8951 (tptp) REVERT: j 191 HIS cc_start: 0.8548 (m-70) cc_final: 0.8292 (t-170) REVERT: k 25 LYS cc_start: 0.9077 (mtpp) cc_final: 0.8789 (mmmt) REVERT: k 171 ASP cc_start: 0.8926 (m-30) cc_final: 0.8699 (m-30) REVERT: l 79 THR cc_start: 0.8339 (OUTLIER) cc_final: 0.8100 (t) REVERT: l 120 MET cc_start: 0.9110 (ttp) cc_final: 0.8526 (tmm) REVERT: m 5 MET cc_start: 0.4513 (mmm) cc_final: 0.4138 (mmt) REVERT: m 47 MET cc_start: 0.7895 (mtt) cc_final: 0.7631 (mtp) REVERT: n 74 MET cc_start: 0.6700 (mmp) cc_final: 0.6389 (mmp) outliers start: 40 outliers final: 35 residues processed: 478 average time/residue: 1.0599 time to fit residues: 805.1510 Evaluate side-chains 488 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 450 time to evaluate : 4.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 406 GLN Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain E residue 277 LYS Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain F residue 294 ASP Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain H residue 17 PHE Chi-restraints excluded: chain I residue 91 CYS Chi-restraints excluded: chain I residue 134 ASP Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain J residue 91 CYS Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 181 GLU Chi-restraints excluded: chain L residue 53 GLU Chi-restraints excluded: chain M residue 25 LYS Chi-restraints excluded: chain N residue 91 CYS Chi-restraints excluded: chain N residue 157 THR Chi-restraints excluded: chain h residue 91 CYS Chi-restraints excluded: chain h residue 120 MET Chi-restraints excluded: chain h residue 188 ILE Chi-restraints excluded: chain i residue 70 ILE Chi-restraints excluded: chain i residue 92 MET Chi-restraints excluded: chain i residue 190 THR Chi-restraints excluded: chain j residue 81 GLN Chi-restraints excluded: chain j residue 91 CYS Chi-restraints excluded: chain k residue 23 LEU Chi-restraints excluded: chain k residue 41 ASN Chi-restraints excluded: chain l residue 16 SER Chi-restraints excluded: chain l residue 79 THR Chi-restraints excluded: chain m residue 92 MET Chi-restraints excluded: chain n residue 91 CYS Chi-restraints excluded: chain n residue 167 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 415 optimal weight: 8.9990 chunk 437 optimal weight: 20.0000 chunk 399 optimal weight: 5.9990 chunk 425 optimal weight: 0.7980 chunk 256 optimal weight: 3.9990 chunk 185 optimal weight: 6.9990 chunk 334 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 384 optimal weight: 9.9990 chunk 402 optimal weight: 10.0000 chunk 424 optimal weight: 2.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 ASN ** n 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.139 37818 Z= 0.255 Angle : 0.523 24.397 51085 Z= 0.291 Chirality : 0.041 0.722 5873 Planarity : 0.003 0.105 6627 Dihedral : 6.736 105.939 5309 Min Nonbonded Distance : 1.719 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.92 % Allowed : 9.56 % Favored : 89.52 % Cbeta Deviations : 0.02 % 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: 0.74 (0.12), residues: 4743 helix: 1.65 (0.11), residues: 2313 sheet: 0.08 (0.16), residues: 892 loop : -1.02 (0.15), residues: 1538 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS j 138 PHE 0.013 0.001 PHE K 17 TYR 0.016 0.001 TYR A 96 ARG 0.020 0.000 ARG m 172 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9486 Ramachandran restraints generated. 4743 Oldfield, 0 Emsley, 4743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9486 Ramachandran restraints generated. 4743 Oldfield, 0 Emsley, 4743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Evaluate side-chains 487 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 450 time to evaluate : 4.567 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: A 130 GLU cc_start: 0.8728 (tt0) cc_final: 0.8362 (tm-30) REVERT: A 144 ASP cc_start: 0.8090 (p0) cc_final: 0.7515 (p0) REVERT: A 205 GLU cc_start: 0.8458 (pm20) cc_final: 0.8153 (pt0) REVERT: A 237 GLN cc_start: 0.9027 (mp10) cc_final: 0.8814 (mp10) REVERT: C 256 LYS cc_start: 0.8954 (mttp) cc_final: 0.8739 (tptt) REVERT: C 263 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7332 (mp0) REVERT: C 283 GLU cc_start: 0.7937 (tm-30) cc_final: 0.7448 (tm-30) REVERT: D 390 MET cc_start: 0.8907 (mtt) cc_final: 0.8680 (mtt) REVERT: F 363 MET cc_start: 0.8722 (mtp) cc_final: 0.8250 (mtp) REVERT: H 70 ILE cc_start: 0.8855 (mp) cc_final: 0.8625 (mm) REVERT: J 129 GLN cc_start: 0.8116 (mm-40) cc_final: 0.7755 (mm-40) REVERT: K 143 LEU cc_start: 0.9462 (mm) cc_final: 0.9025 (tt) REVERT: M 26 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8104 (tm-30) REVERT: M 98 MET cc_start: 0.9044 (tpp) cc_final: 0.8802 (tpp) REVERT: h 84 LYS cc_start: 0.8259 (mmtt) cc_final: 0.8012 (mmtt) REVERT: h 153 MET cc_start: 0.9126 (mmm) cc_final: 0.8816 (tpp) REVERT: i 49 PHE cc_start: 0.7852 (t80) cc_final: 0.7507 (t80) REVERT: j 108 LYS cc_start: 0.9202 (tptt) cc_final: 0.8951 (tptp) REVERT: j 191 HIS cc_start: 0.8548 (m-70) cc_final: 0.8292 (t-170) REVERT: k 25 LYS cc_start: 0.9077 (mtpp) cc_final: 0.8789 (mmmt) REVERT: k 171 ASP cc_start: 0.8926 (m-30) cc_final: 0.8699 (m-30) REVERT: l 79 THR cc_start: 0.8339 (OUTLIER) cc_final: 0.8100 (t) REVERT: l 120 MET cc_start: 0.9107 (ttp) cc_final: 0.8526 (tmm) REVERT: m 5 MET cc_start: 0.4526 (mmm) cc_final: 0.4138 (mmt) REVERT: m 47 MET cc_start: 0.7895 (mtt) cc_final: 0.7631 (mtp) REVERT: n 74 MET cc_start: 0.6700 (mmp) cc_final: 0.6389 (mmp) outliers start: 37 outliers final: 35 residues processed: 474 average time/residue: 1.0294 time to fit residues: 771.8845 Evaluate side-chains 487 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 450 time to evaluate : 4.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 406 GLN Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain E residue 277 LYS Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain F residue 294 ASP Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain H residue 17 PHE Chi-restraints excluded: chain I residue 91 CYS Chi-restraints excluded: chain I residue 134 ASP Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain J residue 91 CYS Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 181 GLU Chi-restraints excluded: chain L residue 53 GLU Chi-restraints excluded: chain M residue 25 LYS Chi-restraints excluded: chain N residue 91 CYS Chi-restraints excluded: chain N residue 157 THR Chi-restraints excluded: chain h residue 91 CYS Chi-restraints excluded: chain h residue 120 MET Chi-restraints excluded: chain h residue 188 ILE Chi-restraints excluded: chain i residue 70 ILE Chi-restraints excluded: chain i residue 92 MET Chi-restraints excluded: chain i residue 190 THR Chi-restraints excluded: chain j residue 81 GLN Chi-restraints excluded: chain j residue 91 CYS Chi-restraints excluded: chain k residue 23 LEU Chi-restraints excluded: chain k residue 41 ASN Chi-restraints excluded: chain l residue 16 SER Chi-restraints excluded: chain l residue 79 THR Chi-restraints excluded: chain m residue 92 MET Chi-restraints excluded: chain n residue 91 CYS Chi-restraints excluded: chain n residue 167 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 279 optimal weight: 2.9990 chunk 450 optimal weight: 6.9990 chunk 274 optimal weight: 3.9990 chunk 213 optimal weight: 1.9990 chunk 312 optimal weight: 0.9980 chunk 472 optimal weight: 9.9990 chunk 434 optimal weight: 0.9990 chunk 376 optimal weight: 7.9990 chunk 39 optimal weight: 6.9990 chunk 290 optimal weight: 0.9980 chunk 230 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: i 41 ASN ** n 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.3930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 37818 Z= 0.164 Angle : 0.446 5.837 51085 Z= 0.228 Chirality : 0.040 0.151 5873 Planarity : 0.003 0.045 6627 Dihedral : 6.567 97.712 5309 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.85 % Allowed : 9.66 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.12), residues: 4743 helix: 1.78 (0.11), residues: 2323 sheet: 0.08 (0.17), residues: 856 loop : -0.80 (0.15), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 95 PHE 0.014 0.001 PHE l 49 TYR 0.012 0.001 TYR j 128 ARG 0.008 0.000 ARG B 100 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9486 Ramachandran restraints generated. 4743 Oldfield, 0 Emsley, 4743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9486 Ramachandran restraints generated. 4743 Oldfield, 0 Emsley, 4743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Evaluate side-chains 501 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 467 time to evaluate : 4.569 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: A 130 GLU cc_start: 0.8724 (tt0) cc_final: 0.8357 (tm-30) REVERT: A 144 ASP cc_start: 0.7965 (p0) cc_final: 0.7422 (p0) REVERT: A 156 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.7246 (tt0) REVERT: A 205 GLU cc_start: 0.8433 (pm20) cc_final: 0.8150 (pt0) REVERT: C 256 LYS cc_start: 0.8972 (mttp) cc_final: 0.8757 (tptt) REVERT: C 263 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7188 (mp0) REVERT: C 283 GLU cc_start: 0.7883 (tm-30) cc_final: 0.7399 (tm-30) REVERT: D 390 MET cc_start: 0.8899 (mtt) cc_final: 0.8669 (mtt) REVERT: F 363 MET cc_start: 0.8735 (mtp) cc_final: 0.8247 (mtp) REVERT: H 41 ASN cc_start: 0.8370 (m110) cc_final: 0.7978 (m110) REVERT: H 70 ILE cc_start: 0.8810 (OUTLIER) cc_final: 0.8589 (mm) REVERT: K 143 LEU cc_start: 0.9462 (mm) cc_final: 0.9034 (tt) REVERT: L 9 GLN cc_start: 0.7882 (mm-40) cc_final: 0.7645 (tp40) REVERT: M 26 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8116 (tm-30) REVERT: M 98 MET cc_start: 0.9001 (tpp) cc_final: 0.8741 (tpp) REVERT: h 84 LYS cc_start: 0.8264 (mmtt) cc_final: 0.8015 (mmtt) REVERT: h 153 MET cc_start: 0.9130 (mmm) cc_final: 0.8842 (tpp) REVERT: i 49 PHE cc_start: 0.7834 (t80) cc_final: 0.7490 (t80) REVERT: j 25 LYS cc_start: 0.8979 (mmmt) cc_final: 0.8638 (mmtm) REVERT: j 108 LYS cc_start: 0.9190 (tptt) cc_final: 0.8937 (tptp) REVERT: j 191 HIS cc_start: 0.8551 (m-70) cc_final: 0.8297 (t-170) REVERT: k 25 LYS cc_start: 0.9066 (mtpp) cc_final: 0.8775 (mmmt) REVERT: k 171 ASP cc_start: 0.8956 (m-30) cc_final: 0.8721 (m-30) REVERT: l 79 THR cc_start: 0.8350 (OUTLIER) cc_final: 0.8104 (t) REVERT: l 120 MET cc_start: 0.9057 (ttp) cc_final: 0.8536 (tmm) REVERT: m 47 MET cc_start: 0.7927 (mtt) cc_final: 0.7671 (mtp) REVERT: m 101 PHE cc_start: 0.7945 (t80) cc_final: 0.7595 (t80) REVERT: m 165 GLU cc_start: 0.8991 (mt-10) cc_final: 0.8611 (mt-10) REVERT: n 74 MET cc_start: 0.6691 (mmp) cc_final: 0.6465 (mmp) outliers start: 34 outliers final: 28 residues processed: 486 average time/residue: 1.0341 time to fit residues: 792.0066 Evaluate side-chains 488 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 456 time to evaluate : 4.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain E residue 277 LYS Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain F residue 294 ASP Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain H residue 17 PHE Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain I residue 134 ASP Chi-restraints excluded: chain J residue 91 CYS Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 181 GLU Chi-restraints excluded: chain L residue 53 GLU Chi-restraints excluded: chain M residue 25 LYS Chi-restraints excluded: chain h residue 91 CYS Chi-restraints excluded: chain h residue 120 MET Chi-restraints excluded: chain h residue 188 ILE Chi-restraints excluded: chain i residue 70 ILE Chi-restraints excluded: chain i residue 92 MET Chi-restraints excluded: chain i residue 190 THR Chi-restraints excluded: chain j residue 81 GLN Chi-restraints excluded: chain k residue 23 LEU Chi-restraints excluded: chain k residue 41 ASN Chi-restraints excluded: chain l residue 17 PHE Chi-restraints excluded: chain l residue 79 THR Chi-restraints excluded: chain m residue 92 MET Chi-restraints excluded: chain n residue 91 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 298 optimal weight: 4.9990 chunk 400 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 chunk 346 optimal weight: 0.6980 chunk 55 optimal weight: 5.9990 chunk 104 optimal weight: 0.1980 chunk 376 optimal weight: 6.9990 chunk 157 optimal weight: 2.9990 chunk 386 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 GLN i 41 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.104330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.071941 restraints weight = 261853.909| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 3.17 r_work: 0.2881 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2750 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2750 r_free = 0.2750 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2750 r_free = 0.2750 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2750 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 37818 Z= 0.165 Angle : 0.445 7.775 51085 Z= 0.225 Chirality : 0.039 0.145 5873 Planarity : 0.003 0.045 6627 Dihedral : 6.321 89.195 5309 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.77 % Allowed : 9.94 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.12), residues: 4743 helix: 1.90 (0.11), residues: 2323 sheet: 0.17 (0.17), residues: 856 loop : -0.74 (0.15), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS j 138 PHE 0.014 0.001 PHE l 49 TYR 0.012 0.001 TYR j 128 ARG 0.004 0.000 ARG M 15 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16762.69 seconds wall clock time: 290 minutes 42.96 seconds (17442.96 seconds total)