Starting phenix.real_space_refine on Sat Aug 23 04:30:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hgp_34745/08_2025/8hgp_34745.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hgp_34745/08_2025/8hgp_34745.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hgp_34745/08_2025/8hgp_34745.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hgp_34745/08_2025/8hgp_34745.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hgp_34745/08_2025/8hgp_34745.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hgp_34745/08_2025/8hgp_34745.map" } resolution = 4.53 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 315 atoms to isotropic. 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 110 5.16 5 C 5672 2.51 5 N 1629 2.21 5 O 1758 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9169 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 4345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 563, 4345 Classifications: {'peptide': 563} Link IDs: {'PTRANS': 35, 'TRANS': 527} Chain breaks: 1 Chain: "A" Number of atoms: 4391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 4391 Classifications: {'peptide': 568} Link IDs: {'PTRANS': 26, 'TRANS': 541} Chain: "C" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 327 Classifications: {'peptide': 41} Link IDs: {'TRANS': 40} Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Residues with excluded nonbonded symmetry interactions: 9 residue: pdb=" N ASN A 182 " occ=0.00 ... (6 atoms not shown) pdb=" ND2 ASN A 182 " occ=0.00 residue: pdb=" N HIS A 183 " occ=0.00 ... (8 atoms not shown) pdb=" NE2 HIS A 183 " occ=0.00 residue: pdb=" N LEU A 184 " occ=0.00 ... (6 atoms not shown) pdb=" CD2 LEU A 184 " occ=0.00 residue: pdb=" N GLY A 203 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY A 203 " occ=0.00 residue: pdb=" N CYS A 329 " occ=0.00 ... (4 atoms not shown) pdb=" SG CYS A 329 " occ=0.00 residue: pdb=" N GLU A 330 " occ=0.00 ... (7 atoms not shown) pdb=" OE2 GLU A 330 " occ=0.00 residue: pdb=" N GLY A 331 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY A 331 " occ=0.00 residue: pdb=" N PRO A 332 " occ=0.00 ... (5 atoms not shown) pdb=" CD PRO A 332 " occ=0.00 residue: pdb=" N CYS A 333 " occ=0.00 ... (4 atoms not shown) pdb=" SG CYS A 333 " occ=0.00 Time building chain proxies: 1.95, per 1000 atoms: 0.21 Number of scatterers: 9169 At special positions: 0 Unit cell: (78.11, 131.61, 127.33, 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 110 16.00 O 1758 8.00 N 1629 7.00 C 5672 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=47, symmetry=0 Simple disulfide: pdb=" SG CYS B 26 " - pdb=" SG CYS B 53 " distance=2.03 Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS B 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 195 " - pdb=" SG CYS B 204 " distance=2.03 Simple disulfide: pdb=" SG CYS B 199 " - pdb=" SG CYS B 212 " distance=2.03 Simple disulfide: pdb=" SG CYS B 220 " - pdb=" SG CYS B 227 " distance=2.03 Simple disulfide: pdb=" SG CYS B 224 " - pdb=" SG CYS B 235 " distance=2.03 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 244 " distance=2.03 Simple disulfide: pdb=" SG CYS B 240 " - pdb=" SG CYS B 252 " distance=2.03 Simple disulfide: pdb=" SG CYS B 255 " - pdb=" SG CYS B 264 " distance=2.03 Simple disulfide: pdb=" SG CYS B 268 " - pdb=" SG CYS B 295 " distance=2.03 Simple disulfide: pdb=" SG CYS B 299 " - pdb=" SG CYS B 311 " distance=2.03 Simple disulfide: pdb=" SG CYS B 315 " - pdb=" SG CYS B 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 334 " - pdb=" SG CYS B 338 " distance=2.03 Simple disulfide: pdb=" SG CYS B 342 " - pdb=" SG CYS B 367 " distance=2.03 Simple disulfide: pdb=" SG CYS B 475 " - pdb=" SG CYS B 504 " distance=2.03 Simple disulfide: pdb=" SG CYS B 511 " - pdb=" SG CYS B 520 " distance=2.03 Simple disulfide: pdb=" SG CYS B 515 " - pdb=" SG CYS B 528 " distance=2.03 Simple disulfide: pdb=" SG CYS B 531 " - pdb=" SG CYS B 540 " distance=2.03 Simple disulfide: pdb=" SG CYS B 544 " - pdb=" SG CYS B 560 " distance=2.03 Simple disulfide: pdb=" SG CYS B 563 " - pdb=" SG CYS B 576 " distance=2.03 Simple disulfide: pdb=" SG CYS B 567 " - pdb=" SG CYS B 584 " distance=2.03 Simple disulfide: pdb=" SG CYS B 587 " - pdb=" SG CYS B 596 " distance=2.03 Simple disulfide: pdb=" SG CYS A 31 " - pdb=" SG CYS A 58 " distance=2.03 Simple disulfide: pdb=" SG CYS A 157 " - pdb=" SG CYS A 187 " distance=2.03 Simple disulfide: pdb=" SG CYS A 190 " - pdb=" SG CYS A 199 " distance=2.03 Simple disulfide: pdb=" SG CYS A 194 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS A 215 " - pdb=" SG CYS A 223 " distance=2.03 Simple disulfide: pdb=" SG CYS A 219 " - pdb=" SG CYS A 231 " distance=2.03 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 240 " distance=2.03 Simple disulfide: pdb=" SG CYS A 236 " - pdb=" SG CYS A 248 " distance=2.03 Simple disulfide: pdb=" SG CYS A 251 " - pdb=" SG CYS A 260 " distance=2.03 Simple disulfide: pdb=" SG CYS A 264 " - pdb=" SG CYS A 291 " distance=2.04 Simple disulfide: pdb=" SG CYS A 295 " - pdb=" SG CYS A 307 " distance=2.03 Simple disulfide: pdb=" SG CYS A 311 " - pdb=" SG CYS A 326 " distance=2.03 Simple disulfide: pdb=" SG CYS A 329 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A 337 " - pdb=" SG CYS A 362 " distance=2.03 Simple disulfide: pdb=" SG CYS A 470 " - pdb=" SG CYS A 499 " distance=2.04 Simple disulfide: pdb=" SG CYS A 506 " - pdb=" SG CYS A 515 " distance=2.03 Simple disulfide: pdb=" SG CYS A 510 " - pdb=" SG CYS A 523 " distance=2.04 Simple disulfide: pdb=" SG CYS A 526 " - pdb=" SG CYS A 535 " distance=2.03 Simple disulfide: pdb=" SG CYS A 539 " - pdb=" SG CYS A 555 " distance=2.04 Simple disulfide: pdb=" SG CYS A 558 " - pdb=" SG CYS A 571 " distance=2.03 Simple disulfide: pdb=" SG CYS A 562 " - pdb=" SG CYS A 579 " distance=2.03 Simple disulfide: pdb=" SG CYS A 582 " - pdb=" SG CYS A 591 " distance=2.03 Simple disulfide: pdb=" SG CYS C 6 " - pdb=" SG CYS C 19 " distance=2.03 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS C 30 " distance=2.03 Simple disulfide: pdb=" SG CYS C 32 " - pdb=" SG CYS C 41 " 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 Links applied ALPHA1-3 " BMA D 3 " - " MAN D 4 " BETA1-3 " NAG D 2 " - " BMA D 3 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A 801 " - " ASN A 56 " " NAG A 802 " - " ASN A 175 " " NAG D 1 " - " ASN A 352 " " NAG E 1 " - " ASN B 259 " Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 365.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2162 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 19 sheets defined 11.2% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'B' and resid 41 through 50 Processing helix chain 'B' and resid 71 through 75 removed outlier: 3.849A pdb=" N GLN B 75 " --> pdb=" O SER B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 173 removed outlier: 3.964A pdb=" N ILE B 172 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 365 Processing helix chain 'B' and resid 377 through 382 removed outlier: 3.905A pdb=" N PHE B 381 " --> pdb=" O PRO B 378 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP B 382 " --> pdb=" O GLU B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 402 removed outlier: 3.726A pdb=" N GLN B 398 " --> pdb=" O GLU B 395 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL B 399 " --> pdb=" O GLN B 396 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE B 400 " --> pdb=" O LEU B 397 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU B 401 " --> pdb=" O GLN B 398 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N THR B 402 " --> pdb=" O VAL B 399 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 395 through 402' Processing helix chain 'B' and resid 422 through 426 removed outlier: 3.568A pdb=" N GLN B 426 " --> pdb=" O SER B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 439 Processing helix chain 'B' and resid 501 through 506 removed outlier: 4.128A pdb=" N GLY B 506 " --> pdb=" O ASP B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.977A pdb=" N GLY B 518 " --> pdb=" O CYS B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 584 removed outlier: 3.577A pdb=" N GLN B 583 " --> pdb=" O GLU B 580 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N CYS B 584 " --> pdb=" O ALA B 581 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 580 through 584' Processing helix chain 'A' and resid 43 through 55 Processing helix chain 'A' and resid 76 through 82 removed outlier: 3.620A pdb=" N LYS A 80 " --> pdb=" O SER A 77 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR A 81 " --> pdb=" O PHE A 78 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE A 82 " --> pdb=" O LEU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 198 removed outlier: 3.871A pdb=" N GLY A 197 " --> pdb=" O CYS A 194 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER A 198 " --> pdb=" O PRO A 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 194 through 198' Processing helix chain 'A' and resid 354 through 360 removed outlier: 4.334A pdb=" N LYS A 357 " --> pdb=" O THR A 354 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N HIS A 358 " --> pdb=" O ASN A 355 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS A 360 " --> pdb=" O LYS A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 397 removed outlier: 3.604A pdb=" N LEU A 392 " --> pdb=" O PRO A 389 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP A 393 " --> pdb=" O GLN A 390 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE A 394 " --> pdb=" O GLU A 391 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU A 395 " --> pdb=" O LEU A 392 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR A 397 " --> pdb=" O ILE A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 421 removed outlier: 3.854A pdb=" N PHE A 420 " --> pdb=" O LEU A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 434 Processing helix chain 'A' and resid 476 through 480 Processing helix chain 'A' and resid 519 through 523 removed outlier: 4.462A pdb=" N CYS A 523 " --> pdb=" O PRO A 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 11 removed outlier: 3.588A pdb=" N MET C 10 " --> pdb=" O SER C 7 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN C 11 " --> pdb=" O SER C 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 7 through 11' Processing sheet with id=AA1, first strand: chain 'B' and resid 55 through 56 Processing sheet with id=AA2, first strand: chain 'B' and resid 60 through 63 Processing sheet with id=AA3, first strand: chain 'B' and resid 272 through 274 Processing sheet with id=AA4, first strand: chain 'B' and resid 289 through 291 removed outlier: 3.604A pdb=" N TYR B 289 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL B 296 " --> pdb=" O TYR B 289 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 319 through 320 removed outlier: 3.573A pdb=" N GLU B 332 " --> pdb=" O GLN B 320 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 342 through 343 removed outlier: 6.665A pdb=" N CYS B 342 " --> pdb=" O PHE B 371 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 374 through 376 removed outlier: 5.179A pdb=" N TYR B 441 " --> pdb=" O LEU B 465 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N LEU B 467 " --> pdb=" O TYR B 441 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU B 443 " --> pdb=" O LEU B 467 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N HIS B 469 " --> pdb=" O LEU B 443 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU B 445 " --> pdb=" O HIS B 469 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ALA B 466 " --> pdb=" O LEU B 494 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 553 through 555 removed outlier: 3.588A pdb=" N LEU B 561 " --> pdb=" O TYR B 554 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 30 through 31 removed outlier: 3.632A pdb=" N ILE A 107 " --> pdb=" O GLU A 142 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 40 through 41 removed outlier: 6.270A pdb=" N GLN A 40 " --> pdb=" O CYS C 32 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 66 through 70 removed outlier: 6.354A pdb=" N ILE A 67 " --> pdb=" O ALA A 92 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ASN A 94 " --> pdb=" O ILE A 67 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N TYR A 69 " --> pdb=" O ASN A 94 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N VAL A 89 " --> pdb=" O ALA A 120 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N LEU A 122 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE A 91 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU A 119 " --> pdb=" O ARG A 149 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N SER A 151 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL A 121 " --> pdb=" O SER A 151 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 236 through 240 removed outlier: 3.509A pdb=" N ALA A 237 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N VAL A 250 " --> pdb=" O ALA A 237 " (cutoff:3.500A) removed outlier: 8.996A pdb=" N GLY A 239 " --> pdb=" O CYS A 248 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N CYS A 248 " --> pdb=" O GLY A 239 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 254 through 255 removed outlier: 4.560A pdb=" N PHE A 254 " --> pdb=" O LYS A 261 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LYS A 261 " --> pdb=" O PHE A 254 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 307 through 308 removed outlier: 3.940A pdb=" N CYS A 326 " --> pdb=" O VAL A 301 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 364 through 365 Processing sheet with id=AB7, first strand: chain 'A' and resid 369 through 371 removed outlier: 7.330A pdb=" N ILE A 462 " --> pdb=" O SER A 437 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ALA A 439 " --> pdb=" O ILE A 462 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS A 489 " --> pdb=" O VAL A 461 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 548 through 549 removed outlier: 3.730A pdb=" N PHE A 549 " --> pdb=" O ILE A 556 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE A 556 " --> pdb=" O PHE A 549 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 585 through 587 removed outlier: 3.737A pdb=" N TYR A 585 " --> pdb=" O VAL A 592 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL A 592 " --> pdb=" O TYR A 585 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 36 through 37 81 hydrogen bonds defined for protein. 174 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: 1.25 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3115 1.35 - 1.46: 1988 1.46 - 1.58: 4129 1.58 - 1.70: 0 1.70 - 1.82: 126 Bond restraints: 9358 Sorted by residual: bond pdb=" C5 MAN D 4 " pdb=" O5 MAN D 4 " ideal model delta sigma weight residual 1.418 1.475 -0.057 2.00e-02 2.50e+03 8.22e+00 bond pdb=" C PRO B 593 " pdb=" N PRO B 594 " ideal model delta sigma weight residual 1.334 1.397 -0.063 2.34e-02 1.83e+03 7.32e+00 bond pdb=" C LYS B 336 " pdb=" N PRO B 337 " ideal model delta sigma weight residual 1.334 1.393 -0.059 2.34e-02 1.83e+03 6.28e+00 bond pdb=" C1 NAG A 801 " pdb=" O5 NAG A 801 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.32e+00 bond pdb=" C1 MAN D 4 " pdb=" O5 MAN D 4 " ideal model delta sigma weight residual 1.399 1.442 -0.043 2.00e-02 2.50e+03 4.62e+00 ... (remaining 9353 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 12358 1.88 - 3.76: 273 3.76 - 5.64: 36 5.64 - 7.52: 9 7.52 - 9.40: 4 Bond angle restraints: 12680 Sorted by residual: angle pdb=" C ALA B 324 " pdb=" N GLU B 325 " pdb=" CA GLU B 325 " ideal model delta sigma weight residual 121.54 129.31 -7.77 1.91e+00 2.74e-01 1.65e+01 angle pdb=" C GLU A 204 " pdb=" N GLU A 205 " pdb=" CA GLU A 205 " ideal model delta sigma weight residual 121.54 128.87 -7.33 1.91e+00 2.74e-01 1.47e+01 angle pdb=" CA PRO B 593 " pdb=" C PRO B 593 " pdb=" N PRO B 594 " ideal model delta sigma weight residual 117.93 122.18 -4.25 1.20e+00 6.94e-01 1.25e+01 angle pdb=" N LEU A 509 " pdb=" CA LEU A 509 " pdb=" C LEU A 509 " ideal model delta sigma weight residual 111.74 116.29 -4.55 1.35e+00 5.49e-01 1.14e+01 angle pdb=" N PRO B 593 " pdb=" CA PRO B 593 " pdb=" C PRO B 593 " ideal model delta sigma weight residual 110.70 114.75 -4.05 1.22e+00 6.72e-01 1.10e+01 ... (remaining 12675 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.72: 5691 22.72 - 45.43: 153 45.43 - 68.15: 33 68.15 - 90.86: 19 90.86 - 113.58: 7 Dihedral angle restraints: 5903 sinusoidal: 2540 harmonic: 3363 Sorted by residual: dihedral pdb=" CB CYS B 299 " pdb=" SG CYS B 299 " pdb=" SG CYS B 311 " pdb=" CB CYS B 311 " ideal model delta sinusoidal sigma weight residual -86.00 -175.48 89.48 1 1.00e+01 1.00e-02 9.51e+01 dihedral pdb=" CB CYS B 544 " pdb=" SG CYS B 544 " pdb=" SG CYS B 560 " pdb=" CB CYS B 560 " ideal model delta sinusoidal sigma weight residual 93.00 -179.23 -87.77 1 1.00e+01 1.00e-02 9.23e+01 dihedral pdb=" CB CYS A 215 " pdb=" SG CYS A 215 " pdb=" SG CYS A 223 " pdb=" CB CYS A 223 " ideal model delta sinusoidal sigma weight residual -86.00 -172.55 86.55 1 1.00e+01 1.00e-02 9.02e+01 ... (remaining 5900 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1233 0.078 - 0.155: 178 0.155 - 0.233: 3 0.233 - 0.311: 2 0.311 - 0.388: 1 Chirality restraints: 1417 Sorted by residual: chirality pdb=" C2 NAG A 802 " pdb=" C1 NAG A 802 " pdb=" C3 NAG A 802 " pdb=" N2 NAG A 802 " both_signs ideal model delta sigma weight residual False -2.49 -2.10 -0.39 2.00e-01 2.50e+01 3.77e+00 chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 352 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.96e+00 ... (remaining 1414 not shown) Planarity restraints: 1673 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 511 " 0.040 5.00e-02 4.00e+02 6.15e-02 6.05e+00 pdb=" N PRO A 512 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO A 512 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 512 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 519 " 0.035 5.00e-02 4.00e+02 5.32e-02 4.52e+00 pdb=" N PRO A 520 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 520 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 520 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 550 " -0.034 5.00e-02 4.00e+02 5.01e-02 4.02e+00 pdb=" N PRO B 551 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 551 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 551 " -0.028 5.00e-02 4.00e+02 ... (remaining 1670 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2178 2.80 - 3.32: 7398 3.32 - 3.85: 14321 3.85 - 4.37: 16134 4.37 - 4.90: 27582 Nonbonded interactions: 67613 Sorted by model distance: nonbonded pdb=" OH TYR B 163 " pdb=" O HIS B 193 " model vdw 2.270 3.040 nonbonded pdb=" O VAL B 356 " pdb=" OG SER B 380 " model vdw 2.328 3.040 nonbonded pdb=" NH1 ARG B 103 " pdb=" O LEU B 256 " model vdw 2.392 3.120 nonbonded pdb=" OG SER B 373 " pdb=" O TYR B 409 " model vdw 2.396 3.040 nonbonded pdb=" NH2 ARG B 34 " pdb=" OD1 ASN B 438 " model vdw 2.398 3.120 ... (remaining 67608 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.330 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6390 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 : 0.003 0.063 9413 Z= 0.180 Angle : 0.703 12.013 12798 Z= 0.382 Chirality : 0.052 0.388 1417 Planarity : 0.007 0.061 1669 Dihedral : 10.200 113.578 3600 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 0.20 % Allowed : 0.78 % Favored : 99.02 % 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 aren not related in a simple way. whole: -3.92 (0.19), residues: 1164 helix: -3.84 (0.43), residues: 41 sheet: -2.91 (0.57), residues: 67 loop : -2.85 (0.15), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 536 TYR 0.012 0.001 TYR B 554 PHE 0.017 0.001 PHE A 404 TRP 0.012 0.001 TRP B 452 HIS 0.011 0.001 HIS B 48 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 9358) covalent geometry : angle 0.67972 (12680) SS BOND : bond 0.00237 ( 47) SS BOND : angle 0.98931 ( 94) hydrogen bonds : bond 0.30789 ( 81) hydrogen bonds : angle 9.11590 ( 174) link_ALPHA1-3 : bond 0.01525 ( 1) link_ALPHA1-3 : angle 3.10665 ( 3) link_BETA1-3 : bond 0.01442 ( 1) link_BETA1-3 : angle 7.24006 ( 3) link_BETA1-4 : bond 0.00695 ( 2) link_BETA1-4 : angle 2.05562 ( 6) link_NAG-ASN : bond 0.00743 ( 4) link_NAG-ASN : angle 3.64396 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 394 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 GLN cc_start: 0.5362 (pp30) cc_final: 0.4620 (mm-40) REVERT: B 31 MET cc_start: 0.7681 (mtp) cc_final: 0.7319 (ptp) REVERT: B 46 LEU cc_start: 0.8532 (mt) cc_final: 0.8168 (mt) REVERT: B 54 GLN cc_start: 0.6707 (mt0) cc_final: 0.6494 (tp-100) REVERT: B 56 VAL cc_start: 0.7921 (t) cc_final: 0.7391 (t) REVERT: B 59 ASN cc_start: 0.6879 (m-40) cc_final: 0.6397 (m-40) REVERT: B 64 TYR cc_start: 0.7601 (m-80) cc_final: 0.7142 (m-80) REVERT: B 65 LEU cc_start: 0.8315 (mt) cc_final: 0.8109 (mt) REVERT: B 74 LEU cc_start: 0.8494 (mt) cc_final: 0.8247 (mt) REVERT: B 75 GLN cc_start: 0.7729 (pt0) cc_final: 0.7504 (pt0) REVERT: B 79 GLU cc_start: 0.6741 (tt0) cc_final: 0.6199 (tt0) REVERT: B 81 GLN cc_start: 0.6821 (mt0) cc_final: 0.6445 (mt0) REVERT: B 85 LEU cc_start: 0.8257 (tp) cc_final: 0.7186 (mt) REVERT: B 91 VAL cc_start: 0.7907 (m) cc_final: 0.7347 (p) REVERT: B 92 ARG cc_start: 0.7556 (mtt90) cc_final: 0.7145 (mmm-85) REVERT: B 93 GLN cc_start: 0.8562 (pp30) cc_final: 0.8131 (pp30) REVERT: B 100 ARG cc_start: 0.7709 (tpp80) cc_final: 0.7472 (mmm-85) REVERT: B 103 ARG cc_start: 0.7084 (mtt-85) cc_final: 0.6672 (tpp80) REVERT: B 105 THR cc_start: 0.7413 (p) cc_final: 0.6406 (t) REVERT: B 106 GLN cc_start: 0.7453 (mt0) cc_final: 0.6879 (mp-120) REVERT: B 160 GLN cc_start: 0.7577 (mm-40) cc_final: 0.6707 (tp-100) REVERT: B 167 ILE cc_start: 0.8461 (mm) cc_final: 0.8205 (mm) REVERT: B 185 ASP cc_start: 0.6906 (t0) cc_final: 0.6446 (t0) REVERT: B 193 HIS cc_start: 0.7972 (m90) cc_final: 0.7337 (m90) REVERT: B 248 LYS cc_start: 0.8559 (mmtt) cc_final: 0.7936 (mmtt) REVERT: B 251 ASP cc_start: 0.7697 (p0) cc_final: 0.7359 (p0) REVERT: B 265 GLU cc_start: 0.6626 (pm20) cc_final: 0.6276 (pm20) REVERT: B 271 LEU cc_start: 0.8310 (mp) cc_final: 0.7992 (mm) REVERT: B 275 ASN cc_start: 0.8240 (t0) cc_final: 0.7631 (t0) REVERT: B 288 ARG cc_start: 0.7796 (mmt180) cc_final: 0.7407 (mmp80) REVERT: B 300 PRO cc_start: 0.7941 (Cg_exo) cc_final: 0.7456 (Cg_endo) REVERT: B 303 TYR cc_start: 0.7536 (m-80) cc_final: 0.7052 (m-80) REVERT: B 320 GLN cc_start: 0.6366 (mt0) cc_final: 0.6080 (mt0) REVERT: B 323 THR cc_start: 0.7139 (m) cc_final: 0.6647 (t) REVERT: B 332 GLU cc_start: 0.7442 (mt-10) cc_final: 0.6486 (mp0) REVERT: B 374 LEU cc_start: 0.7242 (mt) cc_final: 0.7001 (mt) REVERT: B 407 THR cc_start: 0.8040 (p) cc_final: 0.7597 (m) REVERT: B 409 TYR cc_start: 0.7101 (p90) cc_final: 0.6872 (p90) REVERT: B 411 TYR cc_start: 0.6729 (t80) cc_final: 0.6439 (t80) REVERT: B 420 PRO cc_start: 0.8345 (Cg_endo) cc_final: 0.8057 (Cg_exo) REVERT: B 421 ASP cc_start: 0.7769 (p0) cc_final: 0.7394 (p0) REVERT: B 426 GLN cc_start: 0.7495 (pt0) cc_final: 0.6460 (pp30) REVERT: B 429 GLN cc_start: 0.6604 (mt0) cc_final: 0.6299 (mt0) REVERT: B 432 ARG cc_start: 0.7486 (mmt180) cc_final: 0.6526 (tpp-160) REVERT: B 434 ARG cc_start: 0.7237 (mtt90) cc_final: 0.6018 (mtt90) REVERT: B 443 LEU cc_start: 0.7593 (tp) cc_final: 0.7246 (mm) REVERT: B 444 THR cc_start: 0.7127 (m) cc_final: 0.6618 (m) REVERT: B 452 TRP cc_start: 0.7786 (p90) cc_final: 0.7220 (p90) REVERT: B 481 PRO cc_start: 0.8311 (Cg_endo) cc_final: 0.7750 (Cg_exo) REVERT: B 483 ASP cc_start: 0.8442 (m-30) cc_final: 0.7763 (t70) REVERT: B 487 ARG cc_start: 0.7826 (mmt-90) cc_final: 0.7358 (tpp80) REVERT: B 517 ARG cc_start: 0.8311 (mtt180) cc_final: 0.8108 (mtt180) REVERT: B 556 ASN cc_start: 0.7970 (t0) cc_final: 0.7349 (t0) REVERT: B 566 GLU cc_start: 0.7185 (mm-30) cc_final: 0.6484 (tm-30) REVERT: B 577 PHE cc_start: 0.8115 (m-80) cc_final: 0.7860 (m-80) REVERT: B 580 GLU cc_start: 0.8487 (tp30) cc_final: 0.8148 (tp30) REVERT: A 36 ASN cc_start: 0.8103 (p0) cc_final: 0.7592 (p0) REVERT: A 37 LYS cc_start: 0.7941 (ptpt) cc_final: 0.7718 (ptpp) REVERT: A 46 ASP cc_start: 0.7385 (t70) cc_final: 0.6643 (t70) REVERT: A 47 HIS cc_start: 0.7807 (t-90) cc_final: 0.6617 (t70) REVERT: A 61 VAL cc_start: 0.8276 (t) cc_final: 0.8031 (t) REVERT: A 65 LEU cc_start: 0.7749 (tp) cc_final: 0.7477 (tt) REVERT: A 74 TYR cc_start: 0.7696 (m-80) cc_final: 0.6862 (m-80) REVERT: A 85 VAL cc_start: 0.8529 (t) cc_final: 0.8298 (p) REVERT: A 122 LEU cc_start: 0.7460 (mt) cc_final: 0.7113 (mm) REVERT: A 137 MET cc_start: 0.7960 (mtm) cc_final: 0.7582 (mtm) REVERT: A 143 ILE cc_start: 0.8856 (mt) cc_final: 0.8535 (mm) REVERT: A 144 LEU cc_start: 0.8089 (mt) cc_final: 0.7832 (mt) REVERT: A 156 LEU cc_start: 0.7413 (tp) cc_final: 0.7075 (tt) REVERT: A 162 ILE cc_start: 0.8768 (mm) cc_final: 0.8425 (mm) REVERT: A 163 GLN cc_start: 0.8701 (pt0) cc_final: 0.8048 (tt0) REVERT: A 172 PHE cc_start: 0.7404 (m-10) cc_final: 0.7014 (m-10) REVERT: A 209 LYS cc_start: 0.8044 (mttt) cc_final: 0.7431 (mtmm) REVERT: A 226 LYS cc_start: 0.7885 (mtpt) cc_final: 0.7390 (mtpt) REVERT: A 227 SER cc_start: 0.8152 (t) cc_final: 0.7879 (p) REVERT: A 230 ASP cc_start: 0.8359 (m-30) cc_final: 0.8076 (m-30) REVERT: A 233 HIS cc_start: 0.7507 (t-90) cc_final: 0.6877 (t-90) REVERT: A 253 LYS cc_start: 0.8022 (tptm) cc_final: 0.7335 (tptm) REVERT: A 257 GLU cc_start: 0.8338 (mm-30) cc_final: 0.7953 (mm-30) REVERT: A 261 LYS cc_start: 0.7161 (mttm) cc_final: 0.6884 (mttm) REVERT: A 268 MET cc_start: 0.6175 (mtm) cc_final: 0.4995 (mtm) REVERT: A 277 MET cc_start: 0.6327 (mtt) cc_final: 0.5339 (mtt) REVERT: A 293 LYS cc_start: 0.8027 (mtpp) cc_final: 0.7468 (mmmt) REVERT: A 316 TYR cc_start: 0.7526 (t80) cc_final: 0.7063 (t80) REVERT: A 318 MET cc_start: 0.7687 (tpp) cc_final: 0.6812 (tpp) REVERT: A 358 HIS cc_start: 0.7969 (m90) cc_final: 0.7545 (m90) REVERT: A 360 LYS cc_start: 0.8702 (tttt) cc_final: 0.8472 (tttt) REVERT: A 365 ILE cc_start: 0.8183 (mm) cc_final: 0.7890 (mm) REVERT: A 368 ASP cc_start: 0.5199 (m-30) cc_final: 0.4276 (m-30) REVERT: A 369 LEU cc_start: 0.7330 (mt) cc_final: 0.7083 (mm) REVERT: A 372 LEU cc_start: 0.8657 (mt) cc_final: 0.8391 (mt) REVERT: A 396 LYS cc_start: 0.8131 (tppp) cc_final: 0.7686 (tppp) REVERT: A 399 LYS cc_start: 0.8326 (mmtt) cc_final: 0.7854 (mmtt) REVERT: A 401 ILE cc_start: 0.7884 (mt) cc_final: 0.7512 (mt) REVERT: A 404 PHE cc_start: 0.7548 (p90) cc_final: 0.6203 (p90) REVERT: A 421 GLU cc_start: 0.8651 (tt0) cc_final: 0.8039 (tt0) REVERT: A 429 ARG cc_start: 0.7201 (mtt180) cc_final: 0.6876 (mtt-85) REVERT: A 430 THR cc_start: 0.7427 (m) cc_final: 0.6067 (t) REVERT: A 431 LYS cc_start: 0.8218 (mtmm) cc_final: 0.7929 (mtmt) REVERT: A 432 GLN cc_start: 0.8489 (tp-100) cc_final: 0.8255 (tp-100) REVERT: A 433 HIS cc_start: 0.8295 (m-70) cc_final: 0.8060 (m-70) REVERT: A 455 GLU cc_start: 0.6230 (tt0) cc_final: 0.5953 (tt0) REVERT: A 489 LYS cc_start: 0.7830 (ttmp) cc_final: 0.7570 (mtpp) REVERT: A 534 GLU cc_start: 0.6860 (pt0) cc_final: 0.6269 (pt0) REVERT: C 5 LYS cc_start: 0.8063 (mttt) cc_final: 0.7821 (tppp) REVERT: C 18 GLN cc_start: 0.7594 (tt0) cc_final: 0.7259 (pm20) REVERT: C 22 LEU cc_start: 0.7549 (mt) cc_final: 0.7276 (mt) REVERT: C 25 MET cc_start: 0.7937 (mmp) cc_final: 0.7163 (mmp) REVERT: C 29 TYR cc_start: 0.5004 (t80) cc_final: 0.3865 (t80) outliers start: 2 outliers final: 1 residues processed: 396 average time/residue: 0.0997 time to fit residues: 52.2063 Evaluate side-chains 347 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 346 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 0.0030 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.3980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 0.5980 overall best weight: 0.4190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 68 ASN B 158 ASN B 260 HIS B 302 ASN ** B 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 32 GLN A 47 HIS A 57 ASN A 64 ASN A 158 ASN A 408 GLN A 432 GLN A 433 HIS A 486 GLN A 493 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.142455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.116433 restraints weight = 16777.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.121996 restraints weight = 9248.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.125929 restraints weight = 5806.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.128717 restraints weight = 3941.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.130697 restraints weight = 2842.915| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6571 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9413 Z= 0.154 Angle : 0.657 9.673 12798 Z= 0.329 Chirality : 0.047 0.274 1417 Planarity : 0.005 0.052 1669 Dihedral : 9.148 89.842 1426 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % 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 aren not related in a simple way. whole: -3.36 (0.21), residues: 1164 helix: -2.67 (0.61), residues: 63 sheet: -2.69 (0.55), residues: 71 loop : -2.43 (0.17), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 224 TYR 0.013 0.001 TYR B 301 PHE 0.019 0.001 PHE A 180 TRP 0.011 0.001 TRP A 477 HIS 0.006 0.001 HIS A 507 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 9358) covalent geometry : angle 0.63522 (12680) SS BOND : bond 0.00388 ( 47) SS BOND : angle 1.60406 ( 94) hydrogen bonds : bond 0.04329 ( 81) hydrogen bonds : angle 6.85160 ( 174) link_ALPHA1-3 : bond 0.02415 ( 1) link_ALPHA1-3 : angle 2.33895 ( 3) link_BETA1-3 : bond 0.00514 ( 1) link_BETA1-3 : angle 4.42471 ( 3) link_BETA1-4 : bond 0.00479 ( 2) link_BETA1-4 : angle 1.06644 ( 6) link_NAG-ASN : bond 0.00457 ( 4) link_NAG-ASN : angle 2.75672 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 380 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 GLN cc_start: 0.6194 (pp30) cc_final: 0.4848 (mm-40) REVERT: B 30 ASP cc_start: 0.6745 (t0) cc_final: 0.6541 (t0) REVERT: B 31 MET cc_start: 0.7775 (mtp) cc_final: 0.7438 (ptp) REVERT: B 32 LYS cc_start: 0.8176 (mptt) cc_final: 0.7690 (mmtt) REVERT: B 44 ASP cc_start: 0.7206 (t0) cc_final: 0.6629 (t0) REVERT: B 46 LEU cc_start: 0.8777 (mt) cc_final: 0.8519 (mt) REVERT: B 54 GLN cc_start: 0.7055 (mt0) cc_final: 0.6678 (tp-100) REVERT: B 56 VAL cc_start: 0.8132 (t) cc_final: 0.7650 (t) REVERT: B 73 PHE cc_start: 0.8104 (p90) cc_final: 0.7772 (p90) REVERT: B 74 LEU cc_start: 0.8361 (mt) cc_final: 0.8144 (mt) REVERT: B 75 GLN cc_start: 0.7756 (pt0) cc_final: 0.7413 (pt0) REVERT: B 79 GLU cc_start: 0.7197 (tt0) cc_final: 0.6554 (tt0) REVERT: B 81 GLN cc_start: 0.6720 (mt0) cc_final: 0.6225 (mt0) REVERT: B 93 GLN cc_start: 0.8494 (pp30) cc_final: 0.7750 (tm-30) REVERT: B 94 VAL cc_start: 0.8944 (t) cc_final: 0.8612 (t) REVERT: B 105 THR cc_start: 0.7841 (p) cc_final: 0.6883 (t) REVERT: B 106 GLN cc_start: 0.7709 (mt0) cc_final: 0.7167 (mp-120) REVERT: B 116 VAL cc_start: 0.6977 (t) cc_final: 0.6544 (p) REVERT: B 138 ARG cc_start: 0.7342 (mmm-85) cc_final: 0.6520 (mmm160) REVERT: B 160 GLN cc_start: 0.7415 (mm-40) cc_final: 0.7124 (tp40) REVERT: B 171 ASP cc_start: 0.8065 (t70) cc_final: 0.7766 (t70) REVERT: B 173 PHE cc_start: 0.6767 (m-10) cc_final: 0.6491 (m-10) REVERT: B 185 ASP cc_start: 0.7064 (t0) cc_final: 0.6767 (t0) REVERT: B 193 HIS cc_start: 0.7878 (m90) cc_final: 0.7249 (m90) REVERT: B 211 ASP cc_start: 0.8070 (m-30) cc_final: 0.7689 (m-30) REVERT: B 213 GLN cc_start: 0.7678 (tm-30) cc_final: 0.7406 (tm-30) REVERT: B 217 ARG cc_start: 0.7606 (ttt-90) cc_final: 0.7330 (mtp-110) REVERT: B 248 LYS cc_start: 0.8644 (mmtt) cc_final: 0.8076 (mmtt) REVERT: B 253 LEU cc_start: 0.7563 (mt) cc_final: 0.7066 (mt) REVERT: B 265 GLU cc_start: 0.6910 (pm20) cc_final: 0.6558 (pm20) REVERT: B 271 LEU cc_start: 0.8606 (mp) cc_final: 0.8348 (mt) REVERT: B 274 TYR cc_start: 0.6847 (t80) cc_final: 0.6432 (t80) REVERT: B 275 ASN cc_start: 0.8208 (t0) cc_final: 0.7540 (t0) REVERT: B 282 MET cc_start: 0.8056 (mtp) cc_final: 0.7465 (mtp) REVERT: B 303 TYR cc_start: 0.7899 (m-80) cc_final: 0.7289 (m-80) REVERT: B 320 GLN cc_start: 0.6607 (mt0) cc_final: 0.6227 (mt0) REVERT: B 323 THR cc_start: 0.6510 (m) cc_final: 0.6309 (p) REVERT: B 332 GLU cc_start: 0.7325 (mt-10) cc_final: 0.6504 (mp0) REVERT: B 376 PHE cc_start: 0.8128 (m-10) cc_final: 0.7557 (m-10) REVERT: B 377 LEU cc_start: 0.8419 (tp) cc_final: 0.8152 (tt) REVERT: B 398 GLN cc_start: 0.8082 (mm-40) cc_final: 0.7802 (mm-40) REVERT: B 407 THR cc_start: 0.7586 (p) cc_final: 0.7270 (m) REVERT: B 411 TYR cc_start: 0.7206 (t80) cc_final: 0.6736 (t80) REVERT: B 420 PRO cc_start: 0.8425 (Cg_endo) cc_final: 0.7978 (Cg_exo) REVERT: B 421 ASP cc_start: 0.7721 (p0) cc_final: 0.7382 (p0) REVERT: B 422 LEU cc_start: 0.8619 (tp) cc_final: 0.7745 (pp) REVERT: B 426 GLN cc_start: 0.7743 (pt0) cc_final: 0.7047 (pp30) REVERT: B 430 VAL cc_start: 0.7372 (p) cc_final: 0.7025 (t) REVERT: B 434 ARG cc_start: 0.7549 (mtt90) cc_final: 0.7335 (mpt-90) REVERT: B 436 LEU cc_start: 0.7955 (mt) cc_final: 0.7450 (mt) REVERT: B 443 LEU cc_start: 0.7916 (tp) cc_final: 0.7425 (mm) REVERT: B 444 THR cc_start: 0.7560 (m) cc_final: 0.7302 (m) REVERT: B 452 TRP cc_start: 0.7716 (p90) cc_final: 0.7278 (p90) REVERT: B 467 LEU cc_start: 0.7134 (tp) cc_final: 0.6816 (tp) REVERT: B 481 PRO cc_start: 0.8280 (Cg_endo) cc_final: 0.7701 (Cg_exo) REVERT: B 482 TRP cc_start: 0.8546 (m100) cc_final: 0.8318 (m100) REVERT: B 488 ASN cc_start: 0.7898 (t0) cc_final: 0.7661 (t0) REVERT: B 494 LEU cc_start: 0.8534 (mt) cc_final: 0.8138 (mt) REVERT: B 556 ASN cc_start: 0.8080 (t0) cc_final: 0.7464 (t0) REVERT: B 566 GLU cc_start: 0.7537 (mm-30) cc_final: 0.6616 (tm-30) REVERT: B 577 PHE cc_start: 0.8100 (m-80) cc_final: 0.7880 (m-80) REVERT: B 580 GLU cc_start: 0.8433 (tp30) cc_final: 0.8057 (tp30) REVERT: B 592 ASP cc_start: 0.7748 (t0) cc_final: 0.7541 (m-30) REVERT: A 29 LYS cc_start: 0.7920 (pttm) cc_final: 0.7438 (pttm) REVERT: A 36 ASN cc_start: 0.8250 (p0) cc_final: 0.7782 (p0) REVERT: A 46 ASP cc_start: 0.7377 (t70) cc_final: 0.6841 (t70) REVERT: A 47 HIS cc_start: 0.7971 (t70) cc_final: 0.6819 (t70) REVERT: A 51 LEU cc_start: 0.8763 (tp) cc_final: 0.8508 (tp) REVERT: A 55 PHE cc_start: 0.7873 (m-10) cc_final: 0.7395 (m-10) REVERT: A 62 LEU cc_start: 0.8473 (mt) cc_final: 0.8222 (mm) REVERT: A 65 LEU cc_start: 0.7865 (tp) cc_final: 0.7452 (tt) REVERT: A 74 TYR cc_start: 0.7828 (m-80) cc_final: 0.6940 (m-80) REVERT: A 80 LYS cc_start: 0.8291 (mttm) cc_final: 0.7892 (mttm) REVERT: A 83 GLN cc_start: 0.7972 (mm110) cc_final: 0.7528 (mm110) REVERT: A 93 LEU cc_start: 0.8253 (mp) cc_final: 0.8031 (mt) REVERT: A 105 GLN cc_start: 0.8072 (mt0) cc_final: 0.7332 (mm110) REVERT: A 110 ASN cc_start: 0.7942 (m-40) cc_final: 0.7572 (p0) REVERT: A 114 GLU cc_start: 0.7399 (tt0) cc_final: 0.6946 (tt0) REVERT: A 132 LEU cc_start: 0.7848 (tp) cc_final: 0.7598 (mm) REVERT: A 143 ILE cc_start: 0.8964 (mt) cc_final: 0.8641 (mm) REVERT: A 163 GLN cc_start: 0.8637 (pt0) cc_final: 0.7972 (tt0) REVERT: A 176 MET cc_start: 0.7950 (ptp) cc_final: 0.7565 (ptt) REVERT: A 209 LYS cc_start: 0.8118 (mttt) cc_final: 0.7511 (mtmm) REVERT: A 226 LYS cc_start: 0.7871 (mtpt) cc_final: 0.7283 (mtpt) REVERT: A 233 HIS cc_start: 0.7628 (t-90) cc_final: 0.7040 (t-90) REVERT: A 253 LYS cc_start: 0.8137 (tptm) cc_final: 0.7430 (tptm) REVERT: A 256 ASP cc_start: 0.7026 (t70) cc_final: 0.6675 (t0) REVERT: A 261 LYS cc_start: 0.7380 (mttm) cc_final: 0.6888 (mttm) REVERT: A 262 ASP cc_start: 0.7622 (t0) cc_final: 0.7214 (t0) REVERT: A 268 MET cc_start: 0.6130 (mtm) cc_final: 0.4959 (mtm) REVERT: A 277 MET cc_start: 0.6307 (mtt) cc_final: 0.5219 (mtt) REVERT: A 293 LYS cc_start: 0.7907 (mtpp) cc_final: 0.7323 (mmmt) REVERT: A 316 TYR cc_start: 0.7487 (t80) cc_final: 0.7059 (t80) REVERT: A 318 MET cc_start: 0.7784 (tpp) cc_final: 0.6983 (tpp) REVERT: A 338 ASN cc_start: 0.7046 (p0) cc_final: 0.5703 (p0) REVERT: A 345 PHE cc_start: 0.8208 (m-80) cc_final: 0.7925 (m-80) REVERT: A 358 HIS cc_start: 0.8317 (m90) cc_final: 0.7765 (m90) REVERT: A 360 LYS cc_start: 0.8693 (tttt) cc_final: 0.8346 (tttt) REVERT: A 368 ASP cc_start: 0.5204 (m-30) cc_final: 0.3890 (m-30) REVERT: A 396 LYS cc_start: 0.8254 (tppp) cc_final: 0.7815 (tppp) REVERT: A 404 PHE cc_start: 0.7336 (p90) cc_final: 0.6013 (p90) REVERT: A 414 ARG cc_start: 0.6781 (ttm-80) cc_final: 0.6121 (ttt180) REVERT: A 421 GLU cc_start: 0.8688 (tt0) cc_final: 0.8050 (tt0) REVERT: A 430 THR cc_start: 0.7788 (m) cc_final: 0.6514 (p) REVERT: A 432 GLN cc_start: 0.8653 (tp40) cc_final: 0.8066 (tp-100) REVERT: A 433 HIS cc_start: 0.8317 (m90) cc_final: 0.8015 (m90) REVERT: A 476 ASN cc_start: 0.7764 (t0) cc_final: 0.7384 (t0) REVERT: A 489 LYS cc_start: 0.7867 (ttmm) cc_final: 0.7638 (mtpp) REVERT: A 496 GLU cc_start: 0.7558 (mp0) cc_final: 0.7269 (mp0) REVERT: A 551 GLU cc_start: 0.8642 (pt0) cc_final: 0.8187 (pm20) REVERT: C 18 GLN cc_start: 0.7793 (tt0) cc_final: 0.7310 (pm20) REVERT: C 22 LEU cc_start: 0.7599 (mt) cc_final: 0.7281 (mt) REVERT: C 25 MET cc_start: 0.7954 (mmp) cc_final: 0.7299 (mmp) outliers start: 0 outliers final: 0 residues processed: 380 average time/residue: 0.0970 time to fit residues: 49.0536 Evaluate side-chains 346 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 346 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 25 optimal weight: 0.0470 chunk 112 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 6 optimal weight: 0.0370 chunk 113 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 overall best weight: 0.5356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 HIS B 302 ASN ** B 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 32 GLN A 110 ASN A 145 HIS ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.131994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.106317 restraints weight = 16656.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.111743 restraints weight = 9355.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.115654 restraints weight = 5929.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.118453 restraints weight = 4044.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.120484 restraints weight = 2922.344| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6666 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9413 Z= 0.172 Angle : 0.656 9.522 12798 Z= 0.333 Chirality : 0.047 0.285 1417 Planarity : 0.005 0.051 1669 Dihedral : 8.330 87.906 1426 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % 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 aren not related in a simple way. whole: -2.99 (0.23), residues: 1164 helix: -2.05 (0.70), residues: 57 sheet: -2.31 (0.57), residues: 76 loop : -2.19 (0.18), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 252 TYR 0.012 0.001 TYR A 88 PHE 0.017 0.002 PHE B 486 TRP 0.021 0.002 TRP B 415 HIS 0.005 0.001 HIS A 507 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 9358) covalent geometry : angle 0.63546 (12680) SS BOND : bond 0.00567 ( 47) SS BOND : angle 1.47564 ( 94) hydrogen bonds : bond 0.04554 ( 81) hydrogen bonds : angle 6.44623 ( 174) link_ALPHA1-3 : bond 0.01954 ( 1) link_ALPHA1-3 : angle 2.36457 ( 3) link_BETA1-3 : bond 0.00169 ( 1) link_BETA1-3 : angle 4.08383 ( 3) link_BETA1-4 : bond 0.00214 ( 2) link_BETA1-4 : angle 0.96099 ( 6) link_NAG-ASN : bond 0.00516 ( 4) link_NAG-ASN : angle 2.92590 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 378 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 GLN cc_start: 0.6604 (pp30) cc_final: 0.5036 (mm-40) REVERT: B 31 MET cc_start: 0.7728 (mtp) cc_final: 0.7071 (ptp) REVERT: B 44 ASP cc_start: 0.7374 (t0) cc_final: 0.6491 (t0) REVERT: B 46 LEU cc_start: 0.8829 (mt) cc_final: 0.8393 (mt) REVERT: B 47 ARG cc_start: 0.7948 (ttp80) cc_final: 0.7418 (ttp80) REVERT: B 54 GLN cc_start: 0.7097 (mt0) cc_final: 0.6831 (mp10) REVERT: B 55 VAL cc_start: 0.7493 (t) cc_final: 0.6659 (t) REVERT: B 56 VAL cc_start: 0.7968 (t) cc_final: 0.7759 (m) REVERT: B 59 ASN cc_start: 0.7164 (m-40) cc_final: 0.6934 (m-40) REVERT: B 61 GLU cc_start: 0.6931 (tm-30) cc_final: 0.5755 (tm-30) REVERT: B 65 LEU cc_start: 0.8308 (mt) cc_final: 0.8058 (mt) REVERT: B 73 PHE cc_start: 0.8150 (p90) cc_final: 0.7888 (p90) REVERT: B 75 GLN cc_start: 0.7839 (pt0) cc_final: 0.7489 (pt0) REVERT: B 79 GLU cc_start: 0.7048 (tt0) cc_final: 0.6419 (tt0) REVERT: B 81 GLN cc_start: 0.6772 (mt0) cc_final: 0.6203 (mt0) REVERT: B 85 LEU cc_start: 0.8367 (tp) cc_final: 0.8145 (tp) REVERT: B 100 ARG cc_start: 0.8031 (ttm-80) cc_final: 0.7474 (mmm-85) REVERT: B 103 ARG cc_start: 0.7225 (mtt90) cc_final: 0.6718 (ttm110) REVERT: B 105 THR cc_start: 0.8007 (p) cc_final: 0.7556 (t) REVERT: B 106 GLN cc_start: 0.7726 (mt0) cc_final: 0.7383 (mp10) REVERT: B 112 TYR cc_start: 0.7212 (m-80) cc_final: 0.6814 (m-80) REVERT: B 143 ARG cc_start: 0.7765 (mtt180) cc_final: 0.7418 (mtt180) REVERT: B 153 VAL cc_start: 0.7589 (t) cc_final: 0.7386 (t) REVERT: B 167 ILE cc_start: 0.8731 (mm) cc_final: 0.8191 (mm) REVERT: B 169 TRP cc_start: 0.8423 (m100) cc_final: 0.6679 (m100) REVERT: B 173 PHE cc_start: 0.6916 (m-10) cc_final: 0.6323 (m-10) REVERT: B 185 ASP cc_start: 0.7081 (t0) cc_final: 0.5865 (t0) REVERT: B 193 HIS cc_start: 0.7915 (m90) cc_final: 0.7317 (m90) REVERT: B 211 ASP cc_start: 0.8018 (m-30) cc_final: 0.7338 (m-30) REVERT: B 248 LYS cc_start: 0.8716 (mmtt) cc_final: 0.8076 (mmtt) REVERT: B 265 GLU cc_start: 0.7024 (pm20) cc_final: 0.6465 (pm20) REVERT: B 267 HIS cc_start: 0.7384 (m170) cc_final: 0.7153 (m170) REVERT: B 271 LEU cc_start: 0.8578 (mp) cc_final: 0.8350 (mt) REVERT: B 274 TYR cc_start: 0.6990 (t80) cc_final: 0.6520 (t80) REVERT: B 275 ASN cc_start: 0.8135 (t0) cc_final: 0.7545 (t0) REVERT: B 282 MET cc_start: 0.8215 (mtp) cc_final: 0.7908 (mtp) REVERT: B 286 GLU cc_start: 0.8255 (pp20) cc_final: 0.8022 (mp0) REVERT: B 288 ARG cc_start: 0.7952 (mmt-90) cc_final: 0.7714 (mmt-90) REVERT: B 303 TYR cc_start: 0.7997 (m-80) cc_final: 0.7512 (m-80) REVERT: B 311 CYS cc_start: 0.3986 (p) cc_final: 0.3231 (m) REVERT: B 320 GLN cc_start: 0.6734 (mt0) cc_final: 0.6425 (mt0) REVERT: B 332 GLU cc_start: 0.7309 (mt-10) cc_final: 0.6983 (mt-10) REVERT: B 364 PHE cc_start: 0.8564 (m-80) cc_final: 0.7821 (m-80) REVERT: B 371 PHE cc_start: 0.7837 (m-10) cc_final: 0.7614 (m-10) REVERT: B 377 LEU cc_start: 0.8477 (tp) cc_final: 0.8146 (tt) REVERT: B 397 LEU cc_start: 0.8723 (mt) cc_final: 0.8304 (tt) REVERT: B 398 GLN cc_start: 0.8209 (mm-40) cc_final: 0.7971 (mm-40) REVERT: B 407 THR cc_start: 0.7798 (p) cc_final: 0.7370 (m) REVERT: B 411 TYR cc_start: 0.7261 (t80) cc_final: 0.6424 (t80) REVERT: B 420 PRO cc_start: 0.8476 (Cg_endo) cc_final: 0.8083 (Cg_exo) REVERT: B 421 ASP cc_start: 0.7674 (p0) cc_final: 0.7327 (p0) REVERT: B 426 GLN cc_start: 0.7919 (pt0) cc_final: 0.7217 (pp30) REVERT: B 430 VAL cc_start: 0.7606 (p) cc_final: 0.7137 (t) REVERT: B 436 LEU cc_start: 0.7920 (mt) cc_final: 0.7704 (mp) REVERT: B 443 LEU cc_start: 0.8014 (tp) cc_final: 0.7433 (mm) REVERT: B 444 THR cc_start: 0.7484 (m) cc_final: 0.6985 (m) REVERT: B 451 SER cc_start: 0.8068 (p) cc_final: 0.7535 (m) REVERT: B 452 TRP cc_start: 0.7840 (p90) cc_final: 0.7500 (p90) REVERT: B 455 LEU cc_start: 0.7087 (mt) cc_final: 0.6882 (mt) REVERT: B 467 LEU cc_start: 0.7226 (tp) cc_final: 0.6959 (tp) REVERT: B 481 PRO cc_start: 0.8170 (Cg_endo) cc_final: 0.7672 (Cg_exo) REVERT: B 482 TRP cc_start: 0.8661 (m100) cc_final: 0.8335 (m100) REVERT: B 483 ASP cc_start: 0.8475 (m-30) cc_final: 0.7688 (t0) REVERT: B 494 LEU cc_start: 0.8693 (mt) cc_final: 0.8324 (mt) REVERT: B 539 GLU cc_start: 0.7324 (tm-30) cc_final: 0.7122 (tp30) REVERT: B 556 ASN cc_start: 0.8142 (t0) cc_final: 0.7517 (t0) REVERT: B 566 GLU cc_start: 0.7675 (mm-30) cc_final: 0.6540 (tm-30) REVERT: B 577 PHE cc_start: 0.8256 (m-80) cc_final: 0.7975 (m-80) REVERT: B 580 GLU cc_start: 0.8415 (tp30) cc_final: 0.8032 (tp30) REVERT: A 36 ASN cc_start: 0.8311 (p0) cc_final: 0.7857 (p0) REVERT: A 46 ASP cc_start: 0.7290 (t70) cc_final: 0.6567 (t70) REVERT: A 47 HIS cc_start: 0.8087 (t70) cc_final: 0.7005 (t70) REVERT: A 51 LEU cc_start: 0.8859 (tp) cc_final: 0.8624 (tp) REVERT: A 55 PHE cc_start: 0.7905 (m-10) cc_final: 0.7645 (m-10) REVERT: A 61 VAL cc_start: 0.8165 (m) cc_final: 0.7890 (p) REVERT: A 67 ILE cc_start: 0.8360 (mt) cc_final: 0.8134 (mm) REVERT: A 74 TYR cc_start: 0.7981 (m-80) cc_final: 0.7008 (m-80) REVERT: A 80 LYS cc_start: 0.8395 (mttm) cc_final: 0.8089 (mttm) REVERT: A 98 ARG cc_start: 0.7577 (ttt90) cc_final: 0.7137 (tpp80) REVERT: A 110 ASN cc_start: 0.7924 (m110) cc_final: 0.7704 (p0) REVERT: A 112 TYR cc_start: 0.6659 (m-80) cc_final: 0.6344 (m-10) REVERT: A 163 GLN cc_start: 0.8505 (pt0) cc_final: 0.8240 (tt0) REVERT: A 176 MET cc_start: 0.8211 (ptp) cc_final: 0.7863 (ptt) REVERT: A 209 LYS cc_start: 0.8242 (mttt) cc_final: 0.7645 (mtmm) REVERT: A 229 SER cc_start: 0.8173 (p) cc_final: 0.7657 (t) REVERT: A 233 HIS cc_start: 0.7336 (t-90) cc_final: 0.7048 (t-90) REVERT: A 257 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8130 (mm-30) REVERT: A 268 MET cc_start: 0.6096 (mtm) cc_final: 0.4829 (mtm) REVERT: A 277 MET cc_start: 0.6208 (mtt) cc_final: 0.5154 (mtt) REVERT: A 293 LYS cc_start: 0.8007 (mtpp) cc_final: 0.7449 (tppt) REVERT: A 338 ASN cc_start: 0.7195 (p0) cc_final: 0.6369 (p0) REVERT: A 344 GLU cc_start: 0.7250 (tt0) cc_final: 0.7019 (tt0) REVERT: A 345 PHE cc_start: 0.8292 (m-80) cc_final: 0.7479 (m-80) REVERT: A 358 HIS cc_start: 0.8469 (m90) cc_final: 0.8220 (m90) REVERT: A 360 LYS cc_start: 0.8715 (tttt) cc_final: 0.8368 (tttt) REVERT: A 396 LYS cc_start: 0.8353 (tppp) cc_final: 0.7871 (tppp) REVERT: A 404 PHE cc_start: 0.7594 (p90) cc_final: 0.6591 (p90) REVERT: A 421 GLU cc_start: 0.8662 (tt0) cc_final: 0.6997 (tt0) REVERT: A 429 ARG cc_start: 0.7916 (mtt180) cc_final: 0.7440 (mtt-85) REVERT: A 430 THR cc_start: 0.7705 (m) cc_final: 0.6856 (m) REVERT: A 432 GLN cc_start: 0.8682 (tp40) cc_final: 0.8059 (tp-100) REVERT: A 433 HIS cc_start: 0.8301 (m90) cc_final: 0.8009 (m90) REVERT: A 435 GLN cc_start: 0.8690 (tt0) cc_final: 0.8481 (tt0) REVERT: A 451 ARG cc_start: 0.7111 (mtt90) cc_final: 0.5551 (ptp-110) REVERT: A 463 ILE cc_start: 0.6808 (mt) cc_final: 0.6589 (mp) REVERT: A 476 ASN cc_start: 0.7787 (t0) cc_final: 0.7390 (t0) REVERT: A 487 LYS cc_start: 0.7749 (mtmm) cc_final: 0.7463 (mtmm) REVERT: A 489 LYS cc_start: 0.7817 (ttmm) cc_final: 0.7512 (mtpp) REVERT: A 496 GLU cc_start: 0.7560 (mp0) cc_final: 0.7289 (mp0) REVERT: A 521 ARG cc_start: 0.7871 (ptt180) cc_final: 0.6777 (ptt180) REVERT: A 551 GLU cc_start: 0.8662 (pt0) cc_final: 0.8198 (pm20) REVERT: C 22 LEU cc_start: 0.7616 (mt) cc_final: 0.7299 (mt) REVERT: C 25 MET cc_start: 0.7960 (mmp) cc_final: 0.7424 (mmp) outliers start: 0 outliers final: 0 residues processed: 378 average time/residue: 0.1014 time to fit residues: 50.4099 Evaluate side-chains 350 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 350 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 41 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 21 optimal weight: 0.0980 chunk 91 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 109 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 565 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.127476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.101455 restraints weight = 16628.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.106893 restraints weight = 9456.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.110775 restraints weight = 6013.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.113564 restraints weight = 4111.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.115538 restraints weight = 2973.947| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6755 moved from start: 0.4275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9413 Z= 0.219 Angle : 0.710 10.752 12798 Z= 0.362 Chirality : 0.048 0.283 1417 Planarity : 0.005 0.051 1669 Dihedral : 8.098 87.553 1426 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.31 % Favored : 89.69 % Rotamer: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % 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 aren not related in a simple way. whole: -2.76 (0.23), residues: 1164 helix: -2.02 (0.70), residues: 48 sheet: -1.65 (0.66), residues: 64 loop : -2.06 (0.18), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 188 TYR 0.039 0.002 TYR A 117 PHE 0.010 0.002 PHE B 486 TRP 0.019 0.003 TRP A 200 HIS 0.008 0.002 HIS A 507 Details of bonding type rmsd covalent geometry : bond 0.00435 ( 9358) covalent geometry : angle 0.69158 (12680) SS BOND : bond 0.00389 ( 47) SS BOND : angle 1.44411 ( 94) hydrogen bonds : bond 0.04174 ( 81) hydrogen bonds : angle 6.07435 ( 174) link_ALPHA1-3 : bond 0.02460 ( 1) link_ALPHA1-3 : angle 2.59409 ( 3) link_BETA1-3 : bond 0.00646 ( 1) link_BETA1-3 : angle 3.64647 ( 3) link_BETA1-4 : bond 0.00343 ( 2) link_BETA1-4 : angle 1.14339 ( 6) link_NAG-ASN : bond 0.00679 ( 4) link_NAG-ASN : angle 3.12345 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 380 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 GLN cc_start: 0.6986 (pp30) cc_final: 0.5304 (mm-40) REVERT: B 31 MET cc_start: 0.7702 (mtp) cc_final: 0.6579 (ptp) REVERT: B 32 LYS cc_start: 0.8229 (mmtp) cc_final: 0.7647 (mmtt) REVERT: B 44 ASP cc_start: 0.7533 (t0) cc_final: 0.6649 (t0) REVERT: B 46 LEU cc_start: 0.8822 (mt) cc_final: 0.8284 (mt) REVERT: B 47 ARG cc_start: 0.8025 (ttp80) cc_final: 0.7479 (ttp80) REVERT: B 59 ASN cc_start: 0.7242 (m-40) cc_final: 0.6822 (m-40) REVERT: B 61 GLU cc_start: 0.6828 (tm-30) cc_final: 0.3642 (tm-30) REVERT: B 64 TYR cc_start: 0.7742 (m-80) cc_final: 0.7369 (m-80) REVERT: B 65 LEU cc_start: 0.8252 (mt) cc_final: 0.8037 (mt) REVERT: B 75 GLN cc_start: 0.7941 (pt0) cc_final: 0.7622 (pt0) REVERT: B 78 GLN cc_start: 0.7797 (pm20) cc_final: 0.7518 (pm20) REVERT: B 81 GLN cc_start: 0.6576 (mt0) cc_final: 0.6204 (mt0) REVERT: B 100 ARG cc_start: 0.8069 (ttm-80) cc_final: 0.7694 (mmm-85) REVERT: B 105 THR cc_start: 0.8058 (p) cc_final: 0.7663 (t) REVERT: B 106 GLN cc_start: 0.7797 (mt0) cc_final: 0.7412 (mp-120) REVERT: B 109 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7746 (mt-10) REVERT: B 143 ARG cc_start: 0.7752 (mtt180) cc_final: 0.7430 (mtt180) REVERT: B 160 GLN cc_start: 0.7197 (tp40) cc_final: 0.6955 (tp40) REVERT: B 169 TRP cc_start: 0.8395 (m100) cc_final: 0.6421 (m100) REVERT: B 173 PHE cc_start: 0.6892 (m-10) cc_final: 0.6446 (m-10) REVERT: B 182 THR cc_start: 0.7595 (p) cc_final: 0.7209 (p) REVERT: B 184 ILE cc_start: 0.8724 (mm) cc_final: 0.8422 (mm) REVERT: B 185 ASP cc_start: 0.6903 (t0) cc_final: 0.6653 (t0) REVERT: B 211 ASP cc_start: 0.8023 (m-30) cc_final: 0.7751 (m-30) REVERT: B 226 ARG cc_start: 0.7683 (mmp80) cc_final: 0.7409 (mmp-170) REVERT: B 237 HIS cc_start: 0.7554 (t-90) cc_final: 0.7171 (t-90) REVERT: B 239 GLN cc_start: 0.7951 (mm110) cc_final: 0.7621 (mp10) REVERT: B 248 LYS cc_start: 0.8789 (mmtt) cc_final: 0.8081 (mmtt) REVERT: B 274 TYR cc_start: 0.6867 (t80) cc_final: 0.6393 (t80) REVERT: B 275 ASN cc_start: 0.8095 (t0) cc_final: 0.7757 (t0) REVERT: B 282 MET cc_start: 0.8225 (mtp) cc_final: 0.7996 (mtp) REVERT: B 286 GLU cc_start: 0.8340 (pp20) cc_final: 0.7961 (mp0) REVERT: B 288 ARG cc_start: 0.7950 (mmt-90) cc_final: 0.6909 (mmt-90) REVERT: B 303 TYR cc_start: 0.8076 (m-80) cc_final: 0.7666 (m-80) REVERT: B 311 CYS cc_start: 0.4162 (p) cc_final: 0.3479 (m) REVERT: B 319 ASN cc_start: 0.7523 (m-40) cc_final: 0.7196 (m-40) REVERT: B 364 PHE cc_start: 0.8645 (m-80) cc_final: 0.7968 (m-80) REVERT: B 377 LEU cc_start: 0.8568 (tp) cc_final: 0.8262 (tt) REVERT: B 397 LEU cc_start: 0.8826 (mt) cc_final: 0.8611 (tt) REVERT: B 407 THR cc_start: 0.7865 (p) cc_final: 0.7485 (m) REVERT: B 411 TYR cc_start: 0.7385 (t80) cc_final: 0.6543 (t80) REVERT: B 420 PRO cc_start: 0.8493 (Cg_endo) cc_final: 0.8106 (Cg_exo) REVERT: B 421 ASP cc_start: 0.7680 (p0) cc_final: 0.7299 (p0) REVERT: B 422 LEU cc_start: 0.8600 (tp) cc_final: 0.8379 (tp) REVERT: B 426 GLN cc_start: 0.7988 (pt0) cc_final: 0.7214 (pp30) REVERT: B 430 VAL cc_start: 0.7752 (p) cc_final: 0.7343 (t) REVERT: B 436 LEU cc_start: 0.7992 (mt) cc_final: 0.7676 (mp) REVERT: B 444 THR cc_start: 0.7594 (m) cc_final: 0.7213 (m) REVERT: B 451 SER cc_start: 0.8100 (p) cc_final: 0.7613 (m) REVERT: B 452 TRP cc_start: 0.7945 (p90) cc_final: 0.7649 (p90) REVERT: B 455 LEU cc_start: 0.7227 (mt) cc_final: 0.6996 (mt) REVERT: B 481 PRO cc_start: 0.8041 (Cg_endo) cc_final: 0.7434 (Cg_exo) REVERT: B 482 TRP cc_start: 0.8593 (m100) cc_final: 0.8163 (m100) REVERT: B 486 PHE cc_start: 0.8426 (m-10) cc_final: 0.7715 (m-10) REVERT: B 487 ARG cc_start: 0.7821 (mmt90) cc_final: 0.7499 (mtt90) REVERT: B 488 ASN cc_start: 0.8002 (t0) cc_final: 0.7092 (t0) REVERT: B 491 GLN cc_start: 0.5991 (mt0) cc_final: 0.5738 (mt0) REVERT: B 493 LEU cc_start: 0.8126 (tp) cc_final: 0.7584 (tp) REVERT: B 494 LEU cc_start: 0.8673 (mt) cc_final: 0.8464 (mt) REVERT: B 527 GLN cc_start: 0.6918 (pm20) cc_final: 0.5911 (pm20) REVERT: B 556 ASN cc_start: 0.8176 (t0) cc_final: 0.7511 (t0) REVERT: B 566 GLU cc_start: 0.7779 (mm-30) cc_final: 0.6513 (tm-30) REVERT: B 577 PHE cc_start: 0.8328 (m-80) cc_final: 0.7990 (m-80) REVERT: B 580 GLU cc_start: 0.8384 (tp30) cc_final: 0.7957 (tp30) REVERT: A 29 LYS cc_start: 0.7744 (pttm) cc_final: 0.7205 (pttm) REVERT: A 46 ASP cc_start: 0.7224 (t70) cc_final: 0.6579 (t70) REVERT: A 47 HIS cc_start: 0.8019 (t70) cc_final: 0.6873 (t70) REVERT: A 51 LEU cc_start: 0.8933 (tp) cc_final: 0.8660 (tp) REVERT: A 61 VAL cc_start: 0.8239 (m) cc_final: 0.7907 (p) REVERT: A 67 ILE cc_start: 0.8353 (mt) cc_final: 0.8151 (mm) REVERT: A 74 TYR cc_start: 0.8136 (m-80) cc_final: 0.7091 (m-80) REVERT: A 77 SER cc_start: 0.8202 (m) cc_final: 0.6982 (p) REVERT: A 80 LYS cc_start: 0.8412 (mttm) cc_final: 0.8054 (mttm) REVERT: A 102 GLU cc_start: 0.7606 (mt-10) cc_final: 0.7278 (mt-10) REVERT: A 112 TYR cc_start: 0.7363 (m-10) cc_final: 0.6876 (m-10) REVERT: A 119 LEU cc_start: 0.7672 (tp) cc_final: 0.7438 (tp) REVERT: A 122 LEU cc_start: 0.8091 (mp) cc_final: 0.7866 (mp) REVERT: A 135 LEU cc_start: 0.8345 (tp) cc_final: 0.8014 (tp) REVERT: A 137 MET cc_start: 0.8293 (mtm) cc_final: 0.7802 (mtm) REVERT: A 163 GLN cc_start: 0.8388 (pt0) cc_final: 0.8025 (tt0) REVERT: A 176 MET cc_start: 0.8524 (ptp) cc_final: 0.7993 (ptp) REVERT: A 209 LYS cc_start: 0.8262 (mttt) cc_final: 0.7760 (mtmt) REVERT: A 257 GLU cc_start: 0.8505 (mm-30) cc_final: 0.8012 (mm-30) REVERT: A 261 LYS cc_start: 0.7197 (ptmt) cc_final: 0.6780 (ptmt) REVERT: A 268 MET cc_start: 0.6160 (mtm) cc_final: 0.4826 (mtm) REVERT: A 277 MET cc_start: 0.6374 (mtt) cc_final: 0.5153 (mtt) REVERT: A 298 ASN cc_start: 0.8717 (p0) cc_final: 0.8494 (p0) REVERT: A 338 ASN cc_start: 0.7300 (p0) cc_final: 0.7087 (p0) REVERT: A 351 ILE cc_start: 0.7659 (tt) cc_final: 0.7086 (mp) REVERT: A 360 LYS cc_start: 0.8768 (tttt) cc_final: 0.8445 (tttt) REVERT: A 370 HIS cc_start: 0.7974 (m90) cc_final: 0.7633 (m90) REVERT: A 371 ILE cc_start: 0.7809 (mm) cc_final: 0.7559 (mm) REVERT: A 396 LYS cc_start: 0.8526 (tppp) cc_final: 0.8043 (tppp) REVERT: A 404 PHE cc_start: 0.7649 (p90) cc_final: 0.6729 (p90) REVERT: A 407 ILE cc_start: 0.7743 (mt) cc_final: 0.7473 (mm) REVERT: A 421 GLU cc_start: 0.8692 (tt0) cc_final: 0.7624 (tt0) REVERT: A 429 ARG cc_start: 0.8032 (mtt180) cc_final: 0.7579 (mtt-85) REVERT: A 432 GLN cc_start: 0.8627 (tp40) cc_final: 0.7976 (tp-100) REVERT: A 433 HIS cc_start: 0.8371 (m90) cc_final: 0.8035 (m90) REVERT: A 435 GLN cc_start: 0.8791 (tt0) cc_final: 0.8541 (tt0) REVERT: A 445 ILE cc_start: 0.7950 (pt) cc_final: 0.7615 (pt) REVERT: A 454 LYS cc_start: 0.8659 (mmtt) cc_final: 0.8123 (mmtt) REVERT: A 457 SER cc_start: 0.8037 (m) cc_final: 0.7717 (m) REVERT: A 463 ILE cc_start: 0.6942 (mt) cc_final: 0.6615 (mp) REVERT: A 476 ASN cc_start: 0.7822 (t0) cc_final: 0.6758 (t0) REVERT: A 479 LYS cc_start: 0.7907 (mtpt) cc_final: 0.6978 (mtpt) REVERT: A 487 LYS cc_start: 0.7877 (mtmm) cc_final: 0.7623 (mtmm) REVERT: A 489 LYS cc_start: 0.7739 (ttmm) cc_final: 0.7453 (mmmm) REVERT: A 496 GLU cc_start: 0.7542 (mp0) cc_final: 0.7194 (mp0) REVERT: A 551 GLU cc_start: 0.8698 (pt0) cc_final: 0.8252 (pm20) REVERT: A 559 HIS cc_start: 0.7622 (t70) cc_final: 0.7233 (t-170) REVERT: C 25 MET cc_start: 0.7944 (mmp) cc_final: 0.7438 (mmp) outliers start: 0 outliers final: 0 residues processed: 380 average time/residue: 0.0977 time to fit residues: 48.5779 Evaluate side-chains 355 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 355 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 105 optimal weight: 1.9990 chunk 74 optimal weight: 0.2980 chunk 67 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 97 optimal weight: 0.4980 chunk 115 optimal weight: 0.9980 chunk 107 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 64 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 398 GLN ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 83 GLN A 280 ASN A 408 GLN A 584 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.126227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.100980 restraints weight = 16491.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.106271 restraints weight = 9343.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.110030 restraints weight = 5937.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.112752 restraints weight = 4064.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.114759 restraints weight = 2939.447| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6760 moved from start: 0.4712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9413 Z= 0.184 Angle : 0.666 9.920 12798 Z= 0.338 Chirality : 0.048 0.270 1417 Planarity : 0.005 0.047 1669 Dihedral : 7.723 85.797 1426 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.22 % Favored : 89.78 % Rotamer: Outliers : 0.10 % Allowed : 1.76 % Favored : 98.14 % 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 aren not related in a simple way. whole: -2.81 (0.23), residues: 1164 helix: -2.54 (0.59), residues: 63 sheet: -2.02 (0.54), residues: 88 loop : -2.01 (0.19), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 190 TYR 0.015 0.002 TYR A 117 PHE 0.015 0.002 PHE A 78 TRP 0.063 0.003 TRP A 200 HIS 0.008 0.001 HIS A 183 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 9358) covalent geometry : angle 0.64529 (12680) SS BOND : bond 0.00457 ( 47) SS BOND : angle 1.58713 ( 94) hydrogen bonds : bond 0.03968 ( 81) hydrogen bonds : angle 5.86108 ( 174) link_ALPHA1-3 : bond 0.02439 ( 1) link_ALPHA1-3 : angle 2.59482 ( 3) link_BETA1-3 : bond 0.00632 ( 1) link_BETA1-3 : angle 3.68066 ( 3) link_BETA1-4 : bond 0.00369 ( 2) link_BETA1-4 : angle 1.11649 ( 6) link_NAG-ASN : bond 0.00406 ( 4) link_NAG-ASN : angle 2.86905 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 377 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 GLN cc_start: 0.7084 (pp30) cc_final: 0.6009 (mm-40) REVERT: B 31 MET cc_start: 0.7709 (mtp) cc_final: 0.6533 (ptp) REVERT: B 44 ASP cc_start: 0.7410 (t0) cc_final: 0.6602 (t0) REVERT: B 45 MET cc_start: 0.8360 (tmm) cc_final: 0.8097 (tmm) REVERT: B 46 LEU cc_start: 0.8770 (mt) cc_final: 0.8214 (mt) REVERT: B 47 ARG cc_start: 0.8012 (ttp80) cc_final: 0.7464 (ttp80) REVERT: B 55 VAL cc_start: 0.7810 (t) cc_final: 0.7487 (p) REVERT: B 59 ASN cc_start: 0.7252 (m-40) cc_final: 0.6844 (m-40) REVERT: B 61 GLU cc_start: 0.6919 (tm-30) cc_final: 0.3408 (tm-30) REVERT: B 75 GLN cc_start: 0.7942 (pt0) cc_final: 0.7634 (pt0) REVERT: B 78 GLN cc_start: 0.7798 (pm20) cc_final: 0.7421 (pm20) REVERT: B 81 GLN cc_start: 0.6613 (mt0) cc_final: 0.6238 (mt0) REVERT: B 100 ARG cc_start: 0.8094 (ttm-80) cc_final: 0.7675 (mmm-85) REVERT: B 105 THR cc_start: 0.8047 (p) cc_final: 0.7668 (t) REVERT: B 106 GLN cc_start: 0.7780 (mt0) cc_final: 0.7398 (mp-120) REVERT: B 109 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7644 (mt-10) REVERT: B 143 ARG cc_start: 0.7748 (mtt180) cc_final: 0.7453 (mtt180) REVERT: B 155 ILE cc_start: 0.7919 (mp) cc_final: 0.7660 (mp) REVERT: B 164 GLN cc_start: 0.8016 (mm-40) cc_final: 0.7727 (mp-120) REVERT: B 173 PHE cc_start: 0.6813 (m-10) cc_final: 0.6443 (m-10) REVERT: B 182 THR cc_start: 0.7660 (p) cc_final: 0.7329 (p) REVERT: B 184 ILE cc_start: 0.8789 (mm) cc_final: 0.8582 (mm) REVERT: B 185 ASP cc_start: 0.6972 (t0) cc_final: 0.6706 (t0) REVERT: B 193 HIS cc_start: 0.7769 (m90) cc_final: 0.7234 (m90) REVERT: B 211 ASP cc_start: 0.8032 (m-30) cc_final: 0.7730 (m-30) REVERT: B 248 LYS cc_start: 0.8770 (mmtt) cc_final: 0.8124 (mmtt) REVERT: B 267 HIS cc_start: 0.7522 (m170) cc_final: 0.7230 (m170) REVERT: B 271 LEU cc_start: 0.8606 (mt) cc_final: 0.8383 (mt) REVERT: B 274 TYR cc_start: 0.6864 (t80) cc_final: 0.5921 (t80) REVERT: B 275 ASN cc_start: 0.8052 (t0) cc_final: 0.7738 (t0) REVERT: B 286 GLU cc_start: 0.8341 (pp20) cc_final: 0.7618 (tm-30) REVERT: B 303 TYR cc_start: 0.8060 (m-80) cc_final: 0.7611 (m-80) REVERT: B 311 CYS cc_start: 0.4196 (p) cc_final: 0.3503 (m) REVERT: B 313 LEU cc_start: 0.8244 (mt) cc_final: 0.7903 (pt) REVERT: B 320 GLN cc_start: 0.7051 (mt0) cc_final: 0.6747 (mt0) REVERT: B 351 ARG cc_start: 0.7879 (mmp80) cc_final: 0.7674 (tpp-160) REVERT: B 364 PHE cc_start: 0.8675 (m-80) cc_final: 0.7961 (m-80) REVERT: B 376 PHE cc_start: 0.8124 (m-10) cc_final: 0.7859 (m-10) REVERT: B 407 THR cc_start: 0.7876 (p) cc_final: 0.7408 (m) REVERT: B 411 TYR cc_start: 0.7301 (t80) cc_final: 0.6477 (t80) REVERT: B 420 PRO cc_start: 0.8552 (Cg_endo) cc_final: 0.8054 (Cg_exo) REVERT: B 421 ASP cc_start: 0.7613 (p0) cc_final: 0.7345 (p0) REVERT: B 426 GLN cc_start: 0.8039 (pt0) cc_final: 0.7245 (pp30) REVERT: B 430 VAL cc_start: 0.7767 (p) cc_final: 0.7549 (t) REVERT: B 436 LEU cc_start: 0.8035 (mt) cc_final: 0.7668 (mp) REVERT: B 444 THR cc_start: 0.7619 (m) cc_final: 0.7132 (m) REVERT: B 452 TRP cc_start: 0.7890 (p90) cc_final: 0.7317 (p90) REVERT: B 455 LEU cc_start: 0.7148 (mt) cc_final: 0.6893 (mt) REVERT: B 481 PRO cc_start: 0.8080 (Cg_endo) cc_final: 0.7497 (Cg_exo) REVERT: B 482 TRP cc_start: 0.8571 (m100) cc_final: 0.8026 (m100) REVERT: B 483 ASP cc_start: 0.8431 (m-30) cc_final: 0.7715 (t0) REVERT: B 486 PHE cc_start: 0.8534 (m-10) cc_final: 0.7949 (m-10) REVERT: B 487 ARG cc_start: 0.7789 (mmt90) cc_final: 0.7358 (mtt90) REVERT: B 488 ASN cc_start: 0.8082 (t0) cc_final: 0.7500 (t0) REVERT: B 491 GLN cc_start: 0.6128 (mt0) cc_final: 0.5872 (mt0) REVERT: B 493 LEU cc_start: 0.8195 (tp) cc_final: 0.7567 (tp) REVERT: B 494 LEU cc_start: 0.8679 (mt) cc_final: 0.8469 (mt) REVERT: B 527 GLN cc_start: 0.7111 (pm20) cc_final: 0.6051 (pm20) REVERT: B 556 ASN cc_start: 0.8240 (t0) cc_final: 0.7580 (t0) REVERT: B 577 PHE cc_start: 0.8316 (m-80) cc_final: 0.7878 (m-80) REVERT: B 580 GLU cc_start: 0.8385 (tp30) cc_final: 0.7970 (tp30) REVERT: A 29 LYS cc_start: 0.7648 (pttm) cc_final: 0.7082 (pttm) REVERT: A 36 ASN cc_start: 0.8475 (p0) cc_final: 0.8156 (p0) REVERT: A 46 ASP cc_start: 0.7173 (t70) cc_final: 0.6541 (t70) REVERT: A 47 HIS cc_start: 0.8014 (t70) cc_final: 0.6935 (t70) REVERT: A 51 LEU cc_start: 0.8925 (tp) cc_final: 0.8637 (tp) REVERT: A 55 PHE cc_start: 0.7878 (m-10) cc_final: 0.7557 (m-10) REVERT: A 61 VAL cc_start: 0.8329 (m) cc_final: 0.8087 (p) REVERT: A 67 ILE cc_start: 0.8341 (mt) cc_final: 0.8121 (mm) REVERT: A 74 TYR cc_start: 0.8143 (m-80) cc_final: 0.7091 (m-80) REVERT: A 77 SER cc_start: 0.8106 (m) cc_final: 0.6917 (p) REVERT: A 78 PHE cc_start: 0.8681 (p90) cc_final: 0.8300 (p90) REVERT: A 80 LYS cc_start: 0.8406 (mttm) cc_final: 0.8134 (mttm) REVERT: A 111 MET cc_start: 0.7072 (ttt) cc_final: 0.6509 (ttt) REVERT: A 132 LEU cc_start: 0.7657 (tp) cc_final: 0.7432 (tp) REVERT: A 142 GLU cc_start: 0.7151 (tt0) cc_final: 0.6802 (tt0) REVERT: A 163 GLN cc_start: 0.8343 (pt0) cc_final: 0.7953 (tt0) REVERT: A 172 PHE cc_start: 0.7864 (m-10) cc_final: 0.7563 (m-80) REVERT: A 173 LEU cc_start: 0.8035 (mt) cc_final: 0.7733 (mm) REVERT: A 176 MET cc_start: 0.8550 (ptp) cc_final: 0.8004 (ptp) REVERT: A 196 ASN cc_start: 0.8964 (m-40) cc_final: 0.8671 (m110) REVERT: A 209 LYS cc_start: 0.8232 (mttt) cc_final: 0.7655 (mtmm) REVERT: A 229 SER cc_start: 0.7960 (p) cc_final: 0.7560 (t) REVERT: A 230 ASP cc_start: 0.8195 (m-30) cc_final: 0.7478 (p0) REVERT: A 253 LYS cc_start: 0.8041 (tptm) cc_final: 0.7127 (tptm) REVERT: A 257 GLU cc_start: 0.8418 (mm-30) cc_final: 0.8052 (mm-30) REVERT: A 268 MET cc_start: 0.6226 (mtm) cc_final: 0.4908 (mtm) REVERT: A 277 MET cc_start: 0.6341 (mtt) cc_final: 0.5106 (mtt) REVERT: A 293 LYS cc_start: 0.7862 (mtpp) cc_final: 0.6913 (mtpp) REVERT: A 338 ASN cc_start: 0.7333 (p0) cc_final: 0.7028 (p0) REVERT: A 360 LYS cc_start: 0.8656 (tttt) cc_final: 0.8333 (tttt) REVERT: A 370 HIS cc_start: 0.7969 (m90) cc_final: 0.7759 (m90) REVERT: A 396 LYS cc_start: 0.8415 (tppp) cc_final: 0.7858 (tppp) REVERT: A 404 PHE cc_start: 0.7695 (p90) cc_final: 0.6844 (p90) REVERT: A 421 GLU cc_start: 0.8634 (tt0) cc_final: 0.7995 (tt0) REVERT: A 429 ARG cc_start: 0.8032 (mtt180) cc_final: 0.7483 (mtt-85) REVERT: A 432 GLN cc_start: 0.8597 (tp40) cc_final: 0.8057 (tp-100) REVERT: A 433 HIS cc_start: 0.8367 (m90) cc_final: 0.8076 (m90) REVERT: A 454 LYS cc_start: 0.8673 (mmtt) cc_final: 0.8149 (mmtt) REVERT: A 457 SER cc_start: 0.8078 (m) cc_final: 0.7740 (m) REVERT: A 476 ASN cc_start: 0.7816 (t0) cc_final: 0.6741 (t0) REVERT: A 479 LYS cc_start: 0.7869 (mtpt) cc_final: 0.6975 (mtpt) REVERT: A 486 GLN cc_start: 0.6837 (tm-30) cc_final: 0.6611 (tm-30) REVERT: A 487 LYS cc_start: 0.7874 (mtmm) cc_final: 0.7562 (mtmm) REVERT: A 489 LYS cc_start: 0.7729 (ttmm) cc_final: 0.7464 (mmmm) REVERT: A 496 GLU cc_start: 0.7480 (mp0) cc_final: 0.7161 (mp0) REVERT: A 551 GLU cc_start: 0.8686 (pt0) cc_final: 0.8266 (pm20) REVERT: A 554 GLU cc_start: 0.8479 (mt-10) cc_final: 0.8270 (mt-10) REVERT: A 559 HIS cc_start: 0.7604 (t70) cc_final: 0.7215 (t-170) REVERT: C 18 GLN cc_start: 0.8022 (tt0) cc_final: 0.7262 (tt0) REVERT: C 25 MET cc_start: 0.7773 (mmp) cc_final: 0.7477 (mmp) outliers start: 1 outliers final: 0 residues processed: 377 average time/residue: 0.0967 time to fit residues: 47.8350 Evaluate side-chains 354 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 354 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 80 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 113 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 HIS ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 393 GLN B 437 HIS ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 ASN A 435 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.123860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.098977 restraints weight = 16775.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.104213 restraints weight = 9524.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.107928 restraints weight = 6036.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.110590 restraints weight = 4127.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.112538 restraints weight = 2978.248| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6826 moved from start: 0.5437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9413 Z= 0.245 Angle : 0.745 9.324 12798 Z= 0.383 Chirality : 0.050 0.282 1417 Planarity : 0.005 0.055 1669 Dihedral : 7.894 84.131 1426 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.23 % Favored : 86.77 % Rotamer: Outliers : 0.10 % Allowed : 1.67 % Favored : 98.24 % 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 aren not related in a simple way. whole: -2.78 (0.23), residues: 1164 helix: -2.73 (0.57), residues: 60 sheet: -2.23 (0.63), residues: 60 loop : -1.98 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 190 TYR 0.017 0.002 TYR C 29 PHE 0.021 0.002 PHE C 44 TRP 0.057 0.003 TRP A 200 HIS 0.011 0.002 HIS A 507 Details of bonding type rmsd covalent geometry : bond 0.00475 ( 9358) covalent geometry : angle 0.72554 (12680) SS BOND : bond 0.00417 ( 47) SS BOND : angle 1.58522 ( 94) hydrogen bonds : bond 0.04140 ( 81) hydrogen bonds : angle 6.18424 ( 174) link_ALPHA1-3 : bond 0.02325 ( 1) link_ALPHA1-3 : angle 3.10635 ( 3) link_BETA1-3 : bond 0.00846 ( 1) link_BETA1-3 : angle 3.41128 ( 3) link_BETA1-4 : bond 0.00390 ( 2) link_BETA1-4 : angle 1.33275 ( 6) link_NAG-ASN : bond 0.00614 ( 4) link_NAG-ASN : angle 3.25425 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 378 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 GLN cc_start: 0.7004 (pp30) cc_final: 0.6444 (mm-40) REVERT: B 44 ASP cc_start: 0.7562 (t0) cc_final: 0.6746 (t0) REVERT: B 45 MET cc_start: 0.8437 (tmm) cc_final: 0.8085 (tmm) REVERT: B 46 LEU cc_start: 0.8631 (mt) cc_final: 0.8110 (mt) REVERT: B 47 ARG cc_start: 0.7932 (ttp80) cc_final: 0.7464 (ttp80) REVERT: B 55 VAL cc_start: 0.7933 (t) cc_final: 0.6957 (p) REVERT: B 59 ASN cc_start: 0.7169 (m-40) cc_final: 0.6703 (m-40) REVERT: B 61 GLU cc_start: 0.6958 (tm-30) cc_final: 0.6689 (tm-30) REVERT: B 65 LEU cc_start: 0.8309 (mt) cc_final: 0.8095 (mt) REVERT: B 100 ARG cc_start: 0.8176 (ttm-80) cc_final: 0.7796 (mmm-85) REVERT: B 103 ARG cc_start: 0.7407 (ttm-80) cc_final: 0.6958 (ttm110) REVERT: B 105 THR cc_start: 0.7986 (p) cc_final: 0.7721 (t) REVERT: B 106 GLN cc_start: 0.7801 (mt0) cc_final: 0.7493 (mp-120) REVERT: B 112 TYR cc_start: 0.7364 (m-80) cc_final: 0.7084 (m-80) REVERT: B 138 ARG cc_start: 0.7571 (mmm-85) cc_final: 0.6932 (mmm-85) REVERT: B 148 ILE cc_start: 0.7792 (mt) cc_final: 0.7529 (mm) REVERT: B 164 GLN cc_start: 0.8048 (mm-40) cc_final: 0.7843 (mp10) REVERT: B 169 TRP cc_start: 0.8413 (m100) cc_final: 0.7112 (m100) REVERT: B 182 THR cc_start: 0.7709 (p) cc_final: 0.7410 (p) REVERT: B 193 HIS cc_start: 0.7682 (m90) cc_final: 0.7192 (m90) REVERT: B 248 LYS cc_start: 0.8780 (mmtt) cc_final: 0.8045 (mmtt) REVERT: B 253 LEU cc_start: 0.7855 (mt) cc_final: 0.7624 (mt) REVERT: B 265 GLU cc_start: 0.6922 (pm20) cc_final: 0.6490 (pm20) REVERT: B 267 HIS cc_start: 0.7510 (m170) cc_final: 0.7283 (m170) REVERT: B 271 LEU cc_start: 0.8726 (mt) cc_final: 0.8483 (pt) REVERT: B 274 TYR cc_start: 0.6794 (t80) cc_final: 0.6352 (t80) REVERT: B 275 ASN cc_start: 0.8110 (t0) cc_final: 0.7826 (t0) REVERT: B 282 MET cc_start: 0.8178 (mtm) cc_final: 0.7945 (mtm) REVERT: B 286 GLU cc_start: 0.8409 (pp20) cc_final: 0.7690 (tm-30) REVERT: B 303 TYR cc_start: 0.8086 (m-80) cc_final: 0.7665 (m-80) REVERT: B 320 GLN cc_start: 0.7185 (mt0) cc_final: 0.6853 (mt0) REVERT: B 345 LEU cc_start: 0.8105 (mt) cc_final: 0.7698 (mt) REVERT: B 350 LEU cc_start: 0.7830 (mt) cc_final: 0.7519 (mt) REVERT: B 364 PHE cc_start: 0.8698 (m-80) cc_final: 0.8141 (m-80) REVERT: B 376 PHE cc_start: 0.8221 (m-10) cc_final: 0.7994 (m-10) REVERT: B 407 THR cc_start: 0.7880 (p) cc_final: 0.7474 (m) REVERT: B 411 TYR cc_start: 0.7323 (t80) cc_final: 0.6448 (t80) REVERT: B 444 THR cc_start: 0.7668 (m) cc_final: 0.7223 (m) REVERT: B 451 SER cc_start: 0.8107 (p) cc_final: 0.7752 (m) REVERT: B 452 TRP cc_start: 0.7984 (p90) cc_final: 0.7586 (p90) REVERT: B 481 PRO cc_start: 0.8038 (Cg_endo) cc_final: 0.7505 (Cg_exo) REVERT: B 483 ASP cc_start: 0.8446 (m-30) cc_final: 0.7562 (t0) REVERT: B 484 GLN cc_start: 0.8858 (mt0) cc_final: 0.8395 (mm-40) REVERT: B 487 ARG cc_start: 0.7790 (mmt90) cc_final: 0.6744 (ttm-80) REVERT: B 488 ASN cc_start: 0.8122 (t0) cc_final: 0.7508 (t0) REVERT: B 491 GLN cc_start: 0.6132 (mt0) cc_final: 0.5573 (mt0) REVERT: B 493 LEU cc_start: 0.8419 (tp) cc_final: 0.7876 (tp) REVERT: B 494 LEU cc_start: 0.8738 (mt) cc_final: 0.8168 (tt) REVERT: B 527 GLN cc_start: 0.7128 (pm20) cc_final: 0.6179 (pm20) REVERT: B 577 PHE cc_start: 0.8426 (m-80) cc_final: 0.7939 (m-80) REVERT: B 580 GLU cc_start: 0.8354 (tp30) cc_final: 0.8013 (tp30) REVERT: A 46 ASP cc_start: 0.7252 (t70) cc_final: 0.6662 (t70) REVERT: A 47 HIS cc_start: 0.8081 (t70) cc_final: 0.6977 (t70) REVERT: A 51 LEU cc_start: 0.9049 (tp) cc_final: 0.8770 (tp) REVERT: A 61 VAL cc_start: 0.8356 (m) cc_final: 0.8113 (p) REVERT: A 74 TYR cc_start: 0.8188 (m-80) cc_final: 0.7134 (m-80) REVERT: A 75 ASP cc_start: 0.7760 (t70) cc_final: 0.7552 (t0) REVERT: A 77 SER cc_start: 0.8111 (m) cc_final: 0.7887 (p) REVERT: A 88 TYR cc_start: 0.7259 (p90) cc_final: 0.6395 (p90) REVERT: A 111 MET cc_start: 0.7484 (ttt) cc_final: 0.7052 (ttt) REVERT: A 142 GLU cc_start: 0.7218 (tt0) cc_final: 0.6885 (tt0) REVERT: A 149 ARG cc_start: 0.5674 (ttm-80) cc_final: 0.5319 (ttm170) REVERT: A 172 PHE cc_start: 0.7747 (m-10) cc_final: 0.7535 (m-10) REVERT: A 173 LEU cc_start: 0.8019 (mt) cc_final: 0.7800 (mt) REVERT: A 176 MET cc_start: 0.8602 (ptp) cc_final: 0.8175 (ptp) REVERT: A 196 ASN cc_start: 0.8952 (m-40) cc_final: 0.8640 (m110) REVERT: A 209 LYS cc_start: 0.8216 (mttt) cc_final: 0.7718 (mtmt) REVERT: A 212 LYS cc_start: 0.7831 (tttp) cc_final: 0.7600 (tttp) REVERT: A 229 SER cc_start: 0.8029 (p) cc_final: 0.7672 (t) REVERT: A 230 ASP cc_start: 0.8279 (m-30) cc_final: 0.7215 (p0) REVERT: A 257 GLU cc_start: 0.8529 (mm-30) cc_final: 0.8129 (mm-30) REVERT: A 261 LYS cc_start: 0.7522 (ptmt) cc_final: 0.7040 (ptmt) REVERT: A 262 ASP cc_start: 0.8418 (t0) cc_final: 0.8049 (t70) REVERT: A 268 MET cc_start: 0.6362 (mtm) cc_final: 0.4995 (mtm) REVERT: A 277 MET cc_start: 0.6437 (mtt) cc_final: 0.5141 (mtt) REVERT: A 293 LYS cc_start: 0.7824 (mtpp) cc_final: 0.6798 (mtpp) REVERT: A 340 ILE cc_start: 0.7266 (mp) cc_final: 0.6992 (mm) REVERT: A 345 PHE cc_start: 0.8400 (m-80) cc_final: 0.7714 (m-80) REVERT: A 360 LYS cc_start: 0.8708 (tttt) cc_final: 0.8406 (tttt) REVERT: A 396 LYS cc_start: 0.8461 (tppp) cc_final: 0.7896 (tppp) REVERT: A 404 PHE cc_start: 0.7751 (p90) cc_final: 0.6956 (p90) REVERT: A 407 ILE cc_start: 0.7969 (mm) cc_final: 0.7593 (tp) REVERT: A 417 LEU cc_start: 0.7832 (mt) cc_final: 0.7527 (mm) REVERT: A 421 GLU cc_start: 0.8618 (tt0) cc_final: 0.8042 (tt0) REVERT: A 429 ARG cc_start: 0.8067 (mtt180) cc_final: 0.7567 (mtt-85) REVERT: A 431 LYS cc_start: 0.8330 (mtmm) cc_final: 0.7829 (mtmm) REVERT: A 432 GLN cc_start: 0.8580 (tp40) cc_final: 0.8092 (tp-100) REVERT: A 433 HIS cc_start: 0.8329 (m90) cc_final: 0.8016 (m90) REVERT: A 454 LYS cc_start: 0.8726 (mmtt) cc_final: 0.8209 (mmtt) REVERT: A 457 SER cc_start: 0.8238 (m) cc_final: 0.7917 (m) REVERT: A 476 ASN cc_start: 0.7849 (t0) cc_final: 0.6785 (t0) REVERT: A 479 LYS cc_start: 0.7937 (mtpt) cc_final: 0.7042 (mtpt) REVERT: A 487 LYS cc_start: 0.7877 (mtmm) cc_final: 0.7576 (mtmm) REVERT: A 489 LYS cc_start: 0.7842 (ttmm) cc_final: 0.7576 (mtpp) REVERT: A 496 GLU cc_start: 0.7531 (mp0) cc_final: 0.7137 (mp0) REVERT: A 551 GLU cc_start: 0.8635 (pt0) cc_final: 0.8206 (pm20) REVERT: A 554 GLU cc_start: 0.8544 (mt-10) cc_final: 0.8289 (mt-10) REVERT: A 559 HIS cc_start: 0.7650 (t70) cc_final: 0.7271 (t-170) REVERT: C 18 GLN cc_start: 0.7947 (tt0) cc_final: 0.7319 (tt0) REVERT: C 25 MET cc_start: 0.7909 (mmp) cc_final: 0.7381 (mmp) outliers start: 1 outliers final: 0 residues processed: 378 average time/residue: 0.0981 time to fit residues: 49.0732 Evaluate side-chains 357 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 357 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 67 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 21 optimal weight: 0.0370 chunk 42 optimal weight: 0.9980 chunk 32 optimal weight: 0.4980 chunk 80 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 108 optimal weight: 0.0000 overall best weight: 0.4062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 83 GLN A 163 GLN A 280 ASN A 408 GLN A 435 GLN A 552 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.124532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.099651 restraints weight = 16798.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.104856 restraints weight = 9502.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.108579 restraints weight = 6017.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.111210 restraints weight = 4100.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.113116 restraints weight = 2962.527| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6782 moved from start: 0.5537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9413 Z= 0.140 Angle : 0.683 9.294 12798 Z= 0.342 Chirality : 0.048 0.265 1417 Planarity : 0.005 0.081 1669 Dihedral : 7.448 82.980 1426 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 0.20 % Allowed : 0.59 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.59 (0.24), residues: 1164 helix: -2.67 (0.57), residues: 66 sheet: -1.52 (0.64), residues: 71 loop : -1.86 (0.19), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 451 TYR 0.013 0.002 TYR A 113 PHE 0.021 0.002 PHE B 73 TRP 0.085 0.003 TRP A 200 HIS 0.019 0.001 HIS A 183 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 9358) covalent geometry : angle 0.66220 (12680) SS BOND : bond 0.00246 ( 47) SS BOND : angle 1.58634 ( 94) hydrogen bonds : bond 0.03381 ( 81) hydrogen bonds : angle 5.40969 ( 174) link_ALPHA1-3 : bond 0.02029 ( 1) link_ALPHA1-3 : angle 2.73928 ( 3) link_BETA1-3 : bond 0.00884 ( 1) link_BETA1-3 : angle 3.95760 ( 3) link_BETA1-4 : bond 0.00212 ( 2) link_BETA1-4 : angle 1.28643 ( 6) link_NAG-ASN : bond 0.00387 ( 4) link_NAG-ASN : angle 2.69021 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 371 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 GLN cc_start: 0.7423 (pp30) cc_final: 0.6631 (mm-40) REVERT: B 31 MET cc_start: 0.7620 (mtp) cc_final: 0.6639 (ptp) REVERT: B 44 ASP cc_start: 0.7429 (t0) cc_final: 0.6585 (t0) REVERT: B 45 MET cc_start: 0.8305 (tmm) cc_final: 0.8037 (tmm) REVERT: B 46 LEU cc_start: 0.8558 (mt) cc_final: 0.8107 (mt) REVERT: B 47 ARG cc_start: 0.7798 (ttp80) cc_final: 0.7290 (ttp80) REVERT: B 55 VAL cc_start: 0.7623 (t) cc_final: 0.7223 (p) REVERT: B 59 ASN cc_start: 0.7324 (m-40) cc_final: 0.6900 (m-40) REVERT: B 61 GLU cc_start: 0.7136 (tm-30) cc_final: 0.3709 (tm-30) REVERT: B 65 LEU cc_start: 0.8356 (mt) cc_final: 0.8084 (mt) REVERT: B 75 GLN cc_start: 0.7941 (pt0) cc_final: 0.7678 (pt0) REVERT: B 100 ARG cc_start: 0.8134 (ttm-80) cc_final: 0.7750 (mmm-85) REVERT: B 103 ARG cc_start: 0.7393 (ttm-80) cc_final: 0.6696 (mtp85) REVERT: B 106 GLN cc_start: 0.7769 (mt0) cc_final: 0.7462 (mp10) REVERT: B 112 TYR cc_start: 0.7151 (m-80) cc_final: 0.6864 (m-80) REVERT: B 139 GLU cc_start: 0.7196 (mp0) cc_final: 0.6989 (mp0) REVERT: B 182 THR cc_start: 0.7769 (p) cc_final: 0.7425 (p) REVERT: B 184 ILE cc_start: 0.8796 (mm) cc_final: 0.8565 (mm) REVERT: B 193 HIS cc_start: 0.7646 (m90) cc_final: 0.7171 (m90) REVERT: B 237 HIS cc_start: 0.7386 (t-90) cc_final: 0.7004 (t70) REVERT: B 248 LYS cc_start: 0.8710 (mmtt) cc_final: 0.8007 (mmtt) REVERT: B 265 GLU cc_start: 0.7040 (pm20) cc_final: 0.6266 (pm20) REVERT: B 267 HIS cc_start: 0.7730 (m170) cc_final: 0.7192 (m170) REVERT: B 271 LEU cc_start: 0.8658 (mt) cc_final: 0.8422 (pt) REVERT: B 274 TYR cc_start: 0.6701 (t80) cc_final: 0.6301 (t80) REVERT: B 286 GLU cc_start: 0.8342 (pp20) cc_final: 0.7570 (tm-30) REVERT: B 303 TYR cc_start: 0.8023 (m-80) cc_final: 0.7646 (m-80) REVERT: B 320 GLN cc_start: 0.7149 (mt0) cc_final: 0.6774 (mt0) REVERT: B 345 LEU cc_start: 0.8238 (mt) cc_final: 0.7897 (mt) REVERT: B 364 PHE cc_start: 0.8662 (m-80) cc_final: 0.8161 (m-80) REVERT: B 376 PHE cc_start: 0.8096 (m-10) cc_final: 0.7800 (m-10) REVERT: B 405 GLU cc_start: 0.6160 (tp30) cc_final: 0.5520 (tp30) REVERT: B 407 THR cc_start: 0.7989 (p) cc_final: 0.6342 (m) REVERT: B 411 TYR cc_start: 0.7187 (t80) cc_final: 0.5641 (t80) REVERT: B 421 ASP cc_start: 0.7540 (p0) cc_final: 0.7328 (p0) REVERT: B 426 GLN cc_start: 0.7990 (pt0) cc_final: 0.7419 (pp30) REVERT: B 427 ASN cc_start: 0.8290 (m-40) cc_final: 0.7883 (m-40) REVERT: B 430 VAL cc_start: 0.7936 (t) cc_final: 0.7157 (p) REVERT: B 444 THR cc_start: 0.7665 (m) cc_final: 0.6157 (m) REVERT: B 446 GLN cc_start: 0.6829 (mt0) cc_final: 0.6435 (mt0) REVERT: B 451 SER cc_start: 0.8232 (p) cc_final: 0.7817 (m) REVERT: B 452 TRP cc_start: 0.7845 (p90) cc_final: 0.7559 (p90) REVERT: B 467 LEU cc_start: 0.7392 (tp) cc_final: 0.6477 (pt) REVERT: B 481 PRO cc_start: 0.8071 (Cg_endo) cc_final: 0.7527 (Cg_exo) REVERT: B 483 ASP cc_start: 0.8377 (m-30) cc_final: 0.7686 (t0) REVERT: B 487 ARG cc_start: 0.7858 (mmt90) cc_final: 0.7486 (mmt90) REVERT: B 488 ASN cc_start: 0.8164 (t0) cc_final: 0.7587 (t0) REVERT: B 491 GLN cc_start: 0.6212 (mt0) cc_final: 0.5626 (mt0) REVERT: B 527 GLN cc_start: 0.7208 (pm20) cc_final: 0.6433 (pm20) REVERT: B 577 PHE cc_start: 0.8501 (m-80) cc_final: 0.7986 (m-80) REVERT: B 580 GLU cc_start: 0.8328 (tp30) cc_final: 0.7971 (tp30) REVERT: A 45 GLU cc_start: 0.8351 (mp0) cc_final: 0.7968 (mp0) REVERT: A 46 ASP cc_start: 0.7229 (t70) cc_final: 0.6644 (t70) REVERT: A 47 HIS cc_start: 0.7916 (t70) cc_final: 0.6843 (t70) REVERT: A 51 LEU cc_start: 0.8995 (tp) cc_final: 0.8566 (tp) REVERT: A 55 PHE cc_start: 0.7964 (m-10) cc_final: 0.7490 (m-10) REVERT: A 61 VAL cc_start: 0.8266 (m) cc_final: 0.7992 (p) REVERT: A 74 TYR cc_start: 0.8131 (m-80) cc_final: 0.7104 (m-80) REVERT: A 78 PHE cc_start: 0.8695 (p90) cc_final: 0.8376 (p90) REVERT: A 102 GLU cc_start: 0.7478 (mt-10) cc_final: 0.6933 (mt-10) REVERT: A 111 MET cc_start: 0.7484 (ttt) cc_final: 0.6674 (ttt) REVERT: A 112 TYR cc_start: 0.7077 (m-80) cc_final: 0.6168 (m-10) REVERT: A 114 GLU cc_start: 0.7338 (tt0) cc_final: 0.6713 (tt0) REVERT: A 156 LEU cc_start: 0.8334 (mt) cc_final: 0.8086 (mt) REVERT: A 163 GLN cc_start: 0.8548 (tt0) cc_final: 0.8222 (tt0) REVERT: A 176 MET cc_start: 0.8619 (ptp) cc_final: 0.8138 (ptp) REVERT: A 196 ASN cc_start: 0.8846 (m-40) cc_final: 0.8564 (m110) REVERT: A 209 LYS cc_start: 0.8090 (mttt) cc_final: 0.7593 (mtmm) REVERT: A 212 LYS cc_start: 0.7763 (tttp) cc_final: 0.7522 (tttp) REVERT: A 230 ASP cc_start: 0.8190 (m-30) cc_final: 0.7244 (p0) REVERT: A 257 GLU cc_start: 0.8608 (mm-30) cc_final: 0.8077 (mm-30) REVERT: A 261 LYS cc_start: 0.7628 (ptmt) cc_final: 0.7110 (ptmt) REVERT: A 262 ASP cc_start: 0.8394 (t0) cc_final: 0.7513 (t0) REVERT: A 268 MET cc_start: 0.6283 (mtm) cc_final: 0.4829 (mtm) REVERT: A 277 MET cc_start: 0.6373 (mtt) cc_final: 0.5088 (mtt) REVERT: A 293 LYS cc_start: 0.7835 (mtpp) cc_final: 0.6869 (mtpp) REVERT: A 298 ASN cc_start: 0.8741 (p0) cc_final: 0.8442 (p0) REVERT: A 338 ASN cc_start: 0.7391 (p0) cc_final: 0.5982 (p0) REVERT: A 340 ILE cc_start: 0.7254 (mp) cc_final: 0.6985 (mp) REVERT: A 345 PHE cc_start: 0.8370 (m-80) cc_final: 0.7832 (m-80) REVERT: A 358 HIS cc_start: 0.8492 (m-70) cc_final: 0.8240 (m-70) REVERT: A 360 LYS cc_start: 0.8657 (tttt) cc_final: 0.8374 (tttt) REVERT: A 396 LYS cc_start: 0.8396 (tppp) cc_final: 0.7819 (tppp) REVERT: A 404 PHE cc_start: 0.7768 (p90) cc_final: 0.7104 (p90) REVERT: A 417 LEU cc_start: 0.7685 (mt) cc_final: 0.7353 (mt) REVERT: A 421 GLU cc_start: 0.8641 (tt0) cc_final: 0.8008 (tt0) REVERT: A 429 ARG cc_start: 0.8044 (mtt180) cc_final: 0.7487 (mtt-85) REVERT: A 431 LYS cc_start: 0.8314 (mtmm) cc_final: 0.7832 (mtmm) REVERT: A 432 GLN cc_start: 0.8546 (tp40) cc_final: 0.8125 (tp-100) REVERT: A 433 HIS cc_start: 0.8169 (m90) cc_final: 0.7902 (m90) REVERT: A 441 VAL cc_start: 0.7950 (p) cc_final: 0.7183 (p) REVERT: A 451 ARG cc_start: 0.7613 (ptp-110) cc_final: 0.7268 (ptp-170) REVERT: A 454 LYS cc_start: 0.8724 (mmtt) cc_final: 0.8225 (mmtt) REVERT: A 457 SER cc_start: 0.8111 (m) cc_final: 0.7217 (t) REVERT: A 476 ASN cc_start: 0.7828 (t0) cc_final: 0.6879 (t0) REVERT: A 479 LYS cc_start: 0.7884 (mtpt) cc_final: 0.6974 (mtpt) REVERT: A 487 LYS cc_start: 0.7843 (mtmm) cc_final: 0.7447 (mtmm) REVERT: A 496 GLU cc_start: 0.7510 (mp0) cc_final: 0.7113 (mp0) REVERT: A 551 GLU cc_start: 0.8581 (pt0) cc_final: 0.8198 (pm20) REVERT: A 552 ASN cc_start: 0.8813 (OUTLIER) cc_final: 0.7894 (p0) REVERT: A 554 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8236 (mt-10) REVERT: A 559 HIS cc_start: 0.7600 (t70) cc_final: 0.7238 (t-170) REVERT: C 18 GLN cc_start: 0.7954 (tt0) cc_final: 0.7355 (tt0) REVERT: C 25 MET cc_start: 0.7795 (mmp) cc_final: 0.7300 (mmp) outliers start: 2 outliers final: 0 residues processed: 371 average time/residue: 0.0997 time to fit residues: 48.9880 Evaluate side-chains 360 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 359 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 11 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 105 optimal weight: 0.2980 chunk 82 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 113 optimal weight: 0.6980 chunk 84 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 GLN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 HIS ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 83 GLN A 280 ASN ** A 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.121951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.097775 restraints weight = 16746.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.102781 restraints weight = 9466.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.106368 restraints weight = 6013.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.108840 restraints weight = 4102.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.110718 restraints weight = 2976.216| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6828 moved from start: 0.5855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9413 Z= 0.203 Angle : 0.744 10.252 12798 Z= 0.376 Chirality : 0.050 0.261 1417 Planarity : 0.006 0.104 1669 Dihedral : 7.553 80.249 1426 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.68 % Favored : 88.32 % Rotamer: Outliers : 0.10 % Allowed : 1.08 % Favored : 98.82 % 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 aren not related in a simple way. whole: -2.66 (0.23), residues: 1164 helix: -2.78 (0.55), residues: 66 sheet: -1.74 (0.62), residues: 72 loop : -1.89 (0.19), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 226 TYR 0.017 0.002 TYR A 125 PHE 0.021 0.002 PHE B 73 TRP 0.071 0.003 TRP A 200 HIS 0.015 0.002 HIS A 183 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 9358) covalent geometry : angle 0.72378 (12680) SS BOND : bond 0.00399 ( 47) SS BOND : angle 1.61308 ( 94) hydrogen bonds : bond 0.03604 ( 81) hydrogen bonds : angle 5.71262 ( 174) link_ALPHA1-3 : bond 0.02261 ( 1) link_ALPHA1-3 : angle 3.20635 ( 3) link_BETA1-3 : bond 0.00859 ( 1) link_BETA1-3 : angle 3.72165 ( 3) link_BETA1-4 : bond 0.00257 ( 2) link_BETA1-4 : angle 1.27583 ( 6) link_NAG-ASN : bond 0.00399 ( 4) link_NAG-ASN : angle 2.97013 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 379 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 MET cc_start: 0.7684 (mtp) cc_final: 0.6698 (ptp) REVERT: B 44 ASP cc_start: 0.7532 (t0) cc_final: 0.6739 (t0) REVERT: B 45 MET cc_start: 0.8387 (tmm) cc_final: 0.8026 (tmm) REVERT: B 46 LEU cc_start: 0.8651 (mt) cc_final: 0.8099 (mt) REVERT: B 47 ARG cc_start: 0.7846 (ttp80) cc_final: 0.7409 (ttp80) REVERT: B 54 GLN cc_start: 0.7147 (mp10) cc_final: 0.6834 (mp10) REVERT: B 55 VAL cc_start: 0.7784 (t) cc_final: 0.7322 (p) REVERT: B 59 ASN cc_start: 0.7411 (m-40) cc_final: 0.6987 (m-40) REVERT: B 61 GLU cc_start: 0.7099 (tm-30) cc_final: 0.3826 (tm-30) REVERT: B 65 LEU cc_start: 0.8378 (mt) cc_final: 0.8066 (mt) REVERT: B 75 GLN cc_start: 0.8004 (pt0) cc_final: 0.7764 (pt0) REVERT: B 97 GLN cc_start: 0.7857 (mp10) cc_final: 0.7270 (mp10) REVERT: B 100 ARG cc_start: 0.8192 (ttm-80) cc_final: 0.7710 (mmm-85) REVERT: B 103 ARG cc_start: 0.7451 (ttm-80) cc_final: 0.6780 (mtp85) REVERT: B 112 TYR cc_start: 0.7425 (m-80) cc_final: 0.7006 (m-80) REVERT: B 139 GLU cc_start: 0.7339 (mp0) cc_final: 0.7114 (mp0) REVERT: B 154 LEU cc_start: 0.7732 (tt) cc_final: 0.7422 (tp) REVERT: B 182 THR cc_start: 0.7703 (p) cc_final: 0.7356 (p) REVERT: B 184 ILE cc_start: 0.8745 (mm) cc_final: 0.8518 (mm) REVERT: B 190 ARG cc_start: 0.6738 (ttp-110) cc_final: 0.6336 (ttp80) REVERT: B 193 HIS cc_start: 0.7757 (m90) cc_final: 0.7354 (m90) REVERT: B 211 ASP cc_start: 0.8093 (m-30) cc_final: 0.7821 (m-30) REVERT: B 213 GLN cc_start: 0.8039 (tm-30) cc_final: 0.7575 (tm-30) REVERT: B 233 THR cc_start: 0.7907 (m) cc_final: 0.7656 (t) REVERT: B 237 HIS cc_start: 0.7358 (t-90) cc_final: 0.7148 (t-90) REVERT: B 248 LYS cc_start: 0.8754 (mmtt) cc_final: 0.8058 (mmtt) REVERT: B 265 GLU cc_start: 0.6877 (pm20) cc_final: 0.6388 (pm20) REVERT: B 267 HIS cc_start: 0.7782 (m170) cc_final: 0.7212 (m170) REVERT: B 271 LEU cc_start: 0.8681 (mt) cc_final: 0.8461 (pt) REVERT: B 274 TYR cc_start: 0.6595 (t80) cc_final: 0.6262 (t80) REVERT: B 286 GLU cc_start: 0.8377 (pp20) cc_final: 0.7628 (tm-30) REVERT: B 303 TYR cc_start: 0.8037 (m-80) cc_final: 0.7643 (m-80) REVERT: B 320 GLN cc_start: 0.7170 (mt0) cc_final: 0.6789 (mt0) REVERT: B 323 THR cc_start: 0.7534 (t) cc_final: 0.7187 (p) REVERT: B 345 LEU cc_start: 0.8249 (mt) cc_final: 0.7867 (mt) REVERT: B 364 PHE cc_start: 0.8747 (m-80) cc_final: 0.8264 (m-80) REVERT: B 376 PHE cc_start: 0.8133 (m-10) cc_final: 0.7770 (m-10) REVERT: B 405 GLU cc_start: 0.6121 (tp30) cc_final: 0.5496 (tp30) REVERT: B 407 THR cc_start: 0.7956 (p) cc_final: 0.6692 (m) REVERT: B 411 TYR cc_start: 0.7283 (t80) cc_final: 0.5817 (t80) REVERT: B 421 ASP cc_start: 0.7673 (p0) cc_final: 0.7379 (p0) REVERT: B 426 GLN cc_start: 0.7944 (pt0) cc_final: 0.7246 (pt0) REVERT: B 430 VAL cc_start: 0.7824 (t) cc_final: 0.6994 (p) REVERT: B 444 THR cc_start: 0.7668 (m) cc_final: 0.6336 (m) REVERT: B 446 GLN cc_start: 0.6898 (mt0) cc_final: 0.6511 (mt0) REVERT: B 452 TRP cc_start: 0.7920 (p90) cc_final: 0.7422 (p90) REVERT: B 455 LEU cc_start: 0.7255 (mt) cc_final: 0.6973 (mt) REVERT: B 467 LEU cc_start: 0.7616 (tp) cc_final: 0.6634 (pt) REVERT: B 481 PRO cc_start: 0.8033 (Cg_endo) cc_final: 0.7545 (Cg_exo) REVERT: B 482 TRP cc_start: 0.8456 (m100) cc_final: 0.8087 (m100) REVERT: B 483 ASP cc_start: 0.8357 (m-30) cc_final: 0.7658 (t0) REVERT: B 487 ARG cc_start: 0.7833 (mmt90) cc_final: 0.6800 (ttm-80) REVERT: B 488 ASN cc_start: 0.8224 (t0) cc_final: 0.7646 (t0) REVERT: B 491 GLN cc_start: 0.6233 (mt0) cc_final: 0.5665 (mt0) REVERT: B 493 LEU cc_start: 0.8440 (tp) cc_final: 0.7872 (tp) REVERT: B 494 LEU cc_start: 0.8695 (mt) cc_final: 0.8369 (tt) REVERT: B 520 CYS cc_start: 0.4125 (t) cc_final: 0.3852 (m) REVERT: B 577 PHE cc_start: 0.8472 (m-80) cc_final: 0.7981 (m-80) REVERT: A 45 GLU cc_start: 0.8415 (mp0) cc_final: 0.8037 (mp0) REVERT: A 46 ASP cc_start: 0.7243 (t70) cc_final: 0.6692 (t70) REVERT: A 47 HIS cc_start: 0.7917 (t70) cc_final: 0.6820 (t70) REVERT: A 51 LEU cc_start: 0.9015 (tp) cc_final: 0.8578 (tp) REVERT: A 55 PHE cc_start: 0.7906 (m-10) cc_final: 0.7532 (m-10) REVERT: A 74 TYR cc_start: 0.8156 (m-80) cc_final: 0.7079 (m-80) REVERT: A 76 LEU cc_start: 0.8288 (mt) cc_final: 0.8082 (mt) REVERT: A 78 PHE cc_start: 0.8784 (p90) cc_final: 0.8458 (p90) REVERT: A 102 GLU cc_start: 0.7579 (mt-10) cc_final: 0.6991 (mt-10) REVERT: A 111 MET cc_start: 0.7530 (ttt) cc_final: 0.6744 (ttt) REVERT: A 112 TYR cc_start: 0.7190 (m-80) cc_final: 0.6005 (m-10) REVERT: A 114 GLU cc_start: 0.7469 (tt0) cc_final: 0.6793 (tt0) REVERT: A 142 GLU cc_start: 0.7210 (tt0) cc_final: 0.6975 (tt0) REVERT: A 156 LEU cc_start: 0.8319 (mt) cc_final: 0.8075 (mt) REVERT: A 163 GLN cc_start: 0.8648 (tt0) cc_final: 0.8189 (tt0) REVERT: A 166 ASP cc_start: 0.7815 (p0) cc_final: 0.7612 (p0) REVERT: A 173 LEU cc_start: 0.8160 (mt) cc_final: 0.7939 (mt) REVERT: A 196 ASN cc_start: 0.8847 (m-40) cc_final: 0.8579 (m110) REVERT: A 209 LYS cc_start: 0.8127 (mttt) cc_final: 0.7655 (mtmt) REVERT: A 261 LYS cc_start: 0.7732 (ptmt) cc_final: 0.7169 (ptmt) REVERT: A 262 ASP cc_start: 0.8378 (t0) cc_final: 0.7494 (t0) REVERT: A 268 MET cc_start: 0.6351 (mtm) cc_final: 0.4906 (mtm) REVERT: A 277 MET cc_start: 0.6376 (mtt) cc_final: 0.5144 (mtt) REVERT: A 298 ASN cc_start: 0.8838 (p0) cc_final: 0.8539 (p0) REVERT: A 338 ASN cc_start: 0.7369 (p0) cc_final: 0.6209 (p0) REVERT: A 340 ILE cc_start: 0.7312 (mp) cc_final: 0.7051 (mp) REVERT: A 345 PHE cc_start: 0.8349 (m-80) cc_final: 0.7841 (m-80) REVERT: A 358 HIS cc_start: 0.8500 (m-70) cc_final: 0.8215 (m-70) REVERT: A 360 LYS cc_start: 0.8614 (tttt) cc_final: 0.8341 (tttt) REVERT: A 396 LYS cc_start: 0.8431 (tppp) cc_final: 0.7837 (tppp) REVERT: A 404 PHE cc_start: 0.7746 (p90) cc_final: 0.6899 (p90) REVERT: A 407 ILE cc_start: 0.7597 (mm) cc_final: 0.7181 (tp) REVERT: A 408 GLN cc_start: 0.7105 (mm-40) cc_final: 0.6743 (mm110) REVERT: A 420 PHE cc_start: 0.8364 (m-80) cc_final: 0.8163 (m-80) REVERT: A 421 GLU cc_start: 0.8644 (tt0) cc_final: 0.8072 (tt0) REVERT: A 429 ARG cc_start: 0.8016 (mtt180) cc_final: 0.7575 (mtt-85) REVERT: A 431 LYS cc_start: 0.8282 (mtmm) cc_final: 0.7758 (mtmm) REVERT: A 432 GLN cc_start: 0.8461 (tp40) cc_final: 0.8082 (tp-100) REVERT: A 433 HIS cc_start: 0.8156 (m90) cc_final: 0.7816 (m90) REVERT: A 451 ARG cc_start: 0.7834 (ptp-110) cc_final: 0.7549 (ptp-170) REVERT: A 454 LYS cc_start: 0.8730 (mmtt) cc_final: 0.8217 (mmtt) REVERT: A 457 SER cc_start: 0.8104 (m) cc_final: 0.7357 (t) REVERT: A 476 ASN cc_start: 0.7905 (t0) cc_final: 0.7039 (t0) REVERT: A 479 LYS cc_start: 0.7963 (mtpt) cc_final: 0.7059 (mtpt) REVERT: A 487 LYS cc_start: 0.7908 (mtmm) cc_final: 0.7609 (mtmm) REVERT: A 496 GLU cc_start: 0.7458 (mp0) cc_final: 0.7081 (mp0) REVERT: A 552 ASN cc_start: 0.8921 (p0) cc_final: 0.8105 (p0) REVERT: A 554 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8254 (mt-10) REVERT: A 559 HIS cc_start: 0.7637 (t70) cc_final: 0.7127 (t-170) REVERT: C 18 GLN cc_start: 0.7962 (tt0) cc_final: 0.7436 (tt0) REVERT: C 25 MET cc_start: 0.7861 (mmp) cc_final: 0.7344 (mmp) REVERT: C 44 PHE cc_start: 0.8180 (m-80) cc_final: 0.7764 (m-80) outliers start: 1 outliers final: 0 residues processed: 379 average time/residue: 0.0992 time to fit residues: 49.6597 Evaluate side-chains 358 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 358 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 18 optimal weight: 0.4980 chunk 87 optimal weight: 0.4980 chunk 55 optimal weight: 0.0470 chunk 110 optimal weight: 0.6980 chunk 105 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 114 optimal weight: 0.3980 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 GLN ** B 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 GLN A 280 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.123755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.098907 restraints weight = 16706.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.104036 restraints weight = 9426.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.107760 restraints weight = 5971.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.110360 restraints weight = 4074.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.112253 restraints weight = 2946.274| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6793 moved from start: 0.5925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9413 Z= 0.151 Angle : 0.718 9.358 12798 Z= 0.361 Chirality : 0.049 0.269 1417 Planarity : 0.005 0.063 1669 Dihedral : 7.401 79.042 1426 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.14 % Favored : 89.86 % Rotamer: Outliers : 0.10 % Allowed : 0.39 % Favored : 99.51 % 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 aren not related in a simple way. whole: -2.58 (0.24), residues: 1164 helix: -2.68 (0.56), residues: 66 sheet: -1.60 (0.60), residues: 77 loop : -1.84 (0.19), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 252 TYR 0.023 0.002 TYR B 64 PHE 0.018 0.001 PHE B 73 TRP 0.056 0.003 TRP A 200 HIS 0.010 0.001 HIS A 183 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 9358) covalent geometry : angle 0.69984 (12680) SS BOND : bond 0.00339 ( 47) SS BOND : angle 1.53016 ( 94) hydrogen bonds : bond 0.03331 ( 81) hydrogen bonds : angle 5.51051 ( 174) link_ALPHA1-3 : bond 0.02165 ( 1) link_ALPHA1-3 : angle 3.08406 ( 3) link_BETA1-3 : bond 0.01124 ( 1) link_BETA1-3 : angle 3.88880 ( 3) link_BETA1-4 : bond 0.00384 ( 2) link_BETA1-4 : angle 1.24744 ( 6) link_NAG-ASN : bond 0.00337 ( 4) link_NAG-ASN : angle 2.71923 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 370 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 GLN cc_start: 0.7261 (pp30) cc_final: 0.6760 (mm-40) REVERT: B 31 MET cc_start: 0.7691 (mtp) cc_final: 0.6745 (ptp) REVERT: B 44 ASP cc_start: 0.7442 (t0) cc_final: 0.6633 (t0) REVERT: B 45 MET cc_start: 0.8315 (tmm) cc_final: 0.8015 (tmm) REVERT: B 46 LEU cc_start: 0.8626 (mt) cc_final: 0.8137 (mt) REVERT: B 47 ARG cc_start: 0.7823 (ttp80) cc_final: 0.7360 (ttp80) REVERT: B 55 VAL cc_start: 0.7836 (t) cc_final: 0.7459 (p) REVERT: B 59 ASN cc_start: 0.7383 (m-40) cc_final: 0.6965 (m-40) REVERT: B 61 GLU cc_start: 0.7082 (tm-30) cc_final: 0.3863 (tm-30) REVERT: B 65 LEU cc_start: 0.8361 (mt) cc_final: 0.8099 (mt) REVERT: B 75 GLN cc_start: 0.7947 (pt0) cc_final: 0.7728 (pt0) REVERT: B 97 GLN cc_start: 0.7750 (mp10) cc_final: 0.7345 (mp10) REVERT: B 100 ARG cc_start: 0.8170 (ttm-80) cc_final: 0.7633 (mmm-85) REVERT: B 112 TYR cc_start: 0.7222 (m-80) cc_final: 0.6747 (m-80) REVERT: B 143 ARG cc_start: 0.7602 (mpp80) cc_final: 0.7401 (mpp80) REVERT: B 156 GLN cc_start: 0.7843 (tm-30) cc_final: 0.6566 (tm-30) REVERT: B 157 ARG cc_start: 0.7773 (mtm-85) cc_final: 0.7463 (mtm-85) REVERT: B 173 PHE cc_start: 0.7036 (m-10) cc_final: 0.6814 (m-10) REVERT: B 182 THR cc_start: 0.7749 (p) cc_final: 0.7460 (p) REVERT: B 184 ILE cc_start: 0.8795 (mm) cc_final: 0.8553 (mm) REVERT: B 185 ASP cc_start: 0.6549 (t0) cc_final: 0.5806 (t0) REVERT: B 193 HIS cc_start: 0.7863 (m90) cc_final: 0.7474 (m90) REVERT: B 211 ASP cc_start: 0.8174 (m-30) cc_final: 0.7931 (m-30) REVERT: B 213 GLN cc_start: 0.8108 (tm-30) cc_final: 0.7781 (tm-30) REVERT: B 237 HIS cc_start: 0.7375 (t-90) cc_final: 0.6707 (t-90) REVERT: B 239 GLN cc_start: 0.7826 (mm110) cc_final: 0.7513 (mp10) REVERT: B 248 LYS cc_start: 0.8704 (mmtt) cc_final: 0.7972 (mmtt) REVERT: B 267 HIS cc_start: 0.7774 (m170) cc_final: 0.7297 (m170) REVERT: B 271 LEU cc_start: 0.8715 (mt) cc_final: 0.8489 (pt) REVERT: B 274 TYR cc_start: 0.6520 (t80) cc_final: 0.6236 (t80) REVERT: B 286 GLU cc_start: 0.8469 (pp20) cc_final: 0.7559 (tm-30) REVERT: B 303 TYR cc_start: 0.8035 (m-80) cc_final: 0.7632 (m-80) REVERT: B 320 GLN cc_start: 0.7117 (mt0) cc_final: 0.6705 (mt0) REVERT: B 323 THR cc_start: 0.7563 (t) cc_final: 0.7215 (p) REVERT: B 345 LEU cc_start: 0.8289 (mt) cc_final: 0.7963 (mt) REVERT: B 364 PHE cc_start: 0.8733 (m-80) cc_final: 0.8325 (m-80) REVERT: B 376 PHE cc_start: 0.8081 (m-10) cc_final: 0.7717 (m-10) REVERT: B 393 GLN cc_start: 0.7680 (mp10) cc_final: 0.7424 (mp10) REVERT: B 405 GLU cc_start: 0.6091 (tp30) cc_final: 0.5523 (tp30) REVERT: B 411 TYR cc_start: 0.7203 (t80) cc_final: 0.6408 (t80) REVERT: B 430 VAL cc_start: 0.7822 (t) cc_final: 0.6975 (p) REVERT: B 444 THR cc_start: 0.7605 (m) cc_final: 0.7049 (m) REVERT: B 452 TRP cc_start: 0.7888 (p90) cc_final: 0.7200 (p90) REVERT: B 481 PRO cc_start: 0.8071 (Cg_endo) cc_final: 0.7576 (Cg_exo) REVERT: B 482 TRP cc_start: 0.8449 (m100) cc_final: 0.8061 (m100) REVERT: B 483 ASP cc_start: 0.8355 (m-30) cc_final: 0.7646 (t0) REVERT: B 487 ARG cc_start: 0.7871 (mmt90) cc_final: 0.6802 (ttm-80) REVERT: B 488 ASN cc_start: 0.8216 (t0) cc_final: 0.7239 (t0) REVERT: B 491 GLN cc_start: 0.6291 (mt0) cc_final: 0.5736 (mt0) REVERT: B 493 LEU cc_start: 0.8321 (tp) cc_final: 0.7841 (tp) REVERT: B 494 LEU cc_start: 0.8704 (mt) cc_final: 0.8494 (mt) REVERT: B 520 CYS cc_start: 0.4393 (t) cc_final: 0.3845 (m) REVERT: B 527 GLN cc_start: 0.6962 (pm20) cc_final: 0.6192 (pm20) REVERT: B 577 PHE cc_start: 0.8554 (m-80) cc_final: 0.8028 (m-80) REVERT: B 580 GLU cc_start: 0.8325 (tp30) cc_final: 0.7966 (tp30) REVERT: A 28 LYS cc_start: 0.7709 (mtmm) cc_final: 0.7126 (ptpp) REVERT: A 43 THR cc_start: 0.7451 (p) cc_final: 0.7229 (t) REVERT: A 44 PHE cc_start: 0.8263 (m-80) cc_final: 0.7872 (m-10) REVERT: A 45 GLU cc_start: 0.8411 (mp0) cc_final: 0.7947 (mp0) REVERT: A 46 ASP cc_start: 0.7226 (t70) cc_final: 0.6758 (t70) REVERT: A 47 HIS cc_start: 0.7851 (t70) cc_final: 0.6755 (t70) REVERT: A 51 LEU cc_start: 0.9028 (tp) cc_final: 0.8589 (tp) REVERT: A 55 PHE cc_start: 0.7954 (m-10) cc_final: 0.7692 (m-10) REVERT: A 74 TYR cc_start: 0.8107 (m-80) cc_final: 0.7142 (m-80) REVERT: A 75 ASP cc_start: 0.7797 (t70) cc_final: 0.7465 (t0) REVERT: A 76 LEU cc_start: 0.8249 (mt) cc_final: 0.8007 (mt) REVERT: A 77 SER cc_start: 0.8161 (p) cc_final: 0.7503 (p) REVERT: A 78 PHE cc_start: 0.8777 (p90) cc_final: 0.8454 (p90) REVERT: A 80 LYS cc_start: 0.8564 (mttp) cc_final: 0.8185 (mttp) REVERT: A 90 LEU cc_start: 0.8210 (tp) cc_final: 0.7802 (tt) REVERT: A 102 GLU cc_start: 0.7547 (mt-10) cc_final: 0.6930 (mt-10) REVERT: A 103 ASN cc_start: 0.7374 (m-40) cc_final: 0.6841 (m-40) REVERT: A 111 MET cc_start: 0.7428 (ttt) cc_final: 0.6847 (ttt) REVERT: A 112 TYR cc_start: 0.7139 (m-10) cc_final: 0.6413 (m-80) REVERT: A 114 GLU cc_start: 0.7498 (tt0) cc_final: 0.6422 (tt0) REVERT: A 119 LEU cc_start: 0.7505 (tp) cc_final: 0.7035 (tp) REVERT: A 142 GLU cc_start: 0.7193 (tt0) cc_final: 0.6930 (tt0) REVERT: A 149 ARG cc_start: 0.5630 (ttm-80) cc_final: 0.5341 (ttm170) REVERT: A 156 LEU cc_start: 0.8318 (mt) cc_final: 0.8064 (mt) REVERT: A 163 GLN cc_start: 0.8591 (tt0) cc_final: 0.7880 (tt0) REVERT: A 166 ASP cc_start: 0.7807 (p0) cc_final: 0.7476 (p0) REVERT: A 176 MET cc_start: 0.8462 (ptp) cc_final: 0.7890 (ptp) REVERT: A 196 ASN cc_start: 0.8834 (m-40) cc_final: 0.8570 (m110) REVERT: A 209 LYS cc_start: 0.8100 (mttt) cc_final: 0.7616 (mtmt) REVERT: A 256 ASP cc_start: 0.8321 (t70) cc_final: 0.8076 (t0) REVERT: A 261 LYS cc_start: 0.7668 (ptmt) cc_final: 0.7100 (ptmt) REVERT: A 262 ASP cc_start: 0.8342 (t0) cc_final: 0.7941 (t70) REVERT: A 268 MET cc_start: 0.6279 (mtm) cc_final: 0.4867 (mtm) REVERT: A 277 MET cc_start: 0.6421 (mtt) cc_final: 0.5117 (mtt) REVERT: A 298 ASN cc_start: 0.8865 (p0) cc_final: 0.8504 (p0) REVERT: A 316 TYR cc_start: 0.7459 (t80) cc_final: 0.7145 (t80) REVERT: A 358 HIS cc_start: 0.8499 (m-70) cc_final: 0.8208 (m-70) REVERT: A 360 LYS cc_start: 0.8606 (tttt) cc_final: 0.8335 (tttt) REVERT: A 396 LYS cc_start: 0.8459 (tppp) cc_final: 0.7757 (tppp) REVERT: A 404 PHE cc_start: 0.7639 (p90) cc_final: 0.6918 (p90) REVERT: A 407 ILE cc_start: 0.7606 (mm) cc_final: 0.7254 (tp) REVERT: A 408 GLN cc_start: 0.7128 (mm-40) cc_final: 0.6622 (mm-40) REVERT: A 420 PHE cc_start: 0.8344 (m-80) cc_final: 0.8143 (m-80) REVERT: A 421 GLU cc_start: 0.8624 (tt0) cc_final: 0.8053 (tt0) REVERT: A 429 ARG cc_start: 0.8015 (mtt180) cc_final: 0.7506 (mtt-85) REVERT: A 431 LYS cc_start: 0.8219 (mtmm) cc_final: 0.7706 (mtmm) REVERT: A 432 GLN cc_start: 0.8462 (tp40) cc_final: 0.8125 (tp-100) REVERT: A 433 HIS cc_start: 0.8143 (m90) cc_final: 0.7908 (m90) REVERT: A 441 VAL cc_start: 0.7817 (t) cc_final: 0.7571 (m) REVERT: A 451 ARG cc_start: 0.7810 (ptp-110) cc_final: 0.7497 (ptp-170) REVERT: A 454 LYS cc_start: 0.8706 (mmtt) cc_final: 0.8175 (mmtt) REVERT: A 457 SER cc_start: 0.8030 (m) cc_final: 0.7249 (t) REVERT: A 476 ASN cc_start: 0.7881 (t0) cc_final: 0.7101 (t0) REVERT: A 479 LYS cc_start: 0.7982 (mtpt) cc_final: 0.7057 (mtpt) REVERT: A 487 LYS cc_start: 0.7857 (mtmm) cc_final: 0.7603 (mtmm) REVERT: A 496 GLU cc_start: 0.7502 (mp0) cc_final: 0.7189 (mp0) REVERT: A 551 GLU cc_start: 0.8603 (pt0) cc_final: 0.8035 (pm20) REVERT: A 552 ASN cc_start: 0.8960 (p0) cc_final: 0.8140 (p0) REVERT: A 554 GLU cc_start: 0.8474 (mt-10) cc_final: 0.8153 (mt-10) REVERT: A 559 HIS cc_start: 0.7567 (t70) cc_final: 0.7094 (t-170) REVERT: C 18 GLN cc_start: 0.7982 (tt0) cc_final: 0.7449 (tt0) REVERT: C 25 MET cc_start: 0.7843 (mmp) cc_final: 0.7253 (mmp) REVERT: C 44 PHE cc_start: 0.8105 (m-80) cc_final: 0.7778 (m-80) outliers start: 1 outliers final: 0 residues processed: 370 average time/residue: 0.0975 time to fit residues: 48.0289 Evaluate side-chains 361 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 361 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 64 optimal weight: 0.2980 chunk 49 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 93 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN B 160 GLN ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 83 GLN ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.121174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.096698 restraints weight = 16594.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.101686 restraints weight = 9427.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.105273 restraints weight = 6019.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.107792 restraints weight = 4124.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.109731 restraints weight = 2994.225| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6844 moved from start: 0.6252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9413 Z= 0.204 Angle : 0.740 9.087 12798 Z= 0.373 Chirality : 0.050 0.268 1417 Planarity : 0.005 0.062 1669 Dihedral : 7.573 77.811 1426 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.06 % Favored : 86.94 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.67 (0.24), residues: 1164 helix: -2.88 (0.52), residues: 73 sheet: -2.03 (0.62), residues: 65 loop : -1.86 (0.19), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 188 TYR 0.016 0.002 TYR C 29 PHE 0.018 0.002 PHE B 73 TRP 0.061 0.003 TRP A 200 HIS 0.009 0.001 HIS A 507 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 9358) covalent geometry : angle 0.72279 (12680) SS BOND : bond 0.00340 ( 47) SS BOND : angle 1.39976 ( 94) hydrogen bonds : bond 0.03678 ( 81) hydrogen bonds : angle 5.74866 ( 174) link_ALPHA1-3 : bond 0.02250 ( 1) link_ALPHA1-3 : angle 3.33630 ( 3) link_BETA1-3 : bond 0.00964 ( 1) link_BETA1-3 : angle 3.67748 ( 3) link_BETA1-4 : bond 0.00261 ( 2) link_BETA1-4 : angle 1.33714 ( 6) link_NAG-ASN : bond 0.00424 ( 4) link_NAG-ASN : angle 3.02057 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 380 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 GLN cc_start: 0.7202 (pp30) cc_final: 0.6948 (mm-40) REVERT: B 31 MET cc_start: 0.7762 (mtp) cc_final: 0.6768 (ptp) REVERT: B 44 ASP cc_start: 0.7573 (t0) cc_final: 0.6748 (t0) REVERT: B 45 MET cc_start: 0.8402 (tmm) cc_final: 0.8060 (tmm) REVERT: B 46 LEU cc_start: 0.8601 (mt) cc_final: 0.8063 (mt) REVERT: B 47 ARG cc_start: 0.7836 (ttp80) cc_final: 0.7404 (ttp80) REVERT: B 55 VAL cc_start: 0.7901 (t) cc_final: 0.7639 (p) REVERT: B 59 ASN cc_start: 0.7354 (m-40) cc_final: 0.7003 (m-40) REVERT: B 65 LEU cc_start: 0.8383 (mt) cc_final: 0.8103 (mt) REVERT: B 75 GLN cc_start: 0.8017 (pt0) cc_final: 0.7775 (pt0) REVERT: B 97 GLN cc_start: 0.7785 (mp10) cc_final: 0.7403 (mp10) REVERT: B 100 ARG cc_start: 0.8176 (ttm-80) cc_final: 0.7912 (mmm-85) REVERT: B 139 GLU cc_start: 0.7421 (mp0) cc_final: 0.7186 (mp0) REVERT: B 143 ARG cc_start: 0.7667 (mpp80) cc_final: 0.7399 (mpp80) REVERT: B 156 GLN cc_start: 0.7740 (tm-30) cc_final: 0.6355 (tm-30) REVERT: B 157 ARG cc_start: 0.7710 (mtm-85) cc_final: 0.7372 (mtm-85) REVERT: B 172 ILE cc_start: 0.7916 (mt) cc_final: 0.7615 (mt) REVERT: B 182 THR cc_start: 0.7714 (p) cc_final: 0.7322 (p) REVERT: B 184 ILE cc_start: 0.8715 (mm) cc_final: 0.8496 (mm) REVERT: B 185 ASP cc_start: 0.6650 (t0) cc_final: 0.6334 (t0) REVERT: B 193 HIS cc_start: 0.7727 (m90) cc_final: 0.7365 (m90) REVERT: B 213 GLN cc_start: 0.8109 (tm-30) cc_final: 0.7724 (tm-30) REVERT: B 248 LYS cc_start: 0.8691 (mmtt) cc_final: 0.7950 (mmtt) REVERT: B 253 LEU cc_start: 0.7837 (mt) cc_final: 0.7630 (mt) REVERT: B 267 HIS cc_start: 0.7805 (m170) cc_final: 0.7231 (m170) REVERT: B 271 LEU cc_start: 0.8733 (mt) cc_final: 0.8515 (pt) REVERT: B 274 TYR cc_start: 0.6539 (t80) cc_final: 0.6200 (t80) REVERT: B 286 GLU cc_start: 0.8427 (pp20) cc_final: 0.7709 (tm-30) REVERT: B 303 TYR cc_start: 0.8039 (m-80) cc_final: 0.7621 (m-80) REVERT: B 320 GLN cc_start: 0.7128 (mt0) cc_final: 0.6710 (mt0) REVERT: B 323 THR cc_start: 0.7574 (t) cc_final: 0.7196 (p) REVERT: B 345 LEU cc_start: 0.8268 (mt) cc_final: 0.7868 (mt) REVERT: B 349 HIS cc_start: 0.7270 (m90) cc_final: 0.6617 (m90) REVERT: B 350 LEU cc_start: 0.7627 (mt) cc_final: 0.7380 (mt) REVERT: B 364 PHE cc_start: 0.8803 (m-80) cc_final: 0.8404 (m-80) REVERT: B 376 PHE cc_start: 0.8153 (m-10) cc_final: 0.7750 (m-10) REVERT: B 409 TYR cc_start: 0.7146 (p90) cc_final: 0.6928 (p90) REVERT: B 411 TYR cc_start: 0.7244 (t80) cc_final: 0.6488 (t80) REVERT: B 426 GLN cc_start: 0.7725 (pt0) cc_final: 0.7300 (pp30) REVERT: B 444 THR cc_start: 0.7694 (m) cc_final: 0.6699 (m) REVERT: B 452 TRP cc_start: 0.7898 (p90) cc_final: 0.7280 (p90) REVERT: B 467 LEU cc_start: 0.7592 (tp) cc_final: 0.6734 (pt) REVERT: B 481 PRO cc_start: 0.8042 (Cg_endo) cc_final: 0.7537 (Cg_exo) REVERT: B 482 TRP cc_start: 0.8409 (m100) cc_final: 0.8020 (m100) REVERT: B 483 ASP cc_start: 0.8365 (m-30) cc_final: 0.7810 (t0) REVERT: B 487 ARG cc_start: 0.7876 (mmt90) cc_final: 0.6718 (ttm-80) REVERT: B 490 HIS cc_start: 0.8318 (m-70) cc_final: 0.8110 (m-70) REVERT: B 491 GLN cc_start: 0.6274 (mt0) cc_final: 0.6017 (mt0) REVERT: B 493 LEU cc_start: 0.8419 (tp) cc_final: 0.7832 (tp) REVERT: B 494 LEU cc_start: 0.8741 (mt) cc_final: 0.8395 (tt) REVERT: B 520 CYS cc_start: 0.4412 (t) cc_final: 0.3957 (m) REVERT: B 577 PHE cc_start: 0.8526 (m-80) cc_final: 0.8067 (m-80) REVERT: B 580 GLU cc_start: 0.8354 (tp30) cc_final: 0.7989 (tp30) REVERT: A 28 LYS cc_start: 0.7851 (mtmm) cc_final: 0.6797 (mmmm) REVERT: A 43 THR cc_start: 0.7441 (p) cc_final: 0.7196 (t) REVERT: A 45 GLU cc_start: 0.8445 (mp0) cc_final: 0.7975 (mp0) REVERT: A 46 ASP cc_start: 0.7163 (t70) cc_final: 0.6668 (t70) REVERT: A 47 HIS cc_start: 0.7950 (t70) cc_final: 0.6813 (t70) REVERT: A 51 LEU cc_start: 0.9089 (tp) cc_final: 0.8654 (tp) REVERT: A 54 MET cc_start: 0.8239 (tpt) cc_final: 0.7936 (tpt) REVERT: A 55 PHE cc_start: 0.7977 (m-10) cc_final: 0.7693 (m-10) REVERT: A 74 TYR cc_start: 0.8104 (m-80) cc_final: 0.7122 (m-80) REVERT: A 75 ASP cc_start: 0.7773 (t70) cc_final: 0.7490 (t0) REVERT: A 76 LEU cc_start: 0.8273 (mt) cc_final: 0.8051 (mt) REVERT: A 78 PHE cc_start: 0.8812 (p90) cc_final: 0.8461 (p90) REVERT: A 88 TYR cc_start: 0.7126 (p90) cc_final: 0.6485 (p90) REVERT: A 90 LEU cc_start: 0.8177 (tp) cc_final: 0.7770 (tt) REVERT: A 102 GLU cc_start: 0.7475 (mt-10) cc_final: 0.6896 (mt-10) REVERT: A 111 MET cc_start: 0.7676 (ttt) cc_final: 0.7270 (ttt) REVERT: A 114 GLU cc_start: 0.7586 (tt0) cc_final: 0.6747 (tt0) REVERT: A 142 GLU cc_start: 0.7164 (tt0) cc_final: 0.6939 (tt0) REVERT: A 163 GLN cc_start: 0.8398 (tt0) cc_final: 0.7672 (tt0) REVERT: A 166 ASP cc_start: 0.7803 (p0) cc_final: 0.7438 (p0) REVERT: A 176 MET cc_start: 0.8495 (ptp) cc_final: 0.7992 (ptp) REVERT: A 196 ASN cc_start: 0.8858 (m-40) cc_final: 0.8597 (m110) REVERT: A 209 LYS cc_start: 0.8137 (mttt) cc_final: 0.7665 (mtmm) REVERT: A 212 LYS cc_start: 0.8184 (tmtt) cc_final: 0.7976 (tmtt) REVERT: A 213 ILE cc_start: 0.8499 (pt) cc_final: 0.8164 (mm) REVERT: A 226 LYS cc_start: 0.8248 (mtpt) cc_final: 0.7545 (mtpt) REVERT: A 252 ARG cc_start: 0.7193 (mtp85) cc_final: 0.6773 (mtm-85) REVERT: A 256 ASP cc_start: 0.8391 (t70) cc_final: 0.8191 (t0) REVERT: A 261 LYS cc_start: 0.7871 (ptmt) cc_final: 0.7240 (ptmt) REVERT: A 262 ASP cc_start: 0.8351 (t0) cc_final: 0.7966 (t70) REVERT: A 268 MET cc_start: 0.6373 (mtm) cc_final: 0.4916 (mtm) REVERT: A 277 MET cc_start: 0.6394 (mtt) cc_final: 0.5146 (mtt) REVERT: A 298 ASN cc_start: 0.8931 (p0) cc_final: 0.8692 (p0) REVERT: A 316 TYR cc_start: 0.7395 (t80) cc_final: 0.7076 (t80) REVERT: A 328 LYS cc_start: 0.8069 (ttmt) cc_final: 0.7659 (ttmt) REVERT: A 338 ASN cc_start: 0.7674 (p0) cc_final: 0.7206 (p0) REVERT: A 345 PHE cc_start: 0.8279 (m-80) cc_final: 0.8071 (m-80) REVERT: A 358 HIS cc_start: 0.8477 (m-70) cc_final: 0.8201 (m-70) REVERT: A 360 LYS cc_start: 0.8618 (tttt) cc_final: 0.8312 (tttt) REVERT: A 377 ARG cc_start: 0.7735 (ptm-80) cc_final: 0.7188 (ptm-80) REVERT: A 396 LYS cc_start: 0.8578 (tppp) cc_final: 0.7857 (tppp) REVERT: A 404 PHE cc_start: 0.7781 (p90) cc_final: 0.6934 (p90) REVERT: A 420 PHE cc_start: 0.8356 (m-80) cc_final: 0.8127 (m-80) REVERT: A 421 GLU cc_start: 0.8696 (tt0) cc_final: 0.8025 (tt0) REVERT: A 429 ARG cc_start: 0.8067 (mtt180) cc_final: 0.7546 (mtt-85) REVERT: A 432 GLN cc_start: 0.8524 (tp40) cc_final: 0.8105 (tp-100) REVERT: A 433 HIS cc_start: 0.8216 (m90) cc_final: 0.7815 (m90) REVERT: A 451 ARG cc_start: 0.7776 (ptp-110) cc_final: 0.7505 (ptp-170) REVERT: A 454 LYS cc_start: 0.8735 (mmtt) cc_final: 0.8186 (mmtt) REVERT: A 457 SER cc_start: 0.8158 (m) cc_final: 0.7376 (t) REVERT: A 479 LYS cc_start: 0.7981 (mtpt) cc_final: 0.7418 (mtpt) REVERT: A 487 LYS cc_start: 0.7978 (mtmm) cc_final: 0.7721 (mtmm) REVERT: A 496 GLU cc_start: 0.7448 (mp0) cc_final: 0.7108 (mp0) REVERT: A 552 ASN cc_start: 0.8921 (p0) cc_final: 0.8087 (p0) REVERT: A 554 GLU cc_start: 0.8549 (mt-10) cc_final: 0.8149 (mt-10) REVERT: C 18 GLN cc_start: 0.8001 (tt0) cc_final: 0.7634 (tt0) REVERT: C 25 MET cc_start: 0.7867 (mmp) cc_final: 0.7244 (mmp) REVERT: C 44 PHE cc_start: 0.8171 (m-80) cc_final: 0.7857 (m-80) outliers start: 0 outliers final: 0 residues processed: 380 average time/residue: 0.0980 time to fit residues: 49.2311 Evaluate side-chains 363 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 363 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 13 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 56 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 107 optimal weight: 7.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 ASN ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 GLN ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.120027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.096057 restraints weight = 16549.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.101007 restraints weight = 9421.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.104552 restraints weight = 6013.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.107078 restraints weight = 4117.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.108950 restraints weight = 2975.905| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 moved from start: 0.6551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 9413 Z= 0.236 Angle : 0.783 9.088 12798 Z= 0.398 Chirality : 0.051 0.271 1417 Planarity : 0.005 0.063 1669 Dihedral : 7.812 78.092 1426 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.63 % Favored : 87.37 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.67 (0.24), residues: 1164 helix: -2.93 (0.53), residues: 67 sheet: -1.59 (0.59), residues: 77 loop : -1.90 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 217 TYR 0.016 0.002 TYR C 29 PHE 0.020 0.002 PHE B 73 TRP 0.060 0.004 TRP A 200 HIS 0.009 0.002 HIS A 507 Details of bonding type rmsd covalent geometry : bond 0.00460 ( 9358) covalent geometry : angle 0.76412 (12680) SS BOND : bond 0.00357 ( 47) SS BOND : angle 1.54182 ( 94) hydrogen bonds : bond 0.03906 ( 81) hydrogen bonds : angle 5.94211 ( 174) link_ALPHA1-3 : bond 0.02285 ( 1) link_ALPHA1-3 : angle 3.45064 ( 3) link_BETA1-3 : bond 0.01038 ( 1) link_BETA1-3 : angle 3.74643 ( 3) link_BETA1-4 : bond 0.00406 ( 2) link_BETA1-4 : angle 1.34472 ( 6) link_NAG-ASN : bond 0.00500 ( 4) link_NAG-ASN : angle 3.20868 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1664.04 seconds wall clock time: 29 minutes 20.50 seconds (1760.50 seconds total)