Starting phenix.real_space_refine on Wed Mar 4 16:12:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zny_14842/03_2026/7zny_14842.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zny_14842/03_2026/7zny_14842.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zny_14842/03_2026/7zny_14842.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zny_14842/03_2026/7zny_14842.map" model { file = "/net/cci-nas-00/data/ceres_data/7zny_14842/03_2026/7zny_14842.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zny_14842/03_2026/7zny_14842.cif" } resolution = 3.26 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= 0.018 sd= 0.131 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 9442 2.51 5 N 2440 2.21 5 O 2797 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14763 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3722 Classifications: {'peptide': 473} Link IDs: {'PTRANS': 29, 'TRANS': 443} Chain: "B" Number of atoms: 3683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3683 Classifications: {'peptide': 469} Link IDs: {'PTRANS': 29, 'TRANS': 439} Chain: "C" Number of atoms: 3664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3664 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 29, 'TRANS': 437} Chain: "D" Number of atoms: 3694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3694 Classifications: {'peptide': 470} Link IDs: {'PTRANS': 29, 'TRANS': 440} Time building chain proxies: 3.36, per 1000 atoms: 0.23 Number of scatterers: 14763 At special positions: 0 Unit cell: (117.546, 124.004, 161.464, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 84 16.00 O 2797 8.00 N 2440 7.00 C 9442 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 139 " - pdb=" SG CYS B 139 " distance=2.04 Simple disulfide: pdb=" SG CYS A 154 " - pdb=" SG CYS B 154 " distance=2.03 Simple disulfide: pdb=" SG CYS A 188 " - pdb=" SG CYS A 602 " distance=2.03 Simple disulfide: pdb=" SG CYS A 283 " - pdb=" SG CYS A 296 " distance=2.03 Simple disulfide: pdb=" SG CYS A 377 " - pdb=" SG CYS A 490 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 390 " distance=2.03 Simple disulfide: pdb=" SG CYS A 566 " - pdb=" SG CYS A 575 " distance=2.03 Simple disulfide: pdb=" SG CYS B 188 " - pdb=" SG CYS B 602 " distance=2.03 Simple disulfide: pdb=" SG CYS B 283 " - pdb=" SG CYS B 296 " distance=2.03 Simple disulfide: pdb=" SG CYS B 377 " - pdb=" SG CYS B 490 " distance=2.03 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 390 " distance=2.20 Simple disulfide: pdb=" SG CYS B 566 " - pdb=" SG CYS B 575 " distance=2.03 Simple disulfide: pdb=" SG CYS C 139 " - pdb=" SG CYS D 139 " distance=2.02 Simple disulfide: pdb=" SG CYS C 154 " - pdb=" SG CYS D 154 " distance=2.03 Simple disulfide: pdb=" SG CYS C 188 " - pdb=" SG CYS C 602 " distance=2.03 Simple disulfide: pdb=" SG CYS C 283 " - pdb=" SG CYS C 296 " distance=2.03 Simple disulfide: pdb=" SG CYS C 377 " - pdb=" SG CYS C 490 " distance=2.03 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 390 " distance=2.03 Simple disulfide: pdb=" SG CYS C 566 " - pdb=" SG CYS C 575 " distance=2.03 Simple disulfide: pdb=" SG CYS D 188 " - pdb=" SG CYS D 602 " distance=2.03 Simple disulfide: pdb=" SG CYS D 283 " - pdb=" SG CYS D 296 " distance=2.03 Simple disulfide: pdb=" SG CYS D 377 " - pdb=" SG CYS D 490 " distance=2.03 Simple disulfide: pdb=" SG CYS D 382 " - pdb=" SG CYS D 390 " distance=2.03 Simple disulfide: pdb=" SG CYS D 566 " - pdb=" SG CYS D 575 " distance=2.03 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: 1.23 Conformation dependent library (CDL) restraints added in 509.9 milliseconds 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3510 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 36 sheets defined 13.6% alpha, 31.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 143 through 149 removed outlier: 3.674A pdb=" N ASN A 149 " --> pdb=" O LYS A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 180 Proline residue: A 169 - end of helix removed outlier: 4.356A pdb=" N GLY A 180 " --> pdb=" O SER A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 212 Processing helix chain 'A' and resid 305 through 309 removed outlier: 3.975A pdb=" N ASP A 309 " --> pdb=" O HIS A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 381 removed outlier: 4.291A pdb=" N ASN A 376 " --> pdb=" O GLU A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 392 removed outlier: 3.897A pdb=" N CYS A 390 " --> pdb=" O SER A 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 180 Proline residue: B 169 - end of helix removed outlier: 3.638A pdb=" N GLY B 177 " --> pdb=" O SER B 173 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY B 180 " --> pdb=" O SER B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 212 Processing helix chain 'B' and resid 368 through 383 removed outlier: 4.043A pdb=" N GLU B 372 " --> pdb=" O SER B 368 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLU B 373 " --> pdb=" O GLU B 369 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ASN B 376 " --> pdb=" O GLU B 372 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N CYS B 377 " --> pdb=" O GLU B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 392 removed outlier: 4.051A pdb=" N CYS B 390 " --> pdb=" O SER B 386 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLN B 392 " --> pdb=" O PRO B 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 179 Proline residue: C 169 - end of helix removed outlier: 4.592A pdb=" N GLY C 177 " --> pdb=" O SER C 173 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLY C 178 " --> pdb=" O ALA C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 212 removed outlier: 3.618A pdb=" N ARG C 212 " --> pdb=" O SER C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 309 removed outlier: 4.368A pdb=" N ASP C 309 " --> pdb=" O HIS C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 383 removed outlier: 3.667A pdb=" N GLN C 383 " --> pdb=" O GLU C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 392 removed outlier: 4.227A pdb=" N CYS C 390 " --> pdb=" O SER C 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 153 removed outlier: 3.673A pdb=" N TYR D 153 " --> pdb=" O PHE D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 180 Proline residue: D 169 - end of helix removed outlier: 3.572A pdb=" N ALA D 174 " --> pdb=" O ILE D 170 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLY D 177 " --> pdb=" O SER D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 212 Processing helix chain 'D' and resid 277 through 281 removed outlier: 3.844A pdb=" N ALA D 280 " --> pdb=" O ASN D 277 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS D 281 " --> pdb=" O SER D 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 277 through 281' Processing helix chain 'D' and resid 371 through 383 removed outlier: 3.943A pdb=" N GLN D 383 " --> pdb=" O GLU D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 392 removed outlier: 3.871A pdb=" N CYS D 390 " --> pdb=" O SER D 386 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN D 392 " --> pdb=" O PRO D 388 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 138 through 140 removed outlier: 3.756A pdb=" N TRP A 138 " --> pdb=" O ILE C 140 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TRP C 138 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N HIS C 137 " --> pdb=" O ILE D 140 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 193 through 198 removed outlier: 3.540A pdb=" N VAL A 592 " --> pdb=" O TYR A 579 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLU A 582 " --> pdb=" O PRO A 559 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 216 through 217 Processing sheet with id=AA4, first strand: chain 'A' and resid 216 through 217 removed outlier: 3.698A pdb=" N TYR A 228 " --> pdb=" O GLY A 254 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY A 254 " --> pdb=" O TYR A 228 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN A 270 " --> pdb=" O ILE A 253 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N PHE A 255 " --> pdb=" O THR A 268 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N THR A 268 " --> pdb=" O PHE A 255 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N LYS A 257 " --> pdb=" O LEU A 266 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N LEU A 266 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 282 through 283 Processing sheet with id=AA6, first strand: chain 'A' and resid 282 through 283 Processing sheet with id=AA7, first strand: chain 'A' and resid 301 through 303 removed outlier: 4.195A pdb=" N LYS A 344 " --> pdb=" O LEU A 366 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE A 353 " --> pdb=" O THR A 360 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 301 through 303 removed outlier: 4.195A pdb=" N LYS A 344 " --> pdb=" O LEU A 366 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN A 422 " --> pdb=" O THR A 410 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 447 through 448 Processing sheet with id=AB1, first strand: chain 'A' and resid 447 through 448 removed outlier: 7.841A pdb=" N ILE A 463 " --> pdb=" O HIS A 477 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N HIS A 477 " --> pdb=" O ILE A 463 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 506 through 507 removed outlier: 4.284A pdb=" N TYR A 520 " --> pdb=" O TYR A 539 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE A 522 " --> pdb=" O TYR A 537 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 193 through 199 removed outlier: 4.390A pdb=" N THR B 193 " --> pdb=" O SER B 601 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER B 601 " --> pdb=" O THR B 193 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU B 595 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN B 594 " --> pdb=" O GLN B 577 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN B 577 " --> pdb=" O ASN B 594 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 216 through 221 removed outlier: 4.787A pdb=" N ASN B 218 " --> pdb=" O LEU B 233 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU B 233 " --> pdb=" O ASN B 218 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 257 through 258 Processing sheet with id=AB6, first strand: chain 'B' and resid 302 through 303 removed outlier: 4.423A pdb=" N LYS B 344 " --> pdb=" O LEU B 366 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU B 366 " --> pdb=" O LYS B 344 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N MET B 362 " --> pdb=" O ARG B 351 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ARG B 351 " --> pdb=" O MET B 362 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 350 through 355 current: chain 'B' and resid 422 through 426 Processing sheet with id=AB7, first strand: chain 'B' and resid 316 through 321 removed outlier: 6.528A pdb=" N ILE B 285 " --> pdb=" O GLY B 352 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ILE B 354 " --> pdb=" O ILE B 285 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL B 287 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ARG B 351 " --> pdb=" O MET B 362 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N MET B 362 " --> pdb=" O ARG B 351 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 447 through 448 Processing sheet with id=AB9, first strand: chain 'B' and resid 451 through 452 removed outlier: 3.586A pdb=" N LEU B 462 " --> pdb=" O ILE B 452 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE B 463 " --> pdb=" O VAL B 478 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 511 through 512 removed outlier: 3.772A pdb=" N ILE B 534 " --> pdb=" O TYR B 549 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 193 through 199 removed outlier: 3.874A pdb=" N LEU C 595 " --> pdb=" O PHE C 199 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU C 573 " --> pdb=" O ILE C 598 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N PHE C 561 " --> pdb=" O ARG C 580 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 215 through 224 removed outlier: 6.238A pdb=" N ILE C 216 " --> pdb=" O VAL C 235 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N VAL C 235 " --> pdb=" O ILE C 216 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N ASN C 218 " --> pdb=" O LEU C 233 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LEU C 233 " --> pdb=" O ASN C 218 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N PHE C 255 " --> pdb=" O THR C 268 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N THR C 268 " --> pdb=" O PHE C 255 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LYS C 257 " --> pdb=" O LEU C 266 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N LEU C 266 " --> pdb=" O LYS C 257 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 286 through 288 removed outlier: 3.571A pdb=" N GLU C 333 " --> pdb=" O ILE C 315 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 301 through 302 removed outlier: 3.901A pdb=" N LYS C 344 " --> pdb=" O LEU C 366 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU C 366 " --> pdb=" O LYS C 344 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE C 353 " --> pdb=" O THR C 360 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 301 through 302 removed outlier: 3.901A pdb=" N LYS C 344 " --> pdb=" O LEU C 366 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU C 366 " --> pdb=" O LYS C 344 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR C 406 " --> pdb=" O THR C 426 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 350 through 351 removed outlier: 4.125A pdb=" N ARG C 351 " --> pdb=" O MET C 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'C' and resid 440 through 441 Processing sheet with id=AC9, first strand: chain 'C' and resid 511 through 512 Processing sheet with id=AD1, first strand: chain 'D' and resid 193 through 199 removed outlier: 3.706A pdb=" N THR D 193 " --> pdb=" O SER D 601 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER D 601 " --> pdb=" O THR D 193 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU D 595 " --> pdb=" O PHE D 199 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE D 581 " --> pdb=" O THR D 590 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N TRP D 574 " --> pdb=" O CYS D 566 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N CYS D 566 " --> pdb=" O TRP D 574 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N HIS D 576 " --> pdb=" O ILE D 564 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ILE D 564 " --> pdb=" O HIS D 576 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N PHE D 578 " --> pdb=" O LEU D 562 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LEU D 562 " --> pdb=" O PHE D 578 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ARG D 580 " --> pdb=" O ASP D 560 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 215 through 221 removed outlier: 3.921A pdb=" N GLU D 215 " --> pdb=" O VAL D 235 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N MET D 219 " --> pdb=" O THR D 231 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N THR D 231 " --> pdb=" O MET D 219 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N THR D 221 " --> pdb=" O GLY D 229 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N GLY D 229 " --> pdb=" O THR D 221 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET D 263 " --> pdb=" O TRP D 259 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 215 through 221 removed outlier: 3.921A pdb=" N GLU D 215 " --> pdb=" O VAL D 235 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N MET D 219 " --> pdb=" O THR D 231 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N THR D 231 " --> pdb=" O MET D 219 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N THR D 221 " --> pdb=" O GLY D 229 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N GLY D 229 " --> pdb=" O THR D 221 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 330 through 333 removed outlier: 6.909A pdb=" N ILE D 285 " --> pdb=" O GLY D 352 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N ILE D 354 " --> pdb=" O ILE D 285 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL D 287 " --> pdb=" O ILE D 354 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE D 353 " --> pdb=" O THR D 360 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 301 through 303 removed outlier: 3.736A pdb=" N LYS D 344 " --> pdb=" O LEU D 366 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 438 through 441 Processing sheet with id=AD7, first strand: chain 'D' and resid 438 through 441 Processing sheet with id=AD8, first strand: chain 'D' and resid 480 through 481 Processing sheet with id=AD9, first strand: chain 'D' and resid 511 through 512 removed outlier: 3.561A pdb=" N TYR D 520 " --> pdb=" O TYR D 539 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE D 534 " --> pdb=" O TYR D 549 " (cutoff:3.500A) 495 hydrogen bonds defined for protein. 1305 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: 2.61 Time building geometry restraints manager: 1.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3638 1.33 - 1.45: 2963 1.45 - 1.57: 8405 1.57 - 1.69: 0 1.69 - 1.81: 120 Bond restraints: 15126 Sorted by residual: bond pdb=" N ILE B 335 " pdb=" CA ILE B 335 " ideal model delta sigma weight residual 1.461 1.497 -0.036 9.10e-03 1.21e+04 1.60e+01 bond pdb=" N THR A 480 " pdb=" CA THR A 480 " ideal model delta sigma weight residual 1.456 1.497 -0.040 1.21e-02 6.83e+03 1.12e+01 bond pdb=" N GLY B 314 " pdb=" CA GLY B 314 " ideal model delta sigma weight residual 1.444 1.478 -0.034 1.02e-02 9.61e+03 1.11e+01 bond pdb=" N THR C 326 " pdb=" CA THR C 326 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.04e-02 9.25e+03 1.11e+01 bond pdb=" N ILE C 335 " pdb=" CA ILE C 335 " ideal model delta sigma weight residual 1.461 1.490 -0.029 9.10e-03 1.21e+04 1.04e+01 ... (remaining 15121 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 20170 1.95 - 3.90: 401 3.90 - 5.86: 35 5.86 - 7.81: 8 7.81 - 9.76: 4 Bond angle restraints: 20618 Sorted by residual: angle pdb=" C TYR D 491 " pdb=" CA TYR D 491 " pdb=" CB TYR D 491 " ideal model delta sigma weight residual 109.38 116.54 -7.16 1.80e+00 3.09e-01 1.58e+01 angle pdb=" CA GLY B 399 " pdb=" C GLY B 399 " pdb=" O GLY B 399 " ideal model delta sigma weight residual 121.41 118.01 3.40 8.80e-01 1.29e+00 1.50e+01 angle pdb=" N PRO D 185 " pdb=" CA PRO D 185 " pdb=" C PRO D 185 " ideal model delta sigma weight residual 113.53 118.82 -5.29 1.39e+00 5.18e-01 1.45e+01 angle pdb=" CB GLU B 333 " pdb=" CG GLU B 333 " pdb=" CD GLU B 333 " ideal model delta sigma weight residual 112.60 118.58 -5.98 1.70e+00 3.46e-01 1.24e+01 angle pdb=" C ASP A 570 " pdb=" N ASP A 571 " pdb=" CA ASP A 571 " ideal model delta sigma weight residual 121.54 128.22 -6.68 1.91e+00 2.74e-01 1.22e+01 ... (remaining 20613 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 8273 17.95 - 35.89: 700 35.89 - 53.83: 106 53.83 - 71.78: 19 71.78 - 89.72: 3 Dihedral angle restraints: 9101 sinusoidal: 3632 harmonic: 5469 Sorted by residual: dihedral pdb=" CB CYS A 154 " pdb=" SG CYS A 154 " pdb=" SG CYS B 154 " pdb=" CB CYS B 154 " ideal model delta sinusoidal sigma weight residual 93.00 161.31 -68.31 1 1.00e+01 1.00e-02 6.05e+01 dihedral pdb=" CB CYS B 188 " pdb=" SG CYS B 188 " pdb=" SG CYS B 602 " pdb=" CB CYS B 602 " ideal model delta sinusoidal sigma weight residual -86.00 -144.82 58.82 1 1.00e+01 1.00e-02 4.63e+01 dihedral pdb=" CB CYS A 382 " pdb=" SG CYS A 382 " pdb=" SG CYS A 390 " pdb=" CB CYS A 390 " ideal model delta sinusoidal sigma weight residual 93.00 149.15 -56.15 1 1.00e+01 1.00e-02 4.25e+01 ... (remaining 9098 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1930 0.060 - 0.120: 369 0.120 - 0.180: 43 0.180 - 0.240: 8 0.240 - 0.300: 1 Chirality restraints: 2351 Sorted by residual: chirality pdb=" CA LEU A 479 " pdb=" N LEU A 479 " pdb=" C LEU A 479 " pdb=" CB LEU A 479 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" CA VAL D 367 " pdb=" N VAL D 367 " pdb=" C VAL D 367 " pdb=" CB VAL D 367 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA THR C 326 " pdb=" N THR C 326 " pdb=" C THR C 326 " pdb=" CB THR C 326 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 2348 not shown) Planarity restraints: 2638 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS D 490 " 0.027 2.00e-02 2.50e+03 5.29e-02 2.80e+01 pdb=" C CYS D 490 " -0.092 2.00e-02 2.50e+03 pdb=" O CYS D 490 " 0.034 2.00e-02 2.50e+03 pdb=" N TYR D 491 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO D 185 " 0.019 2.00e-02 2.50e+03 3.92e-02 1.54e+01 pdb=" C PRO D 185 " -0.068 2.00e-02 2.50e+03 pdb=" O PRO D 185 " 0.026 2.00e-02 2.50e+03 pdb=" N TYR D 186 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 313 " 0.017 2.00e-02 2.50e+03 3.40e-02 1.16e+01 pdb=" C ASP B 313 " -0.059 2.00e-02 2.50e+03 pdb=" O ASP B 313 " 0.022 2.00e-02 2.50e+03 pdb=" N GLY B 314 " 0.020 2.00e-02 2.50e+03 ... (remaining 2635 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2307 2.77 - 3.30: 13682 3.30 - 3.83: 23264 3.83 - 4.37: 26548 4.37 - 4.90: 48046 Nonbonded interactions: 113847 Sorted by model distance: nonbonded pdb=" OH TYR C 536 " pdb=" OE1 GLN C 577 " model vdw 2.233 3.040 nonbonded pdb=" OH TYR A 228 " pdb=" OE2 GLU A 252 " model vdw 2.243 3.040 nonbonded pdb=" OH TYR A 406 " pdb=" OD1 ASN A 464 " model vdw 2.247 3.040 nonbonded pdb=" OG1 THR C 348 " pdb=" O ASP C 435 " model vdw 2.256 3.040 nonbonded pdb=" OH TYR B 232 " pdb=" OE2 GLU B 252 " model vdw 2.277 3.040 ... (remaining 113842 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 136 through 602) selection = (chain 'B' and resid 136 through 602) selection = chain 'C' selection = (chain 'D' and resid 136 through 602) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.880 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.020 Set refine NCS operators: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.170 15150 Z= 0.225 Angle : 0.636 9.762 20666 Z= 0.364 Chirality : 0.049 0.300 2351 Planarity : 0.005 0.053 2638 Dihedral : 12.596 89.724 5519 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.00 % Allowed : 14.69 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.19), residues: 1871 helix: 1.65 (0.37), residues: 234 sheet: -0.31 (0.21), residues: 667 loop : -1.70 (0.18), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 552 TYR 0.016 0.001 TYR D 439 PHE 0.021 0.001 PHE B 398 TRP 0.023 0.001 TRP B 138 HIS 0.005 0.001 HIS B 532 Details of bonding type rmsd covalent geometry : bond 0.00347 (15126) covalent geometry : angle 0.63358 (20618) SS BOND : bond 0.03472 ( 24) SS BOND : angle 1.28920 ( 48) hydrogen bonds : bond 0.21266 ( 463) hydrogen bonds : angle 8.84798 ( 1305) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.568 Fit side-chains revert: symmetry clash REVERT: A 500 MET cc_start: 0.2654 (mtt) cc_final: 0.0890 (tmm) REVERT: B 316 LEU cc_start: 0.7793 (tp) cc_final: 0.7461 (mt) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.0975 time to fit residues: 18.3566 Evaluate side-chains 100 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 30.0000 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 2.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 346 HIS ** D 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.196564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.153718 restraints weight = 17284.223| |-----------------------------------------------------------------------------| r_work (start): 0.3972 rms_B_bonded: 2.49 r_work: 0.3763 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3595 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.0861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 15150 Z= 0.182 Angle : 0.623 12.040 20666 Z= 0.319 Chirality : 0.049 0.206 2351 Planarity : 0.005 0.048 2638 Dihedral : 4.603 24.737 2046 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 2.87 % Allowed : 14.39 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.19), residues: 1871 helix: 1.66 (0.37), residues: 231 sheet: -0.42 (0.20), residues: 697 loop : -1.66 (0.19), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 563 TYR 0.020 0.001 TYR A 520 PHE 0.017 0.002 PHE B 353 TRP 0.011 0.002 TRP B 138 HIS 0.004 0.001 HIS B 477 Details of bonding type rmsd covalent geometry : bond 0.00429 (15126) covalent geometry : angle 0.61903 (20618) SS BOND : bond 0.00273 ( 24) SS BOND : angle 1.54226 ( 48) hydrogen bonds : bond 0.03954 ( 463) hydrogen bonds : angle 6.31055 ( 1305) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 107 time to evaluate : 0.478 Fit side-chains revert: symmetry clash REVERT: A 500 MET cc_start: 0.3002 (mtt) cc_final: 0.1948 (ttm) REVERT: B 491 TYR cc_start: 0.6097 (m-80) cc_final: 0.5753 (m-80) outliers start: 48 outliers final: 21 residues processed: 146 average time/residue: 0.1016 time to fit residues: 23.7844 Evaluate side-chains 120 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 602 CYS Chi-restraints excluded: chain C residue 154 CYS Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain D residue 272 MET Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 438 ASP Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 568 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 97 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 37 optimal weight: 9.9990 chunk 93 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 chunk 156 optimal weight: 4.9990 chunk 71 optimal weight: 8.9990 chunk 25 optimal weight: 7.9990 chunk 56 optimal weight: 0.6980 chunk 4 optimal weight: 7.9990 chunk 64 optimal weight: 20.0000 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 464 ASN ** A 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 517 ASN ** D 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 402 GLN D 464 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.184356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.133347 restraints weight = 18086.921| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 3.37 r_work: 0.3500 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.082 15150 Z= 0.437 Angle : 0.875 14.447 20666 Z= 0.445 Chirality : 0.056 0.213 2351 Planarity : 0.006 0.053 2638 Dihedral : 5.775 27.216 2046 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 5.25 % Allowed : 14.57 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.71 (0.19), residues: 1871 helix: 1.20 (0.36), residues: 224 sheet: -0.88 (0.20), residues: 692 loop : -1.92 (0.19), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 563 TYR 0.026 0.003 TYR B 547 PHE 0.030 0.003 PHE C 323 TRP 0.018 0.003 TRP C 259 HIS 0.006 0.002 HIS D 576 Details of bonding type rmsd covalent geometry : bond 0.01044 (15126) covalent geometry : angle 0.86977 (20618) SS BOND : bond 0.00620 ( 24) SS BOND : angle 2.17721 ( 48) hydrogen bonds : bond 0.04800 ( 463) hydrogen bonds : angle 6.45405 ( 1305) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 110 time to evaluate : 0.492 Fit side-chains revert: symmetry clash REVERT: A 262 ASP cc_start: 0.7182 (m-30) cc_final: 0.6841 (m-30) REVERT: A 339 HIS cc_start: 0.5598 (OUTLIER) cc_final: 0.4532 (m90) REVERT: A 500 MET cc_start: 0.3257 (mtt) cc_final: 0.2039 (ttm) REVERT: B 257 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.8268 (mttm) REVERT: B 491 TYR cc_start: 0.6025 (m-80) cc_final: 0.5647 (m-80) REVERT: C 217 ILE cc_start: 0.8772 (OUTLIER) cc_final: 0.8499 (pt) REVERT: C 303 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8495 (tp) REVERT: C 500 MET cc_start: 0.2638 (ttp) cc_final: 0.1811 (ttt) outliers start: 88 outliers final: 62 residues processed: 182 average time/residue: 0.0945 time to fit residues: 27.9984 Evaluate side-chains 166 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 100 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 272 MET Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 491 TYR Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 593 GLU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 272 MET Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 377 CYS Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 532 HIS Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 554 THR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 602 CYS Chi-restraints excluded: chain C residue 154 CYS Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain C residue 548 THR Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 272 MET Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 438 ASP Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 490 CYS Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 568 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 179 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 155 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 146 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 170 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 83 optimal weight: 0.2980 chunk 70 optimal weight: 4.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 HIS ** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.189372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.137966 restraints weight = 17619.447| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 3.18 r_work: 0.3582 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15150 Z= 0.160 Angle : 0.623 11.259 20666 Z= 0.315 Chirality : 0.049 0.182 2351 Planarity : 0.005 0.066 2638 Dihedral : 4.973 24.019 2046 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.58 % Allowed : 17.01 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.19), residues: 1871 helix: 1.54 (0.37), residues: 224 sheet: -0.72 (0.20), residues: 699 loop : -1.81 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 552 TYR 0.016 0.001 TYR B 547 PHE 0.014 0.001 PHE B 353 TRP 0.016 0.002 TRP B 138 HIS 0.004 0.001 HIS C 532 Details of bonding type rmsd covalent geometry : bond 0.00376 (15126) covalent geometry : angle 0.61886 (20618) SS BOND : bond 0.00250 ( 24) SS BOND : angle 1.63279 ( 48) hydrogen bonds : bond 0.03304 ( 463) hydrogen bonds : angle 5.71520 ( 1305) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 108 time to evaluate : 0.573 Fit side-chains revert: symmetry clash REVERT: A 339 HIS cc_start: 0.5732 (OUTLIER) cc_final: 0.4426 (m90) REVERT: A 500 MET cc_start: 0.3272 (mtt) cc_final: 0.2459 (ttm) REVERT: B 153 TYR cc_start: 0.7939 (m-10) cc_final: 0.7541 (m-80) REVERT: B 257 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8093 (mttm) REVERT: B 491 TYR cc_start: 0.6168 (m-80) cc_final: 0.5840 (m-80) REVERT: C 207 MET cc_start: 0.8748 (mtp) cc_final: 0.8433 (mtt) REVERT: C 303 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8609 (tp) REVERT: D 261 ASN cc_start: 0.8376 (t0) cc_final: 0.7839 (t0) outliers start: 60 outliers final: 38 residues processed: 157 average time/residue: 0.1001 time to fit residues: 25.4288 Evaluate side-chains 146 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 105 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 272 MET Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 491 TYR Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 554 THR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 602 CYS Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 527 ILE Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 272 MET Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 438 ASP Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 490 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 94 optimal weight: 2.9990 chunk 176 optimal weight: 5.9990 chunk 85 optimal weight: 0.6980 chunk 143 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 160 optimal weight: 0.9990 chunk 146 optimal weight: 0.9990 chunk 138 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 chunk 180 optimal weight: 6.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 471 GLN ** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 532 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.189402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.138564 restraints weight = 17654.343| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 2.91 r_work: 0.3593 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15150 Z= 0.163 Angle : 0.615 10.999 20666 Z= 0.311 Chirality : 0.048 0.218 2351 Planarity : 0.005 0.059 2638 Dihedral : 4.840 20.128 2046 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 4.06 % Allowed : 17.19 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.19), residues: 1871 helix: 1.55 (0.37), residues: 225 sheet: -0.65 (0.20), residues: 685 loop : -1.82 (0.19), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 552 TYR 0.013 0.001 TYR A 520 PHE 0.015 0.001 PHE B 353 TRP 0.016 0.001 TRP B 138 HIS 0.004 0.001 HIS D 532 Details of bonding type rmsd covalent geometry : bond 0.00387 (15126) covalent geometry : angle 0.61174 (20618) SS BOND : bond 0.00292 ( 24) SS BOND : angle 1.50130 ( 48) hydrogen bonds : bond 0.03149 ( 463) hydrogen bonds : angle 5.49746 ( 1305) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 106 time to evaluate : 0.555 Fit side-chains revert: symmetry clash REVERT: A 339 HIS cc_start: 0.5711 (OUTLIER) cc_final: 0.4220 (m90) REVERT: A 500 MET cc_start: 0.3204 (mtt) cc_final: 0.2410 (ttm) REVERT: B 153 TYR cc_start: 0.7913 (m-10) cc_final: 0.7484 (m-80) REVERT: B 257 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.8194 (mttm) REVERT: B 471 GLN cc_start: 0.7902 (OUTLIER) cc_final: 0.7265 (pp30) REVERT: B 479 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7486 (tp) REVERT: B 491 TYR cc_start: 0.6063 (m-80) cc_final: 0.5811 (m-80) REVERT: C 217 ILE cc_start: 0.8662 (OUTLIER) cc_final: 0.8429 (pt) REVERT: C 303 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8689 (tp) REVERT: D 261 ASN cc_start: 0.8334 (t0) cc_final: 0.7841 (t0) outliers start: 68 outliers final: 49 residues processed: 163 average time/residue: 0.0957 time to fit residues: 25.7986 Evaluate side-chains 155 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 100 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 272 MET Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 491 TYR Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 471 GLN Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 554 THR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 602 CYS Chi-restraints excluded: chain C residue 154 CYS Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 272 MET Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 438 ASP Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 490 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 57 optimal weight: 3.9990 chunk 144 optimal weight: 0.0970 chunk 54 optimal weight: 0.9990 chunk 151 optimal weight: 0.9980 chunk 164 optimal weight: 5.9990 chunk 174 optimal weight: 0.2980 chunk 129 optimal weight: 10.0000 chunk 112 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 139 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 577 GLN B 420 GLN B 471 GLN B 477 HIS ** C 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.192740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.152424 restraints weight = 17590.835| |-----------------------------------------------------------------------------| r_work (start): 0.3966 rms_B_bonded: 3.36 r_work: 0.3567 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15150 Z= 0.117 Angle : 0.575 10.874 20666 Z= 0.292 Chirality : 0.047 0.218 2351 Planarity : 0.004 0.058 2638 Dihedral : 4.582 19.886 2046 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 3.52 % Allowed : 18.51 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.19), residues: 1871 helix: 1.68 (0.37), residues: 225 sheet: -0.53 (0.20), residues: 676 loop : -1.77 (0.19), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 552 TYR 0.014 0.001 TYR A 520 PHE 0.013 0.001 PHE B 353 TRP 0.015 0.001 TRP B 138 HIS 0.006 0.001 HIS D 532 Details of bonding type rmsd covalent geometry : bond 0.00272 (15126) covalent geometry : angle 0.57295 (20618) SS BOND : bond 0.00218 ( 24) SS BOND : angle 1.21198 ( 48) hydrogen bonds : bond 0.02901 ( 463) hydrogen bonds : angle 5.23995 ( 1305) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 109 time to evaluate : 0.546 Fit side-chains revert: symmetry clash REVERT: A 500 MET cc_start: 0.3119 (mtt) cc_final: 0.2384 (ttm) REVERT: B 153 TYR cc_start: 0.7963 (m-10) cc_final: 0.7747 (m-80) REVERT: B 257 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8208 (mttm) REVERT: B 479 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7536 (tp) REVERT: B 491 TYR cc_start: 0.6129 (m-80) cc_final: 0.5894 (m-80) REVERT: C 207 MET cc_start: 0.8636 (mtp) cc_final: 0.8389 (mtm) REVERT: C 303 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8680 (tp) REVERT: C 331 VAL cc_start: 0.8237 (OUTLIER) cc_final: 0.7809 (m) REVERT: D 261 ASN cc_start: 0.8317 (t0) cc_final: 0.7894 (t0) outliers start: 59 outliers final: 44 residues processed: 161 average time/residue: 0.1053 time to fit residues: 26.9529 Evaluate side-chains 147 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 99 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 272 MET Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 491 TYR Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 554 THR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 602 CYS Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 154 CYS Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 438 ASP Chi-restraints excluded: chain D residue 490 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 55 optimal weight: 5.9990 chunk 124 optimal weight: 0.8980 chunk 163 optimal weight: 4.9990 chunk 138 optimal weight: 4.9990 chunk 119 optimal weight: 0.0040 chunk 72 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 overall best weight: 1.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 471 GLN C 517 ASN ** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.191366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.143142 restraints weight = 17597.542| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 2.97 r_work: 0.3606 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15150 Z= 0.146 Angle : 0.591 10.679 20666 Z= 0.299 Chirality : 0.048 0.236 2351 Planarity : 0.004 0.059 2638 Dihedral : 4.586 21.715 2046 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 3.94 % Allowed : 17.91 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.27 (0.19), residues: 1871 helix: 1.72 (0.37), residues: 225 sheet: -0.51 (0.20), residues: 676 loop : -1.74 (0.19), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 552 TYR 0.020 0.001 TYR B 547 PHE 0.016 0.001 PHE B 251 TRP 0.016 0.001 TRP B 138 HIS 0.004 0.001 HIS D 532 Details of bonding type rmsd covalent geometry : bond 0.00346 (15126) covalent geometry : angle 0.58638 (20618) SS BOND : bond 0.00255 ( 24) SS BOND : angle 1.56006 ( 48) hydrogen bonds : bond 0.02915 ( 463) hydrogen bonds : angle 5.21005 ( 1305) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 110 time to evaluate : 0.527 Fit side-chains revert: symmetry clash REVERT: A 134 ARG cc_start: 0.7949 (mtt90) cc_final: 0.7642 (mtm-85) REVERT: A 500 MET cc_start: 0.3064 (mtt) cc_final: 0.2350 (ttm) REVERT: B 153 TYR cc_start: 0.7934 (m-10) cc_final: 0.7688 (m-80) REVERT: B 257 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.8239 (mttm) REVERT: B 471 GLN cc_start: 0.7693 (OUTLIER) cc_final: 0.7426 (pp30) REVERT: B 479 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7471 (tp) REVERT: B 491 TYR cc_start: 0.6086 (m-80) cc_final: 0.5820 (m-80) REVERT: C 217 ILE cc_start: 0.8689 (OUTLIER) cc_final: 0.8436 (pt) REVERT: C 303 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8659 (tp) REVERT: D 261 ASN cc_start: 0.8265 (t0) cc_final: 0.7813 (t0) outliers start: 66 outliers final: 54 residues processed: 166 average time/residue: 0.1021 time to fit residues: 27.2475 Evaluate side-chains 162 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 103 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 272 MET Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 491 TYR Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 471 GLN Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 554 THR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 602 CYS Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 154 CYS Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 272 MET Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 438 ASP Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 490 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 3 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 chunk 128 optimal weight: 7.9990 chunk 83 optimal weight: 0.6980 chunk 75 optimal weight: 7.9990 chunk 95 optimal weight: 0.6980 chunk 143 optimal weight: 4.9990 chunk 120 optimal weight: 0.7980 chunk 159 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 471 GLN ** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.191494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.141772 restraints weight = 17718.218| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 2.99 r_work: 0.3608 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15150 Z= 0.145 Angle : 0.591 10.637 20666 Z= 0.297 Chirality : 0.048 0.240 2351 Planarity : 0.004 0.060 2638 Dihedral : 4.563 20.884 2046 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 4.30 % Allowed : 18.21 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.24 (0.19), residues: 1871 helix: 1.75 (0.37), residues: 226 sheet: -0.48 (0.20), residues: 676 loop : -1.74 (0.19), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 468 TYR 0.014 0.001 TYR B 547 PHE 0.015 0.001 PHE B 353 TRP 0.015 0.001 TRP B 138 HIS 0.004 0.001 HIS D 532 Details of bonding type rmsd covalent geometry : bond 0.00342 (15126) covalent geometry : angle 0.58742 (20618) SS BOND : bond 0.00236 ( 24) SS BOND : angle 1.39791 ( 48) hydrogen bonds : bond 0.02875 ( 463) hydrogen bonds : angle 5.16606 ( 1305) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 105 time to evaluate : 0.491 Fit side-chains revert: symmetry clash REVERT: A 134 ARG cc_start: 0.7976 (mtt90) cc_final: 0.7653 (mtm-85) REVERT: A 500 MET cc_start: 0.3018 (mtt) cc_final: 0.2340 (ttm) REVERT: A 534 ILE cc_start: 0.7161 (OUTLIER) cc_final: 0.6921 (tt) REVERT: B 153 TYR cc_start: 0.7900 (m-10) cc_final: 0.7581 (m-80) REVERT: B 257 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8271 (mttm) REVERT: B 471 GLN cc_start: 0.7905 (OUTLIER) cc_final: 0.7336 (pp30) REVERT: B 479 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7460 (tp) REVERT: B 491 TYR cc_start: 0.6104 (m-80) cc_final: 0.5837 (m-80) REVERT: B 500 MET cc_start: 0.2304 (mmt) cc_final: 0.2042 (mmt) REVERT: C 217 ILE cc_start: 0.8678 (OUTLIER) cc_final: 0.8422 (pt) REVERT: C 303 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8648 (tp) REVERT: C 331 VAL cc_start: 0.8248 (OUTLIER) cc_final: 0.7798 (m) REVERT: D 261 ASN cc_start: 0.8257 (t0) cc_final: 0.7795 (t0) outliers start: 72 outliers final: 57 residues processed: 166 average time/residue: 0.0957 time to fit residues: 25.8506 Evaluate side-chains 168 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 104 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 272 MET Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 491 TYR Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 471 GLN Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 554 THR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 602 CYS Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 154 CYS Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 272 MET Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 438 ASP Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 490 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 17 optimal weight: 8.9990 chunk 162 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 167 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 143 optimal weight: 7.9990 chunk 2 optimal weight: 0.3980 chunk 52 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 349 ASN B 471 GLN ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 532 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.191173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.145570 restraints weight = 17732.499| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 2.99 r_work: 0.3606 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15150 Z= 0.168 Angle : 0.603 11.246 20666 Z= 0.305 Chirality : 0.048 0.250 2351 Planarity : 0.005 0.061 2638 Dihedral : 4.606 20.403 2046 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 4.24 % Allowed : 18.21 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.19), residues: 1871 helix: 1.85 (0.37), residues: 219 sheet: -0.54 (0.20), residues: 679 loop : -1.73 (0.19), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 563 TYR 0.013 0.001 TYR B 547 PHE 0.015 0.001 PHE B 353 TRP 0.016 0.001 TRP B 138 HIS 0.004 0.001 HIS D 576 Details of bonding type rmsd covalent geometry : bond 0.00399 (15126) covalent geometry : angle 0.60031 (20618) SS BOND : bond 0.00262 ( 24) SS BOND : angle 1.39480 ( 48) hydrogen bonds : bond 0.02921 ( 463) hydrogen bonds : angle 5.19432 ( 1305) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 108 time to evaluate : 0.451 Fit side-chains revert: symmetry clash REVERT: A 134 ARG cc_start: 0.7835 (mtt90) cc_final: 0.7533 (mtm-85) REVERT: A 500 MET cc_start: 0.3087 (mtt) cc_final: 0.2358 (ttm) REVERT: B 153 TYR cc_start: 0.7917 (m-10) cc_final: 0.7531 (m-80) REVERT: B 154 CYS cc_start: 0.4386 (OUTLIER) cc_final: 0.4049 (t) REVERT: B 257 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8280 (mttm) REVERT: B 479 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7439 (tp) REVERT: B 491 TYR cc_start: 0.6023 (m-80) cc_final: 0.5734 (m-80) REVERT: B 500 MET cc_start: 0.2344 (mmt) cc_final: 0.2073 (mmt) REVERT: C 217 ILE cc_start: 0.8665 (OUTLIER) cc_final: 0.8428 (pt) REVERT: C 303 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8621 (tp) REVERT: D 261 ASN cc_start: 0.8286 (t0) cc_final: 0.7811 (t0) outliers start: 71 outliers final: 65 residues processed: 168 average time/residue: 0.0986 time to fit residues: 26.7198 Evaluate side-chains 174 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 104 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 272 MET Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 491 TYR Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 154 CYS Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 349 ASN Chi-restraints excluded: chain B residue 377 CYS Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 471 GLN Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 519 ARG Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 554 THR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 602 CYS Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 154 CYS Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 272 MET Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 438 ASP Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 475 ILE Chi-restraints excluded: chain D residue 490 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 68 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 164 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 349 ASN ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.190872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.144434 restraints weight = 17705.401| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 3.06 r_work: 0.3603 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.146 15150 Z= 0.183 Angle : 0.846 59.192 20666 Z= 0.485 Chirality : 0.048 0.286 2351 Planarity : 0.006 0.168 2638 Dihedral : 4.621 21.006 2046 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 4.24 % Allowed : 18.27 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.27 (0.19), residues: 1871 helix: 1.85 (0.37), residues: 219 sheet: -0.54 (0.20), residues: 679 loop : -1.73 (0.19), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 552 TYR 0.013 0.001 TYR B 520 PHE 0.015 0.001 PHE B 353 TRP 0.014 0.001 TRP B 138 HIS 0.008 0.001 HIS B 350 Details of bonding type rmsd covalent geometry : bond 0.00414 (15126) covalent geometry : angle 0.84120 (20618) SS BOND : bond 0.00663 ( 24) SS BOND : angle 2.04121 ( 48) hydrogen bonds : bond 0.02915 ( 463) hydrogen bonds : angle 5.19609 ( 1305) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 104 time to evaluate : 0.641 Fit side-chains revert: symmetry clash REVERT: A 134 ARG cc_start: 0.7836 (mtt90) cc_final: 0.7531 (mtm-85) REVERT: A 500 MET cc_start: 0.3084 (mtt) cc_final: 0.2358 (ttm) REVERT: B 153 TYR cc_start: 0.7913 (m-10) cc_final: 0.7537 (m-80) REVERT: B 154 CYS cc_start: 0.4596 (OUTLIER) cc_final: 0.4357 (t) REVERT: B 257 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.8244 (mttm) REVERT: B 349 ASN cc_start: 0.7342 (OUTLIER) cc_final: 0.7042 (p0) REVERT: B 471 GLN cc_start: 0.8046 (OUTLIER) cc_final: 0.7453 (pp30) REVERT: B 479 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7441 (tp) REVERT: B 491 TYR cc_start: 0.6021 (m-80) cc_final: 0.5738 (m-80) REVERT: C 217 ILE cc_start: 0.8661 (OUTLIER) cc_final: 0.8423 (pt) REVERT: C 303 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8621 (tp) REVERT: D 261 ASN cc_start: 0.8277 (t0) cc_final: 0.7802 (t0) outliers start: 71 outliers final: 63 residues processed: 164 average time/residue: 0.0969 time to fit residues: 25.9026 Evaluate side-chains 174 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 104 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 272 MET Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 491 TYR Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 154 CYS Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 349 ASN Chi-restraints excluded: chain B residue 377 CYS Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 471 GLN Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 519 ARG Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 554 THR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 602 CYS Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 154 CYS Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 272 MET Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 438 ASP Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 475 ILE Chi-restraints excluded: chain D residue 490 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 18 optimal weight: 3.9990 chunk 79 optimal weight: 0.0020 chunk 127 optimal weight: 0.9980 chunk 129 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 92 optimal weight: 0.0050 chunk 51 optimal weight: 8.9990 chunk 137 optimal weight: 5.9990 chunk 162 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 overall best weight: 1.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.190834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.142158 restraints weight = 17685.267| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 3.00 r_work: 0.3609 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.150 15150 Z= 0.189 Angle : 0.725 24.210 20666 Z= 0.410 Chirality : 0.048 0.221 2351 Planarity : 0.006 0.167 2638 Dihedral : 4.621 21.006 2046 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 4.18 % Allowed : 18.21 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.19), residues: 1871 helix: 1.85 (0.37), residues: 219 sheet: -0.54 (0.20), residues: 679 loop : -1.73 (0.19), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 552 TYR 0.013 0.001 TYR B 520 PHE 0.015 0.001 PHE B 353 TRP 0.014 0.001 TRP B 138 HIS 0.008 0.001 HIS B 350 Details of bonding type rmsd covalent geometry : bond 0.00421 (15126) covalent geometry : angle 0.71910 (20618) SS BOND : bond 0.00663 ( 24) SS BOND : angle 2.04105 ( 48) hydrogen bonds : bond 0.02915 ( 463) hydrogen bonds : angle 5.19609 ( 1305) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3639.34 seconds wall clock time: 63 minutes 9.30 seconds (3789.30 seconds total)