Starting phenix.real_space_refine on Tue Aug 26 14:09:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9out_70881/08_2025/9out_70881.cif Found real_map, /net/cci-nas-00/data/ceres_data/9out_70881/08_2025/9out_70881.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9out_70881/08_2025/9out_70881.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9out_70881/08_2025/9out_70881.map" model { file = "/net/cci-nas-00/data/ceres_data/9out_70881/08_2025/9out_70881.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9out_70881/08_2025/9out_70881.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.027 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: 4 Type Number sf(0) Gaussians S 322 5.16 5 C 23205 2.51 5 N 6082 2.21 5 O 6930 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36539 Number of models: 1 Model: "" Number of chains: 15 Chain: "C" Number of atoms: 2760 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 349, 2760 Classifications: {'peptide': 349} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 337} Chain: "D" Number of atoms: 2748 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 348, 2748 Classifications: {'peptide': 348} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 336} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 2774 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 352, 2774 Classifications: {'peptide': 352} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 338} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 1100 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 135, 1100 Classifications: {'peptide': 135} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 130} Chain: "J" Number of atoms: 2730 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 346, 2730 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 335} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 2760 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 349, 2760 Classifications: {'peptide': 349} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 337} Chain: "N" Number of atoms: 2764 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 350, 2764 Classifications: {'peptide': 350} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 338} Chain: "A" Number of atoms: 2748 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 348, 2748 Classifications: {'peptide': 348} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 336} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2760 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 349, 2760 Classifications: {'peptide': 349} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 337} Chain breaks: 1 Chain: "E" Number of atoms: 1100 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 135, 1100 Classifications: {'peptide': 135} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 130} Chain: "F" Number of atoms: 2760 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 349, 2760 Classifications: {'peptide': 349} Link IDs: {'PTRANS': 10, 'TRANS': 338} Chain breaks: 1 Chain: "G" Number of atoms: 1290 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 160, 1290 Classifications: {'peptide': 160} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 154} Chain: "K" Number of atoms: 2730 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 346, 2730 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 336} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 2774 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 352, 2774 Classifications: {'peptide': 352} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 338} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "P" Number of atoms: 2741 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 346, 2741 Classifications: {'peptide': 346} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 8, 'TRANS': 335} Chain breaks: 1 Time building chain proxies: 9.10, per 1000 atoms: 0.25 Number of scatterers: 36539 At special positions: 0 Unit cell: (138.467, 153.265, 314.986, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 322 16.00 O 6930 8.00 N 6082 7.00 C 23205 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS J 361 " - pdb=" SG CYS M 361 " distance=2.03 Simple disulfide: pdb=" SG CYS F 361 " - pdb=" SG CYS K 361 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 3.04 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 715.3 nanoseconds 9148 Ramachandran restraints generated. 4574 Oldfield, 0 Emsley, 4574 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8840 Finding SS restraints... Secondary structure from input PDB file: 187 helices and 41 sheets defined 39.9% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'C' and resid 77 through 81 removed outlier: 4.104A pdb=" N LYS C 81 " --> pdb=" O GLU C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 144 Processing helix chain 'C' and resid 145 through 148 Processing helix chain 'C' and resid 150 through 152 No H-bonds generated for 'chain 'C' and resid 150 through 152' Processing helix chain 'C' and resid 187 through 197 Processing helix chain 'C' and resid 215 through 222 removed outlier: 3.638A pdb=" N ARG C 221 " --> pdb=" O ILE C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 230 removed outlier: 3.674A pdb=" N MET C 228 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE C 229 " --> pdb=" O PHE C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 240 removed outlier: 3.698A pdb=" N ASN C 239 " --> pdb=" O GLU C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 260 Processing helix chain 'C' and resid 269 through 281 Processing helix chain 'C' and resid 282 through 295 removed outlier: 3.631A pdb=" N SER C 295 " --> pdb=" O ASP C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 313 Processing helix chain 'C' and resid 314 through 333 removed outlier: 3.663A pdb=" N TYR C 327 " --> pdb=" O ASP C 323 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N SER C 330 " --> pdb=" O ASN C 326 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ASP C 331 " --> pdb=" O TYR C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 345 removed outlier: 4.033A pdb=" N LYS C 339 " --> pdb=" O THR C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 360 removed outlier: 3.535A pdb=" N VAL C 349 " --> pdb=" O HIS C 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 81 removed outlier: 3.548A pdb=" N LYS D 81 " --> pdb=" O GLU D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 144 Processing helix chain 'D' and resid 185 through 196 Processing helix chain 'D' and resid 215 through 222 removed outlier: 3.586A pdb=" N ARG D 221 " --> pdb=" O ILE D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 231 Processing helix chain 'D' and resid 247 through 261 removed outlier: 4.588A pdb=" N GLU D 253 " --> pdb=" O GLU D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 281 removed outlier: 3.667A pdb=" N LEU D 273 " --> pdb=" O MET D 269 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ALA D 275 " --> pdb=" O ASP D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 296 Processing helix chain 'D' and resid 301 through 312 Processing helix chain 'D' and resid 315 through 328 Processing helix chain 'D' and resid 328 through 333 removed outlier: 3.776A pdb=" N LEU D 333 " --> pdb=" O ALA D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 345 removed outlier: 3.915A pdb=" N LYS D 339 " --> pdb=" O THR D 335 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL D 343 " --> pdb=" O LYS D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 360 removed outlier: 3.860A pdb=" N VAL D 349 " --> pdb=" O HIS D 345 " (cutoff:3.500A) Processing helix chain 'H' and resid 139 through 144 Processing helix chain 'H' and resid 145 through 148 Processing helix chain 'H' and resid 150 through 154 removed outlier: 3.568A pdb=" N ASP H 153 " --> pdb=" O LEU H 150 " (cutoff:3.500A) Processing helix chain 'H' and resid 185 through 197 removed outlier: 3.555A pdb=" N TRP H 194 " --> pdb=" O LEU H 190 " (cutoff:3.500A) Processing helix chain 'H' and resid 214 through 222 removed outlier: 4.216A pdb=" N LEU H 218 " --> pdb=" O HIS H 214 " (cutoff:3.500A) Processing helix chain 'H' and resid 222 through 231 Processing helix chain 'H' and resid 232 through 237 removed outlier: 4.516A pdb=" N SER H 236 " --> pdb=" O GLU H 232 " (cutoff:3.500A) Processing helix chain 'H' and resid 247 through 261 removed outlier: 4.473A pdb=" N GLU H 253 " --> pdb=" O GLU H 249 " (cutoff:3.500A) Processing helix chain 'H' and resid 269 through 280 Processing helix chain 'H' and resid 282 through 296 removed outlier: 3.552A pdb=" N VAL H 287 " --> pdb=" O GLU H 283 " (cutoff:3.500A) Processing helix chain 'H' and resid 301 through 313 removed outlier: 3.518A pdb=" N ILE H 305 " --> pdb=" O ASN H 301 " (cutoff:3.500A) Processing helix chain 'H' and resid 314 through 328 Processing helix chain 'H' and resid 329 through 332 removed outlier: 3.540A pdb=" N VAL H 332 " --> pdb=" O ALA H 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 329 through 332' Processing helix chain 'H' and resid 335 through 345 removed outlier: 3.559A pdb=" N LYS H 339 " --> pdb=" O THR H 335 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL H 343 " --> pdb=" O LYS H 339 " (cutoff:3.500A) Processing helix chain 'H' and resid 345 through 360 removed outlier: 3.510A pdb=" N VAL H 349 " --> pdb=" O HIS H 345 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN H 360 " --> pdb=" O LEU H 356 " (cutoff:3.500A) Processing helix chain 'I' and resid 77 through 81 removed outlier: 3.833A pdb=" N LYS I 81 " --> pdb=" O GLU I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 138 through 144 Processing helix chain 'I' and resid 145 through 148 Processing helix chain 'I' and resid 150 through 154 removed outlier: 3.911A pdb=" N ASP I 153 " --> pdb=" O LEU I 150 " (cutoff:3.500A) Processing helix chain 'J' and resid 139 through 144 Processing helix chain 'J' and resid 150 through 154 removed outlier: 3.866A pdb=" N ASP J 153 " --> pdb=" O LEU J 150 " (cutoff:3.500A) Processing helix chain 'J' and resid 187 through 197 removed outlier: 3.510A pdb=" N LEU J 193 " --> pdb=" O GLU J 189 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N TRP J 194 " --> pdb=" O LEU J 190 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLU J 195 " --> pdb=" O GLY J 191 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN J 196 " --> pdb=" O GLY J 192 " (cutoff:3.500A) Processing helix chain 'J' and resid 214 through 221 removed outlier: 4.124A pdb=" N LEU J 218 " --> pdb=" O HIS J 214 " (cutoff:3.500A) Processing helix chain 'J' and resid 222 through 231 removed outlier: 3.649A pdb=" N HIS J 231 " --> pdb=" O ALA J 227 " (cutoff:3.500A) Processing helix chain 'J' and resid 247 through 260 removed outlier: 3.609A pdb=" N GLU J 253 " --> pdb=" O GLU J 249 " (cutoff:3.500A) Processing helix chain 'J' and resid 269 through 280 removed outlier: 3.732A pdb=" N ALA J 275 " --> pdb=" O ASP J 271 " (cutoff:3.500A) Processing helix chain 'J' and resid 282 through 296 Processing helix chain 'J' and resid 301 through 312 Processing helix chain 'J' and resid 314 through 328 Processing helix chain 'J' and resid 335 through 345 Processing helix chain 'J' and resid 345 through 358 removed outlier: 3.657A pdb=" N VAL J 349 " --> pdb=" O HIS J 345 " (cutoff:3.500A) Processing helix chain 'M' and resid 139 through 144 Processing helix chain 'M' and resid 150 through 152 No H-bonds generated for 'chain 'M' and resid 150 through 152' Processing helix chain 'M' and resid 185 through 197 removed outlier: 3.569A pdb=" N GLU M 195 " --> pdb=" O GLY M 191 " (cutoff:3.500A) Processing helix chain 'M' and resid 215 through 222 Processing helix chain 'M' and resid 222 through 231 removed outlier: 3.949A pdb=" N MET M 228 " --> pdb=" O VAL M 224 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N HIS M 231 " --> pdb=" O ALA M 227 " (cutoff:3.500A) Processing helix chain 'M' and resid 233 through 238 removed outlier: 3.500A pdb=" N LYS M 237 " --> pdb=" O MET M 233 " (cutoff:3.500A) Processing helix chain 'M' and resid 247 through 261 Processing helix chain 'M' and resid 265 through 268 removed outlier: 3.510A pdb=" N LYS M 268 " --> pdb=" O ASN M 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 265 through 268' Processing helix chain 'M' and resid 269 through 281 Processing helix chain 'M' and resid 282 through 295 removed outlier: 3.623A pdb=" N SER M 295 " --> pdb=" O ASP M 291 " (cutoff:3.500A) Processing helix chain 'M' and resid 301 through 312 Processing helix chain 'M' and resid 315 through 328 Processing helix chain 'M' and resid 328 through 333 removed outlier: 3.634A pdb=" N LEU M 333 " --> pdb=" O ALA M 329 " (cutoff:3.500A) Processing helix chain 'M' and resid 335 through 345 removed outlier: 3.500A pdb=" N LYS M 339 " --> pdb=" O THR M 335 " (cutoff:3.500A) Processing helix chain 'M' and resid 345 through 358 removed outlier: 3.975A pdb=" N VAL M 349 " --> pdb=" O HIS M 345 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA M 350 " --> pdb=" O PRO M 346 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER M 358 " --> pdb=" O ARG M 354 " (cutoff:3.500A) Processing helix chain 'N' and resid 43 through 48 removed outlier: 3.509A pdb=" N GLU N 47 " --> pdb=" O PHE N 43 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N MET N 48 " --> pdb=" O CYS N 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 43 through 48' Processing helix chain 'N' and resid 60 through 64 removed outlier: 3.702A pdb=" N ASP N 63 " --> pdb=" O GLY N 60 " (cutoff:3.500A) Processing helix chain 'N' and resid 78 through 82 removed outlier: 3.620A pdb=" N LYS N 81 " --> pdb=" O GLU N 78 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ASP N 82 " --> pdb=" O GLU N 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 78 through 82' Processing helix chain 'N' and resid 138 through 144 Processing helix chain 'N' and resid 145 through 148 Processing helix chain 'N' and resid 185 through 197 Processing helix chain 'N' and resid 214 through 222 Processing helix chain 'N' and resid 222 through 229 Processing helix chain 'N' and resid 247 through 261 Processing helix chain 'N' and resid 269 through 281 Processing helix chain 'N' and resid 282 through 295 Processing helix chain 'N' and resid 301 through 312 Processing helix chain 'N' and resid 314 through 328 Processing helix chain 'N' and resid 328 through 333 removed outlier: 3.560A pdb=" N LEU N 333 " --> pdb=" O ALA N 329 " (cutoff:3.500A) Processing helix chain 'N' and resid 335 through 345 removed outlier: 3.527A pdb=" N LYS N 339 " --> pdb=" O THR N 335 " (cutoff:3.500A) Processing helix chain 'N' and resid 345 through 358 removed outlier: 3.623A pdb=" N VAL N 349 " --> pdb=" O HIS N 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 81 removed outlier: 3.683A pdb=" N LYS A 81 " --> pdb=" O GLU A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 144 Processing helix chain 'A' and resid 150 through 154 removed outlier: 3.691A pdb=" N ASP A 153 " --> pdb=" O LEU A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 196 removed outlier: 3.617A pdb=" N TRP A 194 " --> pdb=" O LEU A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 222 removed outlier: 3.731A pdb=" N ALA A 219 " --> pdb=" O LYS A 215 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ARG A 221 " --> pdb=" O ILE A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 231 removed outlier: 3.618A pdb=" N ALA A 227 " --> pdb=" O PRO A 223 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLU A 230 " --> pdb=" O SER A 226 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N HIS A 231 " --> pdb=" O ALA A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 259 removed outlier: 4.422A pdb=" N GLU A 253 " --> pdb=" O GLU A 249 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE A 258 " --> pdb=" O MET A 254 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR A 259 " --> pdb=" O MET A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 269 through 280 removed outlier: 3.613A pdb=" N LEU A 274 " --> pdb=" O ALA A 270 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ALA A 275 " --> pdb=" O ASP A 271 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS A 279 " --> pdb=" O ALA A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 296 Processing helix chain 'A' and resid 301 through 312 Processing helix chain 'A' and resid 315 through 328 Processing helix chain 'A' and resid 328 through 333 removed outlier: 3.854A pdb=" N LEU A 333 " --> pdb=" O ALA A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 345 removed outlier: 3.613A pdb=" N LYS A 339 " --> pdb=" O THR A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 360 removed outlier: 3.727A pdb=" N VAL A 349 " --> pdb=" O HIS A 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 81 removed outlier: 3.701A pdb=" N LYS B 81 " --> pdb=" O GLU B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 144 Processing helix chain 'B' and resid 150 through 152 No H-bonds generated for 'chain 'B' and resid 150 through 152' Processing helix chain 'B' and resid 186 through 197 removed outlier: 3.986A pdb=" N LEU B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 222 Processing helix chain 'B' and resid 222 through 230 removed outlier: 3.893A pdb=" N MET B 228 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N PHE B 229 " --> pdb=" O PHE B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 260 Processing helix chain 'B' and resid 269 through 281 Processing helix chain 'B' and resid 282 through 295 removed outlier: 3.928A pdb=" N SER B 295 " --> pdb=" O ASP B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 313 Processing helix chain 'B' and resid 314 through 328 Processing helix chain 'B' and resid 328 through 333 removed outlier: 3.851A pdb=" N LEU B 333 " --> pdb=" O ALA B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 345 removed outlier: 3.702A pdb=" N LYS B 339 " --> pdb=" O THR B 335 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET B 341 " --> pdb=" O GLY B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 360 Processing helix chain 'E' and resid 138 through 143 Processing helix chain 'E' and resid 150 through 154 removed outlier: 3.994A pdb=" N ASP E 153 " --> pdb=" O LEU E 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 81 Processing helix chain 'F' and resid 138 through 144 Processing helix chain 'F' and resid 145 through 148 Processing helix chain 'F' and resid 150 through 152 No H-bonds generated for 'chain 'F' and resid 150 through 152' Processing helix chain 'F' and resid 185 through 197 removed outlier: 3.699A pdb=" N LEU F 190 " --> pdb=" O LEU F 186 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU F 193 " --> pdb=" O GLU F 189 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TRP F 194 " --> pdb=" O LEU F 190 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU F 195 " --> pdb=" O GLY F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 215 through 222 removed outlier: 3.694A pdb=" N ARG F 221 " --> pdb=" O ILE F 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 229 Processing helix chain 'F' and resid 233 through 238 removed outlier: 3.634A pdb=" N LYS F 238 " --> pdb=" O GLU F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 260 removed outlier: 3.811A pdb=" N GLU F 253 " --> pdb=" O GLU F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 268 removed outlier: 3.760A pdb=" N LYS F 268 " --> pdb=" O ASN F 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 265 through 268' Processing helix chain 'F' and resid 269 through 280 removed outlier: 3.662A pdb=" N LEU F 273 " --> pdb=" O MET F 269 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU F 274 " --> pdb=" O ALA F 270 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ALA F 275 " --> pdb=" O ASP F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 295 removed outlier: 3.760A pdb=" N SER F 295 " --> pdb=" O ASP F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 312 Processing helix chain 'F' and resid 314 through 333 removed outlier: 5.799A pdb=" N SER F 330 " --> pdb=" O ASN F 326 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ASP F 331 " --> pdb=" O TYR F 327 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU F 333 " --> pdb=" O ALA F 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 345 removed outlier: 3.918A pdb=" N LYS F 339 " --> pdb=" O THR F 335 " (cutoff:3.500A) Processing helix chain 'F' and resid 347 through 358 removed outlier: 4.020A pdb=" N GLU F 351 " --> pdb=" O HIS F 347 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 81 removed outlier: 3.625A pdb=" N LYS G 81 " --> pdb=" O GLU G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 144 Processing helix chain 'G' and resid 150 through 154 removed outlier: 4.199A pdb=" N ASP G 153 " --> pdb=" O LEU G 150 " (cutoff:3.500A) Processing helix chain 'K' and resid 77 through 81 removed outlier: 3.617A pdb=" N LYS K 81 " --> pdb=" O GLU K 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 139 through 144 Processing helix chain 'K' and resid 145 through 148 Processing helix chain 'K' and resid 150 through 152 No H-bonds generated for 'chain 'K' and resid 150 through 152' Processing helix chain 'K' and resid 185 through 197 removed outlier: 3.684A pdb=" N LEU K 190 " --> pdb=" O LEU K 186 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TRP K 194 " --> pdb=" O LEU K 190 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU K 195 " --> pdb=" O GLY K 191 " (cutoff:3.500A) Processing helix chain 'K' and resid 214 through 222 removed outlier: 4.021A pdb=" N LEU K 218 " --> pdb=" O HIS K 214 " (cutoff:3.500A) Processing helix chain 'K' and resid 222 through 230 removed outlier: 4.450A pdb=" N GLU K 230 " --> pdb=" O SER K 226 " (cutoff:3.500A) Processing helix chain 'K' and resid 247 through 260 removed outlier: 4.011A pdb=" N GLU K 253 " --> pdb=" O GLU K 249 " (cutoff:3.500A) Processing helix chain 'K' and resid 269 through 280 removed outlier: 3.509A pdb=" N LYS K 279 " --> pdb=" O ALA K 275 " (cutoff:3.500A) Processing helix chain 'K' and resid 282 through 296 removed outlier: 3.699A pdb=" N VAL K 287 " --> pdb=" O GLU K 283 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N CYS K 289 " --> pdb=" O LEU K 285 " (cutoff:3.500A) Processing helix chain 'K' and resid 301 through 312 Processing helix chain 'K' and resid 314 through 328 Processing helix chain 'K' and resid 335 through 345 Processing helix chain 'K' and resid 345 through 359 removed outlier: 3.673A pdb=" N VAL K 349 " --> pdb=" O HIS K 345 " (cutoff:3.500A) Processing helix chain 'L' and resid 40 through 44 Processing helix chain 'L' and resid 138 through 144 Processing helix chain 'L' and resid 145 through 148 Processing helix chain 'L' and resid 150 through 154 Processing helix chain 'L' and resid 185 through 197 Processing helix chain 'L' and resid 214 through 222 removed outlier: 3.804A pdb=" N LEU L 218 " --> pdb=" O HIS L 214 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA L 220 " --> pdb=" O ALA L 216 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG L 221 " --> pdb=" O ILE L 217 " (cutoff:3.500A) Processing helix chain 'L' and resid 222 through 230 removed outlier: 3.577A pdb=" N GLU L 230 " --> pdb=" O SER L 226 " (cutoff:3.500A) Processing helix chain 'L' and resid 232 through 237 removed outlier: 4.354A pdb=" N SER L 236 " --> pdb=" O GLU L 232 " (cutoff:3.500A) Processing helix chain 'L' and resid 247 through 261 removed outlier: 4.300A pdb=" N GLU L 253 " --> pdb=" O GLU L 249 " (cutoff:3.500A) Processing helix chain 'L' and resid 266 through 268 No H-bonds generated for 'chain 'L' and resid 266 through 268' Processing helix chain 'L' and resid 269 through 280 Processing helix chain 'L' and resid 282 through 296 Processing helix chain 'L' and resid 301 through 312 Processing helix chain 'L' and resid 314 through 328 Processing helix chain 'L' and resid 335 through 345 removed outlier: 3.662A pdb=" N LYS L 339 " --> pdb=" O THR L 335 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL L 343 " --> pdb=" O LYS L 339 " (cutoff:3.500A) Processing helix chain 'L' and resid 345 through 360 removed outlier: 3.913A pdb=" N VAL L 349 " --> pdb=" O HIS L 345 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA L 350 " --> pdb=" O PRO L 346 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER L 358 " --> pdb=" O ARG L 354 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLN L 360 " --> pdb=" O LEU L 356 " (cutoff:3.500A) Processing helix chain 'P' and resid 43 through 48 Processing helix chain 'P' and resid 60 through 64 removed outlier: 3.874A pdb=" N ASP P 63 " --> pdb=" O GLY P 60 " (cutoff:3.500A) Processing helix chain 'P' and resid 78 through 81 removed outlier: 3.589A pdb=" N LYS P 81 " --> pdb=" O GLU P 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 78 through 81' Processing helix chain 'P' and resid 139 through 144 Processing helix chain 'P' and resid 145 through 148 Processing helix chain 'P' and resid 185 through 197 Processing helix chain 'P' and resid 214 through 222 Processing helix chain 'P' and resid 222 through 229 Processing helix chain 'P' and resid 247 through 260 Processing helix chain 'P' and resid 265 through 268 removed outlier: 3.961A pdb=" N LYS P 268 " --> pdb=" O ASN P 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 265 through 268' Processing helix chain 'P' and resid 269 through 280 Processing helix chain 'P' and resid 282 through 295 Processing helix chain 'P' and resid 301 through 312 Processing helix chain 'P' and resid 314 through 328 Processing helix chain 'P' and resid 328 through 333 removed outlier: 4.046A pdb=" N LEU P 333 " --> pdb=" O ALA P 329 " (cutoff:3.500A) Processing helix chain 'P' and resid 335 through 345 removed outlier: 3.560A pdb=" N LYS P 339 " --> pdb=" O THR P 335 " (cutoff:3.500A) Processing helix chain 'P' and resid 345 through 358 removed outlier: 3.933A pdb=" N VAL P 349 " --> pdb=" O HIS P 345 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 21 through 39 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 21 through 39 current: chain 'C' and resid 113 through 114 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 113 through 114 current: chain 'D' and resid 168 through 169 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 168 through 169 current: chain 'I' and resid 113 through 118 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 113 through 118 current: chain 'J' and resid 113 through 118 No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 52 through 53 removed outlier: 6.810A pdb=" N LYS C 66 " --> pdb=" O VAL C 91 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N LEU C 84 " --> pdb=" O LYS C 135 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N LYS C 135 " --> pdb=" O LEU C 84 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU C 90 " --> pdb=" O LYS C 129 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS C 129 " --> pdb=" O LEU C 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 202 through 206 removed outlier: 3.785A pdb=" N CYS C 202 " --> pdb=" O ALA C 213 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ALA C 213 " --> pdb=" O CYS C 202 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 29 through 31 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 29 through 31 current: chain 'D' and resid 113 through 118 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 113 through 118 current: chain 'H' and resid 113 through 118 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 113 through 118 current: chain 'M' and resid 113 through 118 No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'D' and resid 52 through 53 removed outlier: 3.512A pdb=" N SER D 85 " --> pdb=" O ASN D 72 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N LEU D 86 " --> pdb=" O LYS D 135 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LYS D 135 " --> pdb=" O LEU D 86 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N LEU D 88 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N PHE D 133 " --> pdb=" O LEU D 88 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N LEU D 90 " --> pdb=" O TRP D 131 " (cutoff:3.500A) removed outlier: 8.846A pdb=" N TRP D 131 " --> pdb=" O LEU D 90 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 202 through 203 Processing sheet with id=AA7, first strand: chain 'H' and resid 21 through 22 Processing sheet with id=AA8, first strand: chain 'H' and resid 52 through 53 removed outlier: 3.509A pdb=" N ILE H 52 " --> pdb=" O VAL H 71 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LYS H 66 " --> pdb=" O VAL H 91 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N LEU H 84 " --> pdb=" O LYS H 135 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N LYS H 135 " --> pdb=" O LEU H 84 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU H 90 " --> pdb=" O LYS H 129 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LYS H 129 " --> pdb=" O LEU H 90 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 203 through 206 Processing sheet with id=AB1, first strand: chain 'I' and resid 52 through 53 removed outlier: 6.559A pdb=" N LYS I 66 " --> pdb=" O VAL I 91 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU I 86 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE I 133 " --> pdb=" O LEU I 86 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 67 through 72 removed outlier: 7.578A pdb=" N LEU J 84 " --> pdb=" O LYS J 135 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N LYS J 135 " --> pdb=" O LEU J 84 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TRP J 131 " --> pdb=" O LEU J 88 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 205 through 206 Processing sheet with id=AB4, first strand: chain 'M' and resid 52 through 53 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 52 through 53 current: chain 'M' and resid 83 through 90 removed outlier: 7.515A pdb=" N LEU M 86 " --> pdb=" O LYS M 135 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LYS M 135 " --> pdb=" O LEU M 86 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N LEU M 88 " --> pdb=" O PHE M 133 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N PHE M 133 " --> pdb=" O LEU M 88 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N LEU M 90 " --> pdb=" O TRP M 131 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N TRP M 131 " --> pdb=" O LEU M 90 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 37 through 38 removed outlier: 3.679A pdb=" N LEU N 155 " --> pdb=" O ILE N 38 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 56 through 59 Processing sheet with id=AB7, first strand: chain 'N' and resid 103 through 105 removed outlier: 4.056A pdb=" N LYS N 103 " --> pdb=" O GLU N 160 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLU N 160 " --> pdb=" O LYS N 103 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 209 through 213 removed outlier: 6.684A pdb=" N CYS N 203 " --> pdb=" O VAL N 241 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N ILE N 243 " --> pdb=" O CYS N 203 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N CYS N 205 " --> pdb=" O ILE N 243 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 22 through 38 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 22 through 38 current: chain 'A' and resid 113 through 118 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 113 through 118 current: chain 'B' and resid 113 through 118 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 113 through 118 current: chain 'F' and resid 168 through 169 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 168 through 169 current: chain 'K' and resid 113 through 118 No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 52 through 53 removed outlier: 7.394A pdb=" N LYS A 66 " --> pdb=" O VAL A 91 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N LEU A 84 " --> pdb=" O LYS A 135 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N LYS A 135 " --> pdb=" O LEU A 84 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 209 through 213 removed outlier: 3.808A pdb=" N PHE A 211 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N CYS A 203 " --> pdb=" O VAL A 241 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N ILE A 243 " --> pdb=" O CYS A 203 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N CYS A 205 " --> pdb=" O ILE A 243 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 52 through 53 removed outlier: 6.889A pdb=" N LYS B 66 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N CYS B 68 " --> pdb=" O LEU B 89 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU B 89 " --> pdb=" O CYS B 68 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N LEU B 84 " --> pdb=" O LYS B 135 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N LYS B 135 " --> pdb=" O LEU B 84 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 202 through 206 removed outlier: 3.621A pdb=" N CYS B 202 " --> pdb=" O ALA B 213 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA B 213 " --> pdb=" O CYS B 202 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 34 through 38 removed outlier: 4.864A pdb=" N THR E 156 " --> pdb=" O LEU E 107 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER E 105 " --> pdb=" O PHE E 158 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N PHE E 104 " --> pdb=" O ALA E 116 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ALA E 116 " --> pdb=" O PHE E 104 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 52 through 53 removed outlier: 7.029A pdb=" N LYS E 66 " --> pdb=" O VAL E 91 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER E 85 " --> pdb=" O ASN E 72 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N LEU E 84 " --> pdb=" O LYS E 135 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N LYS E 135 " --> pdb=" O LEU E 84 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N LEU E 86 " --> pdb=" O PHE E 133 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE E 133 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 123 through 125 Processing sheet with id=AC8, first strand: chain 'F' and resid 29 through 39 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 29 through 39 current: chain 'F' and resid 113 through 118 No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'F' and resid 52 through 53 removed outlier: 6.604A pdb=" N LYS F 66 " --> pdb=" O VAL F 91 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 209 through 210 removed outlier: 6.239A pdb=" N CYS F 205 " --> pdb=" O ILE F 243 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 113 through 118 removed outlier: 4.964A pdb=" N LYS G 115 " --> pdb=" O ILE G 106 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ILE G 106 " --> pdb=" O LYS G 115 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU G 107 " --> pdb=" O THR G 156 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N THR G 156 " --> pdb=" O LEU G 107 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU G 155 " --> pdb=" O ILE G 38 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TRP G 36 " --> pdb=" O LEU G 157 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LYS G 28 " --> pdb=" O GLN G 165 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N SER G 167 " --> pdb=" O GLN G 26 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N GLN G 26 " --> pdb=" O SER G 167 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N THR K 25 " --> pdb=" O MET G 35 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N THR G 37 " --> pdb=" O THR K 25 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 52 through 53 removed outlier: 3.534A pdb=" N ILE G 52 " --> pdb=" O VAL G 71 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL G 71 " --> pdb=" O ILE G 52 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N LYS G 66 " --> pdb=" O VAL G 91 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 98 through 99 removed outlier: 3.565A pdb=" N VAL G 98 " --> pdb=" O PHE G 125 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 66 through 72 removed outlier: 6.812A pdb=" N LYS K 66 " --> pdb=" O VAL K 91 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER K 85 " --> pdb=" O ASN K 72 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU K 84 " --> pdb=" O LYS K 135 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N LYS K 135 " --> pdb=" O LEU K 84 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU K 90 " --> pdb=" O LYS K 129 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LYS K 129 " --> pdb=" O LEU K 90 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 205 through 206 Processing sheet with id=AD7, first strand: chain 'L' and resid 29 through 38 removed outlier: 3.644A pdb=" N PHE L 32 " --> pdb=" O VAL L 161 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N THR L 156 " --> pdb=" O LEU L 107 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 66 through 72 removed outlier: 6.741A pdb=" N LYS L 66 " --> pdb=" O VAL L 91 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 98 through 100 Processing sheet with id=AE1, first strand: chain 'L' and resid 203 through 206 Processing sheet with id=AE2, first strand: chain 'P' and resid 36 through 38 removed outlier: 3.715A pdb=" N TRP P 36 " --> pdb=" O LEU P 157 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU P 155 " --> pdb=" O ILE P 38 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'P' and resid 57 through 59 Processing sheet with id=AE4, first strand: chain 'P' and resid 83 through 86 removed outlier: 4.080A pdb=" N ILE P 137 " --> pdb=" O LEU P 84 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N LEU P 86 " --> pdb=" O LYS P 135 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N LYS P 135 " --> pdb=" O LEU P 86 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'P' and resid 209 through 213 removed outlier: 6.806A pdb=" N CYS P 203 " --> pdb=" O VAL P 241 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N ILE P 243 " --> pdb=" O CYS P 203 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N CYS P 205 " --> pdb=" O ILE P 243 " (cutoff:3.500A) 1232 hydrogen bonds defined for protein. 3492 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: 7.28 Time building geometry restraints manager: 4.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11691 1.34 - 1.46: 7874 1.46 - 1.58: 17226 1.58 - 1.70: 0 1.70 - 1.82: 475 Bond restraints: 37266 Sorted by residual: bond pdb=" CB ASP I 63 " pdb=" CG ASP I 63 " ideal model delta sigma weight residual 1.516 1.567 -0.051 2.50e-02 1.60e+03 4.14e+00 bond pdb=" CB GLN H 120 " pdb=" CG GLN H 120 " ideal model delta sigma weight residual 1.520 1.581 -0.061 3.00e-02 1.11e+03 4.14e+00 bond pdb=" N THR N 25 " pdb=" CA THR N 25 " ideal model delta sigma weight residual 1.457 1.484 -0.026 1.29e-02 6.01e+03 4.12e+00 bond pdb=" C GLN F 360 " pdb=" N CYS F 361 " ideal model delta sigma weight residual 1.331 1.370 -0.039 2.07e-02 2.33e+03 3.61e+00 bond pdb=" N ASP I 63 " pdb=" CA ASP I 63 " ideal model delta sigma weight residual 1.459 1.483 -0.024 1.32e-02 5.74e+03 3.40e+00 ... (remaining 37261 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.04: 49474 3.04 - 6.09: 621 6.09 - 9.13: 112 9.13 - 12.18: 21 12.18 - 15.22: 6 Bond angle restraints: 50234 Sorted by residual: angle pdb=" C GLN M 360 " pdb=" N CYS M 361 " pdb=" CA CYS M 361 " ideal model delta sigma weight residual 121.80 135.80 -14.00 2.44e+00 1.68e-01 3.29e+01 angle pdb=" C GLN F 360 " pdb=" N CYS F 361 " pdb=" CA CYS F 361 " ideal model delta sigma weight residual 121.80 134.98 -13.18 2.44e+00 1.68e-01 2.92e+01 angle pdb=" CB MET D 176 " pdb=" CG MET D 176 " pdb=" SD MET D 176 " ideal model delta sigma weight residual 112.70 127.92 -15.22 3.00e+00 1.11e-01 2.57e+01 angle pdb=" C CYS K 44 " pdb=" N ARG K 45 " pdb=" CA ARG K 45 " ideal model delta sigma weight residual 121.54 130.91 -9.37 1.91e+00 2.74e-01 2.41e+01 angle pdb=" C ASN N 169 " pdb=" N ILE N 170 " pdb=" CA ILE N 170 " ideal model delta sigma weight residual 121.97 130.74 -8.77 1.80e+00 3.09e-01 2.37e+01 ... (remaining 50229 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.15: 20699 18.15 - 36.30: 1640 36.30 - 54.45: 252 54.45 - 72.60: 36 72.60 - 90.75: 20 Dihedral angle restraints: 22647 sinusoidal: 9092 harmonic: 13555 Sorted by residual: dihedral pdb=" CB CYS J 361 " pdb=" SG CYS J 361 " pdb=" SG CYS M 361 " pdb=" CB CYS M 361 " ideal model delta sinusoidal sigma weight residual -86.00 -160.40 74.40 1 1.00e+01 1.00e-02 7.02e+01 dihedral pdb=" CB CYS F 361 " pdb=" SG CYS F 361 " pdb=" SG CYS K 361 " pdb=" CB CYS K 361 " ideal model delta sinusoidal sigma weight residual -86.00 -140.75 54.75 1 1.00e+01 1.00e-02 4.06e+01 dihedral pdb=" CA ASN J 174 " pdb=" C ASN J 174 " pdb=" N THR J 175 " pdb=" CA THR J 175 " ideal model delta harmonic sigma weight residual -180.00 -150.47 -29.53 0 5.00e+00 4.00e-02 3.49e+01 ... (remaining 22644 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 4953 0.085 - 0.170: 522 0.170 - 0.255: 30 0.255 - 0.340: 5 0.340 - 0.425: 4 Chirality restraints: 5514 Sorted by residual: chirality pdb=" CB ILE L 38 " pdb=" CA ILE L 38 " pdb=" CG1 ILE L 38 " pdb=" CG2 ILE L 38 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.42 2.00e-01 2.50e+01 4.51e+00 chirality pdb=" CB VAL L 126 " pdb=" CA VAL L 126 " pdb=" CG1 VAL L 126 " pdb=" CG2 VAL L 126 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.40e+00 chirality pdb=" CB ILE N 27 " pdb=" CA ILE N 27 " pdb=" CG1 ILE N 27 " pdb=" CG2 ILE N 27 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.25e+00 ... (remaining 5511 not shown) Planarity restraints: 6442 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS M 361 " -0.063 5.00e-02 4.00e+02 9.52e-02 1.45e+01 pdb=" N PRO M 362 " 0.165 5.00e-02 4.00e+02 pdb=" CA PRO M 362 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO M 362 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP J 338 " -0.026 2.00e-02 2.50e+03 2.24e-02 1.25e+01 pdb=" CG TRP J 338 " 0.059 2.00e-02 2.50e+03 pdb=" CD1 TRP J 338 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP J 338 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP J 338 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP J 338 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP J 338 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP J 338 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP J 338 " -0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP J 338 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS F 361 " 0.056 5.00e-02 4.00e+02 8.56e-02 1.17e+01 pdb=" N PRO F 362 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO F 362 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO F 362 " 0.048 5.00e-02 4.00e+02 ... (remaining 6439 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 16543 2.98 - 3.46: 38034 3.46 - 3.94: 58619 3.94 - 4.42: 64084 4.42 - 4.90: 103833 Nonbonded interactions: 281113 Sorted by model distance: nonbonded pdb=" N VAL M 126 " pdb=" O VAL M 126 " model vdw 2.504 2.496 nonbonded pdb=" N VAL K 126 " pdb=" O VAL K 126 " model vdw 2.523 2.496 nonbonded pdb=" N VAL H 126 " pdb=" O VAL H 126 " model vdw 2.563 2.496 nonbonded pdb=" N VAL D 126 " pdb=" O VAL D 126 " model vdw 2.566 2.496 nonbonded pdb=" N VAL C 126 " pdb=" O VAL C 126 " model vdw 2.575 2.496 ... (remaining 281108 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 20 through 182 or (resid 183 and (name N or name CA or nam \ e C or name O or name CB )) or resid 184 through 361)) selection = (chain 'B' and (resid 20 through 182 or (resid 183 and (name N or name CA or nam \ e C or name O or name CB )) or resid 184 through 248 or (resid 249 and (name N o \ r name CA or name C or name O or name CB )) or resid 250 through 361)) selection = (chain 'C' and (resid 20 through 182 or (resid 183 and (name N or name CA or nam \ e C or name O or name CB )) or resid 184 through 248 or (resid 249 and (name N o \ r name CA or name C or name O or name CB )) or resid 250 through 361)) selection = (chain 'D' and (resid 20 through 182 or (resid 183 and (name N or name CA or nam \ e C or name O or name CB )) or resid 184 through 361)) selection = (chain 'F' and (resid 20 through 182 or (resid 183 and (name N or name CA or nam \ e C or name O or name CB )) or resid 184 through 248 or (resid 249 and (name N o \ r name CA or name C or name O or name CB )) or resid 250 through 361)) selection = (chain 'H' and (resid 20 through 248 or (resid 249 and (name N or name CA or nam \ e C or name O or name CB )) or resid 250 through 361)) selection = (chain 'J' and (resid 20 through 248 or (resid 249 and (name N or name CA or nam \ e C or name O or name CB )) or resid 250 through 361)) selection = (chain 'K' and (resid 20 through 248 or (resid 249 and (name N or name CA or nam \ e C or name O or name CB )) or resid 250 through 361)) selection = (chain 'L' and (resid 20 through 248 or (resid 249 and (name N or name CA or nam \ e C or name O or name CB )) or resid 250 through 361)) selection = (chain 'M' and (resid 20 through 182 or (resid 183 and (name N or name CA or nam \ e C or name O or name CB )) or resid 184 through 248 or (resid 249 and (name N o \ r name CA or name C or name O or name CB )) or resid 250 through 361)) selection = (chain 'N' and (resid 20 through 182 or (resid 183 and (name N or name CA or nam \ e C or name O or name CB )) or resid 184 through 248 or (resid 249 and (name N o \ r name CA or name C or name O or name CB )) or resid 250 through 361)) selection = (chain 'P' and (resid 20 through 182 or (resid 183 and (name N or name CA or nam \ e C or name O or name CB )) or resid 184 through 248 or (resid 249 and (name N o \ r name CA or name C or name O or name CB )) or resid 250 through 361)) } ncs_group { reference = chain 'E' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.050 Extract box with map and model: 0.550 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 32.080 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.100 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 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 0.061 37268 Z= 0.194 Angle : 0.902 15.222 50238 Z= 0.486 Chirality : 0.052 0.425 5514 Planarity : 0.005 0.095 6442 Dihedral : 13.342 90.749 13801 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.60 % Favored : 94.16 % Rotamer: Outliers : 0.05 % Allowed : 0.20 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.12 (0.11), residues: 4574 helix: -1.22 (0.12), residues: 1518 sheet: -0.54 (0.17), residues: 930 loop : -1.90 (0.12), residues: 2126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 121 TYR 0.037 0.002 TYR C 327 PHE 0.042 0.002 PHE M 251 TRP 0.059 0.002 TRP J 338 HIS 0.011 0.001 HIS F 231 Details of bonding type rmsd covalent geometry : bond 0.00389 (37266) covalent geometry : angle 0.90207 (50234) SS BOND : bond 0.00813 ( 2) SS BOND : angle 0.84527 ( 4) hydrogen bonds : bond 0.17605 ( 1232) hydrogen bonds : angle 7.34497 ( 3492) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9148 Ramachandran restraints generated. 4574 Oldfield, 0 Emsley, 4574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9148 Ramachandran restraints generated. 4574 Oldfield, 0 Emsley, 4574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 4030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 388 time to evaluate : 1.428 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 48 MET cc_start: 0.8594 (tmm) cc_final: 0.8232 (mtt) REVERT: C 89 LEU cc_start: 0.8753 (tp) cc_final: 0.8394 (tp) REVERT: C 255 MET cc_start: 0.3313 (tpt) cc_final: 0.2116 (tmm) REVERT: D 117 MET cc_start: 0.7292 (ptp) cc_final: 0.6893 (ptp) REVERT: D 201 ASP cc_start: 0.6581 (m-30) cc_final: 0.6168 (t0) REVERT: D 254 MET cc_start: 0.8416 (ptm) cc_final: 0.7596 (ppp) REVERT: H 228 MET cc_start: 0.7653 (tmm) cc_final: 0.7092 (ppp) REVERT: H 273 LEU cc_start: 0.9624 (mt) cc_final: 0.9323 (mt) REVERT: H 288 MET cc_start: 0.9232 (mpp) cc_final: 0.8904 (mpp) REVERT: J 255 MET cc_start: 0.8227 (ttt) cc_final: 0.7850 (tpt) REVERT: J 288 MET cc_start: 0.8969 (ppp) cc_final: 0.8698 (ppp) REVERT: J 317 LEU cc_start: 0.9592 (tp) cc_final: 0.9279 (tp) REVERT: J 320 GLN cc_start: 0.8416 (mt0) cc_final: 0.8151 (mt0) REVERT: M 178 MET cc_start: 0.6960 (mmm) cc_final: 0.6660 (mmm) REVERT: M 266 LEU cc_start: 0.7486 (tp) cc_final: 0.7128 (pt) REVERT: M 268 LYS cc_start: 0.7940 (pttp) cc_final: 0.7425 (mppt) REVERT: N 254 MET cc_start: 0.8676 (tmm) cc_final: 0.8343 (tmm) REVERT: N 290 GLU cc_start: 0.8927 (mt-10) cc_final: 0.7496 (mt-10) REVERT: N 353 TYR cc_start: 0.8654 (t80) cc_final: 0.8438 (t80) REVERT: A 45 ARG cc_start: 0.7513 (ptt180) cc_final: 0.7279 (ptt180) REVERT: A 48 MET cc_start: 0.7660 (tpp) cc_final: 0.6916 (tpp) REVERT: A 288 MET cc_start: 0.7406 (ptt) cc_final: 0.6294 (ppp) REVERT: B 48 MET cc_start: 0.5900 (tpt) cc_final: 0.5323 (mmt) REVERT: B 176 MET cc_start: 0.7198 (tmm) cc_final: 0.6892 (tpt) REVERT: B 233 MET cc_start: 0.5627 (ppp) cc_final: 0.4357 (tpp) REVERT: B 254 MET cc_start: 0.1435 (ttt) cc_final: 0.1198 (tpp) REVERT: E 48 MET cc_start: 0.8351 (ttt) cc_final: 0.7838 (tpp) REVERT: E 97 GLU cc_start: 0.7746 (mt-10) cc_final: 0.6954 (tp30) REVERT: F 35 MET cc_start: 0.6428 (ppp) cc_final: 0.5525 (ttp) REVERT: F 48 MET cc_start: 0.7105 (mpp) cc_final: 0.6670 (mmm) REVERT: F 178 MET cc_start: 0.6278 (mmm) cc_final: 0.5129 (tpt) REVERT: G 48 MET cc_start: 0.7229 (tmm) cc_final: 0.6720 (tpp) REVERT: K 117 MET cc_start: 0.7389 (pmm) cc_final: 0.5694 (pmm) REVERT: K 178 MET cc_start: 0.5351 (mpp) cc_final: 0.2126 (tmm) REVERT: K 233 MET cc_start: -0.2494 (ppp) cc_final: -0.3099 (ttt) REVERT: L 41 PHE cc_start: 0.9062 (t80) cc_final: 0.8699 (t80) REVERT: L 48 MET cc_start: 0.8732 (mpp) cc_final: 0.8182 (mpp) REVERT: L 69 LEU cc_start: 0.8678 (mm) cc_final: 0.8224 (mp) REVERT: P 55 SER cc_start: 0.6324 (p) cc_final: 0.5979 (t) REVERT: P 254 MET cc_start: 0.7881 (ppp) cc_final: 0.7678 (ppp) outliers start: 2 outliers final: 0 residues processed: 390 average time/residue: 0.2217 time to fit residues: 144.2248 Evaluate side-chains 285 residues out of total 4030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 285 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 432 optimal weight: 8.9990 chunk 197 optimal weight: 7.9990 chunk 388 optimal weight: 0.9980 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 0.3980 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.8980 chunk 401 optimal weight: 10.0000 chunk 424 optimal weight: 7.9990 overall best weight: 3.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 173 GLN C 231 HIS D 40 ASN ** H 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 127 GLN H 231 HIS H 328 HIS H 360 GLN J 231 HIS ** M 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 127 GLN M 320 GLN N 312 HIS B 127 GLN ** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 231 HIS F 312 HIS ** G 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 296 ASN K 360 GLN ** L 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 214 HIS ** P 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 312 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.092196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.072838 restraints weight = 249091.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.071216 restraints weight = 185578.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.071756 restraints weight = 168840.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.071889 restraints weight = 128546.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.072108 restraints weight = 126619.374| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3651 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3651 r_free = 0.3651 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3651 r_free = 0.3651 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3651 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.096 37268 Z= 0.306 Angle : 0.811 17.800 50238 Z= 0.428 Chirality : 0.046 0.308 5514 Planarity : 0.005 0.095 6442 Dihedral : 5.885 24.053 4892 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 20.63 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.47 % Favored : 93.35 % Rotamer: Outliers : 0.45 % Allowed : 6.68 % Favored : 92.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.70 (0.12), residues: 4574 helix: -0.57 (0.12), residues: 1550 sheet: -0.75 (0.17), residues: 916 loop : -1.67 (0.13), residues: 2108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 45 TYR 0.031 0.002 TYR K 87 PHE 0.038 0.003 PHE M 257 TRP 0.039 0.003 TRP D 36 HIS 0.012 0.002 HIS D 214 Details of bonding type rmsd covalent geometry : bond 0.00654 (37266) covalent geometry : angle 0.81134 (50234) SS BOND : bond 0.00357 ( 2) SS BOND : angle 1.50003 ( 4) hydrogen bonds : bond 0.04579 ( 1232) hydrogen bonds : angle 5.89751 ( 3492) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9148 Ramachandran restraints generated. 4574 Oldfield, 0 Emsley, 4574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9148 Ramachandran restraints generated. 4574 Oldfield, 0 Emsley, 4574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 4030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 309 time to evaluate : 1.590 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: C 48 MET cc_start: 0.8669 (tmm) cc_final: 0.8432 (tmm) REVERT: D 48 MET cc_start: 0.6713 (mmt) cc_final: 0.6405 (mmt) REVERT: D 117 MET cc_start: 0.8319 (ptp) cc_final: 0.7831 (ptp) REVERT: H 228 MET cc_start: 0.8527 (tmm) cc_final: 0.8269 (tmm) REVERT: H 273 LEU cc_start: 0.9618 (mt) cc_final: 0.9192 (mt) REVERT: H 288 MET cc_start: 0.9207 (mpp) cc_final: 0.8935 (mtt) REVERT: I 47 GLU cc_start: 0.6702 (pp20) cc_final: 0.6472 (pp20) REVERT: J 255 MET cc_start: 0.8361 (ttt) cc_final: 0.7688 (tpp) REVERT: J 288 MET cc_start: 0.9227 (ppp) cc_final: 0.8902 (ppp) REVERT: J 305 ILE cc_start: 0.9515 (mt) cc_final: 0.9212 (mt) REVERT: J 341 MET cc_start: 0.8864 (ppp) cc_final: 0.8645 (ppp) REVERT: M 117 MET cc_start: 0.6121 (mpp) cc_final: 0.5788 (mpp) REVERT: M 178 MET cc_start: 0.7160 (mmm) cc_final: 0.6808 (mmm) REVERT: M 189 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8005 (mp0) REVERT: M 266 LEU cc_start: 0.7962 (tp) cc_final: 0.7311 (pt) REVERT: M 268 LYS cc_start: 0.8123 (pttp) cc_final: 0.7371 (mppt) REVERT: N 254 MET cc_start: 0.8679 (tmm) cc_final: 0.8247 (tmm) REVERT: N 290 GLU cc_start: 0.8999 (mt-10) cc_final: 0.8636 (mt-10) REVERT: A 48 MET cc_start: 0.8108 (tpp) cc_final: 0.7356 (tpp) REVERT: A 176 MET cc_start: 0.7689 (ttm) cc_final: 0.7336 (ttm) REVERT: A 228 MET cc_start: 0.1461 (tmm) cc_final: 0.1259 (tmm) REVERT: A 288 MET cc_start: 0.7437 (ptt) cc_final: 0.6177 (ppp) REVERT: B 48 MET cc_start: 0.6658 (tpt) cc_final: 0.6411 (mmt) REVERT: B 254 MET cc_start: 0.1184 (ttt) cc_final: 0.0520 (tpt) REVERT: B 288 MET cc_start: 0.5176 (ptm) cc_final: 0.4405 (mtt) REVERT: B 347 HIS cc_start: 0.7815 (t70) cc_final: 0.7609 (t70) REVERT: E 46 GLU cc_start: 0.8898 (pm20) cc_final: 0.8689 (pm20) REVERT: E 112 GLU cc_start: 0.8831 (mt-10) cc_final: 0.8540 (tm-30) REVERT: F 178 MET cc_start: 0.6263 (mmm) cc_final: 0.5192 (tpp) REVERT: F 231 HIS cc_start: 0.8704 (m90) cc_final: 0.8431 (m-70) REVERT: F 341 MET cc_start: 0.8480 (tpp) cc_final: 0.7552 (tpt) REVERT: G 130 ASP cc_start: 0.8154 (p0) cc_final: 0.7868 (p0) REVERT: K 117 MET cc_start: 0.8268 (pmm) cc_final: 0.7403 (pmm) REVERT: K 178 MET cc_start: 0.5502 (mpp) cc_final: 0.1431 (tmm) REVERT: K 228 MET cc_start: 0.3642 (pmm) cc_final: 0.3404 (pmm) REVERT: K 233 MET cc_start: -0.2448 (ppp) cc_final: -0.3592 (ttt) REVERT: L 48 MET cc_start: 0.9144 (mpp) cc_final: 0.8508 (mpp) REVERT: L 89 LEU cc_start: 0.6855 (tt) cc_final: 0.6637 (tt) REVERT: L 117 MET cc_start: 0.6292 (mpp) cc_final: 0.6043 (mmt) REVERT: P 254 MET cc_start: 0.8011 (ppp) cc_final: 0.7807 (ppp) outliers start: 18 outliers final: 9 residues processed: 327 average time/residue: 0.2208 time to fit residues: 122.2173 Evaluate side-chains 261 residues out of total 4030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 251 time to evaluate : 1.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 96 optimal weight: 9.9990 chunk 176 optimal weight: 0.9980 chunk 392 optimal weight: 5.9990 chunk 183 optimal weight: 0.8980 chunk 227 optimal weight: 0.9990 chunk 329 optimal weight: 1.9990 chunk 121 optimal weight: 0.8980 chunk 336 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 106 optimal weight: 10.0000 chunk 436 optimal weight: 40.0000 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 127 GLN H 231 HIS M 127 GLN ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 173 GLN L 326 ASN ** P 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.094763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.075590 restraints weight = 247968.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.074523 restraints weight = 172449.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.075004 restraints weight = 153307.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.075327 restraints weight = 118272.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.075409 restraints weight = 111603.110| |-----------------------------------------------------------------------------| r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3734 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3734 r_free = 0.3734 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3734 r_free = 0.3734 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3734 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 37268 Z= 0.132 Angle : 0.591 10.176 50238 Z= 0.315 Chirality : 0.042 0.204 5514 Planarity : 0.004 0.077 6442 Dihedral : 5.086 22.506 4892 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.68 % Favored : 94.14 % Rotamer: Outliers : 0.02 % Allowed : 2.68 % Favored : 97.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.29 (0.12), residues: 4574 helix: -0.09 (0.13), residues: 1565 sheet: -0.59 (0.17), residues: 924 loop : -1.53 (0.13), residues: 2085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 45 TYR 0.022 0.001 TYR F 24 PHE 0.024 0.001 PHE L 41 TRP 0.021 0.001 TRP J 338 HIS 0.010 0.001 HIS M 214 Details of bonding type rmsd covalent geometry : bond 0.00285 (37266) covalent geometry : angle 0.59065 (50234) SS BOND : bond 0.00065 ( 2) SS BOND : angle 0.63215 ( 4) hydrogen bonds : bond 0.03502 ( 1232) hydrogen bonds : angle 5.23631 ( 3492) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9148 Ramachandran restraints generated. 4574 Oldfield, 0 Emsley, 4574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9148 Ramachandran restraints generated. 4574 Oldfield, 0 Emsley, 4574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 4030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 323 time to evaluate : 1.594 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: C 177 ASN cc_start: 0.8101 (p0) cc_final: 0.7791 (t0) REVERT: C 228 MET cc_start: 0.6311 (pmm) cc_final: 0.6043 (pmm) REVERT: D 117 MET cc_start: 0.8115 (ptp) cc_final: 0.7602 (ptp) REVERT: D 195 GLU cc_start: 0.8428 (tt0) cc_final: 0.8131 (tt0) REVERT: D 201 ASP cc_start: 0.7115 (m-30) cc_final: 0.6661 (t0) REVERT: H 228 MET cc_start: 0.8473 (tmm) cc_final: 0.8174 (tmm) REVERT: H 273 LEU cc_start: 0.9591 (mt) cc_final: 0.9209 (mt) REVERT: I 50 GLU cc_start: 0.7426 (tm-30) cc_final: 0.6884 (tm-30) REVERT: J 255 MET cc_start: 0.8241 (ttt) cc_final: 0.7678 (tpp) REVERT: J 288 MET cc_start: 0.9207 (ppp) cc_final: 0.8974 (ppp) REVERT: J 305 ILE cc_start: 0.9453 (mt) cc_final: 0.9074 (mt) REVERT: J 317 LEU cc_start: 0.9682 (tp) cc_final: 0.9115 (tp) REVERT: J 341 MET cc_start: 0.8890 (ppp) cc_final: 0.8631 (ppp) REVERT: M 117 MET cc_start: 0.5925 (mpp) cc_final: 0.5633 (mpp) REVERT: M 290 GLU cc_start: 0.8286 (tt0) cc_final: 0.7645 (tp30) REVERT: N 280 TYR cc_start: 0.7112 (m-10) cc_final: 0.6744 (m-10) REVERT: N 290 GLU cc_start: 0.9038 (mt-10) cc_final: 0.8608 (mt-10) REVERT: A 48 MET cc_start: 0.8026 (tpp) cc_final: 0.7535 (tpp) REVERT: A 176 MET cc_start: 0.7684 (ttm) cc_final: 0.7321 (ttm) REVERT: A 288 MET cc_start: 0.7547 (ptt) cc_final: 0.6660 (ppp) REVERT: B 48 MET cc_start: 0.6512 (tpt) cc_final: 0.6140 (mmt) REVERT: B 254 MET cc_start: 0.1517 (ttt) cc_final: 0.1125 (tpt) REVERT: B 288 MET cc_start: 0.5043 (ptm) cc_final: 0.4228 (mtt) REVERT: B 347 HIS cc_start: 0.7875 (t70) cc_final: 0.7671 (t70) REVERT: F 96 SER cc_start: 0.8925 (p) cc_final: 0.8572 (t) REVERT: F 117 MET cc_start: 0.7743 (mtp) cc_final: 0.6927 (ttm) REVERT: F 178 MET cc_start: 0.6260 (mmm) cc_final: 0.5401 (tpt) REVERT: F 231 HIS cc_start: 0.8716 (m90) cc_final: 0.8384 (m-70) REVERT: F 254 MET cc_start: 0.5103 (ppp) cc_final: 0.4343 (ppp) REVERT: F 288 MET cc_start: 0.7141 (ptp) cc_final: 0.6809 (ptp) REVERT: F 341 MET cc_start: 0.8222 (tpp) cc_final: 0.7665 (tpt) REVERT: G 117 MET cc_start: 0.6192 (ptp) cc_final: 0.5812 (ptp) REVERT: G 130 ASP cc_start: 0.8128 (p0) cc_final: 0.7769 (p0) REVERT: K 117 MET cc_start: 0.8104 (pmm) cc_final: 0.7259 (pmm) REVERT: K 178 MET cc_start: 0.5359 (mpp) cc_final: 0.1226 (tmm) REVERT: K 233 MET cc_start: -0.3043 (ppp) cc_final: -0.4287 (ttt) REVERT: K 269 MET cc_start: 0.1138 (ptt) cc_final: 0.0580 (ptm) REVERT: L 48 MET cc_start: 0.9189 (mpp) cc_final: 0.8613 (mpp) REVERT: L 89 LEU cc_start: 0.7138 (tt) cc_final: 0.6874 (tt) REVERT: L 233 MET cc_start: -0.1695 (ptt) cc_final: -0.1971 (ptt) outliers start: 1 outliers final: 0 residues processed: 324 average time/residue: 0.2135 time to fit residues: 118.2724 Evaluate side-chains 251 residues out of total 4030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 345 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 126 optimal weight: 0.2980 chunk 19 optimal weight: 8.9990 chunk 237 optimal weight: 9.9990 chunk 99 optimal weight: 0.7980 chunk 239 optimal weight: 30.0000 chunk 321 optimal weight: 10.0000 chunk 198 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 316 GLN H 127 GLN H 231 HIS J 347 HIS A 165 GLN ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 360 GLN ** P 26 GLN ** 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 = 0.4272 r_free = 0.4272 target = 0.095521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.075870 restraints weight = 246322.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.074659 restraints weight = 166132.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.075117 restraints weight = 148415.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.075430 restraints weight = 117739.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.075512 restraints weight = 111628.373| |-----------------------------------------------------------------------------| r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3735 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3735 r_free = 0.3735 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3735 r_free = 0.3735 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3735 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 37268 Z= 0.109 Angle : 0.557 10.157 50238 Z= 0.294 Chirality : 0.041 0.186 5514 Planarity : 0.003 0.076 6442 Dihedral : 4.688 21.925 4892 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.68 % Favored : 94.18 % Rotamer: Outliers : 0.02 % Allowed : 2.71 % Favored : 97.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.12), residues: 4574 helix: 0.23 (0.13), residues: 1573 sheet: -0.47 (0.18), residues: 875 loop : -1.47 (0.13), residues: 2126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 45 TYR 0.019 0.001 TYR F 259 PHE 0.015 0.001 PHE M 257 TRP 0.016 0.001 TRP L 36 HIS 0.006 0.001 HIS M 214 Details of bonding type rmsd covalent geometry : bond 0.00230 (37266) covalent geometry : angle 0.55654 (50234) SS BOND : bond 0.00291 ( 2) SS BOND : angle 0.45346 ( 4) hydrogen bonds : bond 0.03042 ( 1232) hydrogen bonds : angle 4.91286 ( 3492) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9148 Ramachandran restraints generated. 4574 Oldfield, 0 Emsley, 4574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9148 Ramachandran restraints generated. 4574 Oldfield, 0 Emsley, 4574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 4030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 319 time to evaluate : 1.559 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: C 48 MET cc_start: 0.8673 (tmm) cc_final: 0.8373 (tmm) REVERT: D 117 MET cc_start: 0.8283 (ptp) cc_final: 0.7713 (ptp) REVERT: D 195 GLU cc_start: 0.8438 (tt0) cc_final: 0.8155 (tt0) REVERT: D 201 ASP cc_start: 0.7169 (m-30) cc_final: 0.6714 (t0) REVERT: D 353 TYR cc_start: 0.8778 (t80) cc_final: 0.8454 (t80) REVERT: H 228 MET cc_start: 0.8360 (tmm) cc_final: 0.7768 (ppp) REVERT: H 273 LEU cc_start: 0.9614 (mt) cc_final: 0.9218 (mt) REVERT: H 288 MET cc_start: 0.9541 (mtm) cc_final: 0.8975 (ptp) REVERT: I 50 GLU cc_start: 0.7348 (tm-30) cc_final: 0.7074 (tm-30) REVERT: J 255 MET cc_start: 0.8266 (ttt) cc_final: 0.7733 (tpp) REVERT: J 288 MET cc_start: 0.9206 (ppp) cc_final: 0.8929 (ppp) REVERT: J 305 ILE cc_start: 0.9478 (mt) cc_final: 0.9071 (mt) REVERT: J 317 LEU cc_start: 0.9714 (tp) cc_final: 0.9192 (tp) REVERT: J 341 MET cc_start: 0.8865 (ppp) cc_final: 0.8648 (ppp) REVERT: M 48 MET cc_start: 0.8432 (ppp) cc_final: 0.8220 (ppp) REVERT: M 117 MET cc_start: 0.5856 (mpp) cc_final: 0.5533 (mpp) REVERT: M 178 MET cc_start: 0.7306 (mmp) cc_final: 0.7028 (mmp) REVERT: M 266 LEU cc_start: 0.7194 (pt) cc_final: 0.6904 (pt) REVERT: M 268 LYS cc_start: 0.8061 (pttp) cc_final: 0.7180 (mppt) REVERT: N 123 TYR cc_start: 0.6648 (t80) cc_final: 0.6389 (t80) REVERT: N 254 MET cc_start: 0.8728 (tmm) cc_final: 0.8445 (ppp) REVERT: N 280 TYR cc_start: 0.7239 (m-10) cc_final: 0.6746 (m-10) REVERT: N 290 GLU cc_start: 0.8993 (mt-10) cc_final: 0.8491 (mt-10) REVERT: A 176 MET cc_start: 0.7792 (ttm) cc_final: 0.7389 (ttm) REVERT: A 288 MET cc_start: 0.7666 (ptt) cc_final: 0.6787 (ppp) REVERT: B 48 MET cc_start: 0.6481 (tpt) cc_final: 0.5988 (mmt) REVERT: B 254 MET cc_start: 0.1407 (ttt) cc_final: 0.0859 (tpt) REVERT: B 288 MET cc_start: 0.4972 (ptm) cc_final: 0.4269 (mtt) REVERT: F 96 SER cc_start: 0.8835 (p) cc_final: 0.8441 (t) REVERT: F 117 MET cc_start: 0.7819 (mtp) cc_final: 0.6994 (ttm) REVERT: F 178 MET cc_start: 0.6481 (mmm) cc_final: 0.5604 (tpt) REVERT: F 231 HIS cc_start: 0.8754 (m90) cc_final: 0.8454 (m-70) REVERT: F 254 MET cc_start: 0.5144 (ppp) cc_final: 0.4395 (ppp) REVERT: F 255 MET cc_start: 0.5977 (tpt) cc_final: 0.5533 (mtm) REVERT: F 341 MET cc_start: 0.7916 (tpp) cc_final: 0.7579 (tpp) REVERT: G 130 ASP cc_start: 0.8250 (p0) cc_final: 0.7771 (p0) REVERT: K 117 MET cc_start: 0.7827 (pmm) cc_final: 0.6940 (pmm) REVERT: K 178 MET cc_start: 0.5766 (mpp) cc_final: 0.1506 (tmm) REVERT: L 48 MET cc_start: 0.9267 (mpp) cc_final: 0.8687 (mpp) REVERT: L 89 LEU cc_start: 0.7129 (tt) cc_final: 0.6866 (tt) REVERT: L 233 MET cc_start: -0.1639 (ptt) cc_final: -0.2126 (ptt) REVERT: P 178 MET cc_start: 0.7317 (tpp) cc_final: 0.7018 (tpp) REVERT: P 254 MET cc_start: 0.8119 (ppp) cc_final: 0.7896 (ppp) outliers start: 1 outliers final: 0 residues processed: 320 average time/residue: 0.2157 time to fit residues: 117.2515 Evaluate side-chains 248 residues out of total 4030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 1.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 322 optimal weight: 30.0000 chunk 55 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 chunk 315 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 257 optimal weight: 3.9990 chunk 110 optimal weight: 8.9990 chunk 54 optimal weight: 0.5980 chunk 34 optimal weight: 7.9990 chunk 432 optimal weight: 0.0770 overall best weight: 2.1344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 177 ASN D 127 GLN H 231 HIS M 72 ASN M 127 GLN ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 239 ASN ** G 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 GLN ** 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 = 0.4217 r_free = 0.4217 target = 0.092877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.073236 restraints weight = 249061.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.072343 restraints weight = 173113.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.072805 restraints weight = 147469.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.072879 restraints weight = 122296.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.073061 restraints weight = 116365.113| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3681 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3681 r_free = 0.3681 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3681 r_free = 0.3681 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3681 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.4161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 37268 Z= 0.191 Angle : 0.640 12.299 50238 Z= 0.338 Chirality : 0.042 0.270 5514 Planarity : 0.004 0.068 6442 Dihedral : 5.019 23.123 4892 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.84 % Favored : 93.03 % Rotamer: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.13 (0.12), residues: 4574 helix: 0.21 (0.13), residues: 1557 sheet: -0.73 (0.17), residues: 907 loop : -1.45 (0.13), residues: 2110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 45 TYR 0.021 0.002 TYR H 353 PHE 0.031 0.002 PHE M 257 TRP 0.027 0.002 TRP K 36 HIS 0.009 0.001 HIS D 312 Details of bonding type rmsd covalent geometry : bond 0.00411 (37266) covalent geometry : angle 0.63998 (50234) SS BOND : bond 0.01301 ( 2) SS BOND : angle 0.78101 ( 4) hydrogen bonds : bond 0.03478 ( 1232) hydrogen bonds : angle 5.21807 ( 3492) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9148 Ramachandran restraints generated. 4574 Oldfield, 0 Emsley, 4574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9148 Ramachandran restraints generated. 4574 Oldfield, 0 Emsley, 4574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 4030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 1.622 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: C 228 MET cc_start: 0.6396 (pmm) cc_final: 0.5838 (pmm) REVERT: D 117 MET cc_start: 0.8530 (ptp) cc_final: 0.7987 (ptp) REVERT: H 228 MET cc_start: 0.8940 (tmm) cc_final: 0.8574 (tmm) REVERT: H 273 LEU cc_start: 0.9613 (mt) cc_final: 0.9187 (mt) REVERT: H 288 MET cc_start: 0.9512 (mtm) cc_final: 0.8978 (mtp) REVERT: H 341 MET cc_start: 0.9369 (ppp) cc_final: 0.9030 (ppp) REVERT: J 228 MET cc_start: 0.6593 (tmm) cc_final: 0.6123 (ptp) REVERT: J 255 MET cc_start: 0.8270 (ttt) cc_final: 0.7639 (tpp) REVERT: J 288 MET cc_start: 0.9199 (ppp) cc_final: 0.8880 (ppp) REVERT: J 305 ILE cc_start: 0.9449 (mt) cc_final: 0.9050 (mt) REVERT: M 48 MET cc_start: 0.8498 (ppp) cc_final: 0.8298 (ppp) REVERT: M 117 MET cc_start: 0.6056 (mpp) cc_final: 0.5529 (mpp) REVERT: M 178 MET cc_start: 0.7405 (mmp) cc_final: 0.7190 (mmp) REVERT: N 123 TYR cc_start: 0.6798 (t80) cc_final: 0.6509 (t80) REVERT: N 178 MET cc_start: 0.5031 (tpt) cc_final: 0.4538 (tpp) REVERT: N 228 MET cc_start: 0.9068 (ppp) cc_final: 0.8808 (ppp) REVERT: A 48 MET cc_start: 0.7825 (tpp) cc_final: 0.7379 (tpp) REVERT: A 176 MET cc_start: 0.7690 (ttm) cc_final: 0.7366 (ttm) REVERT: A 228 MET cc_start: 0.1593 (tmm) cc_final: 0.1387 (tmm) REVERT: A 288 MET cc_start: 0.7814 (ptt) cc_final: 0.6737 (ppp) REVERT: B 48 MET cc_start: 0.6929 (tpt) cc_final: 0.6123 (mmt) REVERT: B 254 MET cc_start: 0.0224 (ttt) cc_final: -0.0341 (tpt) REVERT: B 288 MET cc_start: 0.5568 (ptm) cc_final: 0.4679 (mtt) REVERT: F 96 SER cc_start: 0.8981 (p) cc_final: 0.8636 (t) REVERT: F 178 MET cc_start: 0.6457 (mmm) cc_final: 0.5524 (tpt) REVERT: F 231 HIS cc_start: 0.8632 (m90) cc_final: 0.8390 (m170) REVERT: F 254 MET cc_start: 0.5428 (ppp) cc_final: 0.4336 (ppp) REVERT: G 87 TYR cc_start: 0.8137 (m-10) cc_final: 0.7741 (m-80) REVERT: G 130 ASP cc_start: 0.8184 (p0) cc_final: 0.7791 (p0) REVERT: K 117 MET cc_start: 0.8068 (pmm) cc_final: 0.7219 (pmm) REVERT: K 178 MET cc_start: 0.5293 (mpp) cc_final: 0.1225 (tmm) REVERT: K 233 MET cc_start: -0.2208 (ppp) cc_final: -0.4058 (ttt) REVERT: L 48 MET cc_start: 0.9323 (mpp) cc_final: 0.8990 (mpp) REVERT: P 254 MET cc_start: 0.8207 (ppp) cc_final: 0.8005 (ppp) outliers start: 0 outliers final: 0 residues processed: 300 average time/residue: 0.2176 time to fit residues: 111.2653 Evaluate side-chains 231 residues out of total 4030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 192 optimal weight: 3.9990 chunk 255 optimal weight: 3.9990 chunk 2 optimal weight: 0.3980 chunk 126 optimal weight: 3.9990 chunk 236 optimal weight: 3.9990 chunk 267 optimal weight: 1.9990 chunk 226 optimal weight: 4.9990 chunk 438 optimal weight: 20.0000 chunk 375 optimal weight: 10.0000 chunk 231 optimal weight: 0.9990 chunk 411 optimal weight: 6.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 108 ASN H 231 HIS ** I 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 127 GLN N 231 HIS ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 ASN E 127 GLN ** F 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 312 HIS F 345 HIS ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 174 ASN ** K 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 72 ASN P 127 GLN P 212 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.092169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.072679 restraints weight = 248206.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.071170 restraints weight = 178254.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.071733 restraints weight = 162113.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.071841 restraints weight = 127427.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.071835 restraints weight = 125569.876| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3639 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3639 r_free = 0.3639 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3639 r_free = 0.3639 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3639 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.4801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 37268 Z= 0.193 Angle : 0.645 11.975 50238 Z= 0.340 Chirality : 0.043 0.252 5514 Planarity : 0.004 0.072 6442 Dihedral : 5.134 24.238 4892 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.11 % Favored : 92.76 % Rotamer: Outliers : 0.05 % Allowed : 2.93 % Favored : 97.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.23 (0.12), residues: 4574 helix: 0.20 (0.13), residues: 1552 sheet: -0.88 (0.17), residues: 905 loop : -1.51 (0.13), residues: 2117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 45 TYR 0.020 0.002 TYR H 353 PHE 0.027 0.002 PHE M 257 TRP 0.031 0.002 TRP M 194 HIS 0.009 0.001 HIS D 312 Details of bonding type rmsd covalent geometry : bond 0.00416 (37266) covalent geometry : angle 0.64466 (50234) SS BOND : bond 0.00169 ( 2) SS BOND : angle 0.61732 ( 4) hydrogen bonds : bond 0.03516 ( 1232) hydrogen bonds : angle 5.22880 ( 3492) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9148 Ramachandran restraints generated. 4574 Oldfield, 0 Emsley, 4574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9148 Ramachandran restraints generated. 4574 Oldfield, 0 Emsley, 4574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 4030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 297 time to evaluate : 1.517 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: C 228 MET cc_start: 0.6367 (pmm) cc_final: 0.5853 (pmm) REVERT: D 48 MET cc_start: 0.6721 (tpt) cc_final: 0.5968 (tpp) REVERT: D 117 MET cc_start: 0.8615 (ptp) cc_final: 0.8124 (ptp) REVERT: H 35 MET cc_start: 0.8266 (ppp) cc_final: 0.7694 (ppp) REVERT: H 228 MET cc_start: 0.9079 (tmm) cc_final: 0.8769 (tmm) REVERT: H 273 LEU cc_start: 0.9587 (mt) cc_final: 0.9083 (mt) REVERT: H 288 MET cc_start: 0.9537 (mtm) cc_final: 0.9033 (mtp) REVERT: H 341 MET cc_start: 0.9460 (ppp) cc_final: 0.9231 (ppp) REVERT: I 155 LEU cc_start: 0.8311 (pt) cc_final: 0.7484 (tp) REVERT: J 254 MET cc_start: 0.9004 (tmm) cc_final: 0.8792 (tmm) REVERT: J 255 MET cc_start: 0.8292 (ttt) cc_final: 0.7809 (ttt) REVERT: J 288 MET cc_start: 0.9237 (ppp) cc_final: 0.8939 (ppp) REVERT: J 305 ILE cc_start: 0.9399 (mt) cc_final: 0.8974 (mt) REVERT: M 48 MET cc_start: 0.8469 (ppp) cc_final: 0.8163 (ppp) REVERT: M 117 MET cc_start: 0.6070 (mpp) cc_final: 0.5525 (mpp) REVERT: M 178 MET cc_start: 0.7654 (mmp) cc_final: 0.7435 (mmp) REVERT: N 123 TYR cc_start: 0.6801 (t80) cc_final: 0.6485 (t80) REVERT: N 178 MET cc_start: 0.5046 (tpt) cc_final: 0.4628 (tpp) REVERT: N 228 MET cc_start: 0.9170 (ppp) cc_final: 0.8855 (ppp) REVERT: N 290 GLU cc_start: 0.8983 (mt-10) cc_final: 0.8622 (mt-10) REVERT: N 317 LEU cc_start: 0.9543 (mt) cc_final: 0.9104 (mt) REVERT: A 176 MET cc_start: 0.7728 (ttm) cc_final: 0.7395 (ttm) REVERT: A 288 MET cc_start: 0.7942 (ptt) cc_final: 0.6978 (ppp) REVERT: B 48 MET cc_start: 0.7261 (tpt) cc_final: 0.6515 (tpp) REVERT: B 254 MET cc_start: 0.0571 (ttt) cc_final: -0.0149 (tpt) REVERT: B 288 MET cc_start: 0.5811 (ptm) cc_final: 0.4967 (mtt) REVERT: F 34 TYR cc_start: 0.5800 (t80) cc_final: 0.5530 (t80) REVERT: F 117 MET cc_start: 0.8292 (ttm) cc_final: 0.7379 (ttm) REVERT: F 231 HIS cc_start: 0.8658 (m90) cc_final: 0.8414 (m170) REVERT: F 254 MET cc_start: 0.5428 (ppp) cc_final: 0.4301 (ppp) REVERT: K 117 MET cc_start: 0.8092 (pmm) cc_final: 0.7775 (pmm) REVERT: K 178 MET cc_start: 0.5563 (mpp) cc_final: 0.1414 (tmm) REVERT: K 341 MET cc_start: 0.6646 (tmm) cc_final: 0.6372 (tmm) REVERT: L 48 MET cc_start: 0.9443 (mpp) cc_final: 0.8947 (mpp) REVERT: L 233 MET cc_start: -0.1515 (ptt) cc_final: -0.2013 (ptt) REVERT: P 178 MET cc_start: 0.7416 (tpp) cc_final: 0.7161 (tpp) REVERT: P 254 MET cc_start: 0.8181 (ppp) cc_final: 0.7969 (ppp) outliers start: 2 outliers final: 0 residues processed: 299 average time/residue: 0.2128 time to fit residues: 108.3862 Evaluate side-chains 238 residues out of total 4030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 101 optimal weight: 0.8980 chunk 394 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 255 optimal weight: 2.9990 chunk 198 optimal weight: 5.9990 chunk 327 optimal weight: 9.9990 chunk 231 optimal weight: 4.9990 chunk 146 optimal weight: 10.0000 chunk 366 optimal weight: 0.0270 chunk 325 optimal weight: 5.9990 overall best weight: 1.7844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 231 HIS ** I 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 177 ASN ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 212 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.092516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.072790 restraints weight = 247721.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.071783 restraints weight = 174511.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.072485 restraints weight = 144713.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.072333 restraints weight = 122042.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.072484 restraints weight = 119329.113| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3660 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3660 r_free = 0.3660 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3660 r_free = 0.3660 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3660 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.5035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 37268 Z= 0.163 Angle : 0.624 11.046 50238 Z= 0.329 Chirality : 0.042 0.239 5514 Planarity : 0.004 0.068 6442 Dihedral : 5.026 24.117 4892 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.93 % Favored : 92.94 % Rotamer: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.16 (0.12), residues: 4574 helix: 0.26 (0.13), residues: 1561 sheet: -0.88 (0.17), residues: 934 loop : -1.47 (0.13), residues: 2079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG D 45 TYR 0.020 0.002 TYR D 327 PHE 0.020 0.002 PHE M 251 TRP 0.033 0.002 TRP B 36 HIS 0.008 0.001 HIS D 312 Details of bonding type rmsd covalent geometry : bond 0.00354 (37266) covalent geometry : angle 0.62395 (50234) SS BOND : bond 0.00107 ( 2) SS BOND : angle 1.29324 ( 4) hydrogen bonds : bond 0.03402 ( 1232) hydrogen bonds : angle 5.19402 ( 3492) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9148 Ramachandran restraints generated. 4574 Oldfield, 0 Emsley, 4574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9148 Ramachandran restraints generated. 4574 Oldfield, 0 Emsley, 4574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 4030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 304 time to evaluate : 1.350 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: C 228 MET cc_start: 0.6321 (pmm) cc_final: 0.5825 (pmm) REVERT: D 117 MET cc_start: 0.8659 (ptp) cc_final: 0.8191 (ptp) REVERT: H 35 MET cc_start: 0.8148 (ppp) cc_final: 0.7644 (ppp) REVERT: H 178 MET cc_start: 0.8780 (mpp) cc_final: 0.8397 (mpp) REVERT: H 228 MET cc_start: 0.8993 (tmm) cc_final: 0.8693 (tmm) REVERT: H 273 LEU cc_start: 0.9562 (mt) cc_final: 0.9043 (mt) REVERT: H 288 MET cc_start: 0.9506 (mtm) cc_final: 0.8976 (ptp) REVERT: H 341 MET cc_start: 0.9499 (ppp) cc_final: 0.9282 (ppp) REVERT: I 112 GLU cc_start: 0.8643 (mt-10) cc_final: 0.8026 (mt-10) REVERT: J 254 MET cc_start: 0.9017 (tmm) cc_final: 0.8752 (tmm) REVERT: J 255 MET cc_start: 0.8251 (ttt) cc_final: 0.7754 (ttt) REVERT: J 288 MET cc_start: 0.9224 (ppp) cc_final: 0.8939 (ppp) REVERT: J 305 ILE cc_start: 0.9439 (mt) cc_final: 0.9024 (mt) REVERT: J 320 GLN cc_start: 0.8720 (mt0) cc_final: 0.8466 (mt0) REVERT: M 48 MET cc_start: 0.8369 (ppp) cc_final: 0.8081 (ppp) REVERT: M 117 MET cc_start: 0.6019 (mpp) cc_final: 0.5475 (mpp) REVERT: M 178 MET cc_start: 0.7424 (mmp) cc_final: 0.7206 (mmp) REVERT: N 123 TYR cc_start: 0.6775 (t80) cc_final: 0.6416 (t80) REVERT: N 228 MET cc_start: 0.9137 (ppp) cc_final: 0.8820 (ppp) REVERT: N 255 MET cc_start: 0.8612 (mtm) cc_final: 0.8402 (mtp) REVERT: N 290 GLU cc_start: 0.8948 (mt-10) cc_final: 0.8569 (mt-10) REVERT: A 48 MET cc_start: 0.7932 (tpp) cc_final: 0.7438 (tpp) REVERT: A 176 MET cc_start: 0.7722 (ttm) cc_final: 0.7406 (ttm) REVERT: A 288 MET cc_start: 0.8017 (ptt) cc_final: 0.7014 (ppp) REVERT: B 48 MET cc_start: 0.7485 (tpt) cc_final: 0.6837 (tpp) REVERT: B 254 MET cc_start: 0.0378 (ttt) cc_final: -0.0356 (tpt) REVERT: B 288 MET cc_start: 0.5926 (ptm) cc_final: 0.5056 (mtt) REVERT: F 34 TYR cc_start: 0.5951 (t80) cc_final: 0.5742 (t80) REVERT: F 96 SER cc_start: 0.8958 (p) cc_final: 0.8591 (t) REVERT: F 178 MET cc_start: 0.7128 (mmm) cc_final: 0.5672 (tpt) REVERT: F 254 MET cc_start: 0.5376 (ppp) cc_final: 0.4307 (ppp) REVERT: K 117 MET cc_start: 0.8182 (pmm) cc_final: 0.7858 (pmm) REVERT: K 178 MET cc_start: 0.5453 (mpp) cc_final: 0.1176 (tmm) REVERT: K 269 MET cc_start: 0.0231 (ptt) cc_final: -0.0451 (ptm) REVERT: L 48 MET cc_start: 0.9441 (mpp) cc_final: 0.8885 (mpp) REVERT: L 176 MET cc_start: 0.8469 (tmm) cc_final: 0.7628 (mmt) REVERT: L 178 MET cc_start: 0.4599 (pmm) cc_final: 0.4194 (pmm) REVERT: L 233 MET cc_start: -0.1519 (ptt) cc_final: -0.1761 (ptt) REVERT: P 178 MET cc_start: 0.7636 (tpp) cc_final: 0.7337 (tpp) REVERT: P 254 MET cc_start: 0.8091 (ppp) cc_final: 0.7875 (ppp) outliers start: 0 outliers final: 0 residues processed: 304 average time/residue: 0.2038 time to fit residues: 105.4653 Evaluate side-chains 241 residues out of total 4030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 241 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 70 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 186 optimal weight: 10.0000 chunk 359 optimal weight: 0.1980 chunk 450 optimal weight: 9.9990 chunk 181 optimal weight: 10.0000 chunk 332 optimal weight: 9.9990 chunk 158 optimal weight: 0.8980 chunk 207 optimal weight: 0.8980 chunk 132 optimal weight: 0.9990 chunk 370 optimal weight: 0.0470 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 196 ASN C 214 HIS H 40 ASN I 62 ASN ** B 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 ASN ** F 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 231 HIS ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 212 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.094307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.074247 restraints weight = 248184.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.073684 restraints weight = 164805.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.073873 restraints weight = 134908.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.073967 restraints weight = 115216.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.074130 restraints weight = 107591.442| |-----------------------------------------------------------------------------| r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3718 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3718 r_free = 0.3718 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3718 r_free = 0.3718 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3718 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.5005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 37268 Z= 0.107 Angle : 0.588 11.623 50238 Z= 0.306 Chirality : 0.042 0.186 5514 Planarity : 0.003 0.066 6442 Dihedral : 4.659 22.228 4892 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.19 % Favored : 93.68 % Rotamer: Outliers : 0.05 % Allowed : 0.84 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.12), residues: 4574 helix: 0.44 (0.13), residues: 1563 sheet: -0.55 (0.18), residues: 874 loop : -1.38 (0.13), residues: 2137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 AARG N 70 TYR 0.038 0.001 TYR F 259 PHE 0.022 0.001 PHE L 41 TRP 0.027 0.001 TRP K 194 HIS 0.005 0.001 HIS D 312 Details of bonding type rmsd covalent geometry : bond 0.00227 (37266) covalent geometry : angle 0.58760 (50234) SS BOND : bond 0.00781 ( 2) SS BOND : angle 1.49115 ( 4) hydrogen bonds : bond 0.03039 ( 1232) hydrogen bonds : angle 4.86633 ( 3492) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9148 Ramachandran restraints generated. 4574 Oldfield, 0 Emsley, 4574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9148 Ramachandran restraints generated. 4574 Oldfield, 0 Emsley, 4574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 4030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 311 time to evaluate : 1.358 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: C 228 MET cc_start: 0.6337 (pmm) cc_final: 0.5422 (tpp) REVERT: D 117 MET cc_start: 0.8105 (ptp) cc_final: 0.7536 (ptp) REVERT: D 201 ASP cc_start: 0.6794 (m-30) cc_final: 0.6525 (t0) REVERT: H 178 MET cc_start: 0.8722 (mpp) cc_final: 0.8345 (mpp) REVERT: H 228 MET cc_start: 0.9024 (tmm) cc_final: 0.8390 (tmm) REVERT: H 231 HIS cc_start: 0.8509 (m-70) cc_final: 0.8149 (p90) REVERT: H 273 LEU cc_start: 0.9523 (mt) cc_final: 0.9019 (mt) REVERT: H 288 MET cc_start: 0.9498 (mtm) cc_final: 0.9017 (ptp) REVERT: I 50 GLU cc_start: 0.7826 (pp20) cc_final: 0.7535 (pp20) REVERT: J 228 MET cc_start: 0.6474 (tmm) cc_final: 0.5747 (ptp) REVERT: J 254 MET cc_start: 0.8977 (tmm) cc_final: 0.8738 (tmm) REVERT: J 255 MET cc_start: 0.8231 (ttt) cc_final: 0.7608 (tpp) REVERT: J 288 MET cc_start: 0.9181 (ppp) cc_final: 0.8885 (ppp) REVERT: J 305 ILE cc_start: 0.9295 (mt) cc_final: 0.8943 (mt) REVERT: M 117 MET cc_start: 0.5662 (mpp) cc_final: 0.5385 (mpp) REVERT: M 178 MET cc_start: 0.7265 (mmp) cc_final: 0.7055 (mmp) REVERT: M 228 MET cc_start: 0.9067 (pmm) cc_final: 0.8674 (pmm) REVERT: M 318 LYS cc_start: 0.9444 (ptmm) cc_final: 0.9210 (pttp) REVERT: N 123 TYR cc_start: 0.6118 (t80) cc_final: 0.5907 (t80) REVERT: N 178 MET cc_start: 0.5293 (mmm) cc_final: 0.4943 (mmm) REVERT: N 280 TYR cc_start: 0.6890 (m-10) cc_final: 0.6604 (m-10) REVERT: N 290 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8129 (mt-10) REVERT: N 317 LEU cc_start: 0.9337 (mt) cc_final: 0.9136 (mt) REVERT: A 48 MET cc_start: 0.7722 (tpp) cc_final: 0.6881 (tpp) REVERT: A 176 MET cc_start: 0.7616 (ttm) cc_final: 0.7335 (ttm) REVERT: A 288 MET cc_start: 0.8081 (ptt) cc_final: 0.7117 (ppp) REVERT: B 48 MET cc_start: 0.7635 (tpt) cc_final: 0.6816 (tpp) REVERT: B 254 MET cc_start: 0.0512 (ttt) cc_final: 0.0080 (tpt) REVERT: B 288 MET cc_start: 0.5457 (ptm) cc_final: 0.4774 (mtt) REVERT: F 96 SER cc_start: 0.8770 (p) cc_final: 0.8431 (t) REVERT: F 178 MET cc_start: 0.7066 (mmm) cc_final: 0.5647 (tpt) REVERT: F 225 PHE cc_start: 0.7916 (m-10) cc_final: 0.7673 (m-10) REVERT: F 254 MET cc_start: 0.5292 (ppp) cc_final: 0.4361 (ppp) REVERT: G 48 MET cc_start: 0.8282 (tmm) cc_final: 0.7878 (tmm) REVERT: G 130 ASP cc_start: 0.7959 (p0) cc_final: 0.7652 (p0) REVERT: K 178 MET cc_start: 0.5424 (mpp) cc_final: 0.1302 (tmm) REVERT: K 233 MET cc_start: -0.2416 (ppp) cc_final: -0.4186 (ttt) REVERT: K 269 MET cc_start: -0.0079 (ptt) cc_final: -0.0681 (ptm) REVERT: L 48 MET cc_start: 0.9388 (mpp) cc_final: 0.8789 (mpp) REVERT: L 89 LEU cc_start: 0.7196 (tt) cc_final: 0.6996 (tt) REVERT: L 176 MET cc_start: 0.8573 (tmm) cc_final: 0.7834 (mmt) REVERT: L 178 MET cc_start: 0.4760 (pmm) cc_final: 0.4395 (pmm) REVERT: L 233 MET cc_start: -0.1896 (ptt) cc_final: -0.2115 (ptt) REVERT: P 178 MET cc_start: 0.7655 (tpp) cc_final: 0.7385 (tpp) REVERT: P 254 MET cc_start: 0.8054 (ppp) cc_final: 0.7847 (ppp) outliers start: 2 outliers final: 0 residues processed: 313 average time/residue: 0.2076 time to fit residues: 110.1829 Evaluate side-chains 240 residues out of total 4030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 172 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 258 optimal weight: 0.9980 chunk 33 optimal weight: 20.0000 chunk 232 optimal weight: 2.9990 chunk 149 optimal weight: 0.9990 chunk 118 optimal weight: 4.9990 chunk 91 optimal weight: 0.0040 chunk 261 optimal weight: 0.0070 chunk 332 optimal weight: 8.9990 chunk 162 optimal weight: 4.9990 overall best weight: 0.5812 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 196 ASN H 127 GLN I 62 ASN ** A 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 231 HIS ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 212 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.094544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.074599 restraints weight = 247772.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.073542 restraints weight = 164533.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.073871 restraints weight = 149298.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.074133 restraints weight = 118141.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.074247 restraints weight = 112996.737| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3704 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3704 r_free = 0.3704 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3704 r_free = 0.3704 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3704 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.5063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 37268 Z= 0.105 Angle : 0.582 10.204 50238 Z= 0.302 Chirality : 0.042 0.201 5514 Planarity : 0.003 0.069 6442 Dihedral : 4.514 21.374 4892 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.23 % Favored : 93.64 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.83 (0.12), residues: 4574 helix: 0.48 (0.13), residues: 1565 sheet: -0.41 (0.18), residues: 874 loop : -1.36 (0.13), residues: 2135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 284 TYR 0.024 0.001 TYR F 259 PHE 0.016 0.001 PHE M 257 TRP 0.025 0.001 TRP P 194 HIS 0.012 0.001 HIS H 231 Details of bonding type rmsd covalent geometry : bond 0.00225 (37266) covalent geometry : angle 0.58141 (50234) SS BOND : bond 0.00171 ( 2) SS BOND : angle 1.39475 ( 4) hydrogen bonds : bond 0.03030 ( 1232) hydrogen bonds : angle 4.78675 ( 3492) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9148 Ramachandran restraints generated. 4574 Oldfield, 0 Emsley, 4574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9148 Ramachandran restraints generated. 4574 Oldfield, 0 Emsley, 4574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 4030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 313 time to evaluate : 1.799 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: C 228 MET cc_start: 0.6450 (pmm) cc_final: 0.5597 (tpp) REVERT: D 48 MET cc_start: 0.6555 (tpt) cc_final: 0.5852 (tpp) REVERT: D 117 MET cc_start: 0.8138 (ptp) cc_final: 0.7554 (ptp) REVERT: D 201 ASP cc_start: 0.7089 (m-30) cc_final: 0.6778 (t0) REVERT: H 178 MET cc_start: 0.8866 (mpp) cc_final: 0.8538 (mpp) REVERT: H 228 MET cc_start: 0.9037 (tmm) cc_final: 0.8755 (tmm) REVERT: H 273 LEU cc_start: 0.9576 (mt) cc_final: 0.9062 (mt) REVERT: H 288 MET cc_start: 0.9524 (mtm) cc_final: 0.9015 (ptp) REVERT: H 341 MET cc_start: 0.9348 (ppp) cc_final: 0.9079 (ppp) REVERT: I 50 GLU cc_start: 0.7699 (pp20) cc_final: 0.7253 (pp20) REVERT: I 112 GLU cc_start: 0.8639 (mt-10) cc_final: 0.8287 (mp0) REVERT: J 254 MET cc_start: 0.9053 (tmm) cc_final: 0.8828 (tmm) REVERT: J 255 MET cc_start: 0.8309 (ttt) cc_final: 0.7687 (tpp) REVERT: J 288 MET cc_start: 0.9252 (ppp) cc_final: 0.8976 (ppp) REVERT: J 305 ILE cc_start: 0.9459 (mt) cc_final: 0.9048 (mt) REVERT: J 320 GLN cc_start: 0.8402 (mp10) cc_final: 0.8106 (mt0) REVERT: M 48 MET cc_start: 0.8258 (ppp) cc_final: 0.7912 (ppp) REVERT: M 117 MET cc_start: 0.5777 (mpp) cc_final: 0.5350 (mpp) REVERT: M 228 MET cc_start: 0.9133 (pmm) cc_final: 0.8687 (pmm) REVERT: M 233 MET cc_start: 0.3157 (ptt) cc_final: 0.2776 (ptt) REVERT: M 318 LYS cc_start: 0.9562 (ptmm) cc_final: 0.9241 (pttp) REVERT: N 123 TYR cc_start: 0.6660 (t80) cc_final: 0.6172 (t80) REVERT: N 290 GLU cc_start: 0.8912 (mt-10) cc_final: 0.8455 (mt-10) REVERT: A 48 MET cc_start: 0.7944 (tpp) cc_final: 0.7213 (tpp) REVERT: A 176 MET cc_start: 0.7780 (ttm) cc_final: 0.7437 (ttm) REVERT: A 288 MET cc_start: 0.8140 (ptt) cc_final: 0.7190 (ppp) REVERT: B 48 MET cc_start: 0.7828 (tpt) cc_final: 0.7250 (tpp) REVERT: B 254 MET cc_start: 0.0428 (ttt) cc_final: -0.0008 (tpt) REVERT: B 288 MET cc_start: 0.5353 (ptm) cc_final: 0.4805 (mtt) REVERT: F 96 SER cc_start: 0.8865 (p) cc_final: 0.8556 (t) REVERT: F 225 PHE cc_start: 0.7885 (m-10) cc_final: 0.7654 (m-10) REVERT: F 254 MET cc_start: 0.5177 (ppp) cc_final: 0.4405 (ppp) REVERT: G 48 MET cc_start: 0.8361 (tmm) cc_final: 0.8009 (tmm) REVERT: K 178 MET cc_start: 0.5590 (mpp) cc_final: 0.1425 (tmm) REVERT: K 233 MET cc_start: -0.1973 (ppp) cc_final: -0.3611 (ttt) REVERT: K 269 MET cc_start: 0.0219 (ptt) cc_final: -0.0353 (ptm) REVERT: L 48 MET cc_start: 0.9481 (mpp) cc_final: 0.8906 (mpp) REVERT: L 176 MET cc_start: 0.8726 (tmm) cc_final: 0.8147 (mmt) REVERT: P 178 MET cc_start: 0.7735 (tpp) cc_final: 0.7505 (tpp) REVERT: P 254 MET cc_start: 0.8074 (ppp) cc_final: 0.7860 (ppp) outliers start: 0 outliers final: 0 residues processed: 313 average time/residue: 0.1954 time to fit residues: 104.0851 Evaluate side-chains 239 residues out of total 4030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 414 optimal weight: 20.0000 chunk 248 optimal weight: 9.9990 chunk 253 optimal weight: 10.0000 chunk 191 optimal weight: 0.0970 chunk 105 optimal weight: 1.9990 chunk 223 optimal weight: 0.9980 chunk 387 optimal weight: 0.9990 chunk 154 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 196 ASN H 127 GLN H 231 HIS I 62 ASN ** J 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 231 HIS ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 212 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.093807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.074489 restraints weight = 248516.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.073609 restraints weight = 166216.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.074033 restraints weight = 148609.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.074072 restraints weight = 116107.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.074547 restraints weight = 112687.607| |-----------------------------------------------------------------------------| r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3717 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3717 r_free = 0.3717 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3717 r_free = 0.3717 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3717 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.5244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 37268 Z= 0.119 Angle : 0.598 11.056 50238 Z= 0.310 Chirality : 0.042 0.230 5514 Planarity : 0.003 0.067 6442 Dihedral : 4.547 22.015 4892 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.62 % Favored : 93.24 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.81 (0.12), residues: 4574 helix: 0.49 (0.13), residues: 1564 sheet: -0.40 (0.18), residues: 896 loop : -1.35 (0.13), residues: 2114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 284 TYR 0.025 0.001 TYR N 280 PHE 0.024 0.001 PHE M 257 TRP 0.032 0.001 TRP B 36 HIS 0.006 0.001 HIS D 312 Details of bonding type rmsd covalent geometry : bond 0.00257 (37266) covalent geometry : angle 0.59766 (50234) SS BOND : bond 0.00204 ( 2) SS BOND : angle 1.16504 ( 4) hydrogen bonds : bond 0.03060 ( 1232) hydrogen bonds : angle 4.78998 ( 3492) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9148 Ramachandran restraints generated. 4574 Oldfield, 0 Emsley, 4574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9148 Ramachandran restraints generated. 4574 Oldfield, 0 Emsley, 4574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 4030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 299 time to evaluate : 1.340 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: C 228 MET cc_start: 0.6362 (pmm) cc_final: 0.5503 (tpp) REVERT: D 48 MET cc_start: 0.6547 (tpt) cc_final: 0.5766 (tpp) REVERT: D 117 MET cc_start: 0.8077 (ptp) cc_final: 0.7488 (ptp) REVERT: D 201 ASP cc_start: 0.6995 (m-30) cc_final: 0.6753 (t0) REVERT: H 228 MET cc_start: 0.9019 (tmm) cc_final: 0.8724 (tmm) REVERT: H 273 LEU cc_start: 0.9535 (mt) cc_final: 0.9011 (mt) REVERT: H 288 MET cc_start: 0.9499 (mtm) cc_final: 0.9013 (ptp) REVERT: H 341 MET cc_start: 0.9340 (ppp) cc_final: 0.9061 (ppp) REVERT: I 112 GLU cc_start: 0.8588 (mt-10) cc_final: 0.8099 (mt-10) REVERT: J 254 MET cc_start: 0.9015 (tmm) cc_final: 0.8775 (tmm) REVERT: J 255 MET cc_start: 0.8250 (ttt) cc_final: 0.7607 (tpp) REVERT: J 288 MET cc_start: 0.9190 (ppp) cc_final: 0.8898 (ppp) REVERT: J 305 ILE cc_start: 0.9443 (mt) cc_final: 0.9042 (mt) REVERT: J 320 GLN cc_start: 0.8360 (mp10) cc_final: 0.8104 (mt0) REVERT: M 48 MET cc_start: 0.8256 (ppp) cc_final: 0.7932 (ppp) REVERT: M 117 MET cc_start: 0.5798 (mpp) cc_final: 0.5362 (mpp) REVERT: M 228 MET cc_start: 0.9190 (pmm) cc_final: 0.8676 (pmm) REVERT: M 233 MET cc_start: 0.3063 (ptt) cc_final: 0.2636 (ptt) REVERT: M 318 LYS cc_start: 0.9553 (ptmm) cc_final: 0.9243 (pttp) REVERT: N 123 TYR cc_start: 0.6450 (t80) cc_final: 0.6040 (t80) REVERT: A 48 MET cc_start: 0.7917 (tpp) cc_final: 0.7224 (tpp) REVERT: A 176 MET cc_start: 0.7713 (ttm) cc_final: 0.7408 (ttm) REVERT: A 288 MET cc_start: 0.8063 (ptt) cc_final: 0.7131 (ppp) REVERT: B 48 MET cc_start: 0.7871 (tpt) cc_final: 0.7352 (tpp) REVERT: B 254 MET cc_start: 0.0421 (ttt) cc_final: -0.0065 (tpt) REVERT: B 288 MET cc_start: 0.5444 (ptm) cc_final: 0.4816 (mtt) REVERT: B 347 HIS cc_start: 0.7754 (t70) cc_final: 0.7542 (t70) REVERT: F 96 SER cc_start: 0.8888 (p) cc_final: 0.8576 (t) REVERT: F 225 PHE cc_start: 0.7928 (m-10) cc_final: 0.7693 (m-10) REVERT: F 254 MET cc_start: 0.5508 (ppp) cc_final: 0.4496 (ppp) REVERT: G 48 MET cc_start: 0.8406 (tmm) cc_final: 0.8034 (tmm) REVERT: K 178 MET cc_start: 0.5345 (mpp) cc_final: 0.1122 (tmm) REVERT: K 233 MET cc_start: -0.2385 (ppp) cc_final: -0.4237 (ttt) REVERT: K 269 MET cc_start: -0.0516 (ptt) cc_final: -0.1332 (ptm) REVERT: L 48 MET cc_start: 0.9400 (mpp) cc_final: 0.8841 (mpp) REVERT: L 176 MET cc_start: 0.8618 (tmm) cc_final: 0.8083 (mmt) REVERT: L 233 MET cc_start: -0.1664 (ptt) cc_final: -0.1929 (ptt) REVERT: P 178 MET cc_start: 0.7625 (tpp) cc_final: 0.7399 (tpp) REVERT: P 254 MET cc_start: 0.8071 (ppp) cc_final: 0.7855 (ppp) outliers start: 0 outliers final: 0 residues processed: 299 average time/residue: 0.1916 time to fit residues: 97.5015 Evaluate side-chains 238 residues out of total 4030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 308 optimal weight: 0.8980 chunk 81 optimal weight: 8.9990 chunk 359 optimal weight: 0.0060 chunk 103 optimal weight: 4.9990 chunk 186 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 221 optimal weight: 1.9990 chunk 352 optimal weight: 0.0980 chunk 183 optimal weight: 3.9990 overall best weight: 1.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 196 ASN H 231 HIS H 326 ASN I 62 ASN ** J 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 231 HIS ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 212 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.093509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.074096 restraints weight = 247084.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.073318 restraints weight = 167973.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.073848 restraints weight = 142085.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.073939 restraints weight = 114053.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.074096 restraints weight = 109464.043| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3709 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3709 r_free = 0.3709 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3709 r_free = 0.3709 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3709 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.5414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 37268 Z= 0.128 Angle : 0.597 10.504 50238 Z= 0.311 Chirality : 0.042 0.224 5514 Planarity : 0.003 0.067 6442 Dihedral : 4.576 22.551 4892 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.71 % Favored : 93.16 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.79 (0.12), residues: 4574 helix: 0.51 (0.13), residues: 1561 sheet: -0.37 (0.18), residues: 903 loop : -1.35 (0.13), residues: 2110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 284 TYR 0.025 0.001 TYR F 259 PHE 0.022 0.001 PHE M 257 TRP 0.033 0.001 TRP B 36 HIS 0.007 0.001 HIS D 312 Details of bonding type rmsd covalent geometry : bond 0.00279 (37266) covalent geometry : angle 0.59703 (50234) SS BOND : bond 0.00183 ( 2) SS BOND : angle 1.18367 ( 4) hydrogen bonds : bond 0.03126 ( 1232) hydrogen bonds : angle 4.81346 ( 3492) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6507.47 seconds wall clock time: 114 minutes 1.16 seconds (6841.16 seconds total)