Starting phenix.real_space_refine on Sat Mar 16 21:03:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e7v_27941/03_2024/8e7v_27941_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e7v_27941/03_2024/8e7v_27941.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e7v_27941/03_2024/8e7v_27941.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e7v_27941/03_2024/8e7v_27941.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e7v_27941/03_2024/8e7v_27941_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e7v_27941/03_2024/8e7v_27941_trim_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.026 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 23451 2.51 5 N 6391 2.21 5 O 7187 1.98 5 H 37552 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 137": "OD1" <-> "OD2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 170": "OD1" <-> "OD2" Residue "A ASP 201": "OD1" <-> "OD2" Residue "A GLU 205": "OE1" <-> "OE2" Residue "A GLU 216": "OE1" <-> "OE2" Residue "A ASP 239": "OD1" <-> "OD2" Residue "A ASP 279": "OD1" <-> "OD2" Residue "A GLU 283": "OE1" <-> "OE2" Residue "A GLU 285": "OE1" <-> "OE2" Residue "A GLU 316": "OE1" <-> "OE2" Residue "A ASP 392": "OD1" <-> "OD2" Residue "B ASP 239": "OD1" <-> "OD2" Residue "B GLU 283": "OE1" <-> "OE2" Residue "B ASP 347": "OD1" <-> "OD2" Residue "B ASP 392": "OD1" <-> "OD2" Residue "B GLU 408": "OE1" <-> "OE2" Residue "C GLU 159": "OE1" <-> "OE2" Residue "C ASP 194": "OD1" <-> "OD2" Residue "C GLU 234": "OE1" <-> "OE2" Residue "C PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 349": "OE1" <-> "OE2" Residue "C ASP 392": "OD1" <-> "OD2" Residue "D GLU 109": "OE1" <-> "OE2" Residue "D ASP 157": "OD1" <-> "OD2" Residue "D ASP 194": "OD1" <-> "OD2" Residue "D ASP 201": "OD1" <-> "OD2" Residue "D GLU 408": "OE1" <-> "OE2" Residue "E ASP 194": "OD1" <-> "OD2" Residue "E ASP 201": "OD1" <-> "OD2" Residue "E PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 279": "OD1" <-> "OD2" Residue "E GLU 283": "OE1" <-> "OE2" Residue "F ASP 75": "OD1" <-> "OD2" Residue "F ARG 100": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ASP 103": "OD1" <-> "OD2" Residue "F GLU 109": "OE1" <-> "OE2" Residue "F ASP 157": "OD1" <-> "OD2" Residue "F GLU 185": "OE1" <-> "OE2" Residue "F PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 285": "OE1" <-> "OE2" Residue "F GLU 293": "OE1" <-> "OE2" Residue "F GLU 320": "OE1" <-> "OE2" Residue "F GLU 391": "OE1" <-> "OE2" Residue "F ASP 392": "OD1" <-> "OD2" Residue "I TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M GLU 14": "OE1" <-> "OE2" Residue "N PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "h GLU 8": "OE1" <-> "OE2" Residue "h PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "h ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "h ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "h TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 GLU 8": "OE1" <-> "OE2" 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 GLU 8": "OE1" <-> "OE2" Residue "k GLU 14": "OE1" <-> "OE2" Residue "k ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "k ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "k GLU 51": "OE1" <-> "OE2" Residue "k ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "k GLU 151": "OE1" <-> "OE2" 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 "l TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "m GLU 14": "OE1" <-> "OE2" 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 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" Residue "n PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 74798 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: 5434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 5434 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 14, 'TRANS': 336} Chain: "D" Number of atoms: 5434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 5434 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 14, 'TRANS': 336} Chain: "E" Number of atoms: 5435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 5435 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 14, 'TRANS': 336} 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: 27.76, per 1000 atoms: 0.37 Number of scatterers: 74798 At special positions: 0 Unit cell: (142.386, 142.386, 196.093, 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 7187 8.00 N 6391 7.00 C 23451 6.00 H 37552 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: 45.93 Conformation dependent library (CDL) restraints added in 6.8 seconds 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 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: 202 helices and 59 sheets defined 45.7% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.92 Creating SS restraints... Processing helix chain 'A' and resid 67 through 77 removed outlier: 3.780A 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: 3.854A pdb=" N ARG A 134 " --> pdb=" O GLU A 130 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU A 135 " --> pdb=" O THR A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 169 Processing helix chain 'A' and resid 173 through 178 removed outlier: 4.003A 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: 3.618A pdb=" N ALA A 210 " --> pdb=" O GLY A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 262 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: 3.749A pdb=" N LYS A 327 " --> pdb=" O ILE A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 344 removed outlier: 3.673A pdb=" N GLU A 344 " --> pdb=" O LEU A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 365 removed outlier: 3.698A pdb=" N ASP A 356 " --> pdb=" O ASP A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 379 Processing helix chain 'A' and resid 381 through 387 Processing helix chain 'A' and resid 400 through 404 Processing helix chain 'B' and resid 67 through 77 removed outlier: 3.613A 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 103 through 105 No H-bonds generated for 'chain 'B' and resid 103 through 105' Processing helix chain 'B' and resid 125 through 135 removed outlier: 3.555A pdb=" N ALA B 129 " --> pdb=" O LYS B 125 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG B 134 " --> pdb=" O GLU B 130 " (cutoff:3.500A) removed outlier: 3.904A 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: 3.539A 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: 4.646A pdb=" N LYS B 213 " --> pdb=" O GLN B 209 " (cutoff:3.500A) removed outlier: 3.902A 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: 3.811A pdb=" N ARG B 261 " --> pdb=" O VAL B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 289 removed outlier: 3.664A pdb=" N GLN B 289 " --> pdb=" O GLU B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 298 removed outlier: 3.682A 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 removed outlier: 3.504A pdb=" N ARG B 365 " --> pdb=" O LYS B 361 " (cutoff:3.500A) 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: 3.921A 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 134 removed outlier: 3.540A pdb=" N ALA C 133 " --> pdb=" O ALA C 129 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG C 134 " --> pdb=" O GLU C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 168 Processing helix chain 'C' and resid 173 through 178 removed outlier: 3.718A 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: 4.630A pdb=" N LYS C 213 " --> pdb=" O GLN C 209 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU C 214 " --> pdb=" O ALA C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 263 Processing helix chain 'C' and resid 283 through 289 removed outlier: 3.816A 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: 3.843A 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 387 removed outlier: 3.574A pdb=" N VAL C 376 " --> pdb=" O ARG C 373 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ASP C 382 " --> pdb=" O ALA C 379 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N MET C 384 " --> pdb=" O LEU C 381 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU C 387 " --> pdb=" O MET C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 404 Processing helix chain 'D' and resid 67 through 77 removed outlier: 4.100A 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: 3.614A pdb=" N ALA D 129 " --> pdb=" O LYS D 125 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG D 134 " --> pdb=" O GLU D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 168 Processing helix chain 'D' and resid 173 through 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: 4.445A pdb=" N LYS D 213 " --> pdb=" O GLN D 209 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU D 214 " --> pdb=" O ALA D 210 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLU D 216 " --> pdb=" O LEU D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 262 Processing helix chain 'D' and resid 283 through 289 removed outlier: 3.718A pdb=" N GLN D 289 " --> pdb=" O GLU D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 298 Processing helix chain 'D' and resid 302 through 307 removed outlier: 3.601A pdb=" N ARG D 307 " --> pdb=" O GLU D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 327 removed outlier: 3.923A pdb=" N LYS D 327 " --> pdb=" O ILE D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 344 removed outlier: 3.520A pdb=" N GLU D 344 " --> pdb=" O LEU D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 365 Processing helix chain 'D' and resid 369 through 379 Processing helix chain 'D' and resid 381 through 387 Processing helix chain 'D' and resid 400 through 404 Processing helix chain 'E' and resid 67 through 77 removed outlier: 3.595A pdb=" N TYR E 77 " --> pdb=" O HIS E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 103 removed outlier: 3.967A pdb=" N GLY E 102 " --> pdb=" O ARG E 98 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N ASP E 103 " --> pdb=" O LEU E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 130 removed outlier: 3.609A pdb=" N ALA E 129 " --> pdb=" O LYS E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 168 removed outlier: 3.704A pdb=" N LYS E 168 " --> pdb=" O LEU E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 178 removed outlier: 4.471A 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: 4.705A pdb=" N LYS E 213 " --> pdb=" O GLN E 209 " (cutoff:3.500A) removed outlier: 3.917A 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: 4.240A pdb=" N GLN E 289 " --> pdb=" O GLU E 285 " (cutoff:3.500A) Processing helix chain 'E' and resid 292 through 298 removed outlier: 3.539A pdb=" N LYS E 297 " --> pdb=" O GLU E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 307 removed outlier: 3.704A pdb=" N ARG E 307 " --> pdb=" O GLU E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 327 removed outlier: 3.656A pdb=" N LYS E 327 " --> pdb=" O ILE E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 344 removed outlier: 3.552A pdb=" N GLU E 344 " --> pdb=" O LEU E 340 " (cutoff:3.500A) Processing helix chain 'E' and resid 352 through 365 Processing helix chain 'E' and resid 370 through 379 removed outlier: 3.534A pdb=" N VAL E 376 " --> pdb=" O ARG E 373 " (cutoff:3.500A) Processing helix chain 'E' and resid 381 through 387 Processing helix chain 'E' and resid 400 through 404 removed outlier: 3.618A 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 Processing helix chain 'F' and resid 82 through 100 Processing helix chain 'F' and resid 125 through 135 removed outlier: 3.593A pdb=" N ALA F 129 " --> pdb=" O LYS F 125 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU F 132 " --> pdb=" O LEU F 128 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA F 133 " --> pdb=" O ALA F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 148 No H-bonds generated for 'chain 'F' and resid 146 through 148' Processing helix chain 'F' and resid 154 through 168 removed outlier: 3.746A pdb=" N ILE F 162 " --> pdb=" O VAL F 158 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS F 168 " --> pdb=" O LYS F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 178 removed outlier: 3.665A pdb=" N ARG F 178 " --> pdb=" O GLN F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 216 removed outlier: 4.186A pdb=" N LYS F 213 " --> pdb=" O GLN F 209 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU F 214 " --> pdb=" O ALA F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 242 No H-bonds generated for 'chain 'F' and resid 240 through 242' Processing helix chain 'F' and resid 253 through 262 Processing helix chain 'F' and resid 281 through 289 removed outlier: 3.993A pdb=" N GLU F 285 " --> pdb=" O ALA F 281 " (cutoff:3.500A) removed outlier: 3.679A 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: 3.712A pdb=" N LYS F 327 " --> pdb=" O ILE F 323 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 344 Processing helix chain 'F' and resid 352 through 365 Processing helix chain 'F' and resid 368 through 387 removed outlier: 3.612A pdb=" N GLY F 371 " --> pdb=" O GLY F 368 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG F 373 " --> pdb=" O ARG F 370 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL F 376 " --> pdb=" O ARG F 373 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ASP F 382 " --> pdb=" O ALA F 379 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR F 383 " --> pdb=" O LEU F 380 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET F 384 " --> pdb=" O LEU F 381 " (cutoff:3.500A) removed outlier: 4.153A 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: 3.654A 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: 3.746A 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: 3.512A pdb=" N VAL H 180 " --> pdb=" O ALA H 176 " (cutoff:3.500A) Processing helix chain 'I' and resid 19 through 26 removed outlier: 3.620A pdb=" N LEU I 23 " --> pdb=" O ILE I 19 " (cutoff:3.500A) removed outlier: 3.720A 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: 3.531A pdb=" N SER I 75 " --> pdb=" O THR I 71 " (cutoff:3.500A) removed outlier: 3.603A 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 169 Processing helix chain 'I' and resid 176 through 182 Processing helix chain 'J' and resid 19 through 26 removed outlier: 3.836A 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: 3.555A 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: 3.688A 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: 3.595A 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: 3.681A pdb=" N GLU L 26 " --> pdb=" O ARG L 22 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 53 removed outlier: 3.559A pdb=" N ALA L 52 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU L 53 " --> pdb=" O PHE L 49 " (cutoff:3.500A) Processing helix chain 'L' and resid 70 through 82 removed outlier: 3.526A 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: 3.836A 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: 3.577A 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: 3.959A 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: 3.594A 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: 4.064A 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 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: 4.200A 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: 3.507A pdb=" N ILE i 76 " --> pdb=" O ALA i 72 " (cutoff:3.500A) Processing helix chain 'i' and resid 97 through 103 Processing helix chain 'i' and resid 132 through 157 Processing helix chain 'i' and resid 161 through 167 Processing helix chain 'i' and resid 176 through 181 Processing helix chain 'j' and resid 19 through 26 removed outlier: 3.875A 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: 3.625A pdb=" N ILE j 76 " --> pdb=" O ALA j 72 " (cutoff:3.500A) Processing helix chain 'j' and resid 97 through 104 Processing helix chain 'j' and resid 132 through 157 Processing helix chain 'j' and resid 161 through 167 Processing helix chain 'j' and resid 176 through 182 Processing helix chain 'k' and resid 19 through 26 removed outlier: 3.523A pdb=" N LYS k 25 " --> pdb=" O SER k 21 " (cutoff:3.500A) removed outlier: 4.082A 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: 3.562A pdb=" N ILE k 76 " --> pdb=" O ALA k 72 " (cutoff:3.500A) Processing helix chain 'k' and resid 97 through 104 Processing helix chain 'k' and resid 132 through 157 removed outlier: 3.502A pdb=" N ILE k 137 " --> pdb=" O THR k 133 " (cutoff:3.500A) 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: 3.894A 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 Processing helix chain 'l' and resid 97 through 104 Processing helix chain 'l' and resid 132 through 157 removed outlier: 3.590A pdb=" N ILE l 137 " --> pdb=" O THR l 133 " (cutoff:3.500A) 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: 3.853A 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: 3.675A pdb=" N ILE m 76 " --> pdb=" O ALA m 72 " (cutoff:3.500A) Processing helix chain 'm' and resid 97 through 103 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: 3.830A 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: 3.563A 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 sheet with id= A, first strand: chain 'A' and resid 116 through 118 removed outlier: 7.807A pdb=" N LEU A 117 " --> pdb=" O PHE A 245 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N CYS A 247 " --> pdb=" O LEU A 117 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 347 through 350 removed outlier: 3.794A pdb=" N LYS A 395 " --> pdb=" O ILE A 412 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 310 through 313 removed outlier: 3.538A pdb=" N ILE B 115 " --> pdb=" O PHE B 245 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR B 141 " --> pdb=" O ILE B 180 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 219 through 222 Processing sheet with id= E, first strand: chain 'B' and resid 348 through 350 removed outlier: 6.557A pdb=" N VAL B 396 " --> pdb=" O GLU B 349 " (cutoff:3.500A) removed outlier: 4.110A 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: 7.164A pdb=" N CYS C 247 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N GLY C 119 " --> pdb=" O CYS C 247 " (cutoff:3.500A) removed outlier: 6.460A 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: 6.639A pdb=" N ILE C 180 " --> pdb=" O THR C 141 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N ALA C 143 " --> pdb=" O ILE C 180 " (cutoff:3.500A) removed outlier: 6.280A 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 Processing sheet with id= I, first strand: chain 'D' and resid 310 through 314 removed outlier: 3.682A pdb=" N GLY D 119 " --> pdb=" O GLY D 249 " (cutoff:3.500A) removed outlier: 3.561A 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 Processing sheet with id= L, first strand: chain 'E' and resid 310 through 314 removed outlier: 3.543A pdb=" N ILE E 115 " --> pdb=" O PHE E 245 " (cutoff:3.500A) removed outlier: 3.636A 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: 3.517A pdb=" N ILE E 398 " --> pdb=" O GLU E 349 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'F' and resid 115 through 118 removed outlier: 7.042A pdb=" N VAL F 310 " --> pdb=" O LEU F 116 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N ILE F 118 " --> pdb=" O VAL F 310 " (cutoff:3.500A) removed outlier: 6.638A 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: 6.640A pdb=" N ILE F 180 " --> pdb=" O THR F 141 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N ALA F 143 " --> pdb=" O ILE F 180 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N TYR F 182 " --> pdb=" O ALA F 143 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LEU F 244 " --> pdb=" O VAL F 181 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ILE F 183 " --> pdb=" O LEU F 244 " (cutoff:3.500A) removed outlier: 6.368A 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 10 removed outlier: 3.723A pdb=" N THR H 10 " --> pdb=" O GLY H 13 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'H' and resid 28 through 32 removed outlier: 6.493A pdb=" N TYR H 60 " --> pdb=" O ILE H 29 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N LEU H 31 " --> pdb=" O TYR H 60 " (cutoff:3.500A) removed outlier: 6.123A 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: 6.445A pdb=" N TYR I 60 " --> pdb=" O ILE I 29 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N LEU I 31 " --> pdb=" O TYR I 60 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N TYR I 62 " --> pdb=" O LEU I 31 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'I' and resid 119 through 121 Processing sheet with id= Y, first strand: chain 'J' and resid 5 through 8 Processing sheet with id= Z, first strand: chain 'J' and resid 28 through 32 removed outlier: 6.498A pdb=" N TYR J 60 " --> pdb=" O ILE J 29 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N LEU J 31 " --> pdb=" O TYR J 60 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N TYR J 62 " --> pdb=" O LEU J 31 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'J' and resid 118 through 121 Processing sheet with id= AB, first strand: chain 'K' and resid 5 through 9 Processing sheet with id= AC, first strand: chain 'K' and resid 28 through 32 removed outlier: 6.552A pdb=" N TYR K 60 " --> pdb=" O ILE K 29 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N LEU K 31 " --> pdb=" O TYR K 60 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N TYR K 62 " --> pdb=" O LEU K 31 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'K' and resid 118 through 121 Processing sheet with id= AE, first strand: chain 'L' and resid 5 through 8 Processing sheet with id= AF, first strand: chain 'L' and resid 28 through 32 removed outlier: 6.541A pdb=" N TYR L 60 " --> pdb=" O ILE L 29 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N LEU L 31 " --> pdb=" O TYR L 60 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N TYR L 62 " --> pdb=" O LEU L 31 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'L' and resid 118 through 121 Processing sheet with id= AH, first strand: chain 'M' and resid 6 through 8 Processing sheet with id= AI, first strand: chain 'M' and resid 28 through 32 removed outlier: 6.368A pdb=" N TYR M 60 " --> pdb=" O ILE M 29 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N LEU M 31 " --> pdb=" O TYR M 60 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N TYR M 62 " --> pdb=" O LEU M 31 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'M' and resid 119 through 121 Processing sheet with id= AK, first strand: chain 'N' and resid 5 through 9 Processing sheet with id= AL, first strand: chain 'N' and resid 28 through 32 removed outlier: 6.585A pdb=" N TYR N 60 " --> pdb=" O ILE N 29 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N LEU N 31 " --> pdb=" O TYR N 60 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N TYR N 62 " --> pdb=" O LEU N 31 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'N' and resid 118 through 121 removed outlier: 3.540A pdb=" N ILE N 121 " --> pdb=" O ARG N 172 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'h' and resid 5 through 9 Processing sheet with id= AO, first strand: chain 'h' and resid 28 through 32 removed outlier: 6.490A pdb=" N TYR h 60 " --> pdb=" O ILE h 29 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N LEU h 31 " --> pdb=" O TYR h 60 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N TYR h 62 " --> pdb=" O LEU h 31 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N SER h 187 " --> pdb=" O CYS h 113 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'h' and resid 119 through 121 Processing sheet with id= AQ, first strand: chain 'i' and resid 28 through 32 removed outlier: 6.561A pdb=" N TYR i 60 " --> pdb=" O ILE i 29 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N LEU i 31 " --> pdb=" O TYR i 60 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N TYR i 62 " --> pdb=" O LEU i 31 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'i' and resid 119 through 121 Processing sheet with id= AS, first strand: chain 'j' and resid 28 through 32 removed outlier: 6.424A pdb=" N TYR j 60 " --> pdb=" O ILE j 29 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N LEU j 31 " --> pdb=" O TYR j 60 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N TYR j 62 " --> pdb=" O LEU j 31 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N CYS j 91 " --> pdb=" O PHE j 112 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU j 114 " --> pdb=" O CYS j 91 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N SER j 187 " --> pdb=" O CYS j 113 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'j' and resid 119 through 121 Processing sheet with id= AU, first strand: chain 'k' and resid 5 through 7 Processing sheet with id= AV, first strand: chain 'k' and resid 28 through 32 removed outlier: 6.481A pdb=" N TYR k 60 " --> pdb=" O ILE k 29 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N LEU k 31 " --> pdb=" O TYR k 60 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N TYR k 62 " --> pdb=" O LEU k 31 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER k 187 " --> pdb=" O CYS k 113 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'k' and resid 119 through 121 Processing sheet with id= AX, first strand: chain 'l' and resid 5 through 7 Processing sheet with id= AY, first strand: chain 'l' and resid 28 through 32 removed outlier: 6.558A pdb=" N TYR l 60 " --> pdb=" O ILE l 29 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N LEU l 31 " --> pdb=" O TYR l 60 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N TYR l 62 " --> pdb=" O LEU l 31 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'l' and resid 112 through 114 removed outlier: 6.704A pdb=" N SER l 187 " --> pdb=" O CYS l 113 " (cutoff:3.500A) No H-bonds generated for sheet with id= AZ Processing sheet with id= BA, first strand: chain 'l' and resid 118 through 121 Processing sheet with id= BB, first strand: chain 'm' and resid 5 through 9 Processing sheet with id= BC, first strand: chain 'm' and resid 28 through 32 removed outlier: 6.566A pdb=" N TYR m 60 " --> pdb=" O ILE m 29 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N LEU m 31 " --> pdb=" O TYR m 60 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N TYR m 62 " --> pdb=" O LEU m 31 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'm' and resid 119 through 121 Processing sheet with id= BE, first strand: chain 'n' and resid 6 through 8 Processing sheet with id= BF, first strand: chain 'n' and resid 28 through 32 removed outlier: 6.455A pdb=" N TYR n 60 " --> pdb=" O ILE n 29 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N LEU n 31 " --> pdb=" O TYR n 60 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N TYR n 62 " --> pdb=" O LEU n 31 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'n' and resid 118 through 121 1563 hydrogen bonds defined for protein. 4248 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: 25.05 Time building geometry restraints manager: 48.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 37518 1.03 - 1.23: 38 1.23 - 1.42: 15052 1.42 - 1.62: 22388 1.62 - 1.81: 362 Bond restraints: 75358 Sorted by residual: bond pdb=" C4 ATP B 501 " pdb=" C5 ATP B 501 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.36e+01 bond pdb=" C4 ATP D 501 " pdb=" C5 ATP D 501 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.19e+01 bond pdb=" C4 ATP A 501 " pdb=" C5 ATP A 501 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.08e+01 bond pdb=" C4 ATP C 501 " pdb=" C5 ATP C 501 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.02e+01 bond pdb=" C5 ATP B 501 " pdb=" C6 ATP B 501 " ideal model delta sigma weight residual 1.409 1.479 -0.070 1.00e-02 1.00e+04 4.88e+01 ... (remaining 75353 not shown) Histogram of bond angle deviations from ideal: 98.87 - 106.36: 1177 106.36 - 113.84: 92986 113.84 - 121.32: 28106 121.32 - 128.80: 14170 128.80 - 136.28: 252 Bond angle restraints: 136691 Sorted by residual: angle pdb=" PB ATP A 501 " pdb=" O3B ATP A 501 " pdb=" PG ATP A 501 " ideal model delta sigma weight residual 139.87 119.58 20.29 1.00e+00 1.00e+00 4.12e+02 angle pdb=" PB ATP C 501 " pdb=" O3B ATP C 501 " pdb=" PG ATP C 501 " ideal model delta sigma weight residual 139.87 119.63 20.24 1.00e+00 1.00e+00 4.10e+02 angle pdb=" PB ATP D 501 " pdb=" O3B ATP D 501 " pdb=" PG ATP D 501 " ideal model delta sigma weight residual 139.87 120.85 19.02 1.00e+00 1.00e+00 3.62e+02 angle pdb=" PB ATP B 501 " pdb=" O3B ATP B 501 " pdb=" PG ATP B 501 " ideal model delta sigma weight residual 139.87 121.02 18.85 1.00e+00 1.00e+00 3.55e+02 angle pdb=" PA ATP A 501 " pdb=" O3A ATP A 501 " pdb=" PB ATP A 501 " ideal model delta sigma weight residual 136.83 119.22 17.61 1.00e+00 1.00e+00 3.10e+02 ... (remaining 136686 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.17: 33165 25.17 - 50.33: 1583 50.33 - 75.50: 338 75.50 - 100.67: 34 100.67 - 125.83: 2 Dihedral angle restraints: 35122 sinusoidal: 19820 harmonic: 15302 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 -60.00 65.83 -125.83 1 2.00e+01 2.50e-03 3.81e+01 dihedral pdb=" O2A ADP F 600 " pdb=" O3A ADP F 600 " pdb=" PA ADP F 600 " pdb=" PB ADP F 600 " ideal model delta sinusoidal sigma weight residual -60.00 49.88 -109.88 1 2.00e+01 2.50e-03 3.22e+01 dihedral pdb=" CA ASP C 347 " pdb=" CB ASP C 347 " pdb=" CG ASP C 347 " pdb=" OD1 ASP C 347 " ideal model delta sinusoidal sigma weight residual -30.00 -88.91 58.91 1 2.00e+01 2.50e-03 1.16e+01 ... (remaining 35119 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 4256 0.042 - 0.084: 1195 0.084 - 0.126: 348 0.126 - 0.168: 73 0.168 - 0.210: 1 Chirality restraints: 5873 Sorted by residual: chirality pdb=" CA GLN A 232 " pdb=" N GLN A 232 " pdb=" C GLN A 232 " pdb=" CB GLN A 232 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA ILE B 301 " pdb=" N ILE B 301 " pdb=" C ILE B 301 " pdb=" CB ILE B 301 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.59e-01 chirality pdb=" CA PRO n 115 " pdb=" N PRO n 115 " pdb=" C PRO n 115 " pdb=" CB PRO n 115 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.47e-01 ... (remaining 5870 not shown) Planarity restraints: 11203 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN D 195 " -0.052 5.00e-02 4.00e+02 7.81e-02 9.75e+00 pdb=" N PRO D 196 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO D 196 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO D 196 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS E 230 " -0.037 5.00e-02 4.00e+02 5.66e-02 5.12e+00 pdb=" N PRO E 231 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO E 231 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO E 231 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 231 " 0.011 2.00e-02 2.50e+03 2.21e-02 4.87e+00 pdb=" C PRO A 231 " -0.038 2.00e-02 2.50e+03 pdb=" O PRO A 231 " 0.014 2.00e-02 2.50e+03 pdb=" N GLN A 232 " 0.013 2.00e-02 2.50e+03 ... (remaining 11200 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.22: 5816 2.22 - 2.82: 167675 2.82 - 3.41: 198910 3.41 - 4.01: 276310 4.01 - 4.60: 431305 Nonbonded interactions: 1080016 Sorted by model distance: nonbonded pdb=" O ALA j 96 " pdb=" H ALA j 100 " model vdw 1.629 1.850 nonbonded pdb=" O ALA l 96 " pdb=" H ALA l 100 " model vdw 1.631 1.850 nonbonded pdb=" O ALA i 96 " pdb=" H ALA i 100 " model vdw 1.632 1.850 nonbonded pdb=" O ALA M 96 " pdb=" H ALA M 100 " model vdw 1.637 1.850 nonbonded pdb=" O ALA h 96 " pdb=" H ALA h 100 " model vdw 1.637 1.850 ... (remaining 1080011 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: 1.000 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: 0.850 Extract box with map and model: 8.530 Check model and map are aligned: 0.880 Set scattering table: 0.530 Process input model: 187.270 Find NCS groups from input model: 3.210 Set up NCS constraints: 0.180 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:2.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 204.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 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 : 0.005 0.080 37806 Z= 0.330 Angle : 0.737 20.290 51070 Z= 0.461 Chirality : 0.044 0.210 5873 Planarity : 0.004 0.078 6624 Dihedral : 13.568 125.834 14448 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % 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: -0.52 (0.11), residues: 4740 helix: 0.38 (0.10), residues: 2274 sheet: -0.78 (0.17), residues: 631 loop : -0.96 (0.13), residues: 1835 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS J 122 PHE 0.026 0.001 PHE I 17 TYR 0.017 0.001 TYR l 182 ARG 0.012 0.000 ARG k 118 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 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 772 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 772 time to evaluate : 5.341 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: A 93 TYR cc_start: 0.8807 (t80) cc_final: 0.8438 (t80) REVERT: A 247 CYS cc_start: 0.8329 (m) cc_final: 0.7799 (m) REVERT: B 82 GLU cc_start: 0.8336 (pm20) cc_final: 0.8066 (pp20) REVERT: B 94 ASN cc_start: 0.8843 (m-40) cc_final: 0.8619 (m110) REVERT: B 142 MET cc_start: 0.7909 (mtp) cc_final: 0.7477 (mtt) REVERT: B 195 ASN cc_start: 0.7838 (m110) cc_final: 0.7635 (m-40) REVERT: D 170 ASP cc_start: 0.8639 (t70) cc_final: 0.8256 (t0) REVERT: D 236 LEU cc_start: 0.8396 (mt) cc_final: 0.8174 (mt) REVERT: E 153 TYR cc_start: 0.7540 (m-80) cc_final: 0.7219 (m-80) REVERT: E 154 VAL cc_start: 0.7201 (p) cc_final: 0.6347 (p) REVERT: E 247 CYS cc_start: 0.9151 (m) cc_final: 0.8847 (m) REVERT: E 283 GLU cc_start: 0.7825 (tt0) cc_final: 0.7569 (mp0) REVERT: E 384 MET cc_start: 0.7107 (mtm) cc_final: 0.6901 (mtp) REVERT: F 159 GLU cc_start: 0.7370 (pp20) cc_final: 0.7050 (pp20) REVERT: F 160 ASN cc_start: 0.8879 (t0) cc_final: 0.8599 (t0) REVERT: F 266 SER cc_start: 0.7816 (p) cc_final: 0.7446 (t) REVERT: I 10 THR cc_start: 0.8577 (p) cc_final: 0.8055 (t) REVERT: M 34 GLN cc_start: 0.8149 (tp40) cc_final: 0.7935 (mm-40) REVERT: N 18 ASP cc_start: 0.7504 (p0) cc_final: 0.7231 (p0) REVERT: N 60 TYR cc_start: 0.8915 (m-80) cc_final: 0.8662 (m-80) REVERT: h 57 LYS cc_start: 0.8935 (mtpp) cc_final: 0.8630 (mtpp) REVERT: n 78 ASP cc_start: 0.8271 (m-30) cc_final: 0.7911 (m-30) outliers start: 0 outliers final: 0 residues processed: 772 average time/residue: 1.0836 time to fit residues: 1304.9762 Evaluate side-chains 467 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 467 time to evaluate : 4.618 ------------------------------------------------------------------------------- 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: 2.9990 chunk 359 optimal weight: 3.9990 chunk 199 optimal weight: 10.0000 chunk 122 optimal weight: 9.9990 chunk 242 optimal weight: 2.9990 chunk 191 optimal weight: 9.9990 chunk 371 optimal weight: 0.6980 chunk 143 optimal weight: 9.9990 chunk 225 optimal weight: 2.9990 chunk 276 optimal weight: 2.9990 chunk 430 optimal weight: 1.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 ASN B 160 ASN B 324 GLN C 342 ASN D 73 HIS E 160 ASN E 233 GLN E 260 HIS E 406 GLN H 41 ASN ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 41 ASN N 41 ASN i 41 ASN i 123 GLN j 41 ASN k 41 ASN l 129 GLN m 41 ASN n 41 ASN n 191 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 37806 Z= 0.304 Angle : 0.545 6.363 51070 Z= 0.291 Chirality : 0.042 0.154 5873 Planarity : 0.004 0.054 6624 Dihedral : 6.589 115.616 5306 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.85 % Allowed : 5.90 % Favored : 93.25 % 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: 0.23 (0.11), residues: 4740 helix: 1.09 (0.10), residues: 2328 sheet: -0.43 (0.18), residues: 654 loop : -0.79 (0.14), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 73 PHE 0.015 0.001 PHE m 17 TYR 0.018 0.001 TYR C 93 ARG 0.007 0.000 ARG E 100 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 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: 34 poor density : 457 time to evaluate : 5.316 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: A 93 TYR cc_start: 0.8854 (t80) cc_final: 0.8504 (t80) REVERT: A 247 CYS cc_start: 0.8516 (m) cc_final: 0.8071 (m) REVERT: B 94 ASN cc_start: 0.8936 (m-40) cc_final: 0.8684 (m-40) REVERT: B 195 ASN cc_start: 0.7650 (m110) cc_final: 0.7432 (m110) REVERT: B 235 PHE cc_start: 0.7646 (m-80) cc_final: 0.7378 (m-10) REVERT: C 342 ASN cc_start: 0.8564 (m-40) cc_final: 0.8271 (m110) REVERT: D 170 ASP cc_start: 0.8743 (t70) cc_final: 0.8292 (t0) REVERT: E 153 TYR cc_start: 0.7711 (m-80) cc_final: 0.7267 (m-80) REVERT: E 154 VAL cc_start: 0.8124 (p) cc_final: 0.7907 (p) REVERT: E 247 CYS cc_start: 0.8961 (m) cc_final: 0.8636 (m) REVERT: E 283 GLU cc_start: 0.7870 (tt0) cc_final: 0.7514 (mp0) REVERT: F 160 ASN cc_start: 0.8728 (t0) cc_final: 0.8164 (t0) REVERT: F 266 SER cc_start: 0.7972 (p) cc_final: 0.7556 (t) REVERT: K 78 ASP cc_start: 0.8140 (m-30) cc_final: 0.7823 (m-30) REVERT: M 78 ASP cc_start: 0.8346 (m-30) cc_final: 0.8063 (m-30) REVERT: M 144 LYS cc_start: 0.8966 (mttt) cc_final: 0.8751 (mtpt) REVERT: N 18 ASP cc_start: 0.7904 (p0) cc_final: 0.7658 (p0) REVERT: N 47 MET cc_start: 0.8798 (mtt) cc_final: 0.8245 (mtt) REVERT: k 84 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8382 (ttpp) REVERT: l 5 MET cc_start: 0.4834 (mmm) cc_final: 0.4469 (mmt) REVERT: l 149 MET cc_start: 0.7927 (mmm) cc_final: 0.7357 (mmt) outliers start: 34 outliers final: 23 residues processed: 477 average time/residue: 0.9918 time to fit residues: 767.7480 Evaluate side-chains 430 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 406 time to evaluate : 4.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain I residue 171 ASP Chi-restraints excluded: chain J residue 18 ASP Chi-restraints excluded: chain J residue 36 GLU Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain K residue 92 MET Chi-restraints excluded: chain M residue 113 CYS Chi-restraints excluded: chain h residue 21 SER Chi-restraints excluded: chain h residue 168 THR Chi-restraints excluded: chain i residue 168 THR Chi-restraints excluded: chain j residue 113 CYS Chi-restraints excluded: chain k residue 41 ASN Chi-restraints excluded: chain k residue 84 LYS Chi-restraints excluded: chain k residue 168 THR Chi-restraints excluded: chain k residue 171 ASP Chi-restraints excluded: chain m residue 18 ASP Chi-restraints excluded: chain n residue 42 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 239 optimal weight: 1.9990 chunk 133 optimal weight: 20.0000 chunk 358 optimal weight: 1.9990 chunk 293 optimal weight: 3.9990 chunk 118 optimal weight: 9.9990 chunk 431 optimal weight: 1.9990 chunk 465 optimal weight: 2.9990 chunk 384 optimal weight: 0.4980 chunk 427 optimal weight: 0.9980 chunk 147 optimal weight: 6.9990 chunk 345 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 114 ASN E 260 HIS F 94 ASN ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 41 ASN j 123 GLN k 41 ASN l 41 ASN l 159 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 37806 Z= 0.206 Angle : 0.458 6.266 51070 Z= 0.238 Chirality : 0.040 0.150 5873 Planarity : 0.003 0.049 6624 Dihedral : 6.591 107.237 5306 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.62 % Allowed : 7.02 % Favored : 92.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.12), residues: 4740 helix: 1.44 (0.11), residues: 2333 sheet: -0.20 (0.18), residues: 647 loop : -0.60 (0.14), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A 260 PHE 0.015 0.001 PHE m 17 TYR 0.009 0.001 TYR F 153 ARG 0.005 0.000 ARG m 15 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 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 438 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 413 time to evaluate : 4.727 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: A 93 TYR cc_start: 0.8845 (t80) cc_final: 0.8481 (t80) REVERT: A 247 CYS cc_start: 0.8640 (m) cc_final: 0.8157 (m) REVERT: B 93 TYR cc_start: 0.8467 (t80) cc_final: 0.8250 (t80) REVERT: B 94 ASN cc_start: 0.8894 (m-40) cc_final: 0.8596 (m-40) REVERT: B 195 ASN cc_start: 0.7498 (m110) cc_final: 0.7220 (m110) REVERT: C 182 TYR cc_start: 0.8436 (t80) cc_final: 0.8027 (t80) REVERT: C 342 ASN cc_start: 0.8548 (m-40) cc_final: 0.8258 (m-40) REVERT: D 170 ASP cc_start: 0.8759 (t70) cc_final: 0.8294 (t0) REVERT: E 153 TYR cc_start: 0.7702 (m-80) cc_final: 0.7182 (m-80) REVERT: E 247 CYS cc_start: 0.9010 (m) cc_final: 0.8720 (m) REVERT: E 283 GLU cc_start: 0.7739 (tt0) cc_final: 0.7451 (mp0) REVERT: F 160 ASN cc_start: 0.8710 (t0) cc_final: 0.8104 (t0) REVERT: F 266 SER cc_start: 0.7962 (p) cc_final: 0.7564 (t) REVERT: K 78 ASP cc_start: 0.8124 (m-30) cc_final: 0.7772 (m-30) REVERT: M 78 ASP cc_start: 0.8279 (m-30) cc_final: 0.7944 (m-30) REVERT: M 144 LYS cc_start: 0.8978 (mttt) cc_final: 0.8766 (mtpt) REVERT: N 47 MET cc_start: 0.8844 (mtt) cc_final: 0.8387 (mtt) REVERT: h 74 MET cc_start: 0.8433 (mmm) cc_final: 0.8055 (mmm) REVERT: i 128 TYR cc_start: 0.8479 (t80) cc_final: 0.8168 (t80) REVERT: k 84 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8368 (ttpp) REVERT: l 5 MET cc_start: 0.4490 (mmm) cc_final: 0.4175 (mmt) REVERT: l 149 MET cc_start: 0.7985 (mmm) cc_final: 0.7474 (mmt) REVERT: n 78 ASP cc_start: 0.8409 (m-30) cc_final: 0.8181 (m-30) outliers start: 25 outliers final: 17 residues processed: 427 average time/residue: 0.9936 time to fit residues: 696.5169 Evaluate side-chains 414 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 396 time to evaluate : 4.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain F residue 68 HIS Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain J residue 16 SER Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain M residue 113 CYS Chi-restraints excluded: chain h residue 168 THR Chi-restraints excluded: chain i residue 168 THR Chi-restraints excluded: chain k residue 84 LYS Chi-restraints excluded: chain k residue 113 CYS Chi-restraints excluded: chain k residue 171 ASP Chi-restraints excluded: chain m residue 18 ASP Chi-restraints excluded: chain n residue 42 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 426 optimal weight: 0.9990 chunk 324 optimal weight: 2.9990 chunk 223 optimal weight: 1.9990 chunk 47 optimal weight: 10.0000 chunk 205 optimal weight: 7.9990 chunk 289 optimal weight: 3.9990 chunk 432 optimal weight: 2.9990 chunk 458 optimal weight: 2.9990 chunk 226 optimal weight: 0.8980 chunk 410 optimal weight: 2.9990 chunk 123 optimal weight: 6.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 230 HIS C 406 GLN D 225 GLN ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 123 GLN i 41 ASN ** k 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 41 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 37806 Z= 0.256 Angle : 0.472 7.449 51070 Z= 0.245 Chirality : 0.040 0.145 5873 Planarity : 0.003 0.040 6624 Dihedral : 6.527 103.298 5306 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.92 % Allowed : 7.74 % Favored : 91.33 % 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: 0.88 (0.12), residues: 4740 helix: 1.63 (0.11), residues: 2324 sheet: 0.04 (0.18), residues: 633 loop : -0.56 (0.14), residues: 1783 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 260 PHE 0.017 0.001 PHE j 17 TYR 0.013 0.001 TYR F 153 ARG 0.003 0.000 ARG L 15 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 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 430 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 393 time to evaluate : 4.779 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: A 93 TYR cc_start: 0.8844 (t80) cc_final: 0.8516 (t80) REVERT: A 247 CYS cc_start: 0.8624 (m) cc_final: 0.8123 (m) REVERT: A 390 MET cc_start: 0.8686 (mtp) cc_final: 0.8244 (mtp) REVERT: B 94 ASN cc_start: 0.8869 (m-40) cc_final: 0.8473 (m110) REVERT: B 195 ASN cc_start: 0.7607 (m110) cc_final: 0.7343 (m-40) REVERT: C 182 TYR cc_start: 0.8530 (t80) cc_final: 0.8178 (t80) REVERT: D 170 ASP cc_start: 0.8762 (t70) cc_final: 0.8320 (t0) REVERT: E 153 TYR cc_start: 0.7765 (m-80) cc_final: 0.7307 (m-80) REVERT: E 247 CYS cc_start: 0.9040 (m) cc_final: 0.8738 (m) REVERT: F 160 ASN cc_start: 0.8702 (t0) cc_final: 0.8171 (t0) REVERT: I 8 GLU cc_start: 0.6970 (tm-30) cc_final: 0.6653 (tm-30) REVERT: K 17 PHE cc_start: 0.8427 (m-80) cc_final: 0.8209 (m-80) REVERT: K 78 ASP cc_start: 0.8244 (m-30) cc_final: 0.7934 (m-30) REVERT: L 53 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7163 (mp0) REVERT: M 34 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.7699 (mp10) REVERT: M 78 ASP cc_start: 0.8425 (m-30) cc_final: 0.8035 (m-30) REVERT: M 144 LYS cc_start: 0.9045 (mttt) cc_final: 0.8835 (mtpt) REVERT: N 80 MET cc_start: 0.9069 (mtp) cc_final: 0.8792 (mtm) REVERT: i 128 TYR cc_start: 0.8508 (t80) cc_final: 0.8207 (t80) REVERT: j 47 MET cc_start: 0.8909 (OUTLIER) cc_final: 0.8704 (mtt) REVERT: k 153 MET cc_start: 0.9017 (ttm) cc_final: 0.8798 (ttm) REVERT: l 5 MET cc_start: 0.4492 (mmm) cc_final: 0.4256 (mmt) REVERT: l 149 MET cc_start: 0.8202 (mmm) cc_final: 0.7760 (mmt) REVERT: m 141 GLU cc_start: 0.8616 (tp30) cc_final: 0.8259 (tp30) outliers start: 37 outliers final: 28 residues processed: 413 average time/residue: 0.9359 time to fit residues: 632.4161 Evaluate side-chains 402 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 371 time to evaluate : 4.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 170 ASP Chi-restraints excluded: chain F residue 68 HIS Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 170 ASP Chi-restraints excluded: chain H residue 113 CYS Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain I residue 144 LYS Chi-restraints excluded: chain J residue 16 SER Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain K residue 92 MET Chi-restraints excluded: chain L residue 17 PHE Chi-restraints excluded: chain L residue 53 GLU Chi-restraints excluded: chain M residue 34 GLN Chi-restraints excluded: chain M residue 113 CYS Chi-restraints excluded: chain h residue 113 CYS Chi-restraints excluded: chain h residue 168 THR Chi-restraints excluded: chain i residue 113 CYS Chi-restraints excluded: chain i residue 168 THR Chi-restraints excluded: chain j residue 47 MET Chi-restraints excluded: chain j residue 113 CYS Chi-restraints excluded: chain k residue 168 THR Chi-restraints excluded: chain k residue 171 ASP Chi-restraints excluded: chain m residue 18 ASP Chi-restraints excluded: chain n residue 42 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 381 optimal weight: 0.9990 chunk 260 optimal weight: 2.9990 chunk 6 optimal weight: 9.9990 chunk 341 optimal weight: 5.9990 chunk 189 optimal weight: 10.0000 chunk 390 optimal weight: 1.9990 chunk 316 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 233 optimal weight: 2.9990 chunk 411 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 237 GLN E 260 HIS ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 41 ASN l 41 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 37806 Z= 0.282 Angle : 0.469 6.306 51070 Z= 0.245 Chirality : 0.040 0.157 5873 Planarity : 0.003 0.043 6624 Dihedral : 6.504 99.410 5306 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.90 % Allowed : 8.09 % Favored : 91.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.12), residues: 4740 helix: 1.66 (0.11), residues: 2336 sheet: 0.07 (0.19), residues: 633 loop : -0.55 (0.14), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS h 122 PHE 0.014 0.001 PHE L 17 TYR 0.012 0.001 TYR F 153 ARG 0.004 0.000 ARG I 15 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 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 408 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 372 time to evaluate : 4.781 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: A 93 TYR cc_start: 0.8838 (t80) cc_final: 0.8535 (t80) REVERT: A 247 CYS cc_start: 0.8681 (m) cc_final: 0.8237 (m) REVERT: A 390 MET cc_start: 0.8628 (mtp) cc_final: 0.8146 (mtp) REVERT: B 94 ASN cc_start: 0.8832 (m-40) cc_final: 0.8510 (m110) REVERT: B 195 ASN cc_start: 0.7639 (m110) cc_final: 0.7372 (m-40) REVERT: C 182 TYR cc_start: 0.8565 (t80) cc_final: 0.8258 (t80) REVERT: D 170 ASP cc_start: 0.8778 (t70) cc_final: 0.8354 (t0) REVERT: E 153 TYR cc_start: 0.7745 (m-80) cc_final: 0.7273 (m-80) REVERT: E 247 CYS cc_start: 0.9062 (m) cc_final: 0.8761 (m) REVERT: F 160 ASN cc_start: 0.8700 (t0) cc_final: 0.8179 (t0) REVERT: F 350 PHE cc_start: 0.7140 (m-80) cc_final: 0.6785 (m-80) REVERT: I 8 GLU cc_start: 0.6998 (tm-30) cc_final: 0.6613 (tm-30) REVERT: L 53 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7143 (mp0) REVERT: M 34 GLN cc_start: 0.8593 (OUTLIER) cc_final: 0.7729 (mp10) REVERT: M 78 ASP cc_start: 0.8433 (m-30) cc_final: 0.8003 (m-30) REVERT: N 80 MET cc_start: 0.9143 (mtp) cc_final: 0.8895 (mtm) REVERT: i 128 TYR cc_start: 0.8484 (t80) cc_final: 0.8186 (t80) REVERT: j 47 MET cc_start: 0.8972 (OUTLIER) cc_final: 0.8712 (mtt) REVERT: l 41 ASN cc_start: 0.8685 (t0) cc_final: 0.8464 (t0) REVERT: m 141 GLU cc_start: 0.8640 (tp30) cc_final: 0.8167 (tp30) outliers start: 36 outliers final: 31 residues processed: 394 average time/residue: 0.9761 time to fit residues: 632.4612 Evaluate side-chains 390 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 356 time to evaluate : 4.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 315 ASN Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain F residue 68 HIS Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 266 SER Chi-restraints excluded: chain H residue 113 CYS Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain I residue 144 LYS Chi-restraints excluded: chain J residue 16 SER Chi-restraints excluded: chain J residue 181 GLU Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain L residue 17 PHE Chi-restraints excluded: chain L residue 53 GLU Chi-restraints excluded: chain M residue 34 GLN Chi-restraints excluded: chain M residue 113 CYS Chi-restraints excluded: chain h residue 113 CYS Chi-restraints excluded: chain h residue 168 THR Chi-restraints excluded: chain i residue 43 ILE Chi-restraints excluded: chain i residue 113 CYS Chi-restraints excluded: chain i residue 168 THR Chi-restraints excluded: chain j residue 47 MET Chi-restraints excluded: chain k residue 41 ASN Chi-restraints excluded: chain k residue 168 THR Chi-restraints excluded: chain k residue 171 ASP Chi-restraints excluded: chain l residue 108 LYS Chi-restraints excluded: chain l residue 113 CYS Chi-restraints excluded: chain m residue 18 ASP Chi-restraints excluded: chain n residue 42 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 154 optimal weight: 8.9990 chunk 412 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 269 optimal weight: 0.9980 chunk 113 optimal weight: 0.8980 chunk 458 optimal weight: 2.9990 chunk 380 optimal weight: 5.9990 chunk 212 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 151 optimal weight: 8.9990 chunk 240 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 GLN B 225 GLN ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 37806 Z= 0.243 Angle : 0.451 6.208 51070 Z= 0.234 Chirality : 0.040 0.144 5873 Planarity : 0.003 0.040 6624 Dihedral : 6.423 95.966 5306 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.87 % Allowed : 8.54 % Favored : 90.59 % 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: 1.03 (0.12), residues: 4740 helix: 1.75 (0.11), residues: 2328 sheet: 0.15 (0.19), residues: 632 loop : -0.49 (0.14), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS l 122 PHE 0.013 0.001 PHE L 17 TYR 0.013 0.001 TYR F 96 ARG 0.003 0.000 ARG E 228 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 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 399 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 364 time to evaluate : 4.750 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: A 93 TYR cc_start: 0.8833 (t80) cc_final: 0.8553 (t80) REVERT: A 247 CYS cc_start: 0.8681 (m) cc_final: 0.8228 (m) REVERT: B 94 ASN cc_start: 0.8787 (m-40) cc_final: 0.8404 (m110) REVERT: B 195 ASN cc_start: 0.7662 (m110) cc_final: 0.7391 (m-40) REVERT: C 182 TYR cc_start: 0.8600 (t80) cc_final: 0.8316 (t80) REVERT: D 170 ASP cc_start: 0.8779 (t70) cc_final: 0.8357 (t0) REVERT: E 153 TYR cc_start: 0.7768 (m-80) cc_final: 0.7259 (m-80) REVERT: E 247 CYS cc_start: 0.9076 (m) cc_final: 0.8776 (m) REVERT: F 96 TYR cc_start: 0.8110 (m-80) cc_final: 0.7594 (m-80) REVERT: F 160 ASN cc_start: 0.8697 (t0) cc_final: 0.8176 (t0) REVERT: I 8 GLU cc_start: 0.7052 (tm-30) cc_final: 0.6697 (tm-30) REVERT: L 53 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7154 (mp0) REVERT: M 34 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.7705 (mp10) REVERT: M 78 ASP cc_start: 0.8428 (m-30) cc_final: 0.7993 (m-30) REVERT: N 2 LEU cc_start: 0.7589 (tp) cc_final: 0.7220 (tt) REVERT: N 80 MET cc_start: 0.9173 (mtp) cc_final: 0.8899 (mtm) REVERT: i 128 TYR cc_start: 0.8485 (t80) cc_final: 0.8199 (t80) REVERT: j 47 MET cc_start: 0.8958 (OUTLIER) cc_final: 0.8746 (mtt) REVERT: l 41 ASN cc_start: 0.8752 (t0) cc_final: 0.8516 (t0) REVERT: m 141 GLU cc_start: 0.8621 (tp30) cc_final: 0.8125 (tp30) outliers start: 35 outliers final: 30 residues processed: 386 average time/residue: 0.9851 time to fit residues: 626.1867 Evaluate side-chains 389 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 356 time to evaluate : 4.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 170 ASP Chi-restraints excluded: chain F residue 68 HIS Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 170 ASP Chi-restraints excluded: chain H residue 113 CYS Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain I residue 144 LYS Chi-restraints excluded: chain J residue 16 SER Chi-restraints excluded: chain J residue 181 GLU Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain L residue 17 PHE Chi-restraints excluded: chain L residue 53 GLU Chi-restraints excluded: chain M residue 34 GLN Chi-restraints excluded: chain M residue 113 CYS Chi-restraints excluded: chain h residue 113 CYS Chi-restraints excluded: chain i residue 113 CYS Chi-restraints excluded: chain i residue 168 THR Chi-restraints excluded: chain j residue 47 MET Chi-restraints excluded: chain j residue 113 CYS Chi-restraints excluded: chain k residue 168 THR Chi-restraints excluded: chain k residue 171 ASP Chi-restraints excluded: chain l residue 108 LYS Chi-restraints excluded: chain l residue 113 CYS Chi-restraints excluded: chain m residue 18 ASP Chi-restraints excluded: chain n residue 42 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 442 optimal weight: 1.9990 chunk 51 optimal weight: 20.0000 chunk 261 optimal weight: 1.9990 chunk 334 optimal weight: 1.9990 chunk 259 optimal weight: 1.9990 chunk 386 optimal weight: 0.8980 chunk 256 optimal weight: 2.9990 chunk 456 optimal weight: 0.6980 chunk 285 optimal weight: 2.9990 chunk 278 optimal weight: 1.9990 chunk 210 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 41 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 37806 Z= 0.175 Angle : 0.429 6.118 51070 Z= 0.220 Chirality : 0.039 0.142 5873 Planarity : 0.003 0.039 6624 Dihedral : 6.200 92.833 5306 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.85 % Allowed : 8.72 % Favored : 90.44 % 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: 1.19 (0.12), residues: 4740 helix: 1.87 (0.11), residues: 2331 sheet: 0.23 (0.19), residues: 632 loop : -0.42 (0.14), residues: 1777 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 260 PHE 0.013 0.001 PHE L 17 TYR 0.013 0.001 TYR F 96 ARG 0.002 0.000 ARG L 118 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 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 402 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 368 time to evaluate : 4.775 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: A 93 TYR cc_start: 0.8821 (t80) cc_final: 0.8528 (t80) REVERT: A 247 CYS cc_start: 0.8680 (m) cc_final: 0.8233 (m) REVERT: B 195 ASN cc_start: 0.7673 (m110) cc_final: 0.7307 (m110) REVERT: C 182 TYR cc_start: 0.8610 (t80) cc_final: 0.8347 (t80) REVERT: D 170 ASP cc_start: 0.8811 (t70) cc_final: 0.8403 (t0) REVERT: E 153 TYR cc_start: 0.7722 (m-80) cc_final: 0.7221 (m-80) REVERT: E 247 CYS cc_start: 0.9097 (m) cc_final: 0.8804 (m) REVERT: F 160 ASN cc_start: 0.8684 (t0) cc_final: 0.8161 (t0) REVERT: F 350 PHE cc_start: 0.7127 (m-80) cc_final: 0.6793 (m-80) REVERT: I 8 GLU cc_start: 0.7064 (tm-30) cc_final: 0.6827 (tm-30) REVERT: L 53 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.6985 (mp0) REVERT: M 34 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.7670 (mp10) REVERT: M 78 ASP cc_start: 0.8473 (m-30) cc_final: 0.8045 (m-30) REVERT: N 2 LEU cc_start: 0.7625 (tp) cc_final: 0.7283 (tt) REVERT: N 80 MET cc_start: 0.9148 (mtp) cc_final: 0.8926 (mtm) REVERT: i 128 TYR cc_start: 0.8481 (t80) cc_final: 0.8199 (t80) REVERT: l 41 ASN cc_start: 0.8740 (t0) cc_final: 0.8503 (t0) outliers start: 34 outliers final: 29 residues processed: 391 average time/residue: 0.9515 time to fit residues: 609.1057 Evaluate side-chains 389 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 358 time to evaluate : 4.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 315 ASN Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 170 ASP Chi-restraints excluded: chain F residue 68 HIS Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain H residue 113 CYS Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain J residue 16 SER Chi-restraints excluded: chain J residue 181 GLU Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain L residue 17 PHE Chi-restraints excluded: chain L residue 53 GLU Chi-restraints excluded: chain M residue 25 LYS Chi-restraints excluded: chain M residue 34 GLN Chi-restraints excluded: chain M residue 113 CYS Chi-restraints excluded: chain h residue 113 CYS Chi-restraints excluded: chain i residue 168 THR Chi-restraints excluded: chain j residue 113 CYS Chi-restraints excluded: chain k residue 113 CYS Chi-restraints excluded: chain k residue 168 THR Chi-restraints excluded: chain k residue 171 ASP Chi-restraints excluded: chain l residue 108 LYS Chi-restraints excluded: chain m residue 18 ASP Chi-restraints excluded: chain n residue 42 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 282 optimal weight: 2.9990 chunk 182 optimal weight: 10.0000 chunk 272 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 88 optimal weight: 5.9990 chunk 290 optimal weight: 1.9990 chunk 311 optimal weight: 3.9990 chunk 225 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 359 optimal weight: 3.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 37806 Z= 0.242 Angle : 0.449 6.152 51070 Z= 0.232 Chirality : 0.040 0.140 5873 Planarity : 0.003 0.039 6624 Dihedral : 6.154 91.684 5306 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.85 % Allowed : 8.79 % Favored : 90.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.12), residues: 4740 helix: 1.89 (0.11), residues: 2333 sheet: 0.27 (0.19), residues: 633 loop : -0.43 (0.14), residues: 1774 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 260 PHE 0.017 0.001 PHE B 235 TYR 0.015 0.001 TYR F 96 ARG 0.002 0.000 ARG E 228 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 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 390 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 356 time to evaluate : 4.851 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: A 247 CYS cc_start: 0.8742 (m) cc_final: 0.8293 (m) REVERT: A 390 MET cc_start: 0.8708 (mtp) cc_final: 0.8232 (mtp) REVERT: B 195 ASN cc_start: 0.7693 (m110) cc_final: 0.7422 (m-40) REVERT: C 77 TYR cc_start: 0.7651 (m-80) cc_final: 0.7289 (m-80) REVERT: C 182 TYR cc_start: 0.8570 (t80) cc_final: 0.8364 (t80) REVERT: D 170 ASP cc_start: 0.8858 (t70) cc_final: 0.8448 (t0) REVERT: E 153 TYR cc_start: 0.7739 (m-80) cc_final: 0.7225 (m-80) REVERT: E 247 CYS cc_start: 0.9104 (m) cc_final: 0.8817 (m) REVERT: F 96 TYR cc_start: 0.7910 (m-80) cc_final: 0.7408 (m-80) REVERT: F 160 ASN cc_start: 0.8692 (t0) cc_final: 0.8174 (t0) REVERT: I 8 GLU cc_start: 0.7247 (tm-30) cc_final: 0.6842 (tm-30) REVERT: K 74 MET cc_start: 0.8597 (mmt) cc_final: 0.8304 (mmt) REVERT: L 53 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7235 (mp0) REVERT: M 34 GLN cc_start: 0.8554 (OUTLIER) cc_final: 0.7710 (mp10) REVERT: M 78 ASP cc_start: 0.8496 (m-30) cc_final: 0.8078 (m-30) REVERT: N 2 LEU cc_start: 0.7588 (tp) cc_final: 0.7275 (tt) REVERT: N 80 MET cc_start: 0.9162 (mtp) cc_final: 0.8946 (mtm) REVERT: i 128 TYR cc_start: 0.8470 (t80) cc_final: 0.8190 (t80) REVERT: l 41 ASN cc_start: 0.8790 (t0) cc_final: 0.8558 (t0) REVERT: m 141 GLU cc_start: 0.8602 (tp30) cc_final: 0.8116 (tp30) outliers start: 34 outliers final: 30 residues processed: 380 average time/residue: 0.9729 time to fit residues: 606.5276 Evaluate side-chains 384 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 352 time to evaluate : 4.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 315 ASN Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 170 ASP Chi-restraints excluded: chain F residue 68 HIS Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 170 ASP Chi-restraints excluded: chain H residue 113 CYS Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain J residue 16 SER Chi-restraints excluded: chain J residue 181 GLU Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain L residue 17 PHE Chi-restraints excluded: chain L residue 53 GLU Chi-restraints excluded: chain M residue 34 GLN Chi-restraints excluded: chain M residue 113 CYS Chi-restraints excluded: chain h residue 113 CYS Chi-restraints excluded: chain i residue 113 CYS Chi-restraints excluded: chain i residue 168 THR Chi-restraints excluded: chain k residue 168 THR Chi-restraints excluded: chain k residue 171 ASP Chi-restraints excluded: chain l residue 108 LYS Chi-restraints excluded: chain m residue 18 ASP Chi-restraints excluded: chain n residue 42 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 415 optimal weight: 3.9990 chunk 437 optimal weight: 0.9990 chunk 399 optimal weight: 6.9990 chunk 425 optimal weight: 0.8980 chunk 256 optimal weight: 2.9990 chunk 185 optimal weight: 7.9990 chunk 334 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 384 optimal weight: 2.9990 chunk 402 optimal weight: 2.9990 chunk 424 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 37806 Z= 0.182 Angle : 0.430 6.048 51070 Z= 0.220 Chirality : 0.039 0.140 5873 Planarity : 0.003 0.039 6624 Dihedral : 6.065 92.573 5306 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.87 % Allowed : 8.76 % Favored : 90.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.12), residues: 4740 helix: 1.96 (0.11), residues: 2333 sheet: 0.27 (0.19), residues: 647 loop : -0.35 (0.14), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 260 PHE 0.013 0.001 PHE L 17 TYR 0.014 0.001 TYR F 96 ARG 0.003 0.000 ARG H 15 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 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 393 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 358 time to evaluate : 4.766 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: A 93 TYR cc_start: 0.8732 (t80) cc_final: 0.8476 (t80) REVERT: A 247 CYS cc_start: 0.8691 (m) cc_final: 0.8219 (m) REVERT: A 390 MET cc_start: 0.8722 (mtp) cc_final: 0.8254 (mtp) REVERT: B 94 ASN cc_start: 0.8653 (m110) cc_final: 0.8293 (m110) REVERT: B 195 ASN cc_start: 0.7636 (m110) cc_final: 0.7368 (m-40) REVERT: C 77 TYR cc_start: 0.7631 (m-80) cc_final: 0.7268 (m-80) REVERT: C 182 TYR cc_start: 0.8615 (t80) cc_final: 0.8408 (t80) REVERT: D 170 ASP cc_start: 0.8850 (t70) cc_final: 0.8442 (t0) REVERT: E 153 TYR cc_start: 0.7713 (m-80) cc_final: 0.7199 (m-80) REVERT: E 247 CYS cc_start: 0.9110 (m) cc_final: 0.8831 (m) REVERT: F 160 ASN cc_start: 0.8623 (t0) cc_final: 0.8107 (t0) REVERT: I 8 GLU cc_start: 0.7207 (tm-30) cc_final: 0.6818 (tm-30) REVERT: L 53 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7147 (mp0) REVERT: L 120 MET cc_start: 0.8505 (ttm) cc_final: 0.8260 (ttm) REVERT: M 34 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.7707 (mp10) REVERT: M 78 ASP cc_start: 0.8479 (m-30) cc_final: 0.8035 (m-30) REVERT: N 2 LEU cc_start: 0.7565 (tp) cc_final: 0.7254 (tt) REVERT: i 128 TYR cc_start: 0.8466 (t80) cc_final: 0.8190 (t80) REVERT: l 41 ASN cc_start: 0.8785 (t0) cc_final: 0.8537 (t0) outliers start: 35 outliers final: 30 residues processed: 382 average time/residue: 0.9534 time to fit residues: 598.7356 Evaluate side-chains 380 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 348 time to evaluate : 4.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 170 ASP Chi-restraints excluded: chain F residue 68 HIS Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 170 ASP Chi-restraints excluded: chain H residue 113 CYS Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain J residue 16 SER Chi-restraints excluded: chain J residue 181 GLU Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain L residue 17 PHE Chi-restraints excluded: chain L residue 53 GLU Chi-restraints excluded: chain M residue 34 GLN Chi-restraints excluded: chain M residue 113 CYS Chi-restraints excluded: chain h residue 113 CYS Chi-restraints excluded: chain i residue 113 CYS Chi-restraints excluded: chain i residue 168 THR Chi-restraints excluded: chain j residue 113 CYS Chi-restraints excluded: chain k residue 168 THR Chi-restraints excluded: chain k residue 171 ASP Chi-restraints excluded: chain l residue 108 LYS Chi-restraints excluded: chain l residue 113 CYS Chi-restraints excluded: chain m residue 18 ASP Chi-restraints excluded: chain n residue 42 LEU 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: 2.9990 chunk 274 optimal weight: 5.9990 chunk 213 optimal weight: 0.6980 chunk 312 optimal weight: 5.9990 chunk 472 optimal weight: 1.9990 chunk 434 optimal weight: 1.9990 chunk 376 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 290 optimal weight: 1.9990 chunk 230 optimal weight: 0.5980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 37806 Z= 0.192 Angle : 0.433 6.009 51070 Z= 0.222 Chirality : 0.039 0.140 5873 Planarity : 0.003 0.039 6624 Dihedral : 5.987 93.979 5306 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.77 % Allowed : 8.89 % Favored : 90.34 % 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: 1.33 (0.12), residues: 4740 helix: 1.99 (0.11), residues: 2336 sheet: 0.33 (0.19), residues: 647 loop : -0.38 (0.14), residues: 1757 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 260 PHE 0.013 0.001 PHE L 17 TYR 0.007 0.001 TYR A 96 ARG 0.003 0.000 ARG I 15 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 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 385 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 354 time to evaluate : 4.756 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: A 93 TYR cc_start: 0.8738 (t80) cc_final: 0.8518 (t80) REVERT: A 247 CYS cc_start: 0.8751 (m) cc_final: 0.8296 (m) REVERT: A 390 MET cc_start: 0.8735 (mtp) cc_final: 0.8272 (mtp) REVERT: B 195 ASN cc_start: 0.7651 (m110) cc_final: 0.7385 (m-40) REVERT: C 77 TYR cc_start: 0.7581 (m-80) cc_final: 0.7253 (m-80) REVERT: D 170 ASP cc_start: 0.8852 (t70) cc_final: 0.8444 (t0) REVERT: E 153 TYR cc_start: 0.7741 (m-80) cc_final: 0.7236 (m-80) REVERT: E 247 CYS cc_start: 0.9115 (m) cc_final: 0.8840 (m) REVERT: F 160 ASN cc_start: 0.8619 (t0) cc_final: 0.8106 (t0) REVERT: F 350 PHE cc_start: 0.7109 (m-80) cc_final: 0.6792 (m-80) REVERT: I 8 GLU cc_start: 0.7213 (tm-30) cc_final: 0.6822 (tm-30) REVERT: L 53 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7180 (mp0) REVERT: L 120 MET cc_start: 0.8531 (ttm) cc_final: 0.8269 (ttm) REVERT: M 34 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.7713 (mp10) REVERT: M 78 ASP cc_start: 0.8479 (m-30) cc_final: 0.8018 (m-30) REVERT: N 2 LEU cc_start: 0.7560 (tp) cc_final: 0.7254 (tt) REVERT: i 128 TYR cc_start: 0.8472 (t80) cc_final: 0.8199 (t80) REVERT: l 41 ASN cc_start: 0.8800 (t0) cc_final: 0.8556 (t0) REVERT: l 149 MET cc_start: 0.8353 (mmt) cc_final: 0.7632 (mmt) REVERT: m 47 MET cc_start: 0.8955 (mtt) cc_final: 0.8640 (mtt) outliers start: 31 outliers final: 29 residues processed: 375 average time/residue: 0.9805 time to fit residues: 602.0504 Evaluate side-chains 379 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 348 time to evaluate : 4.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 315 ASN Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 170 ASP Chi-restraints excluded: chain F residue 68 HIS Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 170 ASP Chi-restraints excluded: chain H residue 113 CYS Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain J residue 16 SER Chi-restraints excluded: chain J residue 181 GLU Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain L residue 17 PHE Chi-restraints excluded: chain L residue 53 GLU Chi-restraints excluded: chain M residue 34 GLN Chi-restraints excluded: chain M residue 113 CYS Chi-restraints excluded: chain h residue 113 CYS Chi-restraints excluded: chain j residue 113 CYS Chi-restraints excluded: chain k residue 168 THR Chi-restraints excluded: chain k residue 171 ASP Chi-restraints excluded: chain l residue 108 LYS Chi-restraints excluded: chain l residue 113 CYS Chi-restraints excluded: chain m residue 18 ASP Chi-restraints excluded: chain n residue 42 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 298 optimal weight: 0.9990 chunk 400 optimal weight: 0.7980 chunk 115 optimal weight: 4.9990 chunk 346 optimal weight: 0.6980 chunk 55 optimal weight: 0.0770 chunk 104 optimal weight: 2.9990 chunk 376 optimal weight: 0.1980 chunk 157 optimal weight: 5.9990 chunk 386 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 overall best weight: 0.5540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 41 ASN ** k 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.127186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.081376 restraints weight = 187249.324| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.28 r_work: 0.2984 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2875 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2875 r_free = 0.2875 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2875 r_free = 0.2875 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2875 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 37806 Z= 0.117 Angle : 0.413 6.139 51070 Z= 0.209 Chirality : 0.039 0.138 5873 Planarity : 0.003 0.039 6624 Dihedral : 5.767 95.167 5306 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.67 % Allowed : 8.99 % Favored : 90.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.12), residues: 4740 helix: 2.14 (0.11), residues: 2320 sheet: 0.40 (0.19), residues: 646 loop : -0.28 (0.14), residues: 1774 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 260 PHE 0.013 0.001 PHE L 17 TYR 0.007 0.001 TYR F 96 ARG 0.002 0.000 ARG K 15 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14435.06 seconds wall clock time: 251 minutes 8.59 seconds (15068.59 seconds total)