Starting phenix.real_space_refine on Tue Sep 15 11:11:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6voh_21264/09_2026/6voh_21264.cif Found real_map, /net/cci-nas-00/data/ceres_data/6voh_21264/09_2026/6voh_21264.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6voh_21264/09_2026/6voh_21264.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6voh_21264/09_2026/6voh_21264.cif" model { file = "/net/cci-nas-00/data/ceres_data/6voh_21264/09_2026/6voh_21264.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6voh_21264/09_2026/6voh_21264.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6voh_21264/09_2026/6voh_21264.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6voh_21264/09_2026/6voh_21264.map" } resolution = 4.16 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= 0.003 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: 5 Type Number sf(0) Gaussians P 14 5.49 5 S 131 5.16 5 C 24854 2.51 5 N 6674 2.21 5 O 7486 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 195 residue(s): 0.08s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 39159 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 3850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3850 Classifications: {'peptide': 501} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 483} Chain: "C" Number of atoms: 3843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3843 Classifications: {'peptide': 500} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 482} Chain: "B" Number of atoms: 3854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 3854 Classifications: {'peptide': 502} Link IDs: {'PTRANS': 17, 'TRANS': 484} Chain: "D" Number of atoms: 3619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3619 Classifications: {'peptide': 478} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 452} Chain: "E" Number of atoms: 3645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3645 Classifications: {'peptide': 481} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 455} Chain: "F" Number of atoms: 3636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3636 Classifications: {'peptide': 480} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 454} Chain: "d" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1384 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 4, 'TRANS': 174} Chain: "g" Number of atoms: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2508 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 12, 'TRANS': 310} Chain: "e" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1007 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 126} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1068 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 3, 'TRANS': 132} Chain: "I" Number of atoms: 1237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1237 Classifications: {'peptide': 153} Link IDs: {'TRANS': 152} Chain: "a" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1741 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 14, 'TRANS': 208} Chain: "T" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "Y" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "X" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "W" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "V" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "U" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "Z" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "S" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "R" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "Q" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "M" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "N" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "O" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "P" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.05, per 1000 atoms: 0.23 Number of scatterers: 39159 At special positions: 0 Unit cell: (163.28, 204.88, 168.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 131 16.00 P 14 15.00 O 7486 8.00 N 6674 7.00 C 24854 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS g 240 " - pdb=" SG CYS g 246 " distance=2.05 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: 3.56 Conformation dependent library (CDL) restraints added in 1.9 seconds 10282 Ramachandran restraints generated. 5141 Oldfield, 0 Emsley, 5141 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9436 Finding SS restraints... Secondary structure from input PDB file: 176 helices and 28 sheets defined 58.9% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.38 Creating SS restraints... Processing helix chain 'A' and resid 10 through 25 Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'A' and resid 175 through 187 removed outlier: 3.797A pdb=" N GLN A 187 " --> pdb=" O THR A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 216 Processing helix chain 'A' and resid 234 through 252 Proline residue: A 240 - end of helix removed outlier: 3.902A pdb=" N PHE A 250 " --> pdb=" O LEU A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 278 removed outlier: 3.525A pdb=" N GLN A 267 " --> pdb=" O ASP A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 287 Processing helix chain 'A' and resid 290 through 300 Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 329 through 337 removed outlier: 3.753A pdb=" N THR A 333 " --> pdb=" O ALA A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 351 Processing helix chain 'A' and resid 367 through 372 removed outlier: 3.561A pdb=" N GLN A 372 " --> pdb=" O SER A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 380 Processing helix chain 'A' and resid 382 through 397 removed outlier: 4.137A pdb=" N GLU A 392 " --> pdb=" O ALA A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 419 removed outlier: 3.699A pdb=" N ALA A 412 " --> pdb=" O GLN A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 443 removed outlier: 4.536A pdb=" N THR A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 447 Processing helix chain 'A' and resid 453 through 468 removed outlier: 3.895A pdb=" N TYR A 457 " --> pdb=" O GLN A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 476 removed outlier: 3.900A pdb=" N GLU A 474 " --> pdb=" O PRO A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 504 removed outlier: 4.093A pdb=" N ALA A 488 " --> pdb=" O GLU A 484 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU A 489 " --> pdb=" O GLU A 485 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU A 490 " --> pdb=" O ALA A 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 20 removed outlier: 3.698A pdb=" N ILE C 13 " --> pdb=" O ILE C 9 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU C 15 " --> pdb=" O LYS C 11 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG C 16 " --> pdb=" O ILE C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 105 removed outlier: 3.504A pdb=" N LEU C 105 " --> pdb=" O GLU C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 157 Processing helix chain 'C' and resid 175 through 187 Processing helix chain 'C' and resid 202 through 216 Processing helix chain 'C' and resid 217 through 222 removed outlier: 3.844A pdb=" N GLU C 220 " --> pdb=" O GLY C 217 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR C 222 " --> pdb=" O MET C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 253 Proline residue: C 240 - end of helix removed outlier: 3.535A pdb=" N TYR C 249 " --> pdb=" O ALA C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 278 Processing helix chain 'C' and resid 283 through 287 Processing helix chain 'C' and resid 290 through 300 Processing helix chain 'C' and resid 329 through 339 Processing helix chain 'C' and resid 346 through 352 Processing helix chain 'C' and resid 373 through 393 removed outlier: 4.481A pdb=" N GLY C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LYS C 382 " --> pdb=" O LYS C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 400 removed outlier: 4.069A pdb=" N GLN C 398 " --> pdb=" O ALA C 395 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA C 400 " --> pdb=" O ALA C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 422 removed outlier: 3.908A pdb=" N GLU C 419 " --> pdb=" O GLN C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 443 Processing helix chain 'C' and resid 452 through 469 removed outlier: 4.596A pdb=" N LYS C 456 " --> pdb=" O ASP C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 480 removed outlier: 4.062A pdb=" N GLN C 473 " --> pdb=" O LYS C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 503 Processing helix chain 'B' and resid 9 through 19 removed outlier: 3.535A pdb=" N GLU B 15 " --> pdb=" O LYS B 11 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLY B 19 " --> pdb=" O GLU B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 158 Processing helix chain 'B' and resid 176 through 187 removed outlier: 3.585A pdb=" N GLN B 187 " --> pdb=" O THR B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 218 through 221 Processing helix chain 'B' and resid 232 through 253 Proline residue: B 240 - end of helix removed outlier: 4.299A pdb=" N PHE B 250 " --> pdb=" O LEU B 246 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG B 253 " --> pdb=" O TYR B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 277 Processing helix chain 'B' and resid 283 through 287 removed outlier: 3.684A pdb=" N ALA B 286 " --> pdb=" O GLY B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 300 Processing helix chain 'B' and resid 330 through 339 Processing helix chain 'B' and resid 346 through 353 removed outlier: 3.803A pdb=" N PHE B 350 " --> pdb=" O SER B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 371 removed outlier: 3.660A pdb=" N ALA B 370 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 396 removed outlier: 4.593A pdb=" N VAL B 379 " --> pdb=" O ALA B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 421 Processing helix chain 'B' and resid 430 through 443 removed outlier: 3.903A pdb=" N GLY B 441 " --> pdb=" O THR B 437 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN B 443 " --> pdb=" O TYR B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 469 removed outlier: 4.463A pdb=" N GLU B 460 " --> pdb=" O LYS B 456 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS B 466 " --> pdb=" O ARG B 462 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N THR B 467 " --> pdb=" O THR B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 479 removed outlier: 3.938A pdb=" N GLN B 473 " --> pdb=" O LYS B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 503 Processing helix chain 'D' and resid 103 through 107 Processing helix chain 'D' and resid 153 through 159 Processing helix chain 'D' and resid 177 through 189 removed outlier: 3.691A pdb=" N LEU D 181 " --> pdb=" O GLY D 177 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE D 182 " --> pdb=" O LYS D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 219 Processing helix chain 'D' and resid 227 through 231 removed outlier: 4.358A pdb=" N LYS D 231 " --> pdb=" O ALA D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 263 removed outlier: 3.641A pdb=" N PHE D 260 " --> pdb=" O MET D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 289 removed outlier: 3.916A pdb=" N PHE D 278 " --> pdb=" O ASN D 274 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL D 279 " --> pdb=" O ILE D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 312 removed outlier: 3.724A pdb=" N ARG D 312 " --> pdb=" O SER D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 333 removed outlier: 4.171A pdb=" N ASP D 332 " --> pdb=" O VAL D 329 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP D 333 " --> pdb=" O PRO D 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 329 through 333' Processing helix chain 'D' and resid 336 through 346 removed outlier: 3.887A pdb=" N THR D 342 " --> pdb=" O ALA D 338 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA D 344 " --> pdb=" O ALA D 340 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N HIS D 345 " --> pdb=" O THR D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 360 removed outlier: 4.149A pdb=" N ALA D 357 " --> pdb=" O SER D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 381 Processing helix chain 'D' and resid 381 through 401 Processing helix chain 'D' and resid 409 through 413 Processing helix chain 'D' and resid 414 through 431 Processing helix chain 'D' and resid 450 through 463 removed outlier: 4.054A pdb=" N ARG D 456 " --> pdb=" O ALA D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 470 through 474 Processing helix chain 'D' and resid 479 through 494 Processing helix chain 'E' and resid 153 through 160 Processing helix chain 'E' and resid 177 through 192 Processing helix chain 'E' and resid 205 through 219 Processing helix chain 'E' and resid 244 through 265 removed outlier: 5.486A pdb=" N GLY E 250 " --> pdb=" O ARG E 246 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LEU E 251 " --> pdb=" O MET E 247 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE E 260 " --> pdb=" O MET E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 290 Processing helix chain 'E' and resid 301 through 311 Processing helix chain 'E' and resid 336 through 344 Processing helix chain 'E' and resid 353 through 360 Processing helix chain 'E' and resid 376 through 381 Processing helix chain 'E' and resid 381 through 402 Processing helix chain 'E' and resid 414 through 432 removed outlier: 3.661A pdb=" N LEU E 419 " --> pdb=" O GLU E 415 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N THR E 420 " --> pdb=" O GLU E 416 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N SER E 432 " --> pdb=" O GLU E 428 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 443 Processing helix chain 'E' and resid 450 through 464 Processing helix chain 'E' and resid 470 through 474 Processing helix chain 'E' and resid 479 through 494 Processing helix chain 'F' and resid 153 through 159 Processing helix chain 'F' and resid 179 through 193 removed outlier: 5.166A pdb=" N LYS F 191 " --> pdb=" O ASN F 187 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA F 192 " --> pdb=" O ASN F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 219 Processing helix chain 'F' and resid 226 through 230 removed outlier: 3.837A pdb=" N SER F 230 " --> pdb=" O ILE F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 263 removed outlier: 5.148A pdb=" N GLY F 250 " --> pdb=" O ARG F 246 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N LEU F 251 " --> pdb=" O MET F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 276 through 289 removed outlier: 4.056A pdb=" N GLY F 282 " --> pdb=" O PHE F 278 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU F 288 " --> pdb=" O GLU F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 311 Processing helix chain 'F' and resid 329 through 333 Processing helix chain 'F' and resid 336 through 341 Processing helix chain 'F' and resid 341 through 346 removed outlier: 3.824A pdb=" N HIS F 345 " --> pdb=" O THR F 341 " (cutoff:3.500A) Processing helix chain 'F' and resid 353 through 359 removed outlier: 4.127A pdb=" N LYS F 359 " --> pdb=" O GLY F 355 " (cutoff:3.500A) Processing helix chain 'F' and resid 376 through 381 Processing helix chain 'F' and resid 381 through 408 removed outlier: 4.659A pdb=" N ASP F 403 " --> pdb=" O LYS F 399 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ILE F 404 " --> pdb=" O GLU F 400 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 431 Processing helix chain 'F' and resid 438 through 443 Processing helix chain 'F' and resid 450 through 463 removed outlier: 3.726A pdb=" N THR F 454 " --> pdb=" O GLY F 450 " (cutoff:3.500A) Processing helix chain 'F' and resid 470 through 474 Processing helix chain 'F' and resid 479 through 496 removed outlier: 3.650A pdb=" N LYS F 495 " --> pdb=" O GLU F 491 " (cutoff:3.500A) Processing helix chain 'd' and resid 73 through 89 Processing helix chain 'd' and resid 91 through 107 Processing helix chain 'd' and resid 109 through 116 Processing helix chain 'd' and resid 121 through 137 Processing helix chain 'd' and resid 139 through 152 Processing helix chain 'd' and resid 153 through 156 removed outlier: 4.255A pdb=" N ASN d 156 " --> pdb=" O GLU d 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 153 through 156' Processing helix chain 'd' and resid 157 through 174 removed outlier: 4.200A pdb=" N GLU d 166 " --> pdb=" O LEU d 162 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ASP d 167 " --> pdb=" O ASN d 163 " (cutoff:3.500A) Processing helix chain 'd' and resid 187 through 203 Processing helix chain 'd' and resid 236 through 249 removed outlier: 3.990A pdb=" N GLN d 240 " --> pdb=" O SER d 236 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU d 249 " --> pdb=" O ALA d 245 " (cutoff:3.500A) Processing helix chain 'g' and resid 43 through 100 removed outlier: 3.599A pdb=" N LEU g 47 " --> pdb=" O ASN g 43 " (cutoff:3.500A) Proline residue: g 84 - end of helix removed outlier: 3.741A pdb=" N TYR g 94 " --> pdb=" O VAL g 90 " (cutoff:3.500A) Processing helix chain 'g' and resid 107 through 111 removed outlier: 3.562A pdb=" N LYS g 111 " --> pdb=" O PRO g 108 " (cutoff:3.500A) Processing helix chain 'g' and resid 132 through 152 removed outlier: 3.879A pdb=" N MET g 136 " --> pdb=" O GLY g 132 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU g 151 " --> pdb=" O GLU g 147 " (cutoff:3.500A) Processing helix chain 'g' and resid 161 through 171 removed outlier: 3.880A pdb=" N ARG g 170 " --> pdb=" O THR g 166 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ARG g 171 " --> pdb=" O TYR g 167 " (cutoff:3.500A) Processing helix chain 'g' and resid 187 through 203 Processing helix chain 'g' and resid 287 through 362 removed outlier: 3.963A pdb=" N LEU g 292 " --> pdb=" O PRO g 288 " (cutoff:3.500A) Proline residue: g 297 - end of helix removed outlier: 3.702A pdb=" N SER g 311 " --> pdb=" O ALA g 307 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASN g 361 " --> pdb=" O VAL g 357 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ALA g 362 " --> pdb=" O ALA g 358 " (cutoff:3.500A) Processing helix chain 'e' and resid 88 through 104 removed outlier: 3.521A pdb=" N ARG e 104 " --> pdb=" O GLU e 100 " (cutoff:3.500A) Processing helix chain 'e' and resid 111 through 126 Processing helix chain 'e' and resid 126 through 131 Processing helix chain 'J' and resid 88 through 219 removed outlier: 4.030A pdb=" N GLU J 96 " --> pdb=" O ILE J 92 " (cutoff:3.500A) Proline residue: J 111 - end of helix removed outlier: 4.042A pdb=" N ASN J 145 " --> pdb=" O GLU J 141 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N MET J 148 " --> pdb=" O ALA J 144 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA J 158 " --> pdb=" O GLU J 154 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU J 197 " --> pdb=" O GLU J 193 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N SER J 205 " --> pdb=" O LYS J 201 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N GLN J 206 " --> pdb=" O SER J 202 " (cutoff:3.500A) Processing helix chain 'I' and resid 31 through 70 removed outlier: 3.538A pdb=" N ASN I 55 " --> pdb=" O ASP I 51 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N GLN I 58 " --> pdb=" O ASP I 54 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG I 59 " --> pdb=" O ASN I 55 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLU I 68 " --> pdb=" O ILE I 64 " (cutoff:3.500A) Processing helix chain 'I' and resid 71 through 104 removed outlier: 3.806A pdb=" N VAL I 97 " --> pdb=" O ASP I 93 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY I 99 " --> pdb=" O PHE I 95 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N SER I 101 " --> pdb=" O VAL I 97 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N GLU I 102 " --> pdb=" O ASN I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 105 through 159 removed outlier: 4.040A pdb=" N THR I 114 " --> pdb=" O LEU I 110 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS I 116 " --> pdb=" O ASN I 112 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N THR I 117 " --> pdb=" O SER I 113 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE I 129 " --> pdb=" O LYS I 125 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLY I 154 " --> pdb=" O GLN I 150 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER I 158 " --> pdb=" O GLY I 154 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N CYS I 159 " --> pdb=" O THR I 155 " (cutoff:3.500A) Processing helix chain 'I' and resid 164 through 182 Processing helix chain 'a' and resid 37 through 53 removed outlier: 3.847A pdb=" N THR a 42 " --> pdb=" O GLN a 38 " (cutoff:3.500A) Processing helix chain 'a' and resid 54 through 56 No H-bonds generated for 'chain 'a' and resid 54 through 56' Processing helix chain 'a' and resid 68 through 88 removed outlier: 4.380A pdb=" N TYR a 74 " --> pdb=" O ASN a 70 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL a 75 " --> pdb=" O PHE a 71 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N THR a 85 " --> pdb=" O ASP a 81 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLN a 86 " --> pdb=" O VAL a 82 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY a 88 " --> pdb=" O LYS a 84 " (cutoff:3.500A) Processing helix chain 'a' and resid 91 through 93 No H-bonds generated for 'chain 'a' and resid 91 through 93' Processing helix chain 'a' and resid 94 through 114 removed outlier: 3.661A pdb=" N MET a 101 " --> pdb=" O PHE a 97 " (cutoff:3.500A) Processing helix chain 'a' and resid 133 through 156 removed outlier: 4.145A pdb=" N THR a 137 " --> pdb=" O ASP a 133 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR a 154 " --> pdb=" O TYR a 150 " (cutoff:3.500A) Processing helix chain 'a' and resid 176 through 208 removed outlier: 3.826A pdb=" N THR a 181 " --> pdb=" O LEU a 177 " (cutoff:3.500A) Proline residue: a 183 - end of helix removed outlier: 3.547A pdb=" N ASN a 193 " --> pdb=" O ARG a 189 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU a 204 " --> pdb=" O VAL a 200 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL a 205 " --> pdb=" O VAL a 201 " (cutoff:3.500A) Processing helix chain 'a' and resid 213 through 244 removed outlier: 3.868A pdb=" N PHE a 218 " --> pdb=" O ILE a 214 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LEU a 219 " --> pdb=" O PRO a 215 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR a 223 " --> pdb=" O LEU a 219 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER a 224 " --> pdb=" O GLY a 220 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ALA a 228 " --> pdb=" O SER a 224 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N LEU a 229 " --> pdb=" O GLY a 225 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE a 230 " --> pdb=" O ILE a 226 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLU a 244 " --> pdb=" O GLY a 240 " (cutoff:3.500A) Processing helix chain 'T' and resid 4 through 42 removed outlier: 4.377A pdb=" N VAL T 10 " --> pdb=" O ALA T 6 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE T 11 " --> pdb=" O ALA T 7 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N GLY T 23 " --> pdb=" O LEU T 19 " (cutoff:3.500A) Proline residue: T 24 - end of helix removed outlier: 3.603A pdb=" N GLN T 42 " --> pdb=" O GLY T 38 " (cutoff:3.500A) Processing helix chain 'T' and resid 46 through 69 removed outlier: 4.008A pdb=" N PHE T 59 " --> pdb=" O LEU T 55 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR T 64 " --> pdb=" O MET T 60 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU T 68 " --> pdb=" O THR T 64 " (cutoff:3.500A) Processing helix chain 'T' and resid 71 through 76 Processing helix chain 'Y' and resid 4 through 42 removed outlier: 3.848A pdb=" N ALA Y 8 " --> pdb=" O LEU Y 4 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ALA Y 13 " --> pdb=" O SER Y 9 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N GLY Y 14 " --> pdb=" O VAL Y 10 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU Y 15 " --> pdb=" O ILE Y 11 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA Y 20 " --> pdb=" O ALA Y 16 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLY Y 23 " --> pdb=" O LEU Y 19 " (cutoff:3.500A) Proline residue: Y 24 - end of helix removed outlier: 4.925A pdb=" N GLY Y 29 " --> pdb=" O GLY Y 25 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N GLN Y 34 " --> pdb=" O THR Y 30 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU Y 37 " --> pdb=" O GLY Y 33 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE Y 39 " --> pdb=" O ALA Y 35 " (cutoff:3.500A) Processing helix chain 'Y' and resid 45 through 76 removed outlier: 4.458A pdb=" N GLY Y 51 " --> pdb=" O GLY Y 47 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N TYR Y 66 " --> pdb=" O ALA Y 62 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLY Y 67 " --> pdb=" O LEU Y 63 " (cutoff:3.500A) Processing helix chain 'X' and resid 4 through 23 removed outlier: 4.198A pdb=" N ILE X 11 " --> pdb=" O ALA X 7 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA X 12 " --> pdb=" O ALA X 8 " (cutoff:3.500A) Processing helix chain 'X' and resid 23 through 42 removed outlier: 3.723A pdb=" N ALA X 35 " --> pdb=" O ALA X 31 " (cutoff:3.500A) Processing helix chain 'X' and resid 45 through 61 removed outlier: 4.965A pdb=" N GLY X 51 " --> pdb=" O GLY X 47 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N THR X 52 " --> pdb=" O LYS X 48 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEU X 55 " --> pdb=" O GLY X 51 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER X 56 " --> pdb=" O THR X 52 " (cutoff:3.500A) Processing helix chain 'X' and resid 61 through 76 Processing helix chain 'W' and resid 6 through 42 removed outlier: 3.690A pdb=" N GLY W 18 " --> pdb=" O GLY W 14 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N GLY W 23 " --> pdb=" O LEU W 19 " (cutoff:3.500A) Proline residue: W 24 - end of helix Processing helix chain 'W' and resid 45 through 76 removed outlier: 4.056A pdb=" N GLY W 67 " --> pdb=" O LEU W 63 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N VAL W 70 " --> pdb=" O TYR W 66 " (cutoff:3.500A) Processing helix chain 'V' and resid 6 through 21 removed outlier: 3.878A pdb=" N SER V 21 " --> pdb=" O VAL V 17 " (cutoff:3.500A) Processing helix chain 'V' and resid 22 through 42 removed outlier: 3.729A pdb=" N VAL V 26 " --> pdb=" O ILE V 22 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE V 39 " --> pdb=" O ALA V 35 " (cutoff:3.500A) Processing helix chain 'V' and resid 45 through 50 removed outlier: 3.518A pdb=" N ARG V 50 " --> pdb=" O GLU V 46 " (cutoff:3.500A) Processing helix chain 'V' and resid 56 through 78 removed outlier: 3.856A pdb=" N TYR V 66 " --> pdb=" O ALA V 62 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLY V 67 " --> pdb=" O LEU V 63 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LEU V 74 " --> pdb=" O VAL V 70 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU V 75 " --> pdb=" O ALA V 71 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA V 77 " --> pdb=" O ALA V 73 " (cutoff:3.500A) Processing helix chain 'U' and resid 4 through 42 removed outlier: 4.250A pdb=" N SER U 21 " --> pdb=" O VAL U 17 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ILE U 22 " --> pdb=" O GLY U 18 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N GLY U 23 " --> pdb=" O LEU U 19 " (cutoff:3.500A) Proline residue: U 24 - end of helix removed outlier: 3.611A pdb=" N GLY U 27 " --> pdb=" O GLY U 23 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLY U 29 " --> pdb=" O GLY U 25 " (cutoff:3.500A) Processing helix chain 'U' and resid 45 through 76 removed outlier: 4.253A pdb=" N GLY U 67 " --> pdb=" O LEU U 63 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE U 76 " --> pdb=" O LEU U 72 " (cutoff:3.500A) Processing helix chain 'Z' and resid 4 through 21 removed outlier: 4.287A pdb=" N SER Z 21 " --> pdb=" O VAL Z 17 " (cutoff:3.500A) Processing helix chain 'Z' and resid 21 through 42 removed outlier: 3.600A pdb=" N ARG Z 41 " --> pdb=" O GLU Z 37 " (cutoff:3.500A) Processing helix chain 'Z' and resid 45 through 76 removed outlier: 3.823A pdb=" N LEU Z 55 " --> pdb=" O GLY Z 51 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE Z 59 " --> pdb=" O LEU Z 55 " (cutoff:3.500A) Processing helix chain 'S' and resid 4 through 21 removed outlier: 3.996A pdb=" N ILE S 11 " --> pdb=" O ALA S 7 " (cutoff:3.500A) Processing helix chain 'S' and resid 21 through 42 removed outlier: 3.558A pdb=" N GLY S 25 " --> pdb=" O SER S 21 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG S 41 " --> pdb=" O GLU S 37 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLN S 42 " --> pdb=" O GLY S 38 " (cutoff:3.500A) Processing helix chain 'S' and resid 45 through 76 removed outlier: 4.417A pdb=" N THR S 52 " --> pdb=" O LYS S 48 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU S 53 " --> pdb=" O ILE S 49 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LEU S 55 " --> pdb=" O GLY S 51 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLY S 67 " --> pdb=" O LEU S 63 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 42 removed outlier: 3.766A pdb=" N ALA R 8 " --> pdb=" O LEU R 4 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY R 18 " --> pdb=" O GLY R 14 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N GLY R 23 " --> pdb=" O LEU R 19 " (cutoff:3.500A) Proline residue: R 24 - end of helix removed outlier: 3.754A pdb=" N THR R 30 " --> pdb=" O VAL R 26 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 76 removed outlier: 3.637A pdb=" N GLY R 67 " --> pdb=" O LEU R 63 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL R 70 " --> pdb=" O TYR R 66 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 42 removed outlier: 3.842A pdb=" N ILE Q 11 " --> pdb=" O ALA Q 7 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N SER Q 21 " --> pdb=" O VAL Q 17 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ILE Q 22 " --> pdb=" O GLY Q 18 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N GLY Q 23 " --> pdb=" O LEU Q 19 " (cutoff:3.500A) Proline residue: Q 24 - end of helix Processing helix chain 'Q' and resid 45 through 76 removed outlier: 3.519A pdb=" N ILE Q 49 " --> pdb=" O ALA Q 45 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLY Q 67 " --> pdb=" O LEU Q 63 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU Q 75 " --> pdb=" O ALA Q 71 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 20 removed outlier: 3.919A pdb=" N ILE M 11 " --> pdb=" O ALA M 7 " (cutoff:3.500A) Processing helix chain 'M' and resid 21 through 42 Processing helix chain 'M' and resid 45 through 76 removed outlier: 4.083A pdb=" N THR M 52 " --> pdb=" O LYS M 48 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE M 59 " --> pdb=" O LEU M 55 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE M 65 " --> pdb=" O GLU M 61 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR M 66 " --> pdb=" O ALA M 62 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLY M 67 " --> pdb=" O LEU M 63 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 37 removed outlier: 4.207A pdb=" N GLY N 23 " --> pdb=" O LEU N 19 " (cutoff:3.500A) Proline residue: N 24 - end of helix Processing helix chain 'N' and resid 41 through 45 removed outlier: 3.611A pdb=" N GLU N 44 " --> pdb=" O ARG N 41 " (cutoff:3.500A) Processing helix chain 'N' and resid 47 through 76 removed outlier: 3.538A pdb=" N LEU N 55 " --> pdb=" O GLY N 51 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLY N 67 " --> pdb=" O LEU N 63 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 42 removed outlier: 3.612A pdb=" N ILE O 11 " --> pdb=" O ALA O 7 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N GLY O 23 " --> pdb=" O LEU O 19 " (cutoff:3.500A) Proline residue: O 24 - end of helix removed outlier: 3.594A pdb=" N GLN O 34 " --> pdb=" O THR O 30 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL O 36 " --> pdb=" O ALA O 32 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N GLU O 37 " --> pdb=" O GLY O 33 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 72 removed outlier: 4.397A pdb=" N GLY O 51 " --> pdb=" O GLY O 47 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU O 54 " --> pdb=" O ARG O 50 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N LEU O 57 " --> pdb=" O LEU O 53 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLY O 67 " --> pdb=" O LEU O 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 4 through 42 removed outlier: 3.905A pdb=" N GLY P 18 " --> pdb=" O GLY P 14 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLY P 23 " --> pdb=" O LEU P 19 " (cutoff:3.500A) Proline residue: P 24 - end of helix removed outlier: 3.981A pdb=" N GLY P 27 " --> pdb=" O GLY P 23 " (cutoff:3.500A) Processing helix chain 'P' and resid 46 through 76 removed outlier: 3.511A pdb=" N LEU P 55 " --> pdb=" O GLY P 51 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY P 67 " --> pdb=" O LEU P 63 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL P 70 " --> pdb=" O TYR P 66 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 91 through 93 removed outlier: 3.638A pdb=" N VAL F 61 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ARG F 75 " --> pdb=" O GLN F 66 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N LEU F 68 " --> pdb=" O ARG F 73 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ARG F 73 " --> pdb=" O LEU F 68 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL F 30 " --> pdb=" O ILE F 27 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ALA F 34 " --> pdb=" O ILE F 23 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ILE F 23 " --> pdb=" O ALA F 34 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLY A 73 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N LEU A 67 " --> pdb=" O ASN A 71 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N ASN A 71 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N HIS A 43 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N VAL A 32 " --> pdb=" O HIS A 43 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N LEU A 53 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLU A 52 " --> pdb=" O ALA A 64 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 98 Processing sheet with id=AA3, first strand: chain 'A' and resid 108 through 109 removed outlier: 5.665A pdb=" N ILE A 109 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N SER A 313 " --> pdb=" O THR A 257 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE A 259 " --> pdb=" O SER A 313 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 61 through 62 removed outlier: 6.617A pdb=" N ARG C 41 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N VAL C 35 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ILE C 39 " --> pdb=" O VAL C 35 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 97 through 99 Processing sheet with id=AA6, first strand: chain 'C' and resid 319 through 321 removed outlier: 6.548A pdb=" N ILE C 168 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ILE C 169 " --> pdb=" O LEU C 345 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 198 through 199 removed outlier: 6.350A pdb=" N ALA C 198 " --> pdb=" O GLU C 227 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 41 through 42 Processing sheet with id=AA9, first strand: chain 'B' and resid 41 through 42 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 61 through 67 current: chain 'D' and resid 46 through 49 removed outlier: 6.889A pdb=" N ARG D 75 " --> pdb=" O GLN D 66 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N LEU D 68 " --> pdb=" O ARG D 73 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ARG D 73 " --> pdb=" O LEU D 68 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N ALA D 34 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N ILE D 23 " --> pdb=" O ALA D 34 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 97 through 98 removed outlier: 4.272A pdb=" N ARG B 128 " --> pdb=" O ILE B 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 108 through 109 removed outlier: 5.642A pdb=" N ILE B 109 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N THR B 228 " --> pdb=" O ILE B 109 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N VAL B 225 " --> pdb=" O CYS B 194 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N TYR B 196 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N GLU B 227 " --> pdb=" O TYR B 196 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ALA B 198 " --> pdb=" O GLU B 227 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU B 258 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR B 315 " --> pdb=" O THR B 257 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 341 through 342 Processing sheet with id=AB4, first strand: chain 'D' and resid 99 through 101 removed outlier: 3.538A pdb=" N SER D 130 " --> pdb=" O VAL D 100 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 323 through 325 removed outlier: 6.536A pdb=" N ILE D 168 " --> pdb=" O GLN D 325 " (cutoff:3.500A) removed outlier: 8.614A pdb=" N THR D 350 " --> pdb=" O LYS D 167 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLY D 169 " --> pdb=" O THR D 350 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N LEU D 352 " --> pdb=" O GLY D 169 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N PHE D 171 " --> pdb=" O LEU D 352 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'E' and resid 25 through 27 removed outlier: 3.511A pdb=" N VAL E 33 " --> pdb=" O VAL E 74 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL E 77 " --> pdb=" O VAL E 65 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N VAL E 65 " --> pdb=" O VAL E 77 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 110 through 111 Processing sheet with id=AB8, first strand: chain 'E' and resid 148 through 149 removed outlier: 4.366A pdb=" N TYR E 162 " --> pdb=" O PHE E 149 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 169 through 170 removed outlier: 7.410A pdb=" N ILE E 324 " --> pdb=" O VAL E 268 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N LEU E 270 " --> pdb=" O ILE E 324 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N ALA E 326 " --> pdb=" O LEU E 270 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ILE E 272 " --> pdb=" O ALA E 326 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL E 196 " --> pdb=" O LEU E 269 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N PHE E 271 " --> pdb=" O VAL E 196 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N VAL E 198 " --> pdb=" O PHE E 271 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 348 through 349 Processing sheet with id=AC2, first strand: chain 'F' and resid 99 through 101 Processing sheet with id=AC3, first strand: chain 'F' and resid 148 through 149 removed outlier: 4.469A pdb=" N TYR F 162 " --> pdb=" O PHE F 149 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 232 through 237 removed outlier: 3.628A pdb=" N PHE F 199 " --> pdb=" O ALA F 233 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N VAL F 198 " --> pdb=" O PHE F 271 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N ASP F 273 " --> pdb=" O VAL F 198 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLY F 200 " --> pdb=" O ASP F 273 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ILE F 168 " --> pdb=" O GLN F 325 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N LYS F 167 " --> pdb=" O ALA F 348 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'd' and resid 212 through 213 removed outlier: 6.519A pdb=" N VAL d 180 " --> pdb=" O VAL d 212 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'g' and resid 158 through 159 removed outlier: 6.742A pdb=" N MET g 121 " --> pdb=" O LEU g 213 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'g' and resid 256 through 259 removed outlier: 3.679A pdb=" N THR g 265 " --> pdb=" O THR g 258 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'g' and resid 283 through 284 removed outlier: 7.354A pdb=" N GLU g 283 " --> pdb=" O ALA e 41 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU e 3 " --> pdb=" O VAL e 19 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL e 19 " --> pdb=" O LEU e 3 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL e 7 " --> pdb=" O TRP e 15 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N TRP e 15 " --> pdb=" O VAL e 7 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N THR e 9 " --> pdb=" O SER e 13 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N SER e 13 " --> pdb=" O THR e 9 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'e' and resid 22 through 23 removed outlier: 4.386A pdb=" N ARG e 50 " --> pdb=" O ILE e 23 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY e 47 " --> pdb=" O LEU e 62 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA e 61 " --> pdb=" O GLU e 82 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'a' and resid 28 through 29 removed outlier: 4.048A pdb=" N GLN a 29 " --> pdb=" O ILE a 35 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE a 35 " --> pdb=" O GLN a 29 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 2262 hydrogen bonds defined for protein. 6618 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: 9.29 Time building geometry restraints manager: 4.74 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: 13121 1.34 - 1.47: 8096 1.47 - 1.59: 18220 1.59 - 1.71: 23 1.71 - 1.84: 249 Bond restraints: 39709 Sorted by residual: bond pdb=" C4 ATP D 601 " pdb=" C5 ATP D 601 " ideal model delta sigma weight residual 1.388 1.473 -0.085 1.00e-02 1.00e+04 7.20e+01 bond pdb=" C4 ATP A 601 " pdb=" C5 ATP A 601 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.47e+01 bond pdb=" C4 ATP B 601 " pdb=" C5 ATP B 601 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.34e+01 bond pdb=" C4 ATP C 601 " pdb=" C5 ATP C 601 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.06e+01 bond pdb=" C5 ATP D 601 " pdb=" C6 ATP D 601 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.37e+01 ... (remaining 39704 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.45: 53531 4.45 - 8.91: 297 8.91 - 13.36: 10 13.36 - 17.81: 4 17.81 - 22.27: 6 Bond angle restraints: 53848 Sorted by residual: angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 117.60 22.27 1.00e+00 1.00e+00 4.96e+02 angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 117.70 22.17 1.00e+00 1.00e+00 4.92e+02 angle pdb=" PB ATP D 601 " pdb=" O3B ATP D 601 " pdb=" PG ATP D 601 " ideal model delta sigma weight residual 139.87 119.31 20.56 1.00e+00 1.00e+00 4.23e+02 angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 119.73 20.14 1.00e+00 1.00e+00 4.06e+02 angle pdb=" PA ATP D 601 " pdb=" O3A ATP D 601 " pdb=" PB ATP D 601 " ideal model delta sigma weight residual 136.83 116.72 20.11 1.00e+00 1.00e+00 4.04e+02 ... (remaining 53843 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.82: 22434 23.82 - 47.65: 1451 47.65 - 71.47: 142 71.47 - 95.30: 49 95.30 - 119.12: 3 Dihedral angle restraints: 24079 sinusoidal: 9348 harmonic: 14731 Sorted by residual: dihedral pdb=" CA PRO R 79 " pdb=" C PRO R 79 " pdb=" N PHE R 80 " pdb=" CA PHE R 80 " ideal model delta harmonic sigma weight residual -180.00 -123.70 -56.30 0 5.00e+00 4.00e-02 1.27e+02 dihedral pdb=" CA ALA D 295 " pdb=" C ALA D 295 " pdb=" N VAL D 296 " pdb=" CA VAL D 296 " ideal model delta harmonic sigma weight residual -180.00 -129.56 -50.44 0 5.00e+00 4.00e-02 1.02e+02 dihedral pdb=" CA ALA E 295 " pdb=" C ALA E 295 " pdb=" N VAL E 296 " pdb=" CA VAL E 296 " ideal model delta harmonic sigma weight residual -180.00 -131.69 -48.31 0 5.00e+00 4.00e-02 9.33e+01 ... (remaining 24076 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 5541 0.070 - 0.141: 822 0.141 - 0.211: 66 0.211 - 0.281: 8 0.281 - 0.351: 3 Chirality restraints: 6440 Sorted by residual: chirality pdb=" CB ILE N 65 " pdb=" CA ILE N 65 " pdb=" CG1 ILE N 65 " pdb=" CG2 ILE N 65 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" CB ILE e 69 " pdb=" CA ILE e 69 " pdb=" CG1 ILE e 69 " pdb=" CG2 ILE e 69 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" CG LEU J 100 " pdb=" CB LEU J 100 " pdb=" CD1 LEU J 100 " pdb=" CD2 LEU J 100 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.99e+00 ... (remaining 6437 not shown) Planarity restraints: 6950 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU O 54 " -0.020 2.00e-02 2.50e+03 4.06e-02 1.65e+01 pdb=" C LEU O 54 " 0.070 2.00e-02 2.50e+03 pdb=" O LEU O 54 " -0.026 2.00e-02 2.50e+03 pdb=" N LEU O 55 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER V 56 " -0.019 2.00e-02 2.50e+03 3.72e-02 1.38e+01 pdb=" C SER V 56 " 0.064 2.00e-02 2.50e+03 pdb=" O SER V 56 " -0.024 2.00e-02 2.50e+03 pdb=" N LEU V 57 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU T 46 " -0.018 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C GLU T 46 " 0.064 2.00e-02 2.50e+03 pdb=" O GLU T 46 " -0.024 2.00e-02 2.50e+03 pdb=" N GLY T 47 " -0.022 2.00e-02 2.50e+03 ... (remaining 6947 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 2103 2.72 - 3.26: 42678 3.26 - 3.81: 66679 3.81 - 4.35: 81599 4.35 - 4.90: 135674 Nonbonded interactions: 328733 Sorted by model distance: nonbonded pdb=" O ALA F 295 " pdb=" N GLY F 297 " model vdw 2.172 3.120 nonbonded pdb=" OG1 THR d 181 " pdb=" OG1 THR d 222 " model vdw 2.176 3.040 nonbonded pdb=" OH TYR N 66 " pdb=" OE2 GLU O 61 " model vdw 2.179 3.040 nonbonded pdb=" O ALA X 20 " pdb=" OG1 THR X 64 " model vdw 2.179 3.040 nonbonded pdb=" OH TYR C 20 " pdb=" OE2 GLU d 249 " model vdw 2.213 3.040 ... (remaining 328728 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 6 through 503 or resid 601)) selection = (chain 'B' and resid 6 through 601) selection = (chain 'C' and (resid 6 through 503 or resid 601)) } ncs_group { reference = (chain 'D' and resid 17 through 494) selection = (chain 'E' and resid 17 through 494) selection = (chain 'F' and resid 17 through 494) } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 3.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.720 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 38.720 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.170 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 39710 Z= 0.282 Angle : 0.988 22.267 53850 Z= 0.609 Chirality : 0.050 0.351 6440 Planarity : 0.006 0.079 6950 Dihedral : 15.528 119.121 14640 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.68 % Favored : 92.02 % Rotamer: Outliers : 0.49 % Allowed : 10.06 % Favored : 89.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.49 % Twisted General : 0.16 % 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 are not related in a simple way. whole: -3.96 (0.10), residues: 5141 helix: -2.04 (0.08), residues: 2735 sheet: -3.77 (0.19), residues: 431 loop : -3.04 (0.12), residues: 1975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 140 TYR 0.022 0.002 TYR B 144 PHE 0.043 0.002 PHE I 145 TRP 0.011 0.001 TRP e 15 HIS 0.007 0.001 HIS F 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00532 / 0.28 (39709) covalent geometry : angle 0.98794 / 0.61 (53848) SS BOND : bond 0.01510 / 0.79 ( 1) SS BOND : angle 2.19905 / 1.47 ( 2) hydrogen bonds : bond 0.13459 / 8.97 ( 2254) hydrogen bonds : angle 6.73653 / 4.57 ( 6618) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10282 Ramachandran restraints generated. 5141 Oldfield, 0 Emsley, 5141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10282 Ramachandran restraints generated. 5141 Oldfield, 0 Emsley, 5141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1034 residues out of total 4097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 1014 time to evaluate : 1.493 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: A 241 TYR cc_start: 0.9330 (m-10) cc_final: 0.9120 (m-10) REVERT: A 251 MET cc_start: 0.8149 (ttp) cc_final: 0.7887 (ttp) REVERT: A 262 ASP cc_start: 0.6930 (t0) cc_final: 0.6382 (t0) REVERT: A 396 PHE cc_start: 0.8243 (t80) cc_final: 0.8003 (t80) REVERT: A 408 GLN cc_start: 0.5557 (tt0) cc_final: 0.4945 (tt0) REVERT: A 413 ARG cc_start: 0.6780 (tpp80) cc_final: 0.6362 (mtt-85) REVERT: C 39 ILE cc_start: 0.8464 (pt) cc_final: 0.8126 (mt) REVERT: C 82 MET cc_start: 0.7829 (mmm) cc_final: 0.7421 (mmm) REVERT: C 128 ARG cc_start: 0.9091 (tpp80) cc_final: 0.7989 (tpp80) REVERT: C 148 GLN cc_start: 0.8491 (mp10) cc_final: 0.8245 (mp10) REVERT: C 185 LEU cc_start: 0.9057 (mt) cc_final: 0.8828 (mp) REVERT: C 202 LYS cc_start: 0.7827 (pttp) cc_final: 0.7563 (ptmt) REVERT: C 251 MET cc_start: 0.8594 (ttp) cc_final: 0.7776 (ttp) REVERT: C 261 TYR cc_start: 0.8916 (m-80) cc_final: 0.8496 (m-80) REVERT: C 274 MET cc_start: 0.8492 (ptm) cc_final: 0.8088 (tmm) REVERT: C 343 ILE cc_start: 0.8919 (pt) cc_final: 0.8638 (pt) REVERT: C 399 PHE cc_start: 0.7831 (m-80) cc_final: 0.7122 (m-80) REVERT: C 405 LYS cc_start: 0.7669 (ttmt) cc_final: 0.7082 (tptp) REVERT: C 436 MET cc_start: 0.7821 (ptp) cc_final: 0.7361 (ptp) REVERT: B 8 GLU cc_start: 0.7195 (mt-10) cc_final: 0.6920 (mt-10) REVERT: B 20 TYR cc_start: 0.5812 (t80) cc_final: 0.5599 (t80) REVERT: B 76 LEU cc_start: 0.8960 (pp) cc_final: 0.8737 (pp) REVERT: B 151 LEU cc_start: 0.9051 (mt) cc_final: 0.8823 (mt) REVERT: B 155 ASP cc_start: 0.8140 (t0) cc_final: 0.7788 (t0) REVERT: B 251 MET cc_start: 0.8730 (ttp) cc_final: 0.8278 (ttp) REVERT: B 292 PHE cc_start: 0.8387 (t80) cc_final: 0.8079 (t80) REVERT: B 298 LEU cc_start: 0.9440 (tp) cc_final: 0.9045 (tp) REVERT: B 321 GLU cc_start: 0.8160 (pt0) cc_final: 0.7344 (pt0) REVERT: B 323 GLN cc_start: 0.7638 (mt0) cc_final: 0.7197 (mm110) REVERT: D 22 ARG cc_start: 0.7504 (ptm-80) cc_final: 0.7219 (ttp-110) REVERT: D 184 GLU cc_start: 0.7712 (tm-30) cc_final: 0.7480 (tm-30) REVERT: D 256 MET cc_start: 0.8649 (ttm) cc_final: 0.8408 (mtt) REVERT: D 292 MET cc_start: 0.9060 (ttt) cc_final: 0.8734 (ttm) REVERT: D 469 LEU cc_start: 0.7247 (mp) cc_final: 0.7023 (mt) REVERT: D 488 MET cc_start: 0.7817 (ttp) cc_final: 0.7420 (ttt) REVERT: E 18 LYS cc_start: 0.6995 (ttpp) cc_final: 0.6320 (pptt) REVERT: E 69 LEU cc_start: 0.8666 (tp) cc_final: 0.8268 (tp) REVERT: E 79 MET cc_start: 0.7931 (mmt) cc_final: 0.7639 (mmt) REVERT: E 158 LEU cc_start: 0.8945 (tp) cc_final: 0.8688 (tp) REVERT: E 247 MET cc_start: 0.8586 (ttp) cc_final: 0.8331 (ttp) REVERT: E 437 VAL cc_start: 0.8043 (t) cc_final: 0.7812 (p) REVERT: E 480 ILE cc_start: 0.8472 (tp) cc_final: 0.8170 (tt) REVERT: E 488 MET cc_start: 0.5892 (ptp) cc_final: 0.5137 (ptm) REVERT: F 79 MET cc_start: 0.8546 (mmt) cc_final: 0.8330 (mmt) REVERT: F 83 ASP cc_start: 0.7799 (m-30) cc_final: 0.7591 (p0) REVERT: F 92 ILE cc_start: 0.8963 (pt) cc_final: 0.8640 (mp) REVERT: F 119 ASP cc_start: 0.7713 (p0) cc_final: 0.7301 (p0) REVERT: F 265 GLU cc_start: 0.8363 (mt-10) cc_final: 0.7977 (pt0) REVERT: F 362 TYR cc_start: 0.7767 (m-80) cc_final: 0.7543 (m-80) REVERT: F 366 ASP cc_start: 0.7998 (t0) cc_final: 0.7564 (t0) REVERT: F 412 GLU cc_start: 0.7110 (tt0) cc_final: 0.6744 (tt0) REVERT: F 456 ARG cc_start: 0.7879 (tpt-90) cc_final: 0.7285 (ttp80) REVERT: d 210 LYS cc_start: 0.7454 (ptpt) cc_final: 0.7116 (ptmm) REVERT: g 185 LEU cc_start: 0.8676 (mt) cc_final: 0.7965 (pp) REVERT: g 209 LYS cc_start: 0.7176 (tptp) cc_final: 0.6961 (tptp) REVERT: g 222 LYS cc_start: 0.7838 (tmmt) cc_final: 0.7553 (mttp) REVERT: g 281 ILE cc_start: 0.7376 (mm) cc_final: 0.6702 (mm) REVERT: e 1 MET cc_start: 0.6889 (ptt) cc_final: 0.6391 (ptm) REVERT: e 18 GLU cc_start: 0.6469 (mp0) cc_final: 0.6211 (mp0) REVERT: e 34 LEU cc_start: 0.7542 (pp) cc_final: 0.7043 (pp) REVERT: e 36 ASN cc_start: 0.7877 (t0) cc_final: 0.7556 (t0) REVERT: e 50 ARG cc_start: 0.7338 (mtm-85) cc_final: 0.6995 (tpp80) REVERT: e 97 GLU cc_start: 0.7656 (tt0) cc_final: 0.7178 (pt0) REVERT: e 125 ARG cc_start: 0.7682 (mmt180) cc_final: 0.7147 (mmt-90) REVERT: J 139 GLN cc_start: 0.5895 (mt0) cc_final: 0.5266 (tm-30) REVERT: J 162 MET cc_start: 0.5131 (mmm) cc_final: 0.4799 (mmt) REVERT: I 90 MET cc_start: 0.7552 (tmm) cc_final: 0.7295 (tmm) REVERT: a 77 GLU cc_start: 0.7695 (mt-10) cc_final: 0.7466 (mt-10) REVERT: a 197 ASP cc_start: 0.6410 (p0) cc_final: 0.6072 (p0) REVERT: a 198 GLU cc_start: 0.5947 (mm-30) cc_final: 0.5315 (tp30) REVERT: T 50 ARG cc_start: 0.3223 (mtp85) cc_final: 0.2553 (ttt-90) REVERT: T 60 MET cc_start: 0.6697 (mtp) cc_final: 0.5644 (mtp) REVERT: Y 41 ARG cc_start: 0.7178 (mtt180) cc_final: 0.6958 (mmp80) REVERT: Y 54 LEU cc_start: 0.6876 (mm) cc_final: 0.6540 (mm) REVERT: Y 76 PHE cc_start: 0.5977 (m-80) cc_final: 0.5302 (m-80) REVERT: X 28 GLN cc_start: 0.5546 (mt0) cc_final: 0.5288 (mp10) REVERT: X 55 LEU cc_start: 0.5483 (tt) cc_final: 0.5029 (mt) REVERT: X 60 MET cc_start: 0.7557 (ttt) cc_final: 0.5854 (ttt) REVERT: W 49 ILE cc_start: 0.6256 (mt) cc_final: 0.5913 (mm) REVERT: Z 48 LYS cc_start: 0.4143 (mttt) cc_final: 0.3674 (mmtp) REVERT: S 22 ILE cc_start: 0.7923 (tp) cc_final: 0.7662 (mt) REVERT: R 66 TYR cc_start: 0.7068 (m-10) cc_final: 0.6833 (m-80) REVERT: M 50 ARG cc_start: 0.6988 (ttm170) cc_final: 0.6089 (ptm160) REVERT: N 50 ARG cc_start: 0.5685 (mtp180) cc_final: 0.5463 (ttp-170) outliers start: 20 outliers final: 4 residues processed: 1027 average time/residue: 0.2632 time to fit residues: 438.7320 Evaluate side-chains 691 residues out of total 4097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 687 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 432 optimal weight: 0.9980 chunk 197 optimal weight: 9.9990 chunk 388 optimal weight: 9.9990 chunk 455 optimal weight: 20.0000 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.4980 chunk 494 optimal weight: 0.7980 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 GLN C 186 ASN C 188 GLN C 256 HIS C 410 GLN D 325 GLN D 479 ASN ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 193 HIS F 66 GLN ** F 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 299 GLN d 139 GLN d 170 ASN d 190 HIS d 199 GLN d 247 GLN ** g 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 301 ASN e 27 ASN I 147 GLN I 180 ASN a 175 ASN Y 78 ASN ** U 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 78 ASN ** Q 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 28 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.139120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.134914 restraints weight = 73366.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.126736 restraints weight = 143095.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.124862 restraints weight = 139018.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.124950 restraints weight = 152250.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.125242 restraints weight = 126111.804| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 39710 Z= 0.169 Angle : 0.753 12.493 53850 Z= 0.383 Chirality : 0.046 0.295 6440 Planarity : 0.006 0.088 6950 Dihedral : 7.083 122.848 5573 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 16.64 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.92 % Favored : 92.84 % Rotamer: Outliers : 0.27 % Allowed : 6.59 % Favored : 93.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.49 % Twisted General : 0.22 % 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 are not related in a simple way. whole: -2.70 (0.11), residues: 5141 helix: -0.89 (0.09), residues: 2761 sheet: -3.38 (0.21), residues: 433 loop : -2.61 (0.13), residues: 1947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG e 120 TYR 0.033 0.002 TYR N 66 PHE 0.047 0.002 PHE I 145 TRP 0.011 0.002 TRP e 15 HIS 0.013 0.001 HIS g 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.17 (39709) covalent geometry : angle 0.75290 / 0.38 (53848) SS BOND : bond 0.01136 / 0.60 ( 1) SS BOND : angle 1.69826 / 1.13 ( 2) hydrogen bonds : bond 0.05080 / 3.41 ( 2254) hydrogen bonds : angle 5.52024 / 3.77 ( 6618) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10282 Ramachandran restraints generated. 5141 Oldfield, 0 Emsley, 5141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10282 Ramachandran restraints generated. 5141 Oldfield, 0 Emsley, 5141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 919 residues out of total 4097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 908 time to evaluate : 1.464 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: A 201 GLN cc_start: 0.6864 (pt0) cc_final: 0.6399 (pt0) REVERT: A 262 ASP cc_start: 0.6624 (t0) cc_final: 0.6422 (t0) REVERT: A 314 MET cc_start: 0.7691 (ttp) cc_final: 0.7454 (ttm) REVERT: C 219 MET cc_start: 0.8474 (tpp) cc_final: 0.8175 (tpp) REVERT: C 241 TYR cc_start: 0.8648 (m-80) cc_final: 0.8432 (m-10) REVERT: C 251 MET cc_start: 0.8587 (ttp) cc_final: 0.8042 (ttp) REVERT: B 8 GLU cc_start: 0.7033 (mt-10) cc_final: 0.6603 (mt-10) REVERT: B 298 LEU cc_start: 0.9140 (tp) cc_final: 0.8900 (tp) REVERT: D 240 ASN cc_start: 0.8309 (p0) cc_final: 0.8057 (p0) REVERT: D 256 MET cc_start: 0.7951 (ttm) cc_final: 0.7750 (mtt) REVERT: D 274 ASN cc_start: 0.8804 (t0) cc_final: 0.8494 (t0) REVERT: D 366 ASP cc_start: 0.7983 (t0) cc_final: 0.7713 (t70) REVERT: E 18 LYS cc_start: 0.7027 (ttpp) cc_final: 0.6492 (pptt) REVERT: E 69 LEU cc_start: 0.8337 (tp) cc_final: 0.8073 (tp) REVERT: E 79 MET cc_start: 0.8321 (mmt) cc_final: 0.8010 (mmt) REVERT: E 246 ARG cc_start: 0.8810 (ptt-90) cc_final: 0.8302 (ttp-110) REVERT: E 437 VAL cc_start: 0.8221 (t) cc_final: 0.7860 (p) REVERT: E 480 ILE cc_start: 0.8448 (tp) cc_final: 0.8130 (tt) REVERT: E 488 MET cc_start: 0.5880 (ptp) cc_final: 0.5655 (ptm) REVERT: F 274 ASN cc_start: 0.7830 (m-40) cc_final: 0.7599 (m-40) REVERT: F 361 ILE cc_start: 0.9236 (mm) cc_final: 0.9001 (mm) REVERT: F 362 TYR cc_start: 0.8321 (m-80) cc_final: 0.7960 (m-80) REVERT: F 366 ASP cc_start: 0.7973 (t0) cc_final: 0.7524 (t0) REVERT: F 389 GLN cc_start: 0.7540 (mm-40) cc_final: 0.7089 (tp-100) REVERT: F 398 TYR cc_start: 0.8585 (t80) cc_final: 0.8384 (t80) REVERT: d 92 LEU cc_start: 0.6727 (tp) cc_final: 0.6354 (pt) REVERT: d 98 ASP cc_start: 0.7136 (m-30) cc_final: 0.6917 (m-30) REVERT: g 129 LEU cc_start: 0.7550 (tp) cc_final: 0.6821 (tp) REVERT: g 185 LEU cc_start: 0.8116 (mt) cc_final: 0.7560 (pt) REVERT: e 1 MET cc_start: 0.7030 (ptt) cc_final: 0.6768 (ptm) REVERT: e 34 LEU cc_start: 0.7576 (pp) cc_final: 0.7197 (pp) REVERT: e 95 THR cc_start: 0.8435 (m) cc_final: 0.6513 (m) REVERT: I 90 MET cc_start: 0.7494 (tmm) cc_final: 0.7022 (tmm) REVERT: I 144 VAL cc_start: 0.7952 (m) cc_final: 0.7698 (m) REVERT: I 179 MET cc_start: 0.4787 (tmm) cc_final: 0.3899 (tmm) REVERT: a 73 GLU cc_start: 0.7245 (tt0) cc_final: 0.6994 (tt0) REVERT: a 161 PHE cc_start: 0.3430 (p90) cc_final: 0.2929 (p90) REVERT: a 197 ASP cc_start: 0.5531 (p0) cc_final: 0.5229 (p0) REVERT: Y 54 LEU cc_start: 0.6708 (mm) cc_final: 0.5077 (tt) REVERT: Y 76 PHE cc_start: 0.4930 (m-80) cc_final: 0.4545 (m-80) REVERT: X 28 GLN cc_start: 0.6787 (mt0) cc_final: 0.6380 (mp10) REVERT: X 53 LEU cc_start: 0.6995 (OUTLIER) cc_final: 0.6343 (mt) REVERT: W 49 ILE cc_start: 0.6048 (mt) cc_final: 0.5637 (mm) REVERT: Z 59 PHE cc_start: 0.6643 (m-80) cc_final: 0.6286 (m-80) REVERT: R 63 LEU cc_start: 0.5940 (tp) cc_final: 0.5683 (tp) REVERT: M 22 ILE cc_start: 0.7766 (mm) cc_final: 0.7426 (mm) REVERT: M 50 ARG cc_start: 0.7098 (ttm170) cc_final: 0.6560 (ptm160) REVERT: M 74 LEU cc_start: 0.6502 (OUTLIER) cc_final: 0.6152 (mm) REVERT: O 55 LEU cc_start: 0.6436 (tp) cc_final: 0.5435 (tp) REVERT: O 59 PHE cc_start: 0.5870 (m-80) cc_final: 0.5092 (m-80) outliers start: 11 outliers final: 3 residues processed: 913 average time/residue: 0.2421 time to fit residues: 366.4269 Evaluate side-chains 658 residues out of total 4097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 653 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 22 optimal weight: 6.9990 chunk 435 optimal weight: 9.9990 chunk 116 optimal weight: 0.9990 chunk 87 optimal weight: 6.9990 chunk 206 optimal weight: 4.9990 chunk 417 optimal weight: 0.9990 chunk 233 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 378 optimal weight: 0.8980 chunk 470 optimal weight: 5.9990 chunk 33 optimal weight: 0.5980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 GLN A 434 GLN C 256 HIS C 409 ASN C 410 GLN ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 GLN ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 133 HIS D 188 ASN ** D 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 325 GLN ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 266 GLN ** F 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 299 GLN d 199 GLN d 247 GLN g 301 ASN I 147 GLN a 175 ASN ** X 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.138920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.134642 restraints weight = 74119.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.125814 restraints weight = 136123.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.123665 restraints weight = 141446.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.123672 restraints weight = 156928.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.124082 restraints weight = 119012.737| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 39710 Z= 0.183 Angle : 0.738 16.454 53850 Z= 0.374 Chirality : 0.046 0.277 6440 Planarity : 0.005 0.072 6950 Dihedral : 6.839 121.021 5573 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 17.46 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.47 % Favored : 92.36 % Rotamer: Outliers : 0.10 % Allowed : 5.57 % Favored : 94.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.49 % Twisted General : 0.20 % 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 are not related in a simple way. whole: -2.21 (0.11), residues: 5141 helix: -0.45 (0.09), residues: 2769 sheet: -3.23 (0.21), residues: 429 loop : -2.46 (0.13), residues: 1943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 279 TYR 0.022 0.002 TYR R 66 PHE 0.050 0.002 PHE I 145 TRP 0.010 0.002 TRP e 15 HIS 0.009 0.001 HIS D 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.18 (39709) covalent geometry : angle 0.73753 / 0.37 (53848) SS BOND : bond 0.03424 / 1.80 ( 1) SS BOND : angle 2.59416 / 1.73 ( 2) hydrogen bonds : bond 0.04888 / 3.27 ( 2254) hydrogen bonds : angle 5.29514 / 3.61 ( 6618) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10282 Ramachandran restraints generated. 5141 Oldfield, 0 Emsley, 5141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10282 Ramachandran restraints generated. 5141 Oldfield, 0 Emsley, 5141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 858 residues out of total 4097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 854 time to evaluate : 1.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 463 THR cc_start: 0.7811 (p) cc_final: 0.7592 (t) REVERT: C 85 GLU cc_start: 0.7807 (tm-30) cc_final: 0.7557 (tm-30) REVERT: C 251 MET cc_start: 0.8496 (ttp) cc_final: 0.8262 (ttp) REVERT: C 274 MET cc_start: 0.8107 (tmm) cc_final: 0.7839 (tmm) REVERT: C 354 ILE cc_start: 0.8333 (mp) cc_final: 0.7858 (mt) REVERT: B 8 GLU cc_start: 0.6816 (mt-10) cc_final: 0.6511 (mt-10) REVERT: B 20 TYR cc_start: 0.4902 (t80) cc_final: 0.4655 (t80) REVERT: B 201 GLN cc_start: 0.7837 (mm-40) cc_final: 0.7617 (mm-40) REVERT: B 298 LEU cc_start: 0.9237 (tp) cc_final: 0.8922 (tp) REVERT: B 416 ARG cc_start: 0.7180 (mpt180) cc_final: 0.6528 (ttp80) REVERT: D 109 ARG cc_start: 0.7872 (mmm-85) cc_final: 0.7647 (mmm-85) REVERT: D 150 GLU cc_start: 0.7931 (tm-30) cc_final: 0.7681 (tm-30) REVERT: E 18 LYS cc_start: 0.7057 (ttpp) cc_final: 0.6475 (pptt) REVERT: E 69 LEU cc_start: 0.8362 (tp) cc_final: 0.7953 (tp) REVERT: E 79 MET cc_start: 0.8216 (mmt) cc_final: 0.7929 (mmt) REVERT: E 222 ILE cc_start: 0.8741 (pt) cc_final: 0.8528 (mp) REVERT: E 239 MET cc_start: 0.8378 (mtp) cc_final: 0.8176 (mtp) REVERT: E 246 ARG cc_start: 0.8810 (ptt-90) cc_final: 0.8379 (ttp-110) REVERT: E 437 VAL cc_start: 0.8305 (t) cc_final: 0.7915 (p) REVERT: E 480 ILE cc_start: 0.8487 (tp) cc_final: 0.8210 (tt) REVERT: F 247 MET cc_start: 0.8371 (mtp) cc_final: 0.8155 (mtp) REVERT: F 362 TYR cc_start: 0.8258 (m-80) cc_final: 0.7922 (m-80) REVERT: F 366 ASP cc_start: 0.7858 (t0) cc_final: 0.7449 (t0) REVERT: F 389 GLN cc_start: 0.7444 (mm-40) cc_final: 0.7187 (tp40) REVERT: F 398 TYR cc_start: 0.8641 (t80) cc_final: 0.8390 (t80) REVERT: F 476 LEU cc_start: 0.8349 (mt) cc_final: 0.7896 (tp) REVERT: d 92 LEU cc_start: 0.6728 (tp) cc_final: 0.6465 (pt) REVERT: g 185 LEU cc_start: 0.8188 (mt) cc_final: 0.7635 (pt) REVERT: e 1 MET cc_start: 0.7009 (ptt) cc_final: 0.6674 (ptm) REVERT: e 34 LEU cc_start: 0.7612 (pp) cc_final: 0.7313 (pp) REVERT: e 95 THR cc_start: 0.7598 (m) cc_final: 0.7174 (m) REVERT: J 88 LEU cc_start: 0.4072 (pt) cc_final: 0.3519 (tp) REVERT: I 90 MET cc_start: 0.7517 (tmm) cc_final: 0.7039 (tmm) REVERT: I 179 MET cc_start: 0.4609 (tmm) cc_final: 0.3702 (tmm) REVERT: a 161 PHE cc_start: 0.3667 (p90) cc_final: 0.3083 (p90) REVERT: T 49 ILE cc_start: 0.5134 (mm) cc_final: 0.4849 (mm) REVERT: Y 50 ARG cc_start: 0.6541 (ttt90) cc_final: 0.5114 (ttt-90) REVERT: Y 76 PHE cc_start: 0.5142 (m-80) cc_final: 0.4742 (m-80) REVERT: X 28 GLN cc_start: 0.7086 (mt0) cc_final: 0.6180 (mp10) REVERT: W 49 ILE cc_start: 0.5814 (mt) cc_final: 0.5599 (mm) REVERT: W 60 MET cc_start: 0.6187 (mmt) cc_final: 0.5285 (tpt) REVERT: R 66 TYR cc_start: 0.6152 (m-80) cc_final: 0.5631 (m-80) REVERT: M 22 ILE cc_start: 0.7746 (mm) cc_final: 0.7441 (mm) REVERT: M 74 LEU cc_start: 0.6615 (OUTLIER) cc_final: 0.6303 (mm) REVERT: O 63 LEU cc_start: 0.5732 (tt) cc_final: 0.5499 (tt) outliers start: 4 outliers final: 0 residues processed: 855 average time/residue: 0.2257 time to fit residues: 323.1530 Evaluate side-chains 632 residues out of total 4097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 631 time to evaluate : 1.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 389 optimal weight: 20.0000 chunk 382 optimal weight: 8.9990 chunk 310 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 chunk 160 optimal weight: 4.9990 chunk 345 optimal weight: 4.9990 chunk 408 optimal weight: 5.9990 chunk 359 optimal weight: 1.9990 chunk 40 optimal weight: 8.9990 chunk 384 optimal weight: 0.5980 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 GLN A 201 GLN A 256 HIS C 409 ASN C 410 GLN B 188 GLN B 408 GLN D 25 GLN D 133 HIS D 188 ASN ** D 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 325 GLN D 472 GLN ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 479 ASN ** F 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 227 ASN ** d 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 147 GLN I 150 GLN ** a 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 175 ASN ** a 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 34 GLN ** U 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.133434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.129337 restraints weight = 75116.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.119462 restraints weight = 125205.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.117441 restraints weight = 143025.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.117433 restraints weight = 170810.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.117572 restraints weight = 124391.812| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 39710 Z= 0.323 Angle : 0.855 13.811 53850 Z= 0.434 Chirality : 0.050 0.286 6440 Planarity : 0.006 0.068 6950 Dihedral : 6.995 114.364 5573 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 19.63 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.20 % Favored : 90.62 % Rotamer: Outliers : 0.02 % Allowed : 7.15 % Favored : 92.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.49 % Twisted General : 0.22 % 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 are not related in a simple way. whole: -2.28 (0.11), residues: 5141 helix: -0.49 (0.09), residues: 2772 sheet: -3.09 (0.21), residues: 438 loop : -2.56 (0.13), residues: 1931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG M 50 TYR 0.031 0.002 TYR X 66 PHE 0.056 0.002 PHE I 145 TRP 0.011 0.002 TRP e 15 HIS 0.015 0.002 HIS g 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00746 / 0.32 (39709) covalent geometry : angle 0.85475 / 0.43 (53848) SS BOND : bond 0.05476 / 2.88 ( 1) SS BOND : angle 2.77008 / 1.85 ( 2) hydrogen bonds : bond 0.05245 / 3.51 ( 2254) hydrogen bonds : angle 5.48827 / 3.75 ( 6618) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10282 Ramachandran restraints generated. 5141 Oldfield, 0 Emsley, 5141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10282 Ramachandran restraints generated. 5141 Oldfield, 0 Emsley, 5141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 800 residues out of total 4097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 799 time to evaluate : 1.515 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: A 337 SER cc_start: 0.8568 (p) cc_final: 0.8294 (p) REVERT: A 463 THR cc_start: 0.7944 (p) cc_final: 0.7614 (t) REVERT: C 148 GLN cc_start: 0.8312 (mp10) cc_final: 0.8107 (mp10) REVERT: C 354 ILE cc_start: 0.8458 (mp) cc_final: 0.8131 (mt) REVERT: B 11 LYS cc_start: 0.7163 (tmtt) cc_final: 0.6898 (tptp) REVERT: B 298 LEU cc_start: 0.9335 (tp) cc_final: 0.8989 (tp) REVERT: D 150 GLU cc_start: 0.8007 (tm-30) cc_final: 0.7699 (tm-30) REVERT: E 18 LYS cc_start: 0.7267 (ttpp) cc_final: 0.6593 (pptt) REVERT: E 69 LEU cc_start: 0.8685 (tp) cc_final: 0.8268 (tp) REVERT: E 79 MET cc_start: 0.8302 (mmt) cc_final: 0.8026 (mmt) REVERT: E 480 ILE cc_start: 0.8622 (tp) cc_final: 0.8335 (tt) REVERT: F 247 MET cc_start: 0.8611 (mtp) cc_final: 0.8247 (mtp) REVERT: F 362 TYR cc_start: 0.8439 (m-80) cc_final: 0.8152 (m-80) REVERT: F 366 ASP cc_start: 0.8022 (t0) cc_final: 0.7637 (t0) REVERT: F 389 GLN cc_start: 0.7520 (mm-40) cc_final: 0.7244 (tp40) REVERT: d 92 LEU cc_start: 0.6935 (tp) cc_final: 0.6559 (pt) REVERT: g 64 MET cc_start: 0.8765 (ttm) cc_final: 0.8395 (ttm) REVERT: g 121 MET cc_start: 0.8226 (ptm) cc_final: 0.7896 (ptt) REVERT: g 185 LEU cc_start: 0.8314 (mt) cc_final: 0.7762 (pt) REVERT: g 231 LEU cc_start: 0.7860 (tt) cc_final: 0.7627 (tp) REVERT: e 1 MET cc_start: 0.7276 (ptt) cc_final: 0.6695 (ptm) REVERT: e 34 LEU cc_start: 0.7858 (pp) cc_final: 0.7536 (pp) REVERT: e 57 TRP cc_start: 0.4291 (p-90) cc_final: 0.3522 (p-90) REVERT: J 88 LEU cc_start: 0.4311 (pt) cc_final: 0.3710 (mt) REVERT: I 90 MET cc_start: 0.7496 (tmm) cc_final: 0.6883 (tmm) REVERT: a 109 ASN cc_start: 0.7230 (t0) cc_final: 0.6698 (t0) REVERT: a 175 ASN cc_start: 0.4403 (OUTLIER) cc_final: 0.4108 (t0) REVERT: T 49 ILE cc_start: 0.5255 (mm) cc_final: 0.5025 (mm) REVERT: T 78 ASN cc_start: 0.4142 (t0) cc_final: 0.3908 (t0) REVERT: Y 50 ARG cc_start: 0.6659 (ttt90) cc_final: 0.4967 (ttt-90) REVERT: Y 76 PHE cc_start: 0.5269 (m-80) cc_final: 0.4949 (m-80) REVERT: X 28 GLN cc_start: 0.6902 (mt0) cc_final: 0.6177 (mp10) REVERT: W 49 ILE cc_start: 0.6276 (mt) cc_final: 0.5924 (mm) REVERT: V 50 ARG cc_start: 0.6995 (mtt90) cc_final: 0.5186 (ttt180) REVERT: V 60 MET cc_start: 0.6991 (mtt) cc_final: 0.6666 (mtt) REVERT: Z 22 ILE cc_start: 0.8271 (mp) cc_final: 0.7993 (mt) REVERT: Z 60 MET cc_start: 0.6379 (mtt) cc_final: 0.6037 (mtt) REVERT: S 64 THR cc_start: 0.6088 (p) cc_final: 0.5825 (p) REVERT: R 66 TYR cc_start: 0.6811 (m-80) cc_final: 0.6239 (m-80) REVERT: Q 60 MET cc_start: 0.5519 (mmm) cc_final: 0.4922 (mmm) REVERT: M 22 ILE cc_start: 0.8173 (mm) cc_final: 0.7952 (mm) REVERT: N 34 GLN cc_start: 0.6689 (pp30) cc_final: 0.6482 (mm110) outliers start: 1 outliers final: 0 residues processed: 799 average time/residue: 0.2262 time to fit residues: 303.1875 Evaluate side-chains 614 residues out of total 4097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 613 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 399 optimal weight: 5.9990 chunk 179 optimal weight: 0.7980 chunk 100 optimal weight: 8.9990 chunk 136 optimal weight: 2.9990 chunk 338 optimal weight: 0.8980 chunk 343 optimal weight: 0.9990 chunk 221 optimal weight: 0.5980 chunk 90 optimal weight: 3.9990 chunk 481 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 259 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 GLN A 434 GLN C 273 GLN C 409 ASN C 410 GLN B 188 GLN ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 266 GLN E 376 GLN ** F 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 299 GLN d 199 GLN ** d 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 97 ASN ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 331 ASN ** a 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.139638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.135515 restraints weight = 73018.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.126163 restraints weight = 126851.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.124564 restraints weight = 117206.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.124481 restraints weight = 113066.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.124721 restraints weight = 93370.574| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 39710 Z= 0.163 Angle : 0.741 12.821 53850 Z= 0.372 Chirality : 0.046 0.304 6440 Planarity : 0.005 0.068 6950 Dihedral : 6.699 118.086 5573 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 17.31 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.10 % Favored : 92.74 % Rotamer: Outliers : 0.02 % Allowed : 3.71 % Favored : 96.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.49 % Twisted General : 0.20 % 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 are not related in a simple way. whole: -1.90 (0.11), residues: 5141 helix: -0.16 (0.09), residues: 2758 sheet: -2.97 (0.21), residues: 470 loop : -2.37 (0.14), residues: 1913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG V 50 TYR 0.033 0.002 TYR M 66 PHE 0.055 0.002 PHE I 145 TRP 0.011 0.001 TRP e 15 HIS 0.005 0.001 HIS d 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (39709) covalent geometry : angle 0.74077 / 0.37 (53848) SS BOND : bond 0.02683 / 1.41 ( 1) SS BOND : angle 3.78505 / 2.52 ( 2) hydrogen bonds : bond 0.04684 / 3.15 ( 2254) hydrogen bonds : angle 5.15827 / 3.51 ( 6618) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10282 Ramachandran restraints generated. 5141 Oldfield, 0 Emsley, 5141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10282 Ramachandran restraints generated. 5141 Oldfield, 0 Emsley, 5141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 875 residues out of total 4097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 874 time to evaluate : 1.209 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: A 201 GLN cc_start: 0.6929 (pt0) cc_final: 0.6707 (pt0) REVERT: A 337 SER cc_start: 0.8260 (p) cc_final: 0.7979 (p) REVERT: C 85 GLU cc_start: 0.7677 (tm-30) cc_final: 0.7427 (tm-30) REVERT: C 261 TYR cc_start: 0.9040 (m-80) cc_final: 0.8741 (m-80) REVERT: C 274 MET cc_start: 0.8006 (tmm) cc_final: 0.7786 (tmm) REVERT: C 354 ILE cc_start: 0.8462 (mp) cc_final: 0.7935 (mt) REVERT: C 451 LEU cc_start: 0.8248 (mt) cc_final: 0.7999 (mt) REVERT: B 20 TYR cc_start: 0.4518 (t80) cc_final: 0.3987 (t80) REVERT: B 292 PHE cc_start: 0.8534 (t80) cc_final: 0.8260 (t80) REVERT: B 416 ARG cc_start: 0.6793 (mpt180) cc_final: 0.6450 (ttp80) REVERT: D 66 GLN cc_start: 0.8720 (mm110) cc_final: 0.8379 (tp40) REVERT: D 150 GLU cc_start: 0.7922 (tm-30) cc_final: 0.7682 (tm-30) REVERT: D 278 PHE cc_start: 0.8034 (t80) cc_final: 0.7809 (t80) REVERT: D 309 LEU cc_start: 0.8919 (mt) cc_final: 0.8430 (mt) REVERT: E 18 LYS cc_start: 0.7015 (ttpp) cc_final: 0.6806 (ptmt) REVERT: E 79 MET cc_start: 0.8368 (mmt) cc_final: 0.8047 (mmt) REVERT: E 146 LEU cc_start: 0.8564 (pt) cc_final: 0.8240 (pt) REVERT: E 239 MET cc_start: 0.8256 (mmm) cc_final: 0.8018 (mmm) REVERT: E 246 ARG cc_start: 0.8803 (ptt-90) cc_final: 0.8540 (ttp-110) REVERT: E 247 MET cc_start: 0.7785 (ttp) cc_final: 0.7508 (ttp) REVERT: E 306 MET cc_start: 0.8706 (ttm) cc_final: 0.8492 (ttp) REVERT: E 437 VAL cc_start: 0.8319 (t) cc_final: 0.7923 (p) REVERT: E 480 ILE cc_start: 0.8467 (tp) cc_final: 0.8185 (tt) REVERT: F 79 MET cc_start: 0.8760 (mmm) cc_final: 0.8536 (mmm) REVERT: F 306 MET cc_start: 0.7833 (tpp) cc_final: 0.7616 (tpt) REVERT: F 362 TYR cc_start: 0.8212 (m-80) cc_final: 0.7972 (m-80) REVERT: F 366 ASP cc_start: 0.7831 (t0) cc_final: 0.7508 (t0) REVERT: F 476 LEU cc_start: 0.8601 (mt) cc_final: 0.8110 (tp) REVERT: d 92 LEU cc_start: 0.6829 (tp) cc_final: 0.6580 (pt) REVERT: d 151 ASP cc_start: 0.6605 (m-30) cc_final: 0.6388 (m-30) REVERT: g 64 MET cc_start: 0.8632 (ttm) cc_final: 0.8309 (ttm) REVERT: g 139 LYS cc_start: 0.7651 (ttpt) cc_final: 0.7322 (mmtm) REVERT: g 185 LEU cc_start: 0.8278 (mt) cc_final: 0.7646 (pt) REVERT: e 1 MET cc_start: 0.7064 (ptt) cc_final: 0.5669 (ttm) REVERT: e 34 LEU cc_start: 0.7789 (pp) cc_final: 0.7373 (pp) REVERT: e 57 TRP cc_start: 0.4186 (p-90) cc_final: 0.3410 (p-90) REVERT: J 88 LEU cc_start: 0.3846 (pt) cc_final: 0.3432 (mt) REVERT: I 90 MET cc_start: 0.7631 (tmm) cc_final: 0.6978 (tmm) REVERT: I 179 MET cc_start: 0.4333 (tmm) cc_final: 0.3362 (tmm) REVERT: a 73 GLU cc_start: 0.7216 (tt0) cc_final: 0.6691 (tt0) REVERT: a 175 ASN cc_start: 0.4329 (t0) cc_final: 0.4111 (t0) REVERT: Y 34 GLN cc_start: 0.6338 (mm110) cc_final: 0.6135 (mt0) REVERT: Y 50 ARG cc_start: 0.6543 (ttt90) cc_final: 0.5088 (ttt-90) REVERT: Y 55 LEU cc_start: 0.6186 (tt) cc_final: 0.5654 (tp) REVERT: X 28 GLN cc_start: 0.7010 (mt0) cc_final: 0.6209 (mp10) REVERT: W 49 ILE cc_start: 0.5973 (mt) cc_final: 0.5718 (mm) REVERT: W 50 ARG cc_start: 0.7104 (mmm160) cc_final: 0.5177 (ttp-170) REVERT: W 54 LEU cc_start: 0.5874 (mm) cc_final: 0.5671 (mm) REVERT: W 60 MET cc_start: 0.6332 (mmt) cc_final: 0.5445 (tpt) REVERT: V 50 ARG cc_start: 0.6535 (mtt90) cc_final: 0.5861 (ttt180) REVERT: U 48 LYS cc_start: 0.2420 (tptt) cc_final: 0.2004 (tptt) REVERT: Z 22 ILE cc_start: 0.8284 (mp) cc_final: 0.8076 (mt) REVERT: S 64 THR cc_start: 0.5993 (p) cc_final: 0.5777 (p) REVERT: R 66 TYR cc_start: 0.6726 (m-80) cc_final: 0.6332 (m-80) REVERT: M 22 ILE cc_start: 0.7871 (mm) cc_final: 0.7549 (mm) REVERT: N 4 LEU cc_start: 0.8104 (pp) cc_final: 0.7858 (pp) outliers start: 1 outliers final: 0 residues processed: 875 average time/residue: 0.2312 time to fit residues: 337.5685 Evaluate side-chains 625 residues out of total 4097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 625 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 206 optimal weight: 0.8980 chunk 218 optimal weight: 3.9990 chunk 228 optimal weight: 3.9990 chunk 437 optimal weight: 0.6980 chunk 246 optimal weight: 0.9990 chunk 176 optimal weight: 0.7980 chunk 241 optimal weight: 0.5980 chunk 266 optimal weight: 0.0970 chunk 115 optimal weight: 0.9980 chunk 149 optimal weight: 4.9990 chunk 377 optimal weight: 2.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 GLN A 423 GLN C 186 ASN ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 ASN B 186 ASN B 188 GLN ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 459 GLN F 210 ASN ** F 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 299 GLN d 193 GLN d 199 GLN ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 27 ASN ** I 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.140939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.136604 restraints weight = 73381.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.128904 restraints weight = 136370.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.126885 restraints weight = 142900.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.127030 restraints weight = 153724.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.127309 restraints weight = 122873.402| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 39710 Z= 0.155 Angle : 0.732 12.352 53850 Z= 0.365 Chirality : 0.046 0.256 6440 Planarity : 0.005 0.066 6950 Dihedral : 6.517 119.455 5573 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.43 % Favored : 92.45 % Rotamer: Outliers : 0.05 % Allowed : 2.88 % Favored : 97.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.14 % 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 are not related in a simple way. whole: -1.64 (0.11), residues: 5141 helix: 0.02 (0.10), residues: 2770 sheet: -2.89 (0.21), residues: 460 loop : -2.21 (0.14), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG e 110 TYR 0.040 0.002 TYR N 66 PHE 0.057 0.002 PHE I 145 TRP 0.011 0.001 TRP e 15 HIS 0.007 0.001 HIS d 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (39709) covalent geometry : angle 0.73199 / 0.37 (53848) SS BOND : bond 0.02680 / 1.41 ( 1) SS BOND : angle 3.67033 / 2.45 ( 2) hydrogen bonds : bond 0.04592 / 3.10 ( 2254) hydrogen bonds : angle 5.05664 / 3.44 ( 6618) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10282 Ramachandran restraints generated. 5141 Oldfield, 0 Emsley, 5141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10282 Ramachandran restraints generated. 5141 Oldfield, 0 Emsley, 5141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 840 residues out of total 4097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 838 time to evaluate : 1.334 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: A 68 GLU cc_start: 0.7306 (tm-30) cc_final: 0.6841 (tt0) REVERT: A 201 GLN cc_start: 0.6835 (pt0) cc_final: 0.6623 (pt0) REVERT: A 337 SER cc_start: 0.8117 (p) cc_final: 0.7856 (p) REVERT: C 261 TYR cc_start: 0.9061 (m-80) cc_final: 0.8785 (m-80) REVERT: C 274 MET cc_start: 0.8146 (tmm) cc_final: 0.7938 (tmm) REVERT: C 399 PHE cc_start: 0.6276 (m-80) cc_final: 0.5950 (m-80) REVERT: B 171 ASP cc_start: 0.9085 (t0) cc_final: 0.8683 (t0) REVERT: B 292 PHE cc_start: 0.8463 (t80) cc_final: 0.8132 (t80) REVERT: B 338 ILE cc_start: 0.8824 (tp) cc_final: 0.8397 (tp) REVERT: B 354 ILE cc_start: 0.9323 (mp) cc_final: 0.9119 (mt) REVERT: B 416 ARG cc_start: 0.7052 (mpt180) cc_final: 0.6363 (ttp80) REVERT: B 445 TYR cc_start: 0.6103 (t80) cc_final: 0.5897 (t80) REVERT: D 66 GLN cc_start: 0.8704 (mm110) cc_final: 0.8498 (tp40) REVERT: D 150 GLU cc_start: 0.7901 (tm-30) cc_final: 0.7675 (tm-30) REVERT: D 151 THR cc_start: 0.8352 (p) cc_final: 0.8128 (p) REVERT: D 157 ASP cc_start: 0.7919 (t0) cc_final: 0.7685 (t0) REVERT: E 69 LEU cc_start: 0.8180 (tp) cc_final: 0.7798 (tp) REVERT: E 79 MET cc_start: 0.8457 (mmt) cc_final: 0.8173 (mmt) REVERT: E 143 ASP cc_start: 0.7874 (t70) cc_final: 0.7489 (m-30) REVERT: E 144 THR cc_start: 0.7555 (p) cc_final: 0.7272 (p) REVERT: E 146 LEU cc_start: 0.8565 (pt) cc_final: 0.8093 (pt) REVERT: E 239 MET cc_start: 0.8127 (mmm) cc_final: 0.7915 (mmm) REVERT: E 246 ARG cc_start: 0.8775 (ptt-90) cc_final: 0.8517 (ttp-110) REVERT: E 306 MET cc_start: 0.8673 (ttm) cc_final: 0.8103 (ttp) REVERT: E 437 VAL cc_start: 0.8228 (t) cc_final: 0.7852 (p) REVERT: E 480 ILE cc_start: 0.8360 (tp) cc_final: 0.8042 (tt) REVERT: F 79 MET cc_start: 0.8860 (mmm) cc_final: 0.8451 (mmm) REVERT: F 278 PHE cc_start: 0.8820 (t80) cc_final: 0.8560 (t80) REVERT: F 362 TYR cc_start: 0.8312 (m-80) cc_final: 0.7965 (m-80) REVERT: F 476 LEU cc_start: 0.8336 (mt) cc_final: 0.8068 (tp) REVERT: g 64 MET cc_start: 0.8620 (ttm) cc_final: 0.8138 (ttm) REVERT: g 139 LYS cc_start: 0.7468 (ttpt) cc_final: 0.6979 (mmtp) REVERT: g 185 LEU cc_start: 0.8172 (mt) cc_final: 0.7553 (pt) REVERT: e 34 LEU cc_start: 0.7478 (pp) cc_final: 0.7166 (pp) REVERT: e 57 TRP cc_start: 0.4190 (p-90) cc_final: 0.3420 (p-90) REVERT: e 125 ARG cc_start: 0.6871 (mmt180) cc_final: 0.5845 (tpp-160) REVERT: J 88 LEU cc_start: 0.3428 (pt) cc_final: 0.3200 (mt) REVERT: I 90 MET cc_start: 0.7489 (tmm) cc_final: 0.7018 (tmm) REVERT: I 179 MET cc_start: 0.3859 (tmm) cc_final: 0.2918 (tmm) REVERT: a 203 VAL cc_start: 0.7642 (m) cc_final: 0.7405 (p) REVERT: T 49 ILE cc_start: 0.4500 (mm) cc_final: 0.4102 (mm) REVERT: Y 50 ARG cc_start: 0.6509 (ttt90) cc_final: 0.5137 (ttt-90) REVERT: X 28 GLN cc_start: 0.6981 (mt0) cc_final: 0.6294 (mp10) REVERT: W 49 ILE cc_start: 0.5842 (mt) cc_final: 0.5576 (mm) REVERT: Z 22 ILE cc_start: 0.8368 (mp) cc_final: 0.8019 (mt) REVERT: R 66 TYR cc_start: 0.6699 (m-80) cc_final: 0.6349 (m-80) REVERT: Q 60 MET cc_start: 0.5236 (mmt) cc_final: 0.4797 (mmm) REVERT: M 22 ILE cc_start: 0.7674 (mm) cc_final: 0.7201 (mm) REVERT: M 42 GLN cc_start: 0.7149 (mt0) cc_final: 0.6921 (mt0) REVERT: N 4 LEU cc_start: 0.8056 (pp) cc_final: 0.7795 (pp) outliers start: 2 outliers final: 0 residues processed: 840 average time/residue: 0.2342 time to fit residues: 330.6256 Evaluate side-chains 641 residues out of total 4097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 641 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 352 optimal weight: 0.9980 chunk 242 optimal weight: 2.9990 chunk 157 optimal weight: 0.0010 chunk 402 optimal weight: 9.9990 chunk 83 optimal weight: 0.4980 chunk 439 optimal weight: 6.9990 chunk 125 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 478 optimal weight: 20.0000 chunk 305 optimal weight: 3.9990 overall best weight: 1.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 423 GLN C 186 ASN C 409 ASN C 410 GLN B 186 ASN B 188 GLN ** B 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 ASN E 266 GLN F 210 ASN ** F 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 299 GLN ** d 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 192 GLN g 228 HIS g 301 ASN ** I 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 175 ASN a 227 GLN ** U 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.140667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.136626 restraints weight = 73179.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.127094 restraints weight = 124144.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.125455 restraints weight = 111487.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.125513 restraints weight = 105142.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.125717 restraints weight = 88909.188| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 39710 Z= 0.167 Angle : 0.736 11.971 53850 Z= 0.368 Chirality : 0.045 0.355 6440 Planarity : 0.005 0.060 6950 Dihedral : 6.453 119.090 5573 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 17.38 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.59 % Favored : 92.30 % Rotamer: Outliers : 0.05 % Allowed : 2.39 % Favored : 97.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.12 % 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 are not related in a simple way. whole: -1.53 (0.11), residues: 5141 helix: 0.09 (0.10), residues: 2772 sheet: -2.71 (0.22), residues: 449 loop : -2.18 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG e 83 TYR 0.041 0.002 TYR N 66 PHE 0.057 0.002 PHE I 145 TRP 0.014 0.002 TRP e 15 HIS 0.011 0.001 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 (39709) covalent geometry : angle 0.73608 / 0.37 (53848) SS BOND : bond 0.01442 / 0.76 ( 1) SS BOND : angle 2.83080 / 1.89 ( 2) hydrogen bonds : bond 0.04581 / 3.09 ( 2254) hydrogen bonds : angle 5.02186 / 3.41 ( 6618) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10282 Ramachandran restraints generated. 5141 Oldfield, 0 Emsley, 5141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10282 Ramachandran restraints generated. 5141 Oldfield, 0 Emsley, 5141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 819 residues out of total 4097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 817 time to evaluate : 1.522 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: A 423 GLN cc_start: 0.6898 (tp-100) cc_final: 0.6633 (mm-40) REVERT: C 261 TYR cc_start: 0.9086 (m-80) cc_final: 0.8782 (m-80) REVERT: C 274 MET cc_start: 0.8171 (tmm) cc_final: 0.7858 (tmm) REVERT: B 171 ASP cc_start: 0.9080 (t0) cc_final: 0.8684 (t0) REVERT: B 292 PHE cc_start: 0.8487 (t80) cc_final: 0.8114 (t80) REVERT: B 416 ARG cc_start: 0.7191 (mpt180) cc_final: 0.6553 (ttp80) REVERT: B 425 GLN cc_start: 0.8289 (tp40) cc_final: 0.7898 (tp40) REVERT: B 445 TYR cc_start: 0.6050 (t80) cc_final: 0.5823 (t80) REVERT: D 157 ASP cc_start: 0.7909 (t0) cc_final: 0.7599 (t0) REVERT: E 18 LYS cc_start: 0.6953 (ttpp) cc_final: 0.5627 (tppt) REVERT: E 69 LEU cc_start: 0.8299 (tp) cc_final: 0.7879 (tp) REVERT: E 79 MET cc_start: 0.8424 (mmt) cc_final: 0.8189 (mmt) REVERT: E 143 ASP cc_start: 0.7858 (t70) cc_final: 0.7385 (m-30) REVERT: E 146 LEU cc_start: 0.8580 (pt) cc_final: 0.8124 (pt) REVERT: E 183 MET cc_start: 0.7946 (tpp) cc_final: 0.7451 (tpp) REVERT: E 212 LEU cc_start: 0.9073 (tp) cc_final: 0.8759 (tp) REVERT: E 246 ARG cc_start: 0.8699 (ptt-90) cc_final: 0.8480 (ttp-110) REVERT: E 267 ASP cc_start: 0.8259 (m-30) cc_final: 0.8035 (m-30) REVERT: E 306 MET cc_start: 0.8626 (ttm) cc_final: 0.8019 (ttp) REVERT: E 437 VAL cc_start: 0.8219 (t) cc_final: 0.7824 (p) REVERT: E 480 ILE cc_start: 0.8415 (tp) cc_final: 0.8057 (tt) REVERT: F 64 GLU cc_start: 0.7496 (tt0) cc_final: 0.7290 (tt0) REVERT: F 79 MET cc_start: 0.8874 (mmm) cc_final: 0.8533 (mmm) REVERT: F 278 PHE cc_start: 0.8821 (t80) cc_final: 0.8529 (t80) REVERT: F 362 TYR cc_start: 0.8323 (m-80) cc_final: 0.7957 (m-80) REVERT: F 366 ASP cc_start: 0.7574 (t0) cc_final: 0.7253 (t0) REVERT: F 476 LEU cc_start: 0.8532 (mt) cc_final: 0.7985 (tp) REVERT: g 64 MET cc_start: 0.8418 (ttm) cc_final: 0.8131 (ttm) REVERT: g 139 LYS cc_start: 0.7594 (ttpt) cc_final: 0.7048 (mmtm) REVERT: g 185 LEU cc_start: 0.7919 (mt) cc_final: 0.7578 (pp) REVERT: e 34 LEU cc_start: 0.7579 (pp) cc_final: 0.7267 (pp) REVERT: e 57 TRP cc_start: 0.4113 (p-90) cc_final: 0.3364 (p-90) REVERT: e 112 LYS cc_start: 0.6256 (mmmt) cc_final: 0.5708 (mmmt) REVERT: e 125 ARG cc_start: 0.7053 (mmt180) cc_final: 0.4883 (mmt180) REVERT: J 88 LEU cc_start: 0.3881 (pt) cc_final: 0.3575 (mt) REVERT: J 116 MET cc_start: 0.5986 (mmm) cc_final: 0.5330 (mmt) REVERT: I 90 MET cc_start: 0.7522 (tmm) cc_final: 0.6986 (tmm) REVERT: I 179 MET cc_start: 0.3981 (tmm) cc_final: 0.3100 (tmm) REVERT: a 221 LEU cc_start: 0.6089 (tt) cc_final: 0.5621 (mp) REVERT: Y 34 GLN cc_start: 0.6936 (mt0) cc_final: 0.6697 (mm110) REVERT: Y 50 ARG cc_start: 0.6663 (ttt90) cc_final: 0.5337 (ttt-90) REVERT: Y 76 PHE cc_start: 0.5783 (m-80) cc_final: 0.5337 (m-80) REVERT: X 28 GLN cc_start: 0.6559 (mt0) cc_final: 0.6195 (mp10) REVERT: W 49 ILE cc_start: 0.5968 (mt) cc_final: 0.5689 (mm) REVERT: W 60 MET cc_start: 0.6281 (mmt) cc_final: 0.5373 (tpt) REVERT: S 49 ILE cc_start: 0.5586 (mt) cc_final: 0.5138 (tt) REVERT: S 64 THR cc_start: 0.6151 (p) cc_final: 0.5890 (p) REVERT: R 66 TYR cc_start: 0.6901 (m-80) cc_final: 0.6592 (m-80) REVERT: Q 28 GLN cc_start: 0.7320 (mp10) cc_final: 0.6754 (mp10) REVERT: M 22 ILE cc_start: 0.7787 (mm) cc_final: 0.7422 (mm) REVERT: M 66 TYR cc_start: 0.7569 (m-80) cc_final: 0.7208 (m-80) REVERT: N 4 LEU cc_start: 0.7946 (pp) cc_final: 0.7653 (pp) outliers start: 2 outliers final: 0 residues processed: 819 average time/residue: 0.2393 time to fit residues: 328.8346 Evaluate side-chains 645 residues out of total 4097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 645 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 355 optimal weight: 4.9990 chunk 376 optimal weight: 5.9990 chunk 304 optimal weight: 20.0000 chunk 77 optimal weight: 0.9980 chunk 165 optimal weight: 0.8980 chunk 319 optimal weight: 2.9990 chunk 173 optimal weight: 1.9990 chunk 207 optimal weight: 4.9990 chunk 137 optimal weight: 2.9990 chunk 140 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 ASN C 410 GLN B 186 ASN B 187 GLN ** B 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 299 GLN d 193 GLN d 199 GLN ** d 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 192 GLN ** g 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 301 ASN I 147 GLN a 227 GLN ** U 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.138394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.134307 restraints weight = 73449.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.124247 restraints weight = 110672.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.122393 restraints weight = 111493.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.122399 restraints weight = 136368.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.122692 restraints weight = 114711.883| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 39710 Z= 0.209 Angle : 0.781 15.658 53850 Z= 0.389 Chirality : 0.047 0.304 6440 Planarity : 0.005 0.082 6950 Dihedral : 6.536 117.616 5573 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 17.41 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.36 % Favored : 91.50 % Rotamer: Outliers : 0.02 % Allowed : 1.59 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.49 % Twisted General : 0.12 % 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 are not related in a simple way. whole: -1.54 (0.12), residues: 5141 helix: 0.08 (0.10), residues: 2770 sheet: -2.82 (0.21), residues: 465 loop : -2.12 (0.14), residues: 1906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG g 170 TYR 0.044 0.002 TYR N 66 PHE 0.061 0.002 PHE I 145 TRP 0.019 0.002 TRP e 15 HIS 0.009 0.001 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.21 (39709) covalent geometry : angle 0.78034 / 0.39 (53848) SS BOND : bond 0.05358 / 2.82 ( 1) SS BOND : angle 4.47192 / 2.98 ( 2) hydrogen bonds : bond 0.04680 / 3.15 ( 2254) hydrogen bonds : angle 5.07270 / 3.44 ( 6618) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10282 Ramachandran restraints generated. 5141 Oldfield, 0 Emsley, 5141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10282 Ramachandran restraints generated. 5141 Oldfield, 0 Emsley, 5141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 796 residues out of total 4097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 795 time to evaluate : 1.548 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: A 68 GLU cc_start: 0.7485 (tm-30) cc_final: 0.6824 (tt0) REVERT: A 337 SER cc_start: 0.7807 (p) cc_final: 0.7582 (p) REVERT: A 423 GLN cc_start: 0.6801 (tp-100) cc_final: 0.6481 (mm-40) REVERT: A 445 TYR cc_start: 0.6607 (m-10) cc_final: 0.6376 (m-10) REVERT: C 274 MET cc_start: 0.8181 (tmm) cc_final: 0.7825 (tmm) REVERT: B 416 ARG cc_start: 0.6901 (mpt180) cc_final: 0.5383 (mmt-90) REVERT: D 157 ASP cc_start: 0.7820 (t0) cc_final: 0.7460 (t0) REVERT: E 69 LEU cc_start: 0.8381 (tp) cc_final: 0.7980 (tp) REVERT: E 79 MET cc_start: 0.8363 (mmt) cc_final: 0.8109 (mmt) REVERT: E 143 ASP cc_start: 0.7833 (t70) cc_final: 0.7552 (m-30) REVERT: E 146 LEU cc_start: 0.8685 (pt) cc_final: 0.8171 (pt) REVERT: E 246 ARG cc_start: 0.8881 (ptt-90) cc_final: 0.8633 (ttp-110) REVERT: E 306 MET cc_start: 0.8613 (ttm) cc_final: 0.8083 (ttp) REVERT: E 379 ILE cc_start: 0.7334 (mt) cc_final: 0.7032 (mt) REVERT: E 437 VAL cc_start: 0.8239 (t) cc_final: 0.7929 (p) REVERT: E 480 ILE cc_start: 0.8460 (tp) cc_final: 0.8144 (tt) REVERT: F 79 MET cc_start: 0.8964 (mmm) cc_final: 0.8396 (mmt) REVERT: F 278 PHE cc_start: 0.8946 (t80) cc_final: 0.8651 (t80) REVERT: F 306 MET cc_start: 0.7928 (tpp) cc_final: 0.7506 (tpt) REVERT: F 362 TYR cc_start: 0.8451 (m-80) cc_final: 0.8017 (m-80) REVERT: F 366 ASP cc_start: 0.7670 (t0) cc_final: 0.7327 (t0) REVERT: F 476 LEU cc_start: 0.8548 (mt) cc_final: 0.8108 (tp) REVERT: g 139 LYS cc_start: 0.7658 (ttpt) cc_final: 0.7126 (mmtm) REVERT: g 185 LEU cc_start: 0.7912 (mt) cc_final: 0.7628 (pp) REVERT: g 187 THR cc_start: 0.7209 (m) cc_final: 0.6894 (m) REVERT: e 57 TRP cc_start: 0.4667 (p-90) cc_final: 0.3510 (p-90) REVERT: e 125 ARG cc_start: 0.7068 (mmt180) cc_final: 0.6028 (tpp-160) REVERT: J 88 LEU cc_start: 0.3821 (pt) cc_final: 0.3509 (mt) REVERT: J 116 MET cc_start: 0.5976 (mmm) cc_final: 0.5289 (mmt) REVERT: I 90 MET cc_start: 0.7496 (tmm) cc_final: 0.6905 (tmm) REVERT: I 179 MET cc_start: 0.4094 (tmm) cc_final: 0.3369 (tmm) REVERT: a 175 ASN cc_start: 0.4292 (t0) cc_final: 0.4033 (t0) REVERT: a 221 LEU cc_start: 0.5707 (tt) cc_final: 0.5397 (mp) REVERT: T 49 ILE cc_start: 0.4536 (mm) cc_final: 0.4316 (mm) REVERT: T 78 ASN cc_start: 0.4154 (t0) cc_final: 0.3897 (t0) REVERT: Y 50 ARG cc_start: 0.6593 (ttt90) cc_final: 0.5157 (ttt-90) REVERT: Y 76 PHE cc_start: 0.5976 (m-80) cc_final: 0.5468 (m-80) REVERT: X 28 GLN cc_start: 0.6687 (mt0) cc_final: 0.6161 (mt0) REVERT: W 49 ILE cc_start: 0.5911 (mt) cc_final: 0.5633 (mm) REVERT: W 60 MET cc_start: 0.6058 (mmt) cc_final: 0.5207 (mmt) REVERT: V 60 MET cc_start: 0.7027 (mtt) cc_final: 0.6401 (mtt) REVERT: S 64 THR cc_start: 0.6304 (p) cc_final: 0.6097 (p) REVERT: R 66 TYR cc_start: 0.6995 (m-80) cc_final: 0.6666 (m-80) REVERT: M 22 ILE cc_start: 0.7990 (mm) cc_final: 0.7593 (mm) REVERT: M 42 GLN cc_start: 0.7210 (mt0) cc_final: 0.6999 (mt0) outliers start: 1 outliers final: 0 residues processed: 796 average time/residue: 0.2416 time to fit residues: 322.8846 Evaluate side-chains 620 residues out of total 4097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 620 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 418 optimal weight: 5.9990 chunk 412 optimal weight: 0.1980 chunk 420 optimal weight: 9.9990 chunk 320 optimal weight: 5.9990 chunk 442 optimal weight: 9.9990 chunk 123 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 220 optimal weight: 2.9990 chunk 421 optimal weight: 9.9990 chunk 367 optimal weight: 9.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 ASN B 186 ASN ** B 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 247 GLN g 192 GLN g 301 ASN X 34 GLN ** W 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 42 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 = 0.3782 r_free = 0.3782 target = 0.138247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.134310 restraints weight = 73445.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.131990 restraints weight = 114945.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.125179 restraints weight = 192657.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.124087 restraints weight = 153699.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.123729 restraints weight = 147468.688| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 39710 Z= 0.215 Angle : 0.794 14.093 53850 Z= 0.398 Chirality : 0.048 0.311 6440 Planarity : 0.005 0.083 6950 Dihedral : 6.605 117.733 5573 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 18.23 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.34 % Favored : 91.52 % Rotamer: Outliers : 0.05 % Allowed : 1.05 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.49 % Twisted General : 0.14 % 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 are not related in a simple way. whole: -1.57 (0.11), residues: 5141 helix: 0.05 (0.10), residues: 2773 sheet: -2.90 (0.21), residues: 474 loop : -2.11 (0.14), residues: 1894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG g 170 TYR 0.040 0.002 TYR N 66 PHE 0.063 0.002 PHE I 145 TRP 0.018 0.002 TRP e 15 HIS 0.009 0.001 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.21 (39709) covalent geometry : angle 0.79422 / 0.40 (53848) SS BOND : bond 0.02128 / 1.12 ( 1) SS BOND : angle 3.29460 / 2.20 ( 2) hydrogen bonds : bond 0.04726 / 3.18 ( 2254) hydrogen bonds : angle 5.11962 / 3.48 ( 6618) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10282 Ramachandran restraints generated. 5141 Oldfield, 0 Emsley, 5141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10282 Ramachandran restraints generated. 5141 Oldfield, 0 Emsley, 5141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 787 residues out of total 4097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 785 time to evaluate : 1.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 SER cc_start: 0.7944 (p) cc_final: 0.7558 (p) REVERT: A 445 TYR cc_start: 0.6616 (m-10) cc_final: 0.6411 (m-10) REVERT: C 148 GLN cc_start: 0.8037 (mp10) cc_final: 0.7809 (mp10) REVERT: C 274 MET cc_start: 0.7992 (tmm) cc_final: 0.7580 (tmm) REVERT: B 416 ARG cc_start: 0.6821 (mpt180) cc_final: 0.6254 (ttp80) REVERT: B 425 GLN cc_start: 0.8437 (tp40) cc_final: 0.7937 (tp40) REVERT: E 69 LEU cc_start: 0.8403 (tp) cc_final: 0.8008 (tp) REVERT: E 79 MET cc_start: 0.8340 (mmt) cc_final: 0.8077 (mmt) REVERT: E 143 ASP cc_start: 0.7868 (t70) cc_final: 0.7463 (m-30) REVERT: E 146 LEU cc_start: 0.8697 (pt) cc_final: 0.8172 (pt) REVERT: E 183 MET cc_start: 0.8112 (tpp) cc_final: 0.7780 (tpp) REVERT: E 212 LEU cc_start: 0.9143 (tp) cc_final: 0.8887 (tp) REVERT: E 234 LEU cc_start: 0.9061 (mt) cc_final: 0.8645 (mt) REVERT: E 246 ARG cc_start: 0.8878 (ptt-90) cc_final: 0.8656 (ttp-110) REVERT: E 247 MET cc_start: 0.7811 (ttp) cc_final: 0.7269 (mtm) REVERT: E 306 MET cc_start: 0.8593 (ttm) cc_final: 0.8132 (ttp) REVERT: E 379 ILE cc_start: 0.7299 (mt) cc_final: 0.7077 (mt) REVERT: E 480 ILE cc_start: 0.8439 (tp) cc_final: 0.8110 (tt) REVERT: F 79 MET cc_start: 0.8903 (mmm) cc_final: 0.8362 (mmt) REVERT: F 278 PHE cc_start: 0.8924 (t80) cc_final: 0.8653 (t80) REVERT: F 362 TYR cc_start: 0.8426 (m-80) cc_final: 0.8048 (m-80) REVERT: F 366 ASP cc_start: 0.7723 (t0) cc_final: 0.7395 (t0) REVERT: F 476 LEU cc_start: 0.8571 (mt) cc_final: 0.8110 (tp) REVERT: g 139 LYS cc_start: 0.7540 (ttpt) cc_final: 0.7128 (mmtm) REVERT: g 185 LEU cc_start: 0.7738 (mt) cc_final: 0.7435 (pt) REVERT: e 57 TRP cc_start: 0.4652 (p-90) cc_final: 0.3479 (p-90) REVERT: e 112 LYS cc_start: 0.5882 (mmmt) cc_final: 0.5616 (mmmt) REVERT: e 125 ARG cc_start: 0.7081 (mmt180) cc_final: 0.6051 (tpp-160) REVERT: J 116 MET cc_start: 0.5879 (mmm) cc_final: 0.5226 (mmt) REVERT: I 90 MET cc_start: 0.7427 (tmm) cc_final: 0.6897 (tmm) REVERT: I 179 MET cc_start: 0.3777 (tmm) cc_final: 0.3116 (tmm) REVERT: a 221 LEU cc_start: 0.5795 (tt) cc_final: 0.5556 (mp) REVERT: T 78 ASN cc_start: 0.4069 (t0) cc_final: 0.3797 (t0) REVERT: Y 34 GLN cc_start: 0.7095 (mt0) cc_final: 0.6783 (mm-40) REVERT: Y 50 ARG cc_start: 0.6484 (ttt90) cc_final: 0.5067 (ttt-90) REVERT: Y 76 PHE cc_start: 0.5744 (m-80) cc_final: 0.5347 (m-80) REVERT: X 28 GLN cc_start: 0.6839 (mt0) cc_final: 0.6399 (mt0) REVERT: X 60 MET cc_start: 0.5732 (ttt) cc_final: 0.5357 (ttt) REVERT: W 49 ILE cc_start: 0.5807 (mt) cc_final: 0.5512 (mm) REVERT: W 60 MET cc_start: 0.5843 (mmt) cc_final: 0.5258 (mmt) REVERT: Z 22 ILE cc_start: 0.8250 (mp) cc_final: 0.7957 (tt) REVERT: Z 34 GLN cc_start: 0.5969 (mm-40) cc_final: 0.5394 (mm-40) REVERT: R 66 TYR cc_start: 0.6947 (m-80) cc_final: 0.6651 (m-80) REVERT: M 42 GLN cc_start: 0.7253 (mt0) cc_final: 0.6807 (mt0) REVERT: N 70 VAL cc_start: 0.7184 (t) cc_final: 0.6970 (t) outliers start: 2 outliers final: 0 residues processed: 787 average time/residue: 0.2404 time to fit residues: 315.9762 Evaluate side-chains 615 residues out of total 4097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 615 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 294 optimal weight: 5.9990 chunk 119 optimal weight: 0.9980 chunk 214 optimal weight: 0.5980 chunk 94 optimal weight: 0.8980 chunk 93 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 291 optimal weight: 0.6980 chunk 440 optimal weight: 7.9990 chunk 441 optimal weight: 8.9990 chunk 192 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 497 GLN ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 GLN B 186 ASN ** B 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 266 GLN ** F 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 299 GLN d 193 GLN d 199 GLN d 247 GLN a 175 ASN ** W 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.141619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.137640 restraints weight = 72620.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.135662 restraints weight = 113396.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.134845 restraints weight = 179362.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.129644 restraints weight = 172365.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.128176 restraints weight = 128263.200| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 39710 Z= 0.160 Angle : 0.767 14.371 53850 Z= 0.379 Chirality : 0.047 0.537 6440 Planarity : 0.005 0.087 6950 Dihedral : 6.484 121.934 5573 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 17.31 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.47 % Favored : 92.43 % Rotamer: Outliers : 0.05 % Allowed : 0.61 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.14 % 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 are not related in a simple way. whole: -1.42 (0.12), residues: 5141 helix: 0.18 (0.10), residues: 2792 sheet: -2.79 (0.21), residues: 471 loop : -2.09 (0.14), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG g 127 TYR 0.036 0.002 TYR N 66 PHE 0.063 0.002 PHE I 145 TRP 0.011 0.001 TRP a 110 HIS 0.007 0.001 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (39709) covalent geometry : angle 0.76681 / 0.38 (53848) SS BOND : bond 0.02082 / 1.10 ( 1) SS BOND : angle 1.86470 / 1.24 ( 2) hydrogen bonds : bond 0.04491 / 3.02 ( 2254) hydrogen bonds : angle 5.00186 / 3.39 ( 6618) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10282 Ramachandran restraints generated. 5141 Oldfield, 0 Emsley, 5141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10282 Ramachandran restraints generated. 5141 Oldfield, 0 Emsley, 5141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 806 residues out of total 4097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 804 time to evaluate : 1.650 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: A 279 ARG cc_start: 0.8664 (tpp-160) cc_final: 0.8344 (ttm-80) REVERT: A 337 SER cc_start: 0.7762 (p) cc_final: 0.7430 (p) REVERT: A 445 TYR cc_start: 0.6548 (m-10) cc_final: 0.6342 (m-10) REVERT: C 148 GLN cc_start: 0.8025 (mp10) cc_final: 0.7684 (mp10) REVERT: C 221 TYR cc_start: 0.9116 (p90) cc_final: 0.8909 (p90) REVERT: C 274 MET cc_start: 0.8021 (tmm) cc_final: 0.7742 (tmm) REVERT: C 300 GLU cc_start: 0.8235 (tp30) cc_final: 0.7713 (tp30) REVERT: B 416 ARG cc_start: 0.6770 (mpt180) cc_final: 0.6317 (ttp80) REVERT: D 343 PHE cc_start: 0.7882 (m-80) cc_final: 0.7623 (m-80) REVERT: E 69 LEU cc_start: 0.8268 (tp) cc_final: 0.7877 (tp) REVERT: E 79 MET cc_start: 0.8433 (mmt) cc_final: 0.8150 (mmt) REVERT: E 143 ASP cc_start: 0.7596 (t70) cc_final: 0.7369 (m-30) REVERT: E 146 LEU cc_start: 0.8547 (pt) cc_final: 0.8037 (pt) REVERT: E 183 MET cc_start: 0.8077 (tpp) cc_final: 0.7748 (tpp) REVERT: E 212 LEU cc_start: 0.9123 (tp) cc_final: 0.8923 (tp) REVERT: E 247 MET cc_start: 0.7572 (ttp) cc_final: 0.7271 (mtm) REVERT: E 306 MET cc_start: 0.8649 (ttm) cc_final: 0.8086 (ttp) REVERT: E 379 ILE cc_start: 0.7332 (mt) cc_final: 0.6981 (mt) REVERT: E 437 VAL cc_start: 0.8149 (t) cc_final: 0.7778 (p) REVERT: E 480 ILE cc_start: 0.8308 (tp) cc_final: 0.8097 (tt) REVERT: E 492 MET cc_start: 0.4681 (mmt) cc_final: 0.4427 (mmt) REVERT: F 40 MET cc_start: 0.7603 (tpp) cc_final: 0.7359 (ttm) REVERT: F 79 MET cc_start: 0.8881 (mmm) cc_final: 0.8402 (mmt) REVERT: F 278 PHE cc_start: 0.8892 (t80) cc_final: 0.8656 (t80) REVERT: F 354 ARG cc_start: 0.7896 (tpt170) cc_final: 0.7628 (tpp80) REVERT: F 362 TYR cc_start: 0.8421 (m-80) cc_final: 0.8001 (m-80) REVERT: F 398 TYR cc_start: 0.8926 (t80) cc_final: 0.8724 (t80) REVERT: F 476 LEU cc_start: 0.8508 (mt) cc_final: 0.7995 (tp) REVERT: d 92 LEU cc_start: 0.7621 (pt) cc_final: 0.7027 (tp) REVERT: g 64 MET cc_start: 0.8710 (ttm) cc_final: 0.8169 (ttm) REVERT: g 185 LEU cc_start: 0.7696 (mt) cc_final: 0.7422 (pt) REVERT: e 34 LEU cc_start: 0.7568 (pp) cc_final: 0.7196 (pp) REVERT: e 57 TRP cc_start: 0.4666 (p-90) cc_final: 0.3389 (p-90) REVERT: e 121 ARG cc_start: 0.6049 (ppt170) cc_final: 0.5658 (ptm160) REVERT: e 125 ARG cc_start: 0.7116 (mmt180) cc_final: 0.6176 (tpp-160) REVERT: J 116 MET cc_start: 0.5934 (mmm) cc_final: 0.5224 (mmt) REVERT: I 90 MET cc_start: 0.7584 (tmm) cc_final: 0.6992 (tmm) REVERT: I 179 MET cc_start: 0.3541 (tmm) cc_final: 0.3003 (tmm) REVERT: a 197 ASP cc_start: 0.5016 (p0) cc_final: 0.4553 (p0) REVERT: T 49 ILE cc_start: 0.4189 (mm) cc_final: 0.3983 (mm) REVERT: Y 34 GLN cc_start: 0.7039 (mt0) cc_final: 0.6604 (mm-40) REVERT: Y 50 ARG cc_start: 0.6400 (ttt90) cc_final: 0.4559 (tmt170) REVERT: Y 76 PHE cc_start: 0.5625 (m-80) cc_final: 0.5262 (m-80) REVERT: X 28 GLN cc_start: 0.6794 (mt0) cc_final: 0.6480 (mt0) REVERT: X 60 MET cc_start: 0.5577 (ttt) cc_final: 0.5223 (ttt) REVERT: W 60 MET cc_start: 0.6298 (mmt) cc_final: 0.5624 (mmt) REVERT: Z 22 ILE cc_start: 0.8172 (mp) cc_final: 0.7884 (tt) REVERT: S 49 ILE cc_start: 0.5562 (mt) cc_final: 0.5105 (tt) REVERT: R 66 TYR cc_start: 0.6835 (m-80) cc_final: 0.6589 (m-80) REVERT: Q 28 GLN cc_start: 0.7426 (mp10) cc_final: 0.6295 (mp10) REVERT: Q 60 MET cc_start: 0.5310 (mmp) cc_final: 0.5005 (mmp) REVERT: M 59 PHE cc_start: 0.6674 (m-80) cc_final: 0.6222 (m-80) outliers start: 2 outliers final: 0 residues processed: 806 average time/residue: 0.2317 time to fit residues: 313.3344 Evaluate side-chains 624 residues out of total 4097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 624 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 459 optimal weight: 0.9990 chunk 121 optimal weight: 0.7980 chunk 383 optimal weight: 0.8980 chunk 266 optimal weight: 0.0050 chunk 431 optimal weight: 0.9990 chunk 221 optimal weight: 0.5980 chunk 291 optimal weight: 0.3980 chunk 153 optimal weight: 1.9990 chunk 488 optimal weight: 2.9990 chunk 242 optimal weight: 0.6980 chunk 296 optimal weight: 8.9990 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 497 GLN ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 ASN ** B 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 210 ASN ** F 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 299 GLN d 147 ASN d 247 GLN ** W 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 28 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.143132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.139100 restraints weight = 72673.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.136065 restraints weight = 123629.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.135174 restraints weight = 208521.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.134858 restraints weight = 182712.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.134712 restraints weight = 123191.006| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 39710 Z= 0.150 Angle : 0.749 13.281 53850 Z= 0.371 Chirality : 0.046 0.439 6440 Planarity : 0.005 0.095 6950 Dihedral : 6.337 124.731 5573 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.31 % Favored : 92.61 % Rotamer: Outliers : 0.05 % Allowed : 0.42 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.14 % 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 are not related in a simple way. whole: -1.26 (0.12), residues: 5141 helix: 0.30 (0.10), residues: 2784 sheet: -2.68 (0.21), residues: 482 loop : -2.00 (0.14), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 429 TYR 0.038 0.002 TYR M 66 PHE 0.065 0.002 PHE I 145 TRP 0.013 0.002 TRP a 110 HIS 0.010 0.001 HIS g 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (39709) covalent geometry : angle 0.74878 / 0.37 (53848) SS BOND : bond 0.01851 / 0.97 ( 1) SS BOND : angle 2.19825 / 1.47 ( 2) hydrogen bonds : bond 0.04395 / 2.94 ( 2254) hydrogen bonds : angle 4.90504 / 3.32 ( 6618) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7554.10 seconds wall clock time: 131 minutes 18.27 seconds (7878.27 seconds total)