Starting phenix.real_space_refine on Sun Feb 18 21:01:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e91_27952/02_2024/8e91_27952_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e91_27952/02_2024/8e91_27952.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e91_27952/02_2024/8e91_27952.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e91_27952/02_2024/8e91_27952.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e91_27952/02_2024/8e91_27952_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e91_27952/02_2024/8e91_27952_trim_updated.pdb" } resolution = 2.57 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.034 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 208 5.16 5 C 23462 2.51 5 N 6399 2.21 5 O 7180 1.98 5 H 37574 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 103": "OD1" <-> "OD2" Residue "A ASP 170": "OD1" <-> "OD2" Residue "A GLU 205": "OE1" <-> "OE2" Residue "A GLU 216": "OE1" <-> "OE2" Residue "A ASP 279": "OD1" <-> "OD2" Residue "A GLU 303": "OE1" <-> "OE2" Residue "A ASP 356": "OD1" <-> "OD2" Residue "B ASP 157": "OD1" <-> "OD2" Residue "B ASP 170": "OD1" <-> "OD2" Residue "B ASP 172": "OD1" <-> "OD2" Residue "B GLU 234": "OE1" <-> "OE2" Residue "B GLU 283": "OE1" <-> "OE2" Residue "B ASP 347": "OD1" <-> "OD2" Residue "B GLU 408": "OE1" <-> "OE2" Residue "C ASP 144": "OD1" <-> "OD2" Residue "C GLU 159": "OE1" <-> "OE2" Residue "C ASP 194": "OD1" <-> "OD2" Residue "C GLU 234": "OE1" <-> "OE2" Residue "C ASP 399": "OD1" <-> "OD2" Residue "D GLU 109": "OE1" <-> "OE2" Residue "D ASP 194": "OD1" <-> "OD2" Residue "D PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 279": "OD1" <-> "OD2" Residue "D ASP 352": "OD1" <-> "OD2" Residue "D ASP 356": "OD1" <-> "OD2" Residue "E ASP 137": "OD1" <-> "OD2" Residue "E GLU 150": "OE1" <-> "OE2" Residue "E TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 352": "OD1" <-> "OD2" Residue "E TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 100": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 109": "OE1" <-> "OE2" Residue "F GLU 130": "OE1" <-> "OE2" Residue "F ASP 137": "OD1" <-> "OD2" Residue "F ASP 144": "OD1" <-> "OD2" Residue "F GLU 159": "OE1" <-> "OE2" Residue "F GLU 185": "OE1" <-> "OE2" Residue "F ASP 239": "OD1" <-> "OD2" Residue "F GLU 293": "OE1" <-> "OE2" Residue "F ASP 352": "OD1" <-> "OD2" Residue "F ASP 382": "OD1" <-> "OD2" Residue "N PHE 173": "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 ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "h ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "h ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "i ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "i ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "i ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "i ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "i ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "j ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "j ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "j ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "j ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "j ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "k ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "k ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "k ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "k ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "k ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "l ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "l ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "l ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "l ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "l ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "m PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "n ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "n ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "n ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "n ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 74842 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 5424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 5424 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 14, 'TRANS': 335} Chain: "B" Number of atoms: 5445 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 351, 5433 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 14, 'TRANS': 336} Conformer: "B" Number of residues, atoms: 351, 5433 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 14, 'TRANS': 336} bond proxies already assigned to first conformer: 5456 Chain: "C" Number of atoms: 5441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 5441 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 14, 'TRANS': 337} Chain: "D" Number of atoms: 5441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 5441 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 14, 'TRANS': 337} Chain: "E" Number of atoms: 5442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 5442 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 14, 'TRANS': 337} Chain: "F" Number of atoms: 5244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 5244 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 13, 'TRANS': 324} Chain breaks: 1 Chain: "H" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "I" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "J" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "K" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "L" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "M" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "N" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "h" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "i" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "j" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "k" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "l" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "m" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "n" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 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, 'AGS': 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, 'AGS': 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: 26.60, per 1000 atoms: 0.36 Number of scatterers: 74842 At special positions: 0 Unit cell: (148.368, 136.004, 193.328, 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 208 16.00 P 16 15.00 Mg 3 11.99 O 7180 8.00 N 6399 7.00 C 23462 6.00 H 37574 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: 48.49 Conformation dependent library (CDL) restraints added in 7.0 seconds 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8794 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 200 helices and 67 sheets defined 45.3% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.99 Creating SS restraints... Processing helix chain 'A' and resid 67 through 77 removed outlier: 3.823A 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: 3.516A pdb=" N ALA A 129 " --> pdb=" O LYS A 125 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ARG A 134 " --> pdb=" O GLU A 130 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU A 135 " --> pdb=" O THR A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 168 Processing helix chain 'A' and resid 173 through 177 Processing helix chain 'A' and resid 186 through 189 Processing helix chain 'A' and resid 205 through 216 removed outlier: 3.610A pdb=" N ALA A 210 " --> pdb=" O GLY A 206 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU A 214 " --> pdb=" O ALA A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 262 Processing helix chain 'A' and resid 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: 3.741A pdb=" N LYS A 327 " --> pdb=" O ILE A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 344 removed outlier: 3.696A pdb=" N GLU A 344 " --> pdb=" O LEU A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 365 removed outlier: 3.820A pdb=" N ASP A 356 " --> pdb=" O ASP A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 379 removed outlier: 3.508A pdb=" N GLU A 377 " --> pdb=" O SER A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 387 Processing helix chain 'A' and resid 400 through 404 Processing helix chain 'B' and resid 67 through 77 removed outlier: 3.581A pdb=" N TYR B 77 " --> pdb=" O HIS B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 100 Processing helix chain 'B' and resid 125 through 135 removed outlier: 3.506A pdb=" N ALA B 129 " --> pdb=" O LYS B 125 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG B 134 " --> pdb=" O GLU B 130 " (cutoff:3.500A) removed outlier: 3.878A 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: 3.521A 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: 4.642A pdb=" N LYS B 213 " --> pdb=" O GLN B 209 " (cutoff:3.500A) removed outlier: 3.900A 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: 3.639A pdb=" N GLN B 289 " --> pdb=" O GLU B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 298 removed outlier: 3.601A pdb=" N LYS B 297 " --> pdb=" O GLU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 306 Processing helix chain 'B' and resid 319 through 325 Processing helix chain 'B' and resid 333 through 342 Processing helix chain 'B' and resid 352 through 365 Processing helix chain 'B' and resid 368 through 379 Processing helix chain 'B' and resid 381 through 387 Processing helix chain 'B' and resid 400 through 404 Processing helix chain 'C' and resid 67 through 77 removed outlier: 3.500A pdb=" N HIS C 73 " --> pdb=" O GLU C 69 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TYR C 77 " --> pdb=" O HIS C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 100 Processing helix chain 'C' and resid 125 through 135 removed outlier: 3.541A pdb=" N ALA C 129 " --> pdb=" O LYS C 125 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG C 134 " --> pdb=" O GLU C 130 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU C 135 " --> pdb=" O THR C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 168 Processing helix chain 'C' and resid 173 through 178 removed outlier: 3.635A 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: 4.116A pdb=" N LEU C 214 " --> pdb=" O ALA C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 263 removed outlier: 3.687A pdb=" N ARG C 261 " --> pdb=" O VAL C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 289 removed outlier: 3.667A 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: 3.756A 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 removed outlier: 3.542A pdb=" N ASP C 356 " --> pdb=" O ASP C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 379 removed outlier: 3.756A pdb=" N VAL C 376 " --> pdb=" O ARG C 373 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU C 377 " --> pdb=" O SER C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 387 Processing helix chain 'C' and resid 400 through 404 Processing helix chain 'D' and resid 67 through 77 removed outlier: 4.064A 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: 3.593A pdb=" N ALA D 129 " --> pdb=" O LYS D 125 " (cutoff:3.500A) removed outlier: 3.767A 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: 4.364A pdb=" N LYS D 213 " --> pdb=" O GLN D 209 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU D 214 " --> pdb=" O ALA D 210 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLU D 216 " --> pdb=" O LEU D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 262 removed outlier: 3.503A pdb=" N ARG D 261 " --> pdb=" O VAL D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 289 removed outlier: 3.718A pdb=" N GLN D 289 " --> pdb=" O GLU D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 298 removed outlier: 3.540A pdb=" N LYS D 297 " --> pdb=" O GLU D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 307 removed outlier: 3.747A pdb=" N ARG D 307 " --> pdb=" O GLU D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 327 removed outlier: 3.792A pdb=" N LYS D 327 " --> pdb=" O ILE D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 342 Processing helix chain 'D' and resid 352 through 365 removed outlier: 3.556A pdb=" N ALA D 364 " --> pdb=" O LYS D 360 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG D 365 " --> pdb=" O LYS D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 379 removed outlier: 3.531A pdb=" N ALA D 378 " --> pdb=" O ILE D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 387 Processing helix chain 'D' and resid 400 through 404 removed outlier: 3.639A pdb=" N ASP D 404 " --> pdb=" O GLU D 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 400 through 404' Processing helix chain 'E' and resid 67 through 77 removed outlier: 3.514A pdb=" N TYR E 77 " --> pdb=" O HIS E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 100 Processing helix chain 'E' and resid 125 through 130 removed outlier: 3.692A pdb=" N ALA E 129 " --> pdb=" O LYS E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 168 Processing helix chain 'E' and resid 173 through 178 removed outlier: 4.149A 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: 4.709A pdb=" N LYS E 213 " --> pdb=" O GLN E 209 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU E 214 " --> pdb=" O ALA E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 263 Processing helix chain 'E' and resid 283 through 289 removed outlier: 4.221A pdb=" N GLN E 289 " --> pdb=" O GLU E 285 " (cutoff:3.500A) Processing helix chain 'E' and resid 292 through 298 removed outlier: 3.561A pdb=" N LYS E 297 " --> pdb=" O GLU E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 307 removed outlier: 3.798A pdb=" N ARG E 307 " --> pdb=" O GLU E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 327 removed outlier: 3.774A pdb=" N LYS E 327 " --> pdb=" O ILE E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 342 Processing helix chain 'E' and resid 352 through 365 removed outlier: 3.588A pdb=" N ALA E 357 " --> pdb=" O GLU E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 379 Processing helix chain 'E' and resid 381 through 387 Processing helix chain 'E' and resid 400 through 404 Processing helix chain 'F' and resid 67 through 77 removed outlier: 3.867A pdb=" N TYR F 77 " --> pdb=" O HIS F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 100 Processing helix chain 'F' and resid 125 through 135 removed outlier: 3.536A pdb=" N ALA F 129 " --> pdb=" O LYS F 125 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU F 130 " --> pdb=" O THR F 126 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU F 132 " --> pdb=" O LEU F 128 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA F 133 " --> pdb=" O ALA F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 154 through 168 removed outlier: 3.926A pdb=" N ILE F 162 " --> pdb=" O VAL F 158 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS F 168 " --> pdb=" O LYS F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 177 Processing helix chain 'F' and resid 205 through 216 removed outlier: 3.541A pdb=" N ALA F 210 " --> pdb=" O GLY F 206 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LYS F 213 " --> pdb=" O GLN F 209 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU F 214 " --> pdb=" O ALA F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 262 Processing helix chain 'F' and resid 282 through 289 removed outlier: 3.669A 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: 3.806A pdb=" N LYS F 327 " --> pdb=" O ILE F 323 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 344 removed outlier: 3.621A pdb=" N GLU F 344 " --> pdb=" O LEU F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 352 through 365 removed outlier: 3.618A pdb=" N ALA F 357 " --> pdb=" O GLU F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 370 through 387 removed outlier: 3.598A pdb=" N ALA F 378 " --> pdb=" O ILE F 375 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ASP F 382 " --> pdb=" O ALA F 379 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR F 383 " --> pdb=" O LEU F 380 " (cutoff:3.500A) removed outlier: 4.219A 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: 3.736A 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: 3.742A 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 Processing helix chain 'I' and resid 19 through 26 removed outlier: 3.651A 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: 3.588A 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: 3.777A 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: 3.608A 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: 3.663A 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: 3.592A 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: 3.640A pdb=" N GLU L 26 " --> pdb=" O ARG L 22 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 53 removed outlier: 3.650A pdb=" N ALA L 52 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU L 53 " --> pdb=" O PHE L 49 " (cutoff:3.500A) Processing helix chain 'L' and resid 70 through 82 removed outlier: 3.597A 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: 3.813A 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: 3.543A pdb=" N ILE M 76 " --> pdb=" O ALA M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 104 Processing helix chain 'M' and resid 132 through 157 Processing helix chain 'M' and resid 161 through 168 Processing helix chain 'M' and resid 176 through 182 Processing helix chain 'N' and resid 19 through 26 removed outlier: 3.983A 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: 3.654A pdb=" N ILE N 76 " --> pdb=" O ALA N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 97 through 104 Processing helix chain 'N' and resid 132 through 157 Processing helix chain 'N' and resid 161 through 167 Processing helix chain 'N' and resid 176 through 182 Processing helix chain 'h' and resid 19 through 26 removed outlier: 3.760A 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: 3.643A pdb=" N ILE h 76 " --> pdb=" O ALA h 72 " (cutoff:3.500A) Processing helix chain 'h' and resid 97 through 104 Processing helix chain 'h' and resid 132 through 157 Processing helix chain 'h' and resid 161 through 168 Processing helix chain 'h' and resid 176 through 182 Processing helix chain 'i' and resid 19 through 26 removed outlier: 3.923A 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: 3.553A pdb=" N ILE i 76 " --> pdb=" O ALA i 72 " (cutoff:3.500A) Processing helix chain 'i' and resid 97 through 104 Processing helix chain 'i' and resid 132 through 157 Processing helix chain 'i' and resid 161 through 168 Processing helix chain 'i' and resid 176 through 181 Processing helix chain 'j' and resid 19 through 26 removed outlier: 3.739A 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: 3.607A 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: 3.945A 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: 3.589A pdb=" N ILE k 76 " --> pdb=" O ALA k 72 " (cutoff:3.500A) Processing helix chain 'k' and resid 97 through 104 Processing helix chain 'k' and resid 132 through 157 Processing helix chain 'k' and resid 161 through 168 Processing helix chain 'k' and resid 176 through 181 Processing helix chain 'l' and resid 19 through 26 removed outlier: 3.779A 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 Processing helix chain 'l' and resid 161 through 168 Processing helix chain 'l' and resid 176 through 182 Processing helix chain 'm' and resid 19 through 26 removed outlier: 3.788A 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: 3.517A 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: 3.534A pdb=" N LEU n 23 " --> pdb=" O ILE n 19 " (cutoff:3.500A) removed outlier: 3.615A 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: 3.535A pdb=" N ILE n 76 " --> pdb=" O ALA n 72 " (cutoff:3.500A) Processing helix chain 'n' and resid 97 through 104 Processing helix chain 'n' and resid 132 through 157 Processing helix chain 'n' and resid 161 through 168 Processing helix chain 'n' and resid 176 through 182 Processing sheet with id= A, first strand: chain 'A' and resid 115 through 118 removed outlier: 3.707A pdb=" N ILE A 115 " --> pdb=" O PHE A 245 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 220 through 222 Processing sheet with id= C, first strand: chain 'A' and resid 347 through 350 removed outlier: 3.876A pdb=" N LYS A 395 " --> pdb=" O ILE A 412 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 310 through 313 removed outlier: 3.766A pdb=" N THR B 141 " --> pdb=" O ILE B 180 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 219 through 222 Processing sheet with id= F, first strand: chain 'B' and resid 347 through 350 removed outlier: 4.065A pdb=" N LYS B 395 " --> pdb=" O ILE B 412 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 310 through 314 removed outlier: 7.140A pdb=" N CYS C 247 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N GLY C 119 " --> pdb=" O CYS C 247 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N GLY C 249 " --> pdb=" O GLY C 119 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 140 through 144 removed outlier: 6.669A pdb=" N ILE C 180 " --> pdb=" O THR C 141 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N ALA C 143 " --> pdb=" O ILE C 180 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N TYR C 182 " --> pdb=" O ALA C 143 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'C' and resid 347 through 350 removed outlier: 3.887A pdb=" N GLU C 349 " --> pdb=" O VAL C 396 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE C 398 " --> pdb=" O GLU C 349 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU C 394 " --> pdb=" O ILE C 412 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ILE C 412 " --> pdb=" O GLU C 394 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N VAL C 396 " --> pdb=" O LEU C 410 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEU C 410 " --> pdb=" O VAL C 396 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 310 through 314 removed outlier: 3.696A pdb=" N GLY D 119 " --> pdb=" O GLY D 249 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR D 141 " --> pdb=" O ILE D 180 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 219 through 222 Processing sheet with id= L, first strand: chain 'D' and resid 347 through 350 removed outlier: 7.177A pdb=" N ILE D 412 " --> pdb=" O GLU D 394 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N VAL D 396 " --> pdb=" O LEU D 410 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N LEU D 410 " --> pdb=" O VAL D 396 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 310 through 314 removed outlier: 3.770A pdb=" N THR E 141 " --> pdb=" O ILE E 180 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 219 through 222 Processing sheet with id= O, first strand: chain 'E' and resid 347 through 350 removed outlier: 3.613A pdb=" N LYS E 395 " --> pdb=" O ILE E 412 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 115 through 118 removed outlier: 6.941A pdb=" N VAL F 310 " --> pdb=" O LEU F 116 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N ILE F 118 " --> pdb=" O VAL F 310 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ALA F 312 " --> pdb=" O ILE F 118 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'F' and resid 140 through 142 removed outlier: 6.898A pdb=" N ILE F 180 " --> pdb=" O THR F 141 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N LEU F 244 " --> pdb=" O VAL F 181 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ILE F 183 " --> pdb=" O LEU F 244 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ILE F 246 " --> pdb=" O ILE F 183 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'F' and resid 219 through 222 Processing sheet with id= S, first strand: chain 'F' and resid 347 through 350 Processing sheet with id= T, first strand: chain 'H' and resid 6 through 9 Processing sheet with id= U, first strand: chain 'H' and resid 28 through 32 removed outlier: 6.407A pdb=" N TYR H 60 " --> pdb=" O ILE H 29 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N LEU H 31 " --> pdb=" O TYR H 60 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N TYR H 62 " --> pdb=" O LEU H 31 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'H' and resid 118 through 121 Processing sheet with id= W, first strand: chain 'I' and resid 5 through 9 Processing sheet with id= X, first strand: chain 'I' and resid 28 through 32 removed outlier: 6.427A pdb=" N TYR I 60 " --> pdb=" O ILE I 29 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N LEU I 31 " --> pdb=" O TYR I 60 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N TYR I 62 " --> pdb=" O LEU I 31 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'I' and resid 118 through 121 Processing sheet with id= Z, first strand: chain 'J' and resid 5 through 9 Processing sheet with id= AA, first strand: chain 'J' and resid 28 through 32 removed outlier: 6.391A pdb=" N TYR J 60 " --> pdb=" O ILE J 29 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N LEU J 31 " --> pdb=" O TYR J 60 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N TYR J 62 " --> pdb=" O LEU J 31 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'J' and resid 112 through 114 removed outlier: 6.675A pdb=" N SER J 187 " --> pdb=" O CYS J 113 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'J' and resid 118 through 121 Processing sheet with id= AD, first strand: chain 'K' and resid 5 through 9 Processing sheet with id= AE, first strand: chain 'K' and resid 28 through 32 removed outlier: 6.442A pdb=" N TYR K 60 " --> pdb=" O ILE K 29 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N LEU K 31 " --> pdb=" O TYR K 60 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N TYR K 62 " --> pdb=" O LEU K 31 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'K' and resid 118 through 121 Processing sheet with id= AG, first strand: chain 'L' and resid 5 through 8 removed outlier: 3.712A pdb=" N ARG L 15 " --> pdb=" O GLU L 8 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'L' and resid 28 through 32 removed outlier: 6.418A pdb=" N TYR L 60 " --> pdb=" O ILE L 29 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N LEU L 31 " --> pdb=" O TYR L 60 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N TYR L 62 " --> pdb=" O LEU L 31 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'L' and resid 112 through 114 removed outlier: 6.680A pdb=" N SER L 187 " --> pdb=" O CYS L 113 " (cutoff:3.500A) No H-bonds generated for sheet with id= AI Processing sheet with id= AJ, first strand: chain 'L' and resid 118 through 121 Processing sheet with id= AK, first strand: chain 'M' and resid 6 through 8 Processing sheet with id= AL, first strand: chain 'M' and resid 28 through 32 removed outlier: 6.382A pdb=" N TYR M 60 " --> pdb=" O ILE M 29 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N LEU M 31 " --> pdb=" O TYR M 60 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N TYR M 62 " --> pdb=" O LEU M 31 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'M' and resid 118 through 121 Processing sheet with id= AN, first strand: chain 'N' and resid 5 through 9 Processing sheet with id= AO, first strand: chain 'N' and resid 28 through 32 removed outlier: 6.488A pdb=" N TYR N 60 " --> pdb=" O ILE N 29 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N LEU N 31 " --> pdb=" O TYR N 60 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N TYR N 62 " --> pdb=" O LEU N 31 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N SER N 187 " --> pdb=" O CYS N 113 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'N' and resid 118 through 121 Processing sheet with id= AQ, first strand: chain 'h' and resid 5 through 9 Processing sheet with id= AR, first strand: chain 'h' and resid 28 through 32 removed outlier: 6.518A pdb=" N TYR h 60 " --> pdb=" O ILE h 29 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N LEU h 31 " --> pdb=" O TYR h 60 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N TYR h 62 " --> pdb=" O LEU h 31 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'h' and resid 112 through 114 removed outlier: 6.718A pdb=" N SER h 187 " --> pdb=" O CYS h 113 " (cutoff:3.500A) No H-bonds generated for sheet with id= AS Processing sheet with id= AT, first strand: chain 'h' and resid 118 through 121 Processing sheet with id= AU, first strand: chain 'i' and resid 5 through 9 Processing sheet with id= AV, first strand: chain 'i' and resid 28 through 32 removed outlier: 6.516A pdb=" N TYR i 60 " --> pdb=" O ILE i 29 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N LEU i 31 " --> pdb=" O TYR i 60 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N TYR i 62 " --> pdb=" O LEU i 31 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N CYS i 91 " --> pdb=" O PHE i 112 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'i' and resid 118 through 121 Processing sheet with id= AX, first strand: chain 'j' and resid 5 through 9 Processing sheet with id= AY, first strand: chain 'j' and resid 28 through 32 removed outlier: 6.650A pdb=" N TYR j 60 " --> pdb=" O ILE j 29 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N LEU j 31 " --> pdb=" O TYR j 60 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N TYR j 62 " --> pdb=" O LEU j 31 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'j' and resid 112 through 114 removed outlier: 6.723A pdb=" N SER j 187 " --> pdb=" O CYS j 113 " (cutoff:3.500A) No H-bonds generated for sheet with id= AZ Processing sheet with id= BA, first strand: chain 'j' and resid 118 through 121 Processing sheet with id= BB, first strand: chain 'k' and resid 5 through 9 Processing sheet with id= BC, first strand: chain 'k' and resid 28 through 32 removed outlier: 6.584A pdb=" N TYR k 60 " --> pdb=" O ILE k 29 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N LEU k 31 " --> pdb=" O TYR k 60 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N TYR k 62 " --> pdb=" O LEU k 31 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'k' and resid 118 through 121 Processing sheet with id= BE, first strand: chain 'l' and resid 5 through 9 Processing sheet with id= BF, first strand: chain 'l' and resid 28 through 32 removed outlier: 6.522A pdb=" N TYR l 60 " --> pdb=" O ILE l 29 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N LEU l 31 " --> pdb=" O TYR l 60 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N TYR l 62 " --> pdb=" O LEU l 31 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'l' and resid 112 through 114 removed outlier: 6.727A pdb=" N SER l 187 " --> pdb=" O CYS l 113 " (cutoff:3.500A) No H-bonds generated for sheet with id= BG Processing sheet with id= BH, first strand: chain 'l' and resid 118 through 121 Processing sheet with id= BI, first strand: chain 'm' and resid 5 through 9 Processing sheet with id= BJ, first strand: chain 'm' and resid 28 through 32 removed outlier: 6.572A pdb=" N TYR m 60 " --> pdb=" O ILE m 29 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N LEU m 31 " --> pdb=" O TYR m 60 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N TYR m 62 " --> pdb=" O LEU m 31 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'm' and resid 118 through 121 Processing sheet with id= BL, first strand: chain 'n' and resid 5 through 9 Processing sheet with id= BM, first strand: chain 'n' and resid 28 through 32 removed outlier: 6.529A pdb=" N TYR n 60 " --> pdb=" O ILE n 29 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N LEU n 31 " --> pdb=" O TYR n 60 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N TYR n 62 " --> pdb=" O LEU n 31 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'n' and resid 112 through 114 removed outlier: 6.607A pdb=" N SER n 187 " --> pdb=" O CYS n 113 " (cutoff:3.500A) No H-bonds generated for sheet with id= BN Processing sheet with id= BO, first strand: chain 'n' and resid 118 through 121 1566 hydrogen bonds defined for protein. 4320 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: 25.22 Time building geometry restraints manager: 51.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.06: 37534 1.06 - 1.28: 6513 1.28 - 1.50: 15124 1.50 - 1.73: 15859 1.73 - 1.95: 372 Bond restraints: 75402 Sorted by residual: bond pdb=" C HIS A 230 " pdb=" N PRO A 231 " ideal model delta sigma weight residual 1.335 1.353 -0.018 1.30e-02 5.92e+03 1.93e+00 bond pdb=" CB PRO J 85 " pdb=" CG PRO J 85 " ideal model delta sigma weight residual 1.492 1.423 0.069 5.00e-02 4.00e+02 1.91e+00 bond pdb=" CB GLU D 234 " pdb=" CG GLU D 234 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.59e+00 bond pdb=" CB PRO I 85 " pdb=" CG PRO I 85 " ideal model delta sigma weight residual 1.492 1.430 0.062 5.00e-02 4.00e+02 1.56e+00 bond pdb=" CA ARG L 12 " pdb=" CB ARG L 12 " ideal model delta sigma weight residual 1.531 1.550 -0.019 1.51e-02 4.39e+03 1.53e+00 ... (remaining 75397 not shown) Histogram of bond angle deviations from ideal: 99.13 - 106.58: 1325 106.58 - 114.03: 93387 114.03 - 121.48: 28040 121.48 - 128.92: 13774 128.92 - 136.37: 240 Bond angle restraints: 136766 Sorted by residual: angle pdb=" CA GLU D 234 " pdb=" CB GLU D 234 " pdb=" CG GLU D 234 " ideal model delta sigma weight residual 114.10 120.24 -6.14 2.00e+00 2.50e-01 9.42e+00 angle pdb=" N ILE B 198 " pdb=" CA ILE B 198 " pdb=" C ILE B 198 " ideal model delta sigma weight residual 112.96 109.90 3.06 1.00e+00 1.00e+00 9.35e+00 angle pdb=" CA ARG L 12 " pdb=" CB ARG L 12 " pdb=" CG ARG L 12 " ideal model delta sigma weight residual 114.10 119.96 -5.86 2.00e+00 2.50e-01 8.58e+00 angle pdb=" CA GLN D 232 " pdb=" CB GLN D 232 " pdb=" CG GLN D 232 " ideal model delta sigma weight residual 114.10 119.89 -5.79 2.00e+00 2.50e-01 8.39e+00 angle pdb=" CA GLN F 225 " pdb=" CB GLN F 225 " pdb=" CG GLN F 225 " ideal model delta sigma weight residual 114.10 119.88 -5.78 2.00e+00 2.50e-01 8.35e+00 ... (remaining 136761 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.98: 33158 23.98 - 47.95: 1506 47.95 - 71.93: 395 71.93 - 95.90: 24 95.90 - 119.88: 2 Dihedral angle restraints: 35085 sinusoidal: 19777 harmonic: 15308 Sorted by residual: 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 -179.88 119.88 1 2.00e+01 2.50e-03 3.60e+01 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 48.59 -108.59 1 2.00e+01 2.50e-03 3.17e+01 dihedral pdb=" C5' ADP F 600 " pdb=" O5' ADP F 600 " pdb=" PA ADP F 600 " pdb=" O2A ADP F 600 " ideal model delta sinusoidal sigma weight residual -60.00 -142.34 82.34 1 2.00e+01 2.50e-03 2.08e+01 ... (remaining 35082 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 3894 0.035 - 0.069: 1232 0.069 - 0.104: 534 0.104 - 0.138: 194 0.138 - 0.173: 28 Chirality restraints: 5882 Sorted by residual: 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 2.61 -0.17 2.00e-01 2.50e+01 7.47e-01 chirality pdb=" CA ASP A 170 " pdb=" N ASP A 170 " pdb=" C ASP A 170 " pdb=" CB ASP A 170 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.33e-01 chirality pdb=" CA VAL F 222 " pdb=" N VAL F 222 " pdb=" C VAL F 222 " pdb=" CB VAL F 222 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 6.85e-01 ... (remaining 5879 not shown) Planarity restraints: 11212 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS E 230 " 0.036 5.00e-02 4.00e+02 5.44e-02 4.73e+00 pdb=" N PRO E 231 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO E 231 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO E 231 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 223 " 0.033 5.00e-02 4.00e+02 5.08e-02 4.13e+00 pdb=" N PRO B 224 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO B 224 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 224 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 155 " -0.010 2.00e-02 2.50e+03 1.98e-02 3.91e+00 pdb=" C GLY A 155 " 0.034 2.00e-02 2.50e+03 pdb=" O GLY A 155 " -0.013 2.00e-02 2.50e+03 pdb=" N GLU A 156 " -0.012 2.00e-02 2.50e+03 ... (remaining 11209 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.22: 5282 2.22 - 2.81: 165434 2.81 - 3.41: 201647 3.41 - 4.00: 278964 4.00 - 4.60: 435110 Nonbonded interactions: 1086437 Sorted by model distance: nonbonded pdb=" O ALA M 96 " pdb=" H ALA M 100 " model vdw 1.623 1.850 nonbonded pdb=" O ALA l 96 " pdb=" H ALA l 100 " model vdw 1.625 1.850 nonbonded pdb=" O ALA h 96 " pdb=" H ALA h 100 " model vdw 1.629 1.850 nonbonded pdb=" O ALA n 96 " pdb=" H ALA n 100 " model vdw 1.631 1.850 nonbonded pdb=" O ALA j 96 " pdb=" H ALA j 100 " model vdw 1.632 1.850 ... (remaining 1086432 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' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.860 Extract box with map and model: 7.740 Check model and map are aligned: 0.850 Set scattering table: 0.540 Process input model: 187.710 Find NCS groups from input model: 2.980 Set up NCS constraints: 0.380 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:10.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 212.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 37828 Z= 0.281 Angle : 0.650 6.139 51098 Z= 0.356 Chirality : 0.044 0.173 5882 Planarity : 0.004 0.054 6629 Dihedral : 12.111 119.879 14400 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % 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: -0.18 (0.11), residues: 4744 helix: 0.57 (0.10), residues: 2271 sheet: -0.46 (0.17), residues: 727 loop : -0.74 (0.14), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS H 122 PHE 0.019 0.001 PHE N 17 TYR 0.010 0.001 TYR C 153 ARG 0.007 0.001 ARG L 12 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 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 914 residues out of total 4014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 914 time to evaluate : 4.584 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 73 HIS cc_start: 0.7995 (t-90) cc_final: 0.7784 (t-170) REVERT: A 182 TYR cc_start: 0.8176 (t80) cc_final: 0.7944 (t80) REVERT: B 94 ASN cc_start: 0.9280 (m-40) cc_final: 0.9073 (m-40) REVERT: B 171 TYR cc_start: 0.8196 (m-10) cc_final: 0.7945 (m-10) REVERT: B 294 ASP cc_start: 0.8028 (m-30) cc_final: 0.7693 (m-30) REVERT: C 160 ASN cc_start: 0.9036 (m110) cc_final: 0.8055 (m110) REVERT: C 283 GLU cc_start: 0.8047 (tm-30) cc_final: 0.7801 (tm-30) REVERT: C 352 ASP cc_start: 0.8263 (m-30) cc_final: 0.8037 (t0) REVERT: D 72 ASN cc_start: 0.8515 (m-40) cc_final: 0.8249 (m-40) REVERT: D 73 HIS cc_start: 0.8675 (t70) cc_final: 0.8473 (t-90) REVERT: D 115 ILE cc_start: 0.9431 (mt) cc_final: 0.9223 (mp) REVERT: D 142 MET cc_start: 0.8271 (mtp) cc_final: 0.7853 (mpt) REVERT: D 205 GLU cc_start: 0.8476 (tt0) cc_final: 0.7923 (tt0) REVERT: D 297 LYS cc_start: 0.9047 (mttt) cc_final: 0.8547 (tptp) REVERT: E 77 TYR cc_start: 0.8487 (m-80) cc_final: 0.8188 (m-80) REVERT: E 96 TYR cc_start: 0.8719 (m-80) cc_final: 0.8359 (m-80) REVERT: E 301 ILE cc_start: 0.8870 (mm) cc_final: 0.8208 (tt) REVERT: F 94 ASN cc_start: 0.9273 (m-40) cc_final: 0.9012 (m-40) REVERT: F 95 HIS cc_start: 0.8924 (t70) cc_final: 0.8714 (t-90) REVERT: F 256 LYS cc_start: 0.9181 (ttmm) cc_final: 0.8685 (tptt) REVERT: F 293 GLU cc_start: 0.8019 (pm20) cc_final: 0.7795 (mp0) REVERT: I 10 THR cc_start: 0.8716 (p) cc_final: 0.8397 (p) REVERT: h 18 ASP cc_start: 0.7101 (p0) cc_final: 0.6897 (p0) REVERT: i 17 PHE cc_start: 0.7332 (m-80) cc_final: 0.7073 (m-80) REVERT: l 7 ILE cc_start: 0.9212 (mm) cc_final: 0.9008 (mm) REVERT: l 57 LYS cc_start: 0.8287 (mtpp) cc_final: 0.8056 (mtmm) REVERT: m 110 LYS cc_start: 0.8861 (mttt) cc_final: 0.8527 (mttt) REVERT: n 60 TYR cc_start: 0.8689 (m-80) cc_final: 0.8482 (m-80) outliers start: 0 outliers final: 3 residues processed: 914 average time/residue: 2.8564 time to fit residues: 3136.1356 Evaluate side-chains 528 residues out of total 4014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 525 time to evaluate : 4.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain i residue 92 MET Chi-restraints excluded: chain l residue 17 PHE Chi-restraints excluded: chain l residue 92 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 400 optimal weight: 3.9990 chunk 359 optimal weight: 2.9990 chunk 199 optimal weight: 20.0000 chunk 122 optimal weight: 10.0000 chunk 242 optimal weight: 3.9990 chunk 191 optimal weight: 10.0000 chunk 371 optimal weight: 1.9990 chunk 143 optimal weight: 10.0000 chunk 225 optimal weight: 2.9990 chunk 276 optimal weight: 3.9990 chunk 430 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN B 72 ASN B 160 ASN B 163 GLN C 94 ASN C 342 ASN E 101 ASN F 72 ASN ** F 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 129 GLN J 159 GLN K 9 GLN K 41 ASN M 41 ASN N 41 ASN h 9 GLN h 34 GLN h 41 ASN h 81 GLN ** i 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 129 GLN j 9 GLN j 41 ASN k 191 HIS l 41 ASN m 9 GLN m 41 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 37828 Z= 0.320 Angle : 0.561 7.018 51098 Z= 0.296 Chirality : 0.042 0.155 5882 Planarity : 0.004 0.075 6629 Dihedral : 5.823 103.409 5263 Min Nonbonded Distance : 1.754 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.72 % Allowed : 9.06 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.11), residues: 4744 helix: 1.14 (0.10), residues: 2332 sheet: -0.37 (0.16), residues: 803 loop : -0.74 (0.14), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS E 260 PHE 0.014 0.001 PHE D 298 TYR 0.013 0.001 TYR F 96 ARG 0.009 0.001 ARG C 178 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 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 614 residues out of total 4014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 545 time to evaluate : 4.651 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 160 ASN cc_start: 0.8433 (t0) cc_final: 0.8111 (t0) REVERT: B 73 HIS cc_start: 0.8175 (m90) cc_final: 0.7665 (m90) REVERT: B 294 ASP cc_start: 0.8254 (m-30) cc_final: 0.8039 (m-30) REVERT: C 160 ASN cc_start: 0.8464 (m110) cc_final: 0.8065 (m110) REVERT: D 73 HIS cc_start: 0.8904 (t70) cc_final: 0.8662 (t-90) REVERT: D 115 ILE cc_start: 0.9376 (mt) cc_final: 0.9175 (mp) REVERT: D 142 MET cc_start: 0.8490 (mtp) cc_final: 0.8169 (mpt) REVERT: D 205 GLU cc_start: 0.8316 (tt0) cc_final: 0.7926 (tt0) REVERT: D 297 LYS cc_start: 0.9063 (mttt) cc_final: 0.8717 (tptp) REVERT: E 178 ARG cc_start: 0.8311 (mtm180) cc_final: 0.8045 (mtp85) REVERT: F 94 ASN cc_start: 0.9435 (m-40) cc_final: 0.8877 (m110) REVERT: F 256 LYS cc_start: 0.9158 (ttmm) cc_final: 0.8865 (mmmt) REVERT: F 377 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8506 (mm-30) REVERT: I 58 ASP cc_start: 0.7563 (p0) cc_final: 0.7357 (p0) REVERT: J 18 ASP cc_start: 0.7380 (p0) cc_final: 0.6996 (p0) REVERT: h 47 MET cc_start: 0.9134 (mtt) cc_final: 0.8918 (mtt) REVERT: h 98 MET cc_start: 0.8446 (tpt) cc_final: 0.8070 (tpt) REVERT: j 36 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7689 (pt0) REVERT: l 57 LYS cc_start: 0.8770 (mtpp) cc_final: 0.8509 (mtmm) REVERT: l 129 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.7656 (tp40) REVERT: m 60 TYR cc_start: 0.8582 (m-80) cc_final: 0.8322 (m-80) REVERT: n 60 TYR cc_start: 0.8861 (m-80) cc_final: 0.8589 (m-80) REVERT: n 74 MET cc_start: 0.8970 (mmp) cc_final: 0.8722 (mmp) outliers start: 69 outliers final: 20 residues processed: 577 average time/residue: 2.5236 time to fit residues: 1789.2979 Evaluate side-chains 514 residues out of total 4014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 491 time to evaluate : 4.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 160 ASN Chi-restraints excluded: chain F residue 377 GLU Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain J residue 14 GLU Chi-restraints excluded: chain J residue 36 GLU Chi-restraints excluded: chain J residue 41 ASN Chi-restraints excluded: chain K residue 36 GLU Chi-restraints excluded: chain L residue 25 LYS Chi-restraints excluded: chain M residue 7 ILE Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain N residue 7 ILE Chi-restraints excluded: chain N residue 129 GLN Chi-restraints excluded: chain i residue 168 THR Chi-restraints excluded: chain j residue 36 GLU Chi-restraints excluded: chain j residue 41 ASN Chi-restraints excluded: chain k residue 36 GLU Chi-restraints excluded: chain l residue 92 MET Chi-restraints excluded: chain l residue 129 GLN Chi-restraints excluded: chain l residue 168 THR Chi-restraints excluded: chain l residue 187 SER Chi-restraints excluded: chain m residue 18 ASP Chi-restraints excluded: chain n residue 2 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 239 optimal weight: 2.9990 chunk 133 optimal weight: 20.0000 chunk 358 optimal weight: 2.9990 chunk 293 optimal weight: 4.9990 chunk 118 optimal weight: 7.9990 chunk 431 optimal weight: 2.9990 chunk 465 optimal weight: 4.9990 chunk 384 optimal weight: 5.9990 chunk 427 optimal weight: 4.9990 chunk 147 optimal weight: 8.9990 chunk 345 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 ASN ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 342 ASN D 73 HIS E 94 ASN ** F 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 GLN H 131 GLN I 9 GLN K 9 GLN K 41 ASN M 41 ASN N 159 GLN h 41 ASN ** i 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 41 ASN ** l 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 9 GLN m 41 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 37828 Z= 0.340 Angle : 0.518 7.106 51098 Z= 0.270 Chirality : 0.042 0.150 5882 Planarity : 0.003 0.047 6629 Dihedral : 5.748 97.594 5258 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.59 % Allowed : 10.13 % Favored : 88.27 % 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: 0.56 (0.12), residues: 4744 helix: 1.37 (0.11), residues: 2331 sheet: 0.15 (0.19), residues: 606 loop : -0.82 (0.13), residues: 1807 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.016 0.002 HIS F 95 PHE 0.018 0.001 PHE B 298 TYR 0.013 0.001 TYR B 182 ARG 0.007 0.000 ARG E 100 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 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 556 residues out of total 4014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 492 time to evaluate : 4.726 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: B 73 HIS cc_start: 0.8127 (m90) cc_final: 0.7554 (m90) REVERT: B 294 ASP cc_start: 0.8407 (m-30) cc_final: 0.8121 (m-30) REVERT: C 160 ASN cc_start: 0.8509 (m110) cc_final: 0.8083 (m110) REVERT: C 283 GLU cc_start: 0.7587 (tm-30) cc_final: 0.7387 (tm-30) REVERT: D 115 ILE cc_start: 0.9339 (mt) cc_final: 0.9125 (mp) REVERT: D 205 GLU cc_start: 0.8375 (tt0) cc_final: 0.7955 (tt0) REVERT: D 297 LYS cc_start: 0.9138 (mttt) cc_final: 0.8741 (tptp) REVERT: F 142 MET cc_start: 0.7471 (tmt) cc_final: 0.7029 (tmt) REVERT: F 256 LYS cc_start: 0.9172 (ttmm) cc_final: 0.8659 (tptt) REVERT: j 36 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7742 (pt0) REVERT: l 60 TYR cc_start: 0.8797 (m-80) cc_final: 0.8506 (m-80) REVERT: l 129 GLN cc_start: 0.7929 (OUTLIER) cc_final: 0.7652 (tp40) REVERT: m 60 TYR cc_start: 0.8768 (m-80) cc_final: 0.8520 (m-80) REVERT: n 60 TYR cc_start: 0.8988 (m-80) cc_final: 0.8724 (m-80) outliers start: 64 outliers final: 27 residues processed: 527 average time/residue: 2.5408 time to fit residues: 1646.8559 Evaluate side-chains 489 residues out of total 4014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 460 time to evaluate : 4.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 LYS Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain D residue 331 ASN Chi-restraints excluded: chain F residue 294 ASP Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain I residue 129 GLN Chi-restraints excluded: chain J residue 36 GLU Chi-restraints excluded: chain J residue 41 ASN Chi-restraints excluded: chain K residue 36 GLU Chi-restraints excluded: chain L residue 25 LYS Chi-restraints excluded: chain M residue 7 ILE Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain N residue 7 ILE Chi-restraints excluded: chain N residue 129 GLN Chi-restraints excluded: chain h residue 36 GLU Chi-restraints excluded: chain h residue 117 SER Chi-restraints excluded: chain i residue 5 MET Chi-restraints excluded: chain i residue 25 LYS Chi-restraints excluded: chain i residue 168 THR Chi-restraints excluded: chain j residue 36 GLU Chi-restraints excluded: chain j residue 98 MET Chi-restraints excluded: chain l residue 15 ARG Chi-restraints excluded: chain l residue 36 GLU Chi-restraints excluded: chain l residue 41 ASN Chi-restraints excluded: chain l residue 92 MET Chi-restraints excluded: chain l residue 129 GLN Chi-restraints excluded: chain l residue 168 THR Chi-restraints excluded: chain n residue 36 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 426 optimal weight: 5.9990 chunk 324 optimal weight: 2.9990 chunk 223 optimal weight: 3.9990 chunk 47 optimal weight: 9.9990 chunk 205 optimal weight: 9.9990 chunk 289 optimal weight: 2.9990 chunk 432 optimal weight: 4.9990 chunk 458 optimal weight: 3.9990 chunk 226 optimal weight: 2.9990 chunk 410 optimal weight: 3.9990 chunk 123 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 GLN E 94 ASN E 101 ASN ** F 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 41 ASN J 9 GLN K 9 GLN ** K 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 41 ASN h 41 ASN ** i 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 9 GLN ** n 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 37828 Z= 0.335 Angle : 0.507 6.912 51098 Z= 0.264 Chirality : 0.042 0.147 5882 Planarity : 0.003 0.086 6629 Dihedral : 5.692 90.470 5258 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.47 % Allowed : 11.00 % Favored : 87.53 % 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: 0.69 (0.12), residues: 4744 helix: 1.47 (0.11), residues: 2335 sheet: 0.10 (0.17), residues: 718 loop : -0.76 (0.14), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS F 95 PHE 0.013 0.001 PHE L 17 TYR 0.014 0.001 TYR B 182 ARG 0.015 0.000 ARG M 15 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 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 526 residues out of total 4014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 467 time to evaluate : 4.663 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: B 294 ASP cc_start: 0.8410 (m-30) cc_final: 0.8157 (m-30) REVERT: C 160 ASN cc_start: 0.8474 (m110) cc_final: 0.7986 (m110) REVERT: C 283 GLU cc_start: 0.7675 (tm-30) cc_final: 0.7375 (tm-30) REVERT: D 191 ARG cc_start: 0.8063 (mtp85) cc_final: 0.7653 (mtm110) REVERT: D 205 GLU cc_start: 0.8302 (tt0) cc_final: 0.7889 (tt0) REVERT: D 297 LYS cc_start: 0.9145 (mttt) cc_final: 0.8778 (tptp) REVERT: E 118 ILE cc_start: 0.8998 (mt) cc_final: 0.8735 (mm) REVERT: F 142 MET cc_start: 0.7472 (tmt) cc_final: 0.7035 (tmt) REVERT: F 256 LYS cc_start: 0.9161 (ttmm) cc_final: 0.8654 (tptt) REVERT: J 34 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.7915 (mp10) REVERT: K 15 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.7664 (ptp-170) REVERT: L 36 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7664 (pp20) REVERT: j 36 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7675 (pt0) REVERT: l 36 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7641 (pp20) REVERT: l 129 GLN cc_start: 0.7959 (OUTLIER) cc_final: 0.7693 (tp40) REVERT: m 36 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7493 (pt0) REVERT: m 60 TYR cc_start: 0.8822 (m-80) cc_final: 0.8588 (m-80) REVERT: n 60 TYR cc_start: 0.9026 (m-80) cc_final: 0.8809 (m-80) REVERT: n 149 MET cc_start: 0.8831 (mmp) cc_final: 0.8559 (mmp) outliers start: 59 outliers final: 30 residues processed: 496 average time/residue: 2.5410 time to fit residues: 1555.5906 Evaluate side-chains 483 residues out of total 4014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 446 time to evaluate : 4.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain D residue 331 ASN Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain H residue 41 ASN Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 129 GLN Chi-restraints excluded: chain J residue 34 GLN Chi-restraints excluded: chain J residue 36 GLU Chi-restraints excluded: chain J residue 41 ASN Chi-restraints excluded: chain K residue 15 ARG Chi-restraints excluded: chain K residue 36 GLU Chi-restraints excluded: chain K residue 108 LYS Chi-restraints excluded: chain K residue 113 CYS Chi-restraints excluded: chain L residue 25 LYS Chi-restraints excluded: chain L residue 36 GLU Chi-restraints excluded: chain M residue 7 ILE Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain N residue 25 LYS Chi-restraints excluded: chain N residue 129 GLN Chi-restraints excluded: chain h residue 15 ARG Chi-restraints excluded: chain h residue 36 GLU Chi-restraints excluded: chain h residue 117 SER Chi-restraints excluded: chain i residue 5 MET Chi-restraints excluded: chain i residue 25 LYS Chi-restraints excluded: chain i residue 168 THR Chi-restraints excluded: chain j residue 36 GLU Chi-restraints excluded: chain j residue 41 ASN Chi-restraints excluded: chain j residue 98 MET Chi-restraints excluded: chain k residue 98 MET Chi-restraints excluded: chain l residue 15 ARG Chi-restraints excluded: chain l residue 36 GLU Chi-restraints excluded: chain l residue 129 GLN Chi-restraints excluded: chain l residue 187 SER Chi-restraints excluded: chain m residue 36 GLU Chi-restraints excluded: chain m residue 98 MET Chi-restraints excluded: chain n residue 36 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 381 optimal weight: 1.9990 chunk 260 optimal weight: 0.8980 chunk 6 optimal weight: 10.0000 chunk 341 optimal weight: 1.9990 chunk 189 optimal weight: 20.0000 chunk 390 optimal weight: 2.9990 chunk 316 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 233 optimal weight: 1.9990 chunk 411 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 ASN ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 GLN C 342 ASN E 101 ASN F 209 GLN F 342 ASN I 41 ASN J 9 GLN K 9 GLN ** K 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 41 ASN h 41 ASN ** i 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 41 ASN ** l 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 9 GLN ** n 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 37828 Z= 0.199 Angle : 0.469 6.834 51098 Z= 0.240 Chirality : 0.040 0.143 5882 Planarity : 0.003 0.030 6629 Dihedral : 5.488 76.840 5255 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.12 % Allowed : 11.73 % Favored : 87.15 % 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: 0.87 (0.12), residues: 4744 helix: 1.63 (0.11), residues: 2339 sheet: 0.29 (0.19), residues: 592 loop : -0.68 (0.14), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS F 95 PHE 0.013 0.001 PHE L 17 TYR 0.013 0.001 TYR B 182 ARG 0.003 0.000 ARG C 191 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 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 511 residues out of total 4014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 466 time to evaluate : 4.736 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: C 160 ASN cc_start: 0.8296 (m110) cc_final: 0.8006 (m110) REVERT: C 283 GLU cc_start: 0.7669 (tm-30) cc_final: 0.7340 (tm-30) REVERT: C 363 MET cc_start: 0.8157 (tpp) cc_final: 0.7955 (tpp) REVERT: D 191 ARG cc_start: 0.8077 (mtp85) cc_final: 0.7629 (mtm110) REVERT: D 205 GLU cc_start: 0.8302 (tt0) cc_final: 0.7884 (tt0) REVERT: D 297 LYS cc_start: 0.9140 (mttt) cc_final: 0.8768 (tptp) REVERT: E 118 ILE cc_start: 0.8988 (mt) cc_final: 0.8733 (mm) REVERT: F 142 MET cc_start: 0.7490 (tmt) cc_final: 0.7031 (tmt) REVERT: F 256 LYS cc_start: 0.9153 (ttmm) cc_final: 0.8696 (tptt) REVERT: K 15 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.7640 (ptp-170) REVERT: M 17 PHE cc_start: 0.8413 (m-80) cc_final: 0.8009 (m-80) REVERT: j 36 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7650 (pt0) REVERT: l 129 GLN cc_start: 0.7932 (OUTLIER) cc_final: 0.7673 (tp40) REVERT: m 60 TYR cc_start: 0.8807 (m-80) cc_final: 0.8556 (m-80) REVERT: m 120 MET cc_start: 0.9171 (OUTLIER) cc_final: 0.8757 (ttm) REVERT: n 25 LYS cc_start: 0.9227 (mtpp) cc_final: 0.9016 (mtmt) REVERT: n 60 TYR cc_start: 0.9009 (m-80) cc_final: 0.8808 (m-80) outliers start: 45 outliers final: 23 residues processed: 489 average time/residue: 2.6076 time to fit residues: 1589.4396 Evaluate side-chains 476 residues out of total 4014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 449 time to evaluate : 4.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain D residue 331 ASN Chi-restraints excluded: chain E residue 101 ASN Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain F residue 294 ASP Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 129 GLN Chi-restraints excluded: chain J residue 34 GLN Chi-restraints excluded: chain K residue 15 ARG Chi-restraints excluded: chain K residue 36 GLU Chi-restraints excluded: chain K residue 108 LYS Chi-restraints excluded: chain K residue 113 CYS Chi-restraints excluded: chain L residue 25 LYS Chi-restraints excluded: chain L residue 113 CYS Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain N residue 25 LYS Chi-restraints excluded: chain N residue 129 GLN Chi-restraints excluded: chain h residue 36 GLU Chi-restraints excluded: chain i residue 25 LYS Chi-restraints excluded: chain j residue 36 GLU Chi-restraints excluded: chain j residue 98 MET Chi-restraints excluded: chain k residue 98 MET Chi-restraints excluded: chain l residue 15 ARG Chi-restraints excluded: chain l residue 129 GLN Chi-restraints excluded: chain l residue 187 SER Chi-restraints excluded: chain m residue 120 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 154 optimal weight: 9.9990 chunk 412 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 269 optimal weight: 0.9990 chunk 113 optimal weight: 10.0000 chunk 458 optimal weight: 0.6980 chunk 380 optimal weight: 3.9990 chunk 212 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 151 optimal weight: 20.0000 chunk 240 optimal weight: 3.9990 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 342 ASN I 41 ASN J 9 GLN ** K 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 41 ASN ** h 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 9 GLN ** n 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 37828 Z= 0.247 Angle : 0.472 6.776 51098 Z= 0.242 Chirality : 0.040 0.142 5882 Planarity : 0.003 0.082 6629 Dihedral : 5.367 60.437 5255 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.95 % Allowed : 12.05 % Favored : 87.01 % 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: 0.96 (0.12), residues: 4744 helix: 1.72 (0.11), residues: 2331 sheet: 0.33 (0.19), residues: 602 loop : -0.66 (0.14), residues: 1811 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS J 122 PHE 0.013 0.001 PHE L 17 TYR 0.011 0.001 TYR B 182 ARG 0.012 0.000 ARG M 15 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 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 497 residues out of total 4014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 459 time to evaluate : 4.745 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: C 160 ASN cc_start: 0.8305 (m110) cc_final: 0.8062 (m110) REVERT: C 283 GLU cc_start: 0.7698 (tm-30) cc_final: 0.7354 (tm-30) REVERT: C 363 MET cc_start: 0.8213 (tpp) cc_final: 0.7895 (tpp) REVERT: D 191 ARG cc_start: 0.8087 (mtp85) cc_final: 0.7643 (mtm110) REVERT: D 205 GLU cc_start: 0.8306 (tt0) cc_final: 0.7898 (tt0) REVERT: D 297 LYS cc_start: 0.9144 (mttt) cc_final: 0.8834 (tptp) REVERT: E 118 ILE cc_start: 0.8976 (mt) cc_final: 0.8716 (mm) REVERT: F 93 TYR cc_start: 0.8637 (t80) cc_final: 0.8168 (t80) REVERT: F 142 MET cc_start: 0.7512 (tmt) cc_final: 0.7091 (tmt) REVERT: F 331 ASN cc_start: 0.8464 (p0) cc_final: 0.8160 (p0) REVERT: K 15 ARG cc_start: 0.7884 (OUTLIER) cc_final: 0.7664 (ptp-170) REVERT: j 36 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7691 (pt0) REVERT: l 129 GLN cc_start: 0.7943 (OUTLIER) cc_final: 0.7695 (tp40) REVERT: m 36 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7538 (pt0) REVERT: m 60 TYR cc_start: 0.8845 (m-80) cc_final: 0.8640 (m-80) REVERT: m 120 MET cc_start: 0.9170 (OUTLIER) cc_final: 0.8745 (ttm) REVERT: n 25 LYS cc_start: 0.9231 (mtpp) cc_final: 0.9007 (mtmt) outliers start: 38 outliers final: 21 residues processed: 475 average time/residue: 2.5279 time to fit residues: 1478.2683 Evaluate side-chains 468 residues out of total 4014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 442 time to evaluate : 4.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain D residue 331 ASN Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain I residue 98 MET Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 129 GLN Chi-restraints excluded: chain K residue 15 ARG Chi-restraints excluded: chain K residue 36 GLU Chi-restraints excluded: chain K residue 108 LYS Chi-restraints excluded: chain K residue 113 CYS Chi-restraints excluded: chain L residue 25 LYS Chi-restraints excluded: chain L residue 113 CYS Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain N residue 25 LYS Chi-restraints excluded: chain N residue 129 GLN Chi-restraints excluded: chain h residue 36 GLU Chi-restraints excluded: chain j residue 36 GLU Chi-restraints excluded: chain j residue 98 MET Chi-restraints excluded: chain k residue 98 MET Chi-restraints excluded: chain l residue 15 ARG Chi-restraints excluded: chain l residue 129 GLN Chi-restraints excluded: chain m residue 36 GLU Chi-restraints excluded: chain m residue 120 MET Chi-restraints excluded: chain n residue 36 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 442 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 261 optimal weight: 0.7980 chunk 334 optimal weight: 3.9990 chunk 259 optimal weight: 0.2980 chunk 386 optimal weight: 3.9990 chunk 256 optimal weight: 2.9990 chunk 456 optimal weight: 3.9990 chunk 285 optimal weight: 0.9990 chunk 278 optimal weight: 2.9990 chunk 210 optimal weight: 2.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 ASN ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 342 ASN I 41 ASN J 9 GLN ** K 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 41 ASN ** h 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 41 ASN l 41 ASN ** l 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 9 GLN ** n 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.3703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 37828 Z= 0.187 Angle : 0.460 6.145 51098 Z= 0.235 Chirality : 0.040 0.141 5882 Planarity : 0.003 0.051 6629 Dihedral : 5.247 61.137 5255 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.97 % Allowed : 12.32 % Favored : 86.71 % 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: 1.06 (0.12), residues: 4744 helix: 1.82 (0.11), residues: 2329 sheet: 0.35 (0.19), residues: 602 loop : -0.61 (0.14), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS m 122 PHE 0.017 0.001 PHE m 101 TYR 0.013 0.001 TYR B 182 ARG 0.005 0.000 ARG M 15 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 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 495 residues out of total 4014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 456 time to evaluate : 4.703 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: C 160 ASN cc_start: 0.8283 (m110) cc_final: 0.8045 (m110) REVERT: C 178 ARG cc_start: 0.8016 (ptp-110) cc_final: 0.7786 (ptp-110) REVERT: C 283 GLU cc_start: 0.7746 (tm-30) cc_final: 0.7391 (tm-30) REVERT: C 363 MET cc_start: 0.8242 (tpp) cc_final: 0.7905 (tpp) REVERT: D 191 ARG cc_start: 0.8067 (mtp85) cc_final: 0.7626 (mtm110) REVERT: D 205 GLU cc_start: 0.8301 (tt0) cc_final: 0.7868 (tt0) REVERT: D 235 PHE cc_start: 0.8441 (m-10) cc_final: 0.7904 (m-80) REVERT: D 297 LYS cc_start: 0.9140 (mttt) cc_final: 0.8839 (tptp) REVERT: F 93 TYR cc_start: 0.8632 (t80) cc_final: 0.8227 (t80) REVERT: F 142 MET cc_start: 0.7545 (tmt) cc_final: 0.7116 (tmt) REVERT: F 331 ASN cc_start: 0.8474 (p0) cc_final: 0.8167 (p0) REVERT: J 18 ASP cc_start: 0.7660 (p0) cc_final: 0.7356 (p0) REVERT: K 15 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7637 (ptp-170) REVERT: L 36 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7600 (pp20) REVERT: n 25 LYS cc_start: 0.9219 (mtpp) cc_final: 0.8988 (mtmt) outliers start: 39 outliers final: 22 residues processed: 475 average time/residue: 2.5559 time to fit residues: 1502.0437 Evaluate side-chains 467 residues out of total 4014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 443 time to evaluate : 5.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain F residue 294 ASP Chi-restraints excluded: chain H residue 41 ASN Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 129 GLN Chi-restraints excluded: chain J residue 41 ASN Chi-restraints excluded: chain K residue 15 ARG Chi-restraints excluded: chain K residue 108 LYS Chi-restraints excluded: chain K residue 113 CYS Chi-restraints excluded: chain L residue 17 PHE Chi-restraints excluded: chain L residue 25 LYS Chi-restraints excluded: chain L residue 36 GLU Chi-restraints excluded: chain L residue 113 CYS Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain N residue 25 LYS Chi-restraints excluded: chain i residue 53 GLU Chi-restraints excluded: chain j residue 98 MET Chi-restraints excluded: chain k residue 98 MET Chi-restraints excluded: chain l residue 15 ARG Chi-restraints excluded: chain l residue 41 ASN Chi-restraints excluded: chain l residue 129 GLN 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: 2.9990 chunk 272 optimal weight: 2.9990 chunk 137 optimal weight: 9.9990 chunk 89 optimal weight: 4.9990 chunk 88 optimal weight: 10.0000 chunk 290 optimal weight: 2.9990 chunk 311 optimal weight: 0.7980 chunk 225 optimal weight: 1.9990 chunk 42 optimal weight: 7.9990 chunk 359 optimal weight: 5.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 ASN I 41 ASN J 9 GLN ** K 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 41 ASN ** h 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 41 ASN ** l 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 9 GLN ** n 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.3762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 37828 Z= 0.247 Angle : 0.470 5.988 51098 Z= 0.240 Chirality : 0.040 0.141 5882 Planarity : 0.003 0.076 6629 Dihedral : 5.220 60.983 5255 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.97 % Allowed : 12.35 % Favored : 86.68 % 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: 1.07 (0.12), residues: 4744 helix: 1.81 (0.11), residues: 2334 sheet: 0.38 (0.19), residues: 602 loop : -0.62 (0.14), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS m 122 PHE 0.015 0.001 PHE E 350 TYR 0.017 0.001 TYR B 182 ARG 0.014 0.000 ARG M 15 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 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 486 residues out of total 4014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 447 time to evaluate : 4.745 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: C 283 GLU cc_start: 0.7758 (tm-30) cc_final: 0.7388 (tm-30) REVERT: C 363 MET cc_start: 0.8282 (tpp) cc_final: 0.7936 (tpp) REVERT: D 191 ARG cc_start: 0.8084 (mtp85) cc_final: 0.7637 (mtm110) REVERT: D 205 GLU cc_start: 0.8296 (tt0) cc_final: 0.7862 (tt0) REVERT: D 297 LYS cc_start: 0.9143 (mttt) cc_final: 0.8846 (tptp) REVERT: E 118 ILE cc_start: 0.8950 (mt) cc_final: 0.8692 (mm) REVERT: F 93 TYR cc_start: 0.8662 (t80) cc_final: 0.8262 (t80) REVERT: F 142 MET cc_start: 0.7563 (tmt) cc_final: 0.7134 (tmt) REVERT: F 331 ASN cc_start: 0.8483 (p0) cc_final: 0.8180 (p0) REVERT: K 15 ARG cc_start: 0.7888 (OUTLIER) cc_final: 0.7636 (ptp-170) REVERT: L 36 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7619 (pp20) REVERT: N 34 GLN cc_start: 0.8443 (mm-40) cc_final: 0.8208 (mm-40) REVERT: h 36 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7689 (pp20) REVERT: i 36 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7433 (pt0) REVERT: j 36 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7702 (pt0) REVERT: l 129 GLN cc_start: 0.7943 (OUTLIER) cc_final: 0.7676 (tp40) outliers start: 39 outliers final: 21 residues processed: 467 average time/residue: 2.5357 time to fit residues: 1461.0916 Evaluate side-chains 468 residues out of total 4014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 441 time to evaluate : 4.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain F residue 294 ASP Chi-restraints excluded: chain H residue 41 ASN Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain I residue 98 MET Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 129 GLN Chi-restraints excluded: chain J residue 41 ASN Chi-restraints excluded: chain K residue 15 ARG Chi-restraints excluded: chain K residue 108 LYS Chi-restraints excluded: chain K residue 113 CYS Chi-restraints excluded: chain L residue 25 LYS Chi-restraints excluded: chain L residue 36 GLU Chi-restraints excluded: chain L residue 113 CYS Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain N residue 25 LYS Chi-restraints excluded: chain h residue 36 GLU Chi-restraints excluded: chain i residue 36 GLU Chi-restraints excluded: chain i residue 53 GLU Chi-restraints excluded: chain j residue 36 GLU Chi-restraints excluded: chain j residue 98 MET Chi-restraints excluded: chain k residue 98 MET Chi-restraints excluded: chain l residue 129 GLN Chi-restraints excluded: chain m residue 98 MET Chi-restraints excluded: chain n residue 36 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 415 optimal weight: 2.9990 chunk 437 optimal weight: 0.8980 chunk 399 optimal weight: 3.9990 chunk 425 optimal weight: 3.9990 chunk 256 optimal weight: 2.9990 chunk 185 optimal weight: 6.9990 chunk 334 optimal weight: 2.9990 chunk 130 optimal weight: 7.9990 chunk 384 optimal weight: 2.9990 chunk 402 optimal weight: 1.9990 chunk 424 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 ASN ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 342 ASN D 83 GLN F 209 GLN I 41 ASN J 9 GLN ** K 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 41 ASN ** h 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 41 ASN l 41 ASN ** l 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 9 GLN ** n 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 37828 Z= 0.229 Angle : 0.469 5.945 51098 Z= 0.240 Chirality : 0.040 0.141 5882 Planarity : 0.003 0.068 6629 Dihedral : 5.192 61.456 5255 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.95 % Allowed : 12.40 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.12), residues: 4744 helix: 1.84 (0.11), residues: 2338 sheet: 0.37 (0.19), residues: 602 loop : -0.60 (0.14), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS m 122 PHE 0.014 0.001 PHE L 17 TYR 0.013 0.001 TYR A 171 ARG 0.013 0.000 ARG M 15 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 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 485 residues out of total 4014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 447 time to evaluate : 4.706 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 163 GLN cc_start: 0.9026 (tt0) cc_final: 0.8540 (tp-100) REVERT: B 142 MET cc_start: 0.8596 (mmm) cc_final: 0.8380 (mmm) REVERT: C 283 GLU cc_start: 0.7777 (tm-30) cc_final: 0.7406 (tm-30) REVERT: C 363 MET cc_start: 0.8296 (tpp) cc_final: 0.8019 (tpp) REVERT: D 191 ARG cc_start: 0.8089 (mtp85) cc_final: 0.7638 (mtm110) REVERT: D 205 GLU cc_start: 0.8281 (tt0) cc_final: 0.7845 (tt0) REVERT: D 297 LYS cc_start: 0.9141 (mttt) cc_final: 0.8854 (tptp) REVERT: E 118 ILE cc_start: 0.8949 (mt) cc_final: 0.8689 (mm) REVERT: F 93 TYR cc_start: 0.8647 (t80) cc_final: 0.8265 (t80) REVERT: F 142 MET cc_start: 0.7555 (tmt) cc_final: 0.7131 (tmt) REVERT: F 331 ASN cc_start: 0.8489 (p0) cc_final: 0.8240 (p0) REVERT: K 15 ARG cc_start: 0.7878 (OUTLIER) cc_final: 0.7599 (ptp-170) REVERT: L 36 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7622 (pp20) REVERT: N 34 GLN cc_start: 0.8445 (mm-40) cc_final: 0.8215 (mm-40) REVERT: j 36 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7716 (pt0) outliers start: 38 outliers final: 20 residues processed: 467 average time/residue: 2.6027 time to fit residues: 1511.3297 Evaluate side-chains 473 residues out of total 4014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 450 time to evaluate : 4.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain F residue 294 ASP Chi-restraints excluded: chain H residue 41 ASN Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 129 GLN Chi-restraints excluded: chain J residue 41 ASN Chi-restraints excluded: chain K residue 15 ARG Chi-restraints excluded: chain K residue 108 LYS Chi-restraints excluded: chain K residue 113 CYS Chi-restraints excluded: chain L residue 25 LYS Chi-restraints excluded: chain L residue 36 GLU Chi-restraints excluded: chain L residue 113 CYS Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain N residue 25 LYS Chi-restraints excluded: chain j residue 36 GLU Chi-restraints excluded: chain j residue 41 ASN Chi-restraints excluded: chain j residue 98 MET Chi-restraints excluded: chain k residue 98 MET Chi-restraints excluded: chain l residue 129 GLN Chi-restraints excluded: chain m residue 98 MET Chi-restraints excluded: chain n residue 36 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 279 optimal weight: 0.9990 chunk 450 optimal weight: 2.9990 chunk 274 optimal weight: 4.9990 chunk 213 optimal weight: 0.8980 chunk 312 optimal weight: 4.9990 chunk 472 optimal weight: 0.0980 chunk 434 optimal weight: 0.9980 chunk 376 optimal weight: 3.9990 chunk 39 optimal weight: 20.0000 chunk 290 optimal weight: 2.9990 chunk 230 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 342 ASN I 41 ASN J 9 GLN ** K 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 41 ASN ** h 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 41 ASN m 9 GLN ** n 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.3881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 37828 Z= 0.163 Angle : 0.461 7.070 51098 Z= 0.234 Chirality : 0.040 0.142 5882 Planarity : 0.003 0.070 6629 Dihedral : 5.136 61.256 5255 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.60 % Allowed : 12.82 % Favored : 86.58 % 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: 1.17 (0.12), residues: 4744 helix: 1.91 (0.11), residues: 2337 sheet: 0.38 (0.19), residues: 602 loop : -0.57 (0.14), residues: 1805 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS F 68 PHE 0.014 0.001 PHE L 17 TYR 0.015 0.001 TYR E 385 ARG 0.019 0.000 ARG M 15 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 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 481 residues out of total 4014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 457 time to evaluate : 5.988 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: A 163 GLN cc_start: 0.9026 (tt0) cc_final: 0.8540 (tp-100) REVERT: B 142 MET cc_start: 0.8580 (mmm) cc_final: 0.8377 (mmm) REVERT: C 283 GLU cc_start: 0.7783 (tm-30) cc_final: 0.7408 (tm-30) REVERT: C 363 MET cc_start: 0.8297 (tpp) cc_final: 0.8016 (tpp) REVERT: D 191 ARG cc_start: 0.8076 (mtp85) cc_final: 0.7627 (mtm110) REVERT: D 205 GLU cc_start: 0.8284 (tt0) cc_final: 0.7858 (tt0) REVERT: D 297 LYS cc_start: 0.9137 (mttt) cc_final: 0.8852 (tptp) REVERT: E 118 ILE cc_start: 0.8957 (mt) cc_final: 0.8702 (mm) REVERT: F 93 TYR cc_start: 0.8645 (t80) cc_final: 0.8265 (t80) REVERT: F 142 MET cc_start: 0.7583 (tmt) cc_final: 0.7157 (tmt) REVERT: F 331 ASN cc_start: 0.8475 (p0) cc_final: 0.8203 (p0) REVERT: J 18 ASP cc_start: 0.7679 (p0) cc_final: 0.7379 (p0) REVERT: K 15 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.7665 (ptp-170) REVERT: L 36 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7599 (pp20) REVERT: M 41 ASN cc_start: 0.8069 (OUTLIER) cc_final: 0.7850 (t0) REVERT: N 34 GLN cc_start: 0.8435 (mm-40) cc_final: 0.8211 (mm-40) outliers start: 24 outliers final: 17 residues processed: 467 average time/residue: 2.5684 time to fit residues: 1484.1356 Evaluate side-chains 467 residues out of total 4014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 447 time to evaluate : 4.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain F residue 294 ASP Chi-restraints excluded: chain H residue 41 ASN Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 129 GLN Chi-restraints excluded: chain J residue 41 ASN Chi-restraints excluded: chain K residue 15 ARG Chi-restraints excluded: chain K residue 108 LYS Chi-restraints excluded: chain K residue 113 CYS Chi-restraints excluded: chain L residue 25 LYS Chi-restraints excluded: chain L residue 36 GLU Chi-restraints excluded: chain L residue 113 CYS Chi-restraints excluded: chain M residue 41 ASN Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain j residue 98 MET Chi-restraints excluded: chain k residue 98 MET Chi-restraints excluded: chain l residue 129 GLN Chi-restraints excluded: chain m residue 98 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 298 optimal weight: 2.9990 chunk 400 optimal weight: 2.9990 chunk 115 optimal weight: 0.2980 chunk 346 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 104 optimal weight: 9.9990 chunk 376 optimal weight: 3.9990 chunk 157 optimal weight: 10.0000 chunk 386 optimal weight: 3.9990 chunk 47 optimal weight: 10.0000 chunk 69 optimal weight: 0.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 41 ASN J 9 GLN ** K 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 41 ASN ** h 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 41 ASN l 41 ASN ** l 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 9 GLN ** n 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.146060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.080183 restraints weight = 153253.663| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 1.99 r_work: 0.2960 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2764 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2764 r_free = 0.2764 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2764 r_free = 0.2764 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2764 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.147 37828 Z= 0.190 Angle : 0.569 59.190 51098 Z= 0.321 Chirality : 0.040 0.231 5882 Planarity : 0.003 0.079 6629 Dihedral : 5.136 61.261 5255 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.65 % Allowed : 12.87 % Favored : 86.48 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.12), residues: 4744 helix: 1.90 (0.11), residues: 2337 sheet: 0.37 (0.19), residues: 602 loop : -0.57 (0.14), residues: 1805 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS F 68 PHE 0.013 0.001 PHE L 17 TYR 0.011 0.001 TYR E 385 ARG 0.003 0.000 ARG j 15 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25712.42 seconds wall clock time: 441 minutes 59.45 seconds (26519.45 seconds total)