Starting phenix.real_space_refine on Thu Jul 2 18:36:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hgp_34745/07_2026/8hgp_34745.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hgp_34745/07_2026/8hgp_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8hgp_34745/07_2026/8hgp_34745.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hgp_34745/07_2026/8hgp_34745.map" model { file = "/net/cci-nas-00/data/ceres_data/8hgp_34745/07_2026/8hgp_34745.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hgp_34745/07_2026/8hgp_34745.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8hgp_34745/07_2026/8hgp_34745.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hgp_34745/07_2026/8hgp_34745.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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 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 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 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: 1.59, per 1000 atoms: 0.17 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: 0.91 Conformation dependent library (CDL) restraints added in 275.5 milliseconds 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: 0.28 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: 1.35 Time building geometry restraints manager: 1.14 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 - 17.90: 5521 17.90 - 35.79: 142 35.79 - 53.69: 55 53.69 - 71.58: 11 71.58 - 89.48: 10 Dihedral angle restraints: 5739 sinusoidal: 2376 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 5736 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: 6.100 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: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.210 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6352 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 : 8.020 75.693 3436 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 are 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/Z covalent geometry : bond 0.00345 / 0.18 ( 9358) covalent geometry : angle 0.67972 / 0.38 (12680) SS BOND : bond 0.00237 / 0.16 ( 47) SS BOND : angle 0.98931 / 0.58 ( 94) hydrogen bonds : bond 0.30789 / 20.56 ( 81) hydrogen bonds : angle 9.11590 / 5.96 ( 174) link_ALPHA1-3 : bond 0.01525 / 0.80 ( 1) link_ALPHA1-3 : angle 3.10665 / 1.63 ( 3) link_BETA1-3 : bond 0.01442 / 0.76 ( 1) link_BETA1-3 : angle 7.24006 / 3.81 ( 3) link_BETA1-4 : bond 0.00695 / 0.35 ( 2) link_BETA1-4 : angle 2.05562 / 1.68 ( 6) link_NAG-ASN : bond 0.00743 / 0.37 ( 4) link_NAG-ASN : angle 3.64396 / 2.24 ( 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 : 0.331 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: 0.7730 (pt0) cc_final: 0.7505 (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: 0.8258 (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: 0.7496 (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: 0.7593 (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: 0.8275 (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: 0.8528 (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: 0.7583 (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: 0.8426 (mm) REVERT: A 163 GLN cc_start: 0.8701 (pt0) cc_final: 0.8049 (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: 0.6885 (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: 0.8059 (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: 0.1047 time to fit residues: 55.4221 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 : 0.239 ------------------------------------------------------------------------------- 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... B 68 ASN ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3934 r_free = 0.3934 target = 0.141939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.116338 restraints weight = 16915.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.121823 restraints weight = 9463.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.125692 restraints weight = 5967.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.128397 restraints weight = 4069.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.130324 restraints weight = 2939.426| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6520 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9413 Z= 0.150 Angle : 0.639 9.563 12798 Z= 0.322 Chirality : 0.047 0.282 1417 Planarity : 0.005 0.052 1669 Dihedral : 4.758 21.705 1262 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 0.00 % Allowed : 1.86 % 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 are not related in a simple way. whole: -3.37 (0.21), residues: 1164 helix: -2.66 (0.64), residues: 57 sheet: -2.72 (0.54), residues: 71 loop : -2.44 (0.17), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 190 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 0.005 0.001 HIS A 507 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.15 ( 9358) covalent geometry : angle 0.61288 / 0.31 (12680) SS BOND : bond 0.00855 / 0.50 ( 47) SS BOND : angle 1.75469 / 1.08 ( 94) hydrogen bonds : bond 0.05021 / 3.32 ( 81) hydrogen bonds : angle 6.92746 / 4.43 ( 174) link_ALPHA1-3 : bond 0.01312 / 0.69 ( 1) link_ALPHA1-3 : angle 2.62115 / 1.36 ( 3) link_BETA1-3 : bond 0.00475 / 0.25 ( 1) link_BETA1-3 : angle 4.01098 / 2.10 ( 3) link_BETA1-4 : bond 0.00337 / 0.16 ( 2) link_BETA1-4 : angle 1.11096 / 0.61 ( 6) link_NAG-ASN : bond 0.00477 / 0.24 ( 4) link_NAG-ASN : angle 2.76494 / 1.58 ( 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 377 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 377 time to evaluate : 0.337 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: 0.6126 (pp30) cc_final: 0.4779 (mm-40) REVERT: B 30 ASP cc_start: 0.6753 (t0) cc_final: 0.6515 (t0) REVERT: B 31 MET cc_start: 0.7751 (mtp) cc_final: 0.7380 (ptp) REVERT: B 32 LYS cc_start: 0.8146 (mptt) cc_final: 0.7724 (mmtt) REVERT: B 44 ASP cc_start: 0.7223 (t0) cc_final: 0.6650 (t0) REVERT: B 46 LEU cc_start: 0.8759 (mt) cc_final: 0.8513 (mt) REVERT: B 54 GLN cc_start: 0.6997 (mt0) cc_final: 0.6620 (tp-100) REVERT: B 56 VAL cc_start: 0.8139 (t) cc_final: 0.7664 (t) REVERT: B 73 PHE cc_start: 0.8090 (p90) cc_final: 0.7775 (p90) REVERT: B 74 LEU cc_start: 0.8388 (mt) cc_final: 0.8140 (mt) REVERT: B 75 GLN cc_start: 0.7746 (pt0) cc_final: 0.7410 (pt0) REVERT: B 79 GLU cc_start: 0.7184 (tt0) cc_final: 0.6552 (tt0) REVERT: B 81 GLN cc_start: 0.6701 (mt0) cc_final: 0.6206 (mt0) REVERT: B 93 GLN cc_start: 0.8462 (pp30) cc_final: 0.7704 (tm-30) REVERT: B 94 VAL cc_start: 0.8931 (t) cc_final: 0.8592 (t) REVERT: B 100 ARG cc_start: 0.7611 (tpp80) cc_final: 0.7409 (tpp80) REVERT: B 105 THR cc_start: 0.7777 (p) cc_final: 0.6857 (t) REVERT: B 106 GLN cc_start: 0.7680 (mt0) cc_final: 0.7134 (mp-120) REVERT: B 116 VAL cc_start: 0.6976 (t) cc_final: 0.6574 (p) REVERT: B 138 ARG cc_start: 0.7326 (mmm-85) cc_final: 0.6517 (mmm160) REVERT: B 156 GLN cc_start: 0.7875 (tm-30) cc_final: 0.7637 (tm-30) REVERT: B 160 GLN cc_start: 0.7462 (mm-40) cc_final: 0.7131 (tp40) REVERT: B 171 ASP cc_start: 0.7984 (t70) cc_final: 0.7695 (t70) REVERT: B 173 PHE cc_start: 0.6731 (m-10) cc_final: 0.6448 (m-10) REVERT: B 185 ASP cc_start: 0.7046 (t0) cc_final: 0.6724 (t0) REVERT: B 193 HIS cc_start: 0.7882 (m90) cc_final: 0.7246 (m90) REVERT: B 211 ASP cc_start: 0.8059 (m-30) cc_final: 0.7648 (m-30) REVERT: B 213 GLN cc_start: 0.7647 (tm-30) cc_final: 0.7355 (tm-30) REVERT: B 217 ARG cc_start: 0.7581 (ttt-90) cc_final: 0.7295 (mtp-110) REVERT: B 248 LYS cc_start: 0.8649 (mmtt) cc_final: 0.8055 (mmtt) REVERT: B 253 LEU cc_start: 0.7562 (mt) cc_final: 0.7015 (mt) REVERT: B 265 GLU cc_start: 0.6923 (pm20) cc_final: 0.6560 (pm20) REVERT: B 271 LEU cc_start: 0.8603 (mp) cc_final: 0.8350 (mt) REVERT: B 274 TYR cc_start: 0.6840 (t80) cc_final: 0.6420 (t80) REVERT: B 275 ASN cc_start: 0.8226 (t0) cc_final: 0.7575 (t0) REVERT: B 282 MET cc_start: 0.8048 (mtp) cc_final: 0.7451 (mtp) REVERT: B 303 TYR cc_start: 0.7903 (m-80) cc_final: 0.7311 (m-80) REVERT: B 320 GLN cc_start: 0.6588 (mt0) cc_final: 0.6278 (mt0) REVERT: B 332 GLU cc_start: 0.7303 (mt-10) cc_final: 0.6458 (mp0) REVERT: B 376 PHE cc_start: 0.8129 (m-10) cc_final: 0.7570 (m-10) REVERT: B 377 LEU cc_start: 0.8396 (tp) cc_final: 0.8156 (tt) REVERT: B 407 THR cc_start: 0.7622 (p) cc_final: 0.7320 (m) REVERT: B 409 TYR cc_start: 0.7170 (p90) cc_final: 0.6963 (p90) REVERT: B 411 TYR cc_start: 0.7168 (t80) cc_final: 0.6714 (t80) REVERT: B 420 PRO cc_start: 0.8436 (Cg_endo) cc_final: 0.7995 (Cg_exo) REVERT: B 421 ASP cc_start: 0.7740 (p0) cc_final: 0.7395 (p0) REVERT: B 422 LEU cc_start: 0.8618 (tp) cc_final: 0.7744 (pp) REVERT: B 426 GLN cc_start: 0.7736 (pt0) cc_final: 0.7046 (pp30) REVERT: B 430 VAL cc_start: 0.7374 (p) cc_final: 0.7019 (t) REVERT: B 434 ARG cc_start: 0.7489 (mtt90) cc_final: 0.7280 (mpt-90) REVERT: B 436 LEU cc_start: 0.7951 (mt) cc_final: 0.7444 (mt) REVERT: B 443 LEU cc_start: 0.7929 (tp) cc_final: 0.7436 (mm) REVERT: B 444 THR cc_start: 0.7499 (m) cc_final: 0.7173 (m) REVERT: B 452 TRP cc_start: 0.7702 (p90) cc_final: 0.7265 (p90) REVERT: B 467 LEU cc_start: 0.7130 (tp) cc_final: 0.6817 (tp) REVERT: B 481 PRO cc_start: 0.8272 (Cg_endo) cc_final: 0.7701 (Cg_exo) REVERT: B 482 TRP cc_start: 0.8536 (m100) cc_final: 0.8313 (m100) REVERT: B 488 ASN cc_start: 0.7963 (t0) cc_final: 0.7729 (t0) REVERT: B 494 LEU cc_start: 0.8555 (mt) cc_final: 0.8149 (mt) REVERT: B 556 ASN cc_start: 0.8072 (t0) cc_final: 0.7458 (t0) REVERT: B 566 GLU cc_start: 0.7572 (mm-30) cc_final: 0.6608 (tm-30) REVERT: B 577 PHE cc_start: 0.8087 (m-80) cc_final: 0.7868 (m-80) REVERT: B 580 GLU cc_start: 0.8424 (tp30) cc_final: 0.8052 (tp30) REVERT: A 29 LYS cc_start: 0.7948 (pttm) cc_final: 0.7468 (pttm) REVERT: A 36 ASN cc_start: 0.8246 (p0) cc_final: 0.7791 (p0) REVERT: A 46 ASP cc_start: 0.7367 (t70) cc_final: 0.6555 (t70) REVERT: A 47 HIS cc_start: 0.7957 (t70) cc_final: 0.6802 (t70) REVERT: A 51 LEU cc_start: 0.8747 (tp) cc_final: 0.8514 (tp) REVERT: A 55 PHE cc_start: 0.7865 (m-10) cc_final: 0.7370 (m-10) REVERT: A 62 LEU cc_start: 0.8470 (mt) cc_final: 0.8212 (mm) REVERT: A 65 LEU cc_start: 0.7917 (tp) cc_final: 0.7526 (tt) REVERT: A 74 TYR cc_start: 0.7803 (m-80) cc_final: 0.6923 (m-80) REVERT: A 80 LYS cc_start: 0.8280 (mttm) cc_final: 0.7872 (mttm) REVERT: A 83 GLN cc_start: 0.7966 (mm110) cc_final: 0.7548 (mm110) REVERT: A 93 LEU cc_start: 0.8255 (mp) cc_final: 0.8031 (mt) REVERT: A 105 GLN cc_start: 0.8044 (mt0) cc_final: 0.7308 (mm110) REVERT: A 110 ASN cc_start: 0.7916 (m-40) cc_final: 0.7550 (p0) REVERT: A 114 GLU cc_start: 0.7362 (tt0) cc_final: 0.6894 (tt0) REVERT: A 132 LEU cc_start: 0.7858 (tp) cc_final: 0.7611 (mm) REVERT: A 143 ILE cc_start: 0.8966 (mt) cc_final: 0.8636 (mm) REVERT: A 163 GLN cc_start: 0.8632 (pt0) cc_final: 0.7975 (tt0) REVERT: A 176 MET cc_start: 0.7948 (ptp) cc_final: 0.7568 (ptt) REVERT: A 209 LYS cc_start: 0.8117 (mttt) cc_final: 0.7510 (mtmm) REVERT: A 226 LYS cc_start: 0.7853 (mtpt) cc_final: 0.7265 (mtpt) REVERT: A 233 HIS cc_start: 0.7608 (t-90) cc_final: 0.7019 (t-90) REVERT: A 253 LYS cc_start: 0.8136 (tptm) cc_final: 0.7441 (tptm) REVERT: A 256 ASP cc_start: 0.6996 (t70) cc_final: 0.6635 (t0) REVERT: A 261 LYS cc_start: 0.7361 (mttm) cc_final: 0.6867 (mttm) REVERT: A 262 ASP cc_start: 0.7603 (t0) cc_final: 0.7180 (t0) REVERT: A 268 MET cc_start: 0.6123 (mtm) cc_final: 0.4946 (mtm) REVERT: A 277 MET cc_start: 0.6301 (mtt) cc_final: 0.5215 (mtt) REVERT: A 285 TYR cc_start: 0.5837 (m-10) cc_final: 0.5635 (m-10) REVERT: A 293 LYS cc_start: 0.7890 (mtpp) cc_final: 0.6964 (mmmt) REVERT: A 316 TYR cc_start: 0.7440 (t80) cc_final: 0.7039 (t80) REVERT: A 318 MET cc_start: 0.7764 (tpp) cc_final: 0.6960 (tpp) REVERT: A 338 ASN cc_start: 0.7008 (p0) cc_final: 0.5712 (p0) REVERT: A 340 ILE cc_start: 0.7695 (mp) cc_final: 0.7475 (mp) REVERT: A 345 PHE cc_start: 0.8160 (m-80) cc_final: 0.7877 (m-80) REVERT: A 358 HIS cc_start: 0.8291 (m90) cc_final: 0.7757 (m90) REVERT: A 360 LYS cc_start: 0.8702 (tttt) cc_final: 0.8356 (tttt) REVERT: A 368 ASP cc_start: 0.5229 (m-30) cc_final: 0.4620 (m-30) REVERT: A 369 LEU cc_start: 0.7308 (mt) cc_final: 0.7025 (mm) REVERT: A 396 LYS cc_start: 0.8242 (tppp) cc_final: 0.7826 (tppp) REVERT: A 404 PHE cc_start: 0.7370 (p90) cc_final: 0.6292 (p90) REVERT: A 421 GLU cc_start: 0.8680 (tt0) cc_final: 0.8045 (tt0) REVERT: A 429 ARG cc_start: 0.7623 (mtt180) cc_final: 0.6969 (mmm-85) REVERT: A 432 GLN cc_start: 0.8641 (tp40) cc_final: 0.8060 (tp-100) REVERT: A 433 HIS cc_start: 0.8306 (m90) cc_final: 0.8011 (m90) REVERT: A 476 ASN cc_start: 0.7734 (t0) cc_final: 0.7386 (t0) REVERT: A 489 LYS cc_start: 0.7897 (ttmm) cc_final: 0.7650 (mtpp) REVERT: A 496 GLU cc_start: 0.7547 (mp0) cc_final: 0.7282 (mp0) REVERT: A 551 GLU cc_start: 0.8619 (pt0) cc_final: 0.8169 (pm20) REVERT: C 18 GLN cc_start: 0.7765 (tt0) cc_final: 0.7294 (pm20) REVERT: C 22 LEU cc_start: 0.7586 (mt) cc_final: 0.7269 (mt) REVERT: C 25 MET cc_start: 0.7928 (mmp) cc_final: 0.7283 (mmp) outliers start: 0 outliers final: 0 residues processed: 377 average time/residue: 0.1052 time to fit residues: 53.1556 Evaluate side-chains 343 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 343 time to evaluate : 0.320 ------------------------------------------------------------------------------- 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: 0.0970 chunk 112 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 92 optimal weight: 0.0980 chunk 87 optimal weight: 2.9990 chunk 6 optimal weight: 0.1980 chunk 113 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 39 optimal weight: 0.0870 chunk 64 optimal weight: 0.6980 overall best weight: 0.2356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 HIS ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.137293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.111247 restraints weight = 16464.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.116859 restraints weight = 9243.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.120870 restraints weight = 5846.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.123484 restraints weight = 3987.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.125622 restraints weight = 2937.758| |-----------------------------------------------------------------------------| r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6527 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9413 Z= 0.109 Angle : 0.587 9.469 12798 Z= 0.297 Chirality : 0.046 0.271 1417 Planarity : 0.004 0.047 1669 Dihedral : 4.595 21.423 1262 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.07 (0.22), residues: 1164 helix: -2.19 (0.69), residues: 57 sheet: -2.24 (0.62), residues: 61 loop : -2.27 (0.17), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 252 TYR 0.012 0.001 TYR B 301 PHE 0.020 0.001 PHE B 486 TRP 0.017 0.001 TRP B 415 HIS 0.004 0.001 HIS A 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 ( 9358) covalent geometry : angle 0.57192 / 0.29 (12680) SS BOND : bond 0.00285 / 0.18 ( 47) SS BOND : angle 1.19047 / 0.77 ( 94) hydrogen bonds : bond 0.04638 / 3.01 ( 81) hydrogen bonds : angle 6.30967 / 3.97 ( 174) link_ALPHA1-3 : bond 0.01451 / 0.76 ( 1) link_ALPHA1-3 : angle 2.10136 / 1.08 ( 3) link_BETA1-3 : bond 0.00701 / 0.37 ( 1) link_BETA1-3 : angle 3.83274 / 2.01 ( 3) link_BETA1-4 : bond 0.00650 / 0.34 ( 2) link_BETA1-4 : angle 0.98321 / 0.66 ( 6) link_NAG-ASN : bond 0.00420 / 0.21 ( 4) link_NAG-ASN : angle 2.42214 / 1.42 ( 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 376 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 376 time to evaluate : 0.257 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: 0.6148 (pp30) cc_final: 0.4915 (mm-40) REVERT: B 31 MET cc_start: 0.7717 (mtp) cc_final: 0.7208 (ptp) REVERT: B 44 ASP cc_start: 0.7259 (t0) cc_final: 0.6490 (t0) REVERT: B 46 LEU cc_start: 0.8762 (mt) cc_final: 0.8441 (mt) REVERT: B 47 ARG cc_start: 0.7878 (ttp80) cc_final: 0.7366 (ttp80) REVERT: B 54 GLN cc_start: 0.7052 (mt0) cc_final: 0.6700 (tp40) REVERT: B 56 VAL cc_start: 0.8055 (t) cc_final: 0.7750 (m) REVERT: B 61 GLU cc_start: 0.7004 (tm-30) cc_final: 0.6008 (tm-30) REVERT: B 65 LEU cc_start: 0.8389 (mt) cc_final: 0.8183 (mt) REVERT: B 73 PHE cc_start: 0.8080 (p90) cc_final: 0.7692 (p90) REVERT: B 75 GLN cc_start: 0.7775 (pt0) cc_final: 0.7383 (pt0) REVERT: B 79 GLU cc_start: 0.7072 (tt0) cc_final: 0.6362 (tt0) REVERT: B 81 GLN cc_start: 0.6731 (mt0) cc_final: 0.6157 (mt0) REVERT: B 93 GLN cc_start: 0.8518 (pp30) cc_final: 0.8230 (tm-30) REVERT: B 100 ARG cc_start: 0.7624 (tpp80) cc_final: 0.7356 (mmm-85) REVERT: B 103 ARG cc_start: 0.7240 (mtt90) cc_final: 0.6720 (ttm110) REVERT: B 105 THR cc_start: 0.7914 (p) cc_final: 0.6992 (t) REVERT: B 106 GLN cc_start: 0.7700 (mt0) cc_final: 0.7198 (mp-120) REVERT: B 112 TYR cc_start: 0.6984 (m-80) cc_final: 0.6727 (m-80) REVERT: B 143 ARG cc_start: 0.7643 (mtt180) cc_final: 0.7291 (mtt180) REVERT: B 173 PHE cc_start: 0.6782 (m-10) cc_final: 0.6236 (m-10) REVERT: B 184 ILE cc_start: 0.8382 (mm) cc_final: 0.8143 (mm) REVERT: B 185 ASP cc_start: 0.7070 (t0) cc_final: 0.6798 (t0) REVERT: B 193 HIS cc_start: 0.7879 (m90) cc_final: 0.7268 (m90) REVERT: B 210 GLU cc_start: 0.7538 (pm20) cc_final: 0.7197 (pm20) REVERT: B 211 ASP cc_start: 0.7963 (m-30) cc_final: 0.7273 (m-30) REVERT: B 237 HIS cc_start: 0.7557 (t-90) cc_final: 0.7351 (t-90) REVERT: B 248 LYS cc_start: 0.8633 (mmtt) cc_final: 0.7987 (mmtt) REVERT: B 253 LEU cc_start: 0.7581 (mt) cc_final: 0.7294 (mt) REVERT: B 265 GLU cc_start: 0.6915 (pm20) cc_final: 0.6383 (pm20) REVERT: B 266 LEU cc_start: 0.8302 (tp) cc_final: 0.8068 (tp) REVERT: B 267 HIS cc_start: 0.7381 (m170) cc_final: 0.6851 (m170) REVERT: B 271 LEU cc_start: 0.8612 (mp) cc_final: 0.8361 (mt) REVERT: B 274 TYR cc_start: 0.6950 (t80) cc_final: 0.6094 (t80) REVERT: B 275 ASN cc_start: 0.8220 (t0) cc_final: 0.7528 (t0) REVERT: B 282 MET cc_start: 0.8179 (mtp) cc_final: 0.7908 (mtp) REVERT: B 286 GLU cc_start: 0.8193 (pp20) cc_final: 0.7977 (mp0) REVERT: B 291 PHE cc_start: 0.7644 (t80) cc_final: 0.7440 (t80) REVERT: B 303 TYR cc_start: 0.7882 (m-80) cc_final: 0.7297 (m-80) REVERT: B 332 GLU cc_start: 0.7388 (mt-10) cc_final: 0.7063 (mt-10) REVERT: B 364 PHE cc_start: 0.8480 (m-80) cc_final: 0.7724 (m-80) REVERT: B 377 LEU cc_start: 0.8397 (tp) cc_final: 0.8157 (tt) REVERT: B 398 GLN cc_start: 0.8094 (mm-40) cc_final: 0.7817 (mm-40) REVERT: B 407 THR cc_start: 0.7743 (p) cc_final: 0.7284 (m) REVERT: B 409 TYR cc_start: 0.7150 (p90) cc_final: 0.6943 (p90) REVERT: B 411 TYR cc_start: 0.7263 (t80) cc_final: 0.6406 (t80) REVERT: B 420 PRO cc_start: 0.8437 (Cg_endo) cc_final: 0.8149 (Cg_exo) REVERT: B 421 ASP cc_start: 0.7641 (p0) cc_final: 0.7359 (p0) REVERT: B 426 GLN cc_start: 0.7873 (pt0) cc_final: 0.7157 (pp30) REVERT: B 436 LEU cc_start: 0.8005 (mt) cc_final: 0.7443 (mt) REVERT: B 443 LEU cc_start: 0.7956 (tp) cc_final: 0.7415 (mm) REVERT: B 444 THR cc_start: 0.7369 (m) cc_final: 0.6801 (m) REVERT: B 451 SER cc_start: 0.8090 (p) cc_final: 0.7629 (m) REVERT: B 452 TRP cc_start: 0.7788 (p90) cc_final: 0.7469 (p90) REVERT: B 467 LEU cc_start: 0.7116 (tp) cc_final: 0.6850 (tp) REVERT: B 481 PRO cc_start: 0.8214 (Cg_endo) cc_final: 0.7692 (Cg_exo) REVERT: B 482 TRP cc_start: 0.8639 (m100) cc_final: 0.8275 (m100) REVERT: B 483 ASP cc_start: 0.8436 (m-30) cc_final: 0.7650 (t0) REVERT: B 494 LEU cc_start: 0.8512 (mt) cc_final: 0.8122 (mt) REVERT: B 556 ASN cc_start: 0.8073 (t0) cc_final: 0.7455 (t0) REVERT: B 566 GLU cc_start: 0.7540 (mm-30) cc_final: 0.6534 (tm-30) REVERT: B 577 PHE cc_start: 0.8116 (m-80) cc_final: 0.7874 (m-80) REVERT: B 580 GLU cc_start: 0.8417 (tp30) cc_final: 0.8042 (tp30) REVERT: A 36 ASN cc_start: 0.8294 (p0) cc_final: 0.7875 (p0) REVERT: A 46 ASP cc_start: 0.7187 (t70) cc_final: 0.6559 (t70) REVERT: A 47 HIS cc_start: 0.7864 (t70) cc_final: 0.6755 (t70) REVERT: A 51 LEU cc_start: 0.8738 (tp) cc_final: 0.8505 (tp) REVERT: A 55 PHE cc_start: 0.7804 (m-10) cc_final: 0.7492 (m-10) REVERT: A 61 VAL cc_start: 0.8107 (m) cc_final: 0.7793 (p) REVERT: A 74 TYR cc_start: 0.7851 (m-80) cc_final: 0.6898 (m-80) REVERT: A 80 LYS cc_start: 0.8274 (mttm) cc_final: 0.8046 (mttm) REVERT: A 83 GLN cc_start: 0.7873 (mm110) cc_final: 0.7094 (mm110) REVERT: A 98 ARG cc_start: 0.7594 (ttt90) cc_final: 0.7229 (tpp80) REVERT: A 102 GLU cc_start: 0.7173 (mt-10) cc_final: 0.6888 (mt-10) REVERT: A 103 ASN cc_start: 0.7290 (m-40) cc_final: 0.6346 (m-40) REVERT: A 107 ILE cc_start: 0.8412 (mm) cc_final: 0.8190 (mm) REVERT: A 110 ASN cc_start: 0.7920 (m110) cc_final: 0.7601 (p0) REVERT: A 112 TYR cc_start: 0.6765 (m-80) cc_final: 0.6560 (m-80) REVERT: A 143 ILE cc_start: 0.8863 (mt) cc_final: 0.8470 (mm) REVERT: A 163 GLN cc_start: 0.8541 (pt0) cc_final: 0.8187 (tt0) REVERT: A 167 ILE cc_start: 0.8461 (mp) cc_final: 0.8250 (mp) REVERT: A 172 PHE cc_start: 0.8102 (m-80) cc_final: 0.7818 (m-10) REVERT: A 176 MET cc_start: 0.8086 (ptp) cc_final: 0.7729 (ptt) REVERT: A 209 LYS cc_start: 0.8135 (mttt) cc_final: 0.7525 (mtmm) REVERT: A 226 LYS cc_start: 0.8085 (mtpt) cc_final: 0.7425 (mtpt) REVERT: A 229 SER cc_start: 0.8242 (p) cc_final: 0.7769 (t) REVERT: A 233 HIS cc_start: 0.7263 (t-90) cc_final: 0.6920 (t-90) REVERT: A 252 ARG cc_start: 0.7305 (mtp85) cc_final: 0.6964 (mtp85) REVERT: A 253 LYS cc_start: 0.8173 (tptm) cc_final: 0.7498 (tptm) REVERT: A 254 PHE cc_start: 0.7219 (m-10) cc_final: 0.5799 (m-80) REVERT: A 255 ARG cc_start: 0.6766 (ttt-90) cc_final: 0.6526 (ttp80) REVERT: A 262 ASP cc_start: 0.7663 (t0) cc_final: 0.7218 (t0) REVERT: A 268 MET cc_start: 0.6095 (mtm) cc_final: 0.4874 (mtm) REVERT: A 277 MET cc_start: 0.6128 (mtt) cc_final: 0.5070 (mtt) REVERT: A 290 THR cc_start: 0.6870 (t) cc_final: 0.6669 (t) REVERT: A 293 LYS cc_start: 0.7670 (mtpp) cc_final: 0.7196 (tppt) REVERT: A 338 ASN cc_start: 0.7136 (p0) cc_final: 0.6372 (p0) REVERT: A 340 ILE cc_start: 0.7549 (mp) cc_final: 0.7316 (mp) REVERT: A 345 PHE cc_start: 0.8184 (m-80) cc_final: 0.7673 (m-80) REVERT: A 358 HIS cc_start: 0.8344 (m90) cc_final: 0.7762 (m90) REVERT: A 360 LYS cc_start: 0.8693 (tttt) cc_final: 0.8343 (tttt) REVERT: A 396 LYS cc_start: 0.8273 (tppp) cc_final: 0.7838 (tppp) REVERT: A 421 GLU cc_start: 0.8653 (tt0) cc_final: 0.8008 (tt0) REVERT: A 430 THR cc_start: 0.7665 (m) cc_final: 0.7233 (t) REVERT: A 431 LYS cc_start: 0.8274 (mtmm) cc_final: 0.7760 (mtmt) REVERT: A 432 GLN cc_start: 0.8672 (tp40) cc_final: 0.8159 (tp-100) REVERT: A 476 ASN cc_start: 0.7707 (t0) cc_final: 0.7293 (t0) REVERT: A 489 LYS cc_start: 0.7726 (ttmm) cc_final: 0.7509 (mmmm) REVERT: A 496 GLU cc_start: 0.7528 (mp0) cc_final: 0.7290 (mp0) REVERT: A 521 ARG cc_start: 0.7772 (ptt180) cc_final: 0.7293 (tmm-80) REVERT: A 551 GLU cc_start: 0.8616 (pt0) cc_final: 0.8158 (pm20) REVERT: C 22 LEU cc_start: 0.7519 (mt) cc_final: 0.7232 (mt) REVERT: C 25 MET cc_start: 0.7927 (mmp) cc_final: 0.7354 (mmp) outliers start: 0 outliers final: 0 residues processed: 376 average time/residue: 0.1043 time to fit residues: 52.1189 Evaluate side-chains 356 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 356 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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: 0.6980 chunk 76 optimal weight: 0.1980 chunk 98 optimal weight: 0.8980 chunk 112 optimal weight: 0.0040 chunk 21 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 85 optimal weight: 0.0000 overall best weight: 0.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 158 ASN B 160 GLN ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 32 GLN ** 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 = 0.3867 r_free = 0.3867 target = 0.134512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.108107 restraints weight = 16692.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.113741 restraints weight = 9427.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.117689 restraints weight = 5992.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.120565 restraints weight = 4101.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.122661 restraints weight = 2963.428| |-----------------------------------------------------------------------------| r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6579 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9413 Z= 0.127 Angle : 0.595 9.414 12798 Z= 0.303 Chirality : 0.046 0.271 1417 Planarity : 0.004 0.042 1669 Dihedral : 4.655 20.880 1262 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.72 (0.23), residues: 1164 helix: -1.40 (0.81), residues: 48 sheet: -1.20 (0.63), residues: 74 loop : -2.10 (0.18), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 190 TYR 0.040 0.002 TYR A 117 PHE 0.009 0.001 PHE B 486 TRP 0.007 0.001 TRP A 477 HIS 0.005 0.001 HIS A 507 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.13 ( 9358) covalent geometry : angle 0.57799 / 0.30 (12680) SS BOND : bond 0.00362 / 0.25 ( 47) SS BOND : angle 1.33089 / 0.88 ( 94) hydrogen bonds : bond 0.04095 / 2.64 ( 81) hydrogen bonds : angle 5.85898 / 3.74 ( 174) link_ALPHA1-3 : bond 0.00951 / 0.50 ( 1) link_ALPHA1-3 : angle 2.09656 / 1.08 ( 3) link_BETA1-3 : bond 0.00715 / 0.38 ( 1) link_BETA1-3 : angle 3.50853 / 1.84 ( 3) link_BETA1-4 : bond 0.00619 / 0.31 ( 2) link_BETA1-4 : angle 0.79640 / 0.50 ( 6) link_NAG-ASN : bond 0.00517 / 0.26 ( 4) link_NAG-ASN : angle 2.51477 / 1.43 ( 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 370 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 370 time to evaluate : 0.341 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: 0.6535 (pp30) cc_final: 0.5334 (mm-40) REVERT: B 31 MET cc_start: 0.7505 (mtp) cc_final: 0.6652 (ptp) REVERT: B 32 LYS cc_start: 0.8251 (mmtm) cc_final: 0.7979 (mmtt) REVERT: B 44 ASP cc_start: 0.7364 (t0) cc_final: 0.6428 (t0) REVERT: B 46 LEU cc_start: 0.8787 (mt) cc_final: 0.8390 (mt) REVERT: B 47 ARG cc_start: 0.7940 (ttp80) cc_final: 0.7345 (ttp80) REVERT: B 54 GLN cc_start: 0.7118 (mt0) cc_final: 0.6659 (tp40) REVERT: B 55 VAL cc_start: 0.7423 (t) cc_final: 0.6736 (t) REVERT: B 59 ASN cc_start: 0.7204 (m-40) cc_final: 0.6941 (m-40) REVERT: B 61 GLU cc_start: 0.6978 (tm-30) cc_final: 0.4832 (tm-30) REVERT: B 64 TYR cc_start: 0.7615 (m-80) cc_final: 0.7116 (m-80) REVERT: B 65 LEU cc_start: 0.8355 (mt) cc_final: 0.8141 (mt) REVERT: B 73 PHE cc_start: 0.8104 (p90) cc_final: 0.7787 (p90) REVERT: B 75 GLN cc_start: 0.7816 (pt0) cc_final: 0.7432 (pt0) REVERT: B 79 GLU cc_start: 0.6966 (tt0) cc_final: 0.6277 (tt0) REVERT: B 81 GLN cc_start: 0.6695 (mt0) cc_final: 0.6156 (mt0) REVERT: B 85 LEU cc_start: 0.8403 (tp) cc_final: 0.8186 (tp) REVERT: B 93 GLN cc_start: 0.8510 (pp30) cc_final: 0.8257 (tm-30) REVERT: B 100 ARG cc_start: 0.7671 (tpp80) cc_final: 0.7454 (mmm-85) REVERT: B 103 ARG cc_start: 0.7270 (mtt90) cc_final: 0.6796 (ttm110) REVERT: B 105 THR cc_start: 0.7945 (p) cc_final: 0.7088 (t) REVERT: B 106 GLN cc_start: 0.7731 (mt0) cc_final: 0.7372 (mp-120) REVERT: B 112 TYR cc_start: 0.7117 (m-80) cc_final: 0.6804 (m-80) REVERT: B 143 ARG cc_start: 0.7667 (mtt180) cc_final: 0.7209 (mtt180) REVERT: B 160 GLN cc_start: 0.7044 (tp-100) cc_final: 0.6830 (tp40) REVERT: B 173 PHE cc_start: 0.6948 (m-10) cc_final: 0.6308 (m-10) REVERT: B 185 ASP cc_start: 0.7037 (t0) cc_final: 0.6811 (t0) REVERT: B 193 HIS cc_start: 0.7900 (m90) cc_final: 0.7289 (m90) REVERT: B 208 SER cc_start: 0.7671 (m) cc_final: 0.7393 (p) REVERT: B 210 GLU cc_start: 0.7479 (pm20) cc_final: 0.6950 (pm20) REVERT: B 211 ASP cc_start: 0.7918 (m-30) cc_final: 0.6793 (m-30) REVERT: B 248 LYS cc_start: 0.8668 (mmtt) cc_final: 0.7996 (mmtt) REVERT: B 253 LEU cc_start: 0.7676 (mt) cc_final: 0.7427 (mt) REVERT: B 265 GLU cc_start: 0.6957 (pm20) cc_final: 0.6410 (pm20) REVERT: B 267 HIS cc_start: 0.7376 (m170) cc_final: 0.7128 (m170) REVERT: B 271 LEU cc_start: 0.8571 (mp) cc_final: 0.8333 (mt) REVERT: B 274 TYR cc_start: 0.6776 (t80) cc_final: 0.6162 (t80) REVERT: B 275 ASN cc_start: 0.8158 (t0) cc_final: 0.7543 (t0) REVERT: B 282 MET cc_start: 0.8196 (mtp) cc_final: 0.7917 (mtp) REVERT: B 286 GLU cc_start: 0.8247 (pp20) cc_final: 0.7972 (mp0) REVERT: B 303 TYR cc_start: 0.7942 (m-80) cc_final: 0.7443 (m-80) REVERT: B 311 CYS cc_start: 0.3993 (p) cc_final: 0.3112 (m) REVERT: B 332 GLU cc_start: 0.7347 (mt-10) cc_final: 0.7064 (mt-10) REVERT: B 364 PHE cc_start: 0.8517 (m-80) cc_final: 0.7746 (m-80) REVERT: B 398 GLN cc_start: 0.8189 (mm-40) cc_final: 0.7874 (mm-40) REVERT: B 407 THR cc_start: 0.7834 (p) cc_final: 0.7285 (m) REVERT: B 409 TYR cc_start: 0.7133 (p90) cc_final: 0.6903 (p90) REVERT: B 411 TYR cc_start: 0.7377 (t80) cc_final: 0.6553 (t80) REVERT: B 420 PRO cc_start: 0.8505 (Cg_endo) cc_final: 0.8172 (Cg_exo) REVERT: B 421 ASP cc_start: 0.7700 (p0) cc_final: 0.7371 (p0) REVERT: B 422 LEU cc_start: 0.8626 (tp) cc_final: 0.8358 (tp) REVERT: B 426 GLN cc_start: 0.7913 (pt0) cc_final: 0.7227 (pp30) REVERT: B 430 VAL cc_start: 0.7742 (p) cc_final: 0.7506 (t) REVERT: B 436 LEU cc_start: 0.8011 (mt) cc_final: 0.7351 (mt) REVERT: B 444 THR cc_start: 0.7450 (m) cc_final: 0.7093 (m) REVERT: B 451 SER cc_start: 0.8087 (p) cc_final: 0.7604 (m) REVERT: B 452 TRP cc_start: 0.7827 (p90) cc_final: 0.7506 (p90) REVERT: B 467 LEU cc_start: 0.7160 (tp) cc_final: 0.6958 (tp) REVERT: B 481 PRO cc_start: 0.8092 (Cg_endo) cc_final: 0.7573 (Cg_exo) REVERT: B 487 ARG cc_start: 0.7911 (mmt90) cc_final: 0.7397 (mtt90) REVERT: B 488 ASN cc_start: 0.7993 (t0) cc_final: 0.7494 (t0) REVERT: B 494 LEU cc_start: 0.8658 (mt) cc_final: 0.8273 (mt) REVERT: B 527 GLN cc_start: 0.6950 (pm20) cc_final: 0.5999 (pm20) REVERT: B 556 ASN cc_start: 0.8134 (t0) cc_final: 0.7489 (t0) REVERT: B 566 GLU cc_start: 0.7659 (mm-30) cc_final: 0.6555 (tm-30) REVERT: B 577 PHE cc_start: 0.8195 (m-80) cc_final: 0.7926 (m-80) REVERT: B 580 GLU cc_start: 0.8408 (tp30) cc_final: 0.8065 (tp30) REVERT: A 29 LYS cc_start: 0.7776 (pttm) cc_final: 0.7325 (pttm) REVERT: A 36 ASN cc_start: 0.8311 (p0) cc_final: 0.7873 (p0) REVERT: A 46 ASP cc_start: 0.7259 (t70) cc_final: 0.6654 (t70) REVERT: A 47 HIS cc_start: 0.7899 (t70) cc_final: 0.6836 (t70) REVERT: A 51 LEU cc_start: 0.8851 (tp) cc_final: 0.8616 (tp) REVERT: A 55 PHE cc_start: 0.7806 (m-10) cc_final: 0.7590 (m-10) REVERT: A 61 VAL cc_start: 0.8161 (m) cc_final: 0.7833 (p) REVERT: A 67 ILE cc_start: 0.8391 (mt) cc_final: 0.8049 (mm) REVERT: A 74 TYR cc_start: 0.7939 (m-80) cc_final: 0.6972 (m-80) REVERT: A 83 GLN cc_start: 0.7824 (mm110) cc_final: 0.7022 (mm110) REVERT: A 98 ARG cc_start: 0.7604 (ttt90) cc_final: 0.7260 (tpp80) REVERT: A 102 GLU cc_start: 0.7371 (mt-10) cc_final: 0.6838 (mt-10) REVERT: A 103 ASN cc_start: 0.7337 (m-40) cc_final: 0.6440 (m-40) REVERT: A 110 ASN cc_start: 0.7987 (m110) cc_final: 0.7714 (p0) REVERT: A 112 TYR cc_start: 0.6687 (m-80) cc_final: 0.6371 (m-80) REVERT: A 119 LEU cc_start: 0.7786 (tp) cc_final: 0.7240 (tp) REVERT: A 122 LEU cc_start: 0.7953 (mp) cc_final: 0.7461 (mm) REVERT: A 138 ARG cc_start: 0.8256 (mtt180) cc_final: 0.7962 (mtt-85) REVERT: A 163 GLN cc_start: 0.8549 (pt0) cc_final: 0.8039 (tt0) REVERT: A 172 PHE cc_start: 0.8187 (m-80) cc_final: 0.7903 (m-10) REVERT: A 176 MET cc_start: 0.8272 (ptp) cc_final: 0.7828 (ptt) REVERT: A 209 LYS cc_start: 0.8199 (mttt) cc_final: 0.7619 (mtmt) REVERT: A 229 SER cc_start: 0.8130 (p) cc_final: 0.7696 (t) REVERT: A 253 LYS cc_start: 0.8146 (tptm) cc_final: 0.7286 (tptm) REVERT: A 255 ARG cc_start: 0.6859 (ttt-90) cc_final: 0.6547 (ttp80) REVERT: A 257 GLU cc_start: 0.8473 (mm-30) cc_final: 0.7696 (mm-30) REVERT: A 261 LYS cc_start: 0.7240 (ptmt) cc_final: 0.6843 (ptmt) REVERT: A 268 MET cc_start: 0.6077 (mtm) cc_final: 0.4890 (mtm) REVERT: A 277 MET cc_start: 0.6178 (mtt) cc_final: 0.5067 (mtt) REVERT: A 290 THR cc_start: 0.6917 (t) cc_final: 0.6511 (t) REVERT: A 293 LYS cc_start: 0.7761 (mtpp) cc_final: 0.6863 (mtpp) REVERT: A 298 ASN cc_start: 0.8321 (p0) cc_final: 0.7453 (p0) REVERT: A 338 ASN cc_start: 0.7284 (p0) cc_final: 0.6293 (p0) REVERT: A 345 PHE cc_start: 0.8242 (m-80) cc_final: 0.7590 (m-80) REVERT: A 358 HIS cc_start: 0.8355 (m90) cc_final: 0.8151 (m90) REVERT: A 360 LYS cc_start: 0.8741 (tttt) cc_final: 0.8395 (tttt) REVERT: A 368 ASP cc_start: 0.5059 (m-30) cc_final: 0.4057 (m-30) REVERT: A 396 LYS cc_start: 0.8353 (tppp) cc_final: 0.7868 (tppp) REVERT: A 404 PHE cc_start: 0.7446 (p90) cc_final: 0.6314 (p90) REVERT: A 421 GLU cc_start: 0.8652 (tt0) cc_final: 0.7663 (tt0) REVERT: A 429 ARG cc_start: 0.7956 (mtt180) cc_final: 0.7312 (mtt-85) REVERT: A 430 THR cc_start: 0.7682 (m) cc_final: 0.6715 (m) REVERT: A 451 ARG cc_start: 0.7079 (mtt90) cc_final: 0.6862 (ptp-170) REVERT: A 457 SER cc_start: 0.7831 (m) cc_final: 0.7502 (m) REVERT: A 460 ASP cc_start: 0.6751 (t70) cc_final: 0.6431 (t70) REVERT: A 463 ILE cc_start: 0.6571 (mt) cc_final: 0.6369 (mp) REVERT: A 476 ASN cc_start: 0.7746 (t0) cc_final: 0.7351 (t0) REVERT: A 487 LYS cc_start: 0.7680 (mtmm) cc_final: 0.7343 (mtmm) REVERT: A 489 LYS cc_start: 0.7699 (ttmm) cc_final: 0.7481 (mmmm) REVERT: A 496 GLU cc_start: 0.7573 (mp0) cc_final: 0.7229 (mp0) REVERT: A 551 GLU cc_start: 0.8654 (pt0) cc_final: 0.8228 (pm20) REVERT: C 22 LEU cc_start: 0.7749 (mt) cc_final: 0.7429 (mt) REVERT: C 25 MET cc_start: 0.7856 (mmp) cc_final: 0.7310 (mmp) outliers start: 0 outliers final: 0 residues processed: 370 average time/residue: 0.0984 time to fit residues: 48.5063 Evaluate side-chains 352 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 352 time to evaluate : 0.208 ------------------------------------------------------------------------------- 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: 0.9990 chunk 74 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 107 optimal weight: 0.0370 chunk 51 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 64 optimal weight: 0.5980 chunk 71 optimal weight: 0.8980 overall best weight: 0.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 158 ASN ** 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 A 280 ASN A 370 HIS A 435 GLN A 468 ASN A 504 GLN A 565 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.127301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.101992 restraints weight = 16568.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.107423 restraints weight = 9344.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.111286 restraints weight = 5932.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.114070 restraints weight = 4049.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.116009 restraints weight = 2923.052| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6684 moved from start: 0.4203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9413 Z= 0.200 Angle : 0.666 10.516 12798 Z= 0.340 Chirality : 0.047 0.284 1417 Planarity : 0.005 0.046 1669 Dihedral : 5.044 19.658 1262 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.14 % Favored : 89.86 % Rotamer: Outliers : 0.10 % Allowed : 1.37 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.57 (0.23), residues: 1164 helix: -1.88 (0.71), residues: 48 sheet: -1.04 (0.63), residues: 79 loop : -1.96 (0.19), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 190 TYR 0.027 0.002 TYR A 117 PHE 0.014 0.002 PHE A 180 TRP 0.014 0.002 TRP A 477 HIS 0.010 0.002 HIS A 507 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.20 ( 9358) covalent geometry : angle 0.64836 / 0.33 (12680) SS BOND : bond 0.00367 / 0.26 ( 47) SS BOND : angle 1.36902 / 0.92 ( 94) hydrogen bonds : bond 0.03929 / 2.48 ( 81) hydrogen bonds : angle 5.98807 / 3.77 ( 174) link_ALPHA1-3 : bond 0.01159 / 0.61 ( 1) link_ALPHA1-3 : angle 2.70810 / 1.41 ( 3) link_BETA1-3 : bond 0.00591 / 0.31 ( 1) link_BETA1-3 : angle 3.31701 / 1.74 ( 3) link_BETA1-4 : bond 0.00417 / 0.21 ( 2) link_BETA1-4 : angle 1.09022 / 0.67 ( 6) link_NAG-ASN : bond 0.00529 / 0.28 ( 4) link_NAG-ASN : angle 2.95769 / 1.60 ( 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 380 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 379 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.7153 (pp30) cc_final: 0.5970 (tm-30) REVERT: B 31 MET cc_start: 0.7486 (mtp) cc_final: 0.6416 (ptp) REVERT: B 32 LYS cc_start: 0.8428 (mmtm) cc_final: 0.8224 (mmtp) REVERT: B 44 ASP cc_start: 0.7478 (t0) cc_final: 0.6660 (t0) REVERT: B 46 LEU cc_start: 0.8818 (mt) cc_final: 0.8299 (mt) REVERT: B 47 ARG cc_start: 0.8080 (ttp80) cc_final: 0.7533 (ttp80) REVERT: B 55 VAL cc_start: 0.7687 (t) cc_final: 0.7179 (p) REVERT: B 59 ASN cc_start: 0.7330 (m-40) cc_final: 0.6883 (m-40) REVERT: B 61 GLU cc_start: 0.6942 (tm-30) cc_final: 0.3534 (tm-30) REVERT: B 64 TYR cc_start: 0.7776 (m-80) cc_final: 0.7314 (m-80) REVERT: B 65 LEU cc_start: 0.8315 (mt) cc_final: 0.8094 (mt) REVERT: B 75 GLN cc_start: 0.7915 (pt0) cc_final: 0.7592 (pt0) REVERT: B 78 GLN cc_start: 0.8504 (mt0) cc_final: 0.8154 (pm20) REVERT: B 81 GLN cc_start: 0.6575 (mt0) cc_final: 0.6130 (mt0) REVERT: B 103 ARG cc_start: 0.7285 (mtt90) cc_final: 0.6874 (ttm110) REVERT: B 105 THR cc_start: 0.8064 (p) cc_final: 0.7284 (t) REVERT: B 106 GLN cc_start: 0.7837 (mt0) cc_final: 0.7446 (mp10) REVERT: B 143 ARG cc_start: 0.7746 (mtt180) cc_final: 0.7412 (mtt180) REVERT: B 173 PHE cc_start: 0.6600 (m-10) cc_final: 0.6149 (m-10) REVERT: B 182 THR cc_start: 0.7543 (p) cc_final: 0.7170 (p) REVERT: B 185 ASP cc_start: 0.7135 (t0) cc_final: 0.6916 (t0) REVERT: B 193 HIS cc_start: 0.7875 (m90) cc_final: 0.7298 (m90) REVERT: B 208 SER cc_start: 0.7771 (m) cc_final: 0.7478 (t) REVERT: B 211 ASP cc_start: 0.7883 (m-30) cc_final: 0.7313 (m-30) REVERT: B 248 LYS cc_start: 0.8763 (mmtt) cc_final: 0.8046 (mmtt) REVERT: B 253 LEU cc_start: 0.7744 (mt) cc_final: 0.7439 (mt) REVERT: B 274 TYR cc_start: 0.6845 (t80) cc_final: 0.6277 (t80) REVERT: B 275 ASN cc_start: 0.8164 (t0) cc_final: 0.7749 (t0) REVERT: B 282 MET cc_start: 0.8183 (mtp) cc_final: 0.7951 (mtp) REVERT: B 286 GLU cc_start: 0.8328 (pp20) cc_final: 0.7480 (tm-30) REVERT: B 288 ARG cc_start: 0.7981 (mmt-90) cc_final: 0.6407 (mmt-90) REVERT: B 303 TYR cc_start: 0.8060 (m-80) cc_final: 0.7639 (m-80) REVERT: B 311 CYS cc_start: 0.4269 (p) cc_final: 0.3502 (m) REVERT: B 320 GLN cc_start: 0.6659 (mt0) cc_final: 0.6009 (mt0) REVERT: B 332 GLU cc_start: 0.7362 (mt-10) cc_final: 0.7067 (mt-10) REVERT: B 361 ILE cc_start: 0.8831 (mm) cc_final: 0.8626 (mm) REVERT: B 364 PHE cc_start: 0.8646 (m-80) cc_final: 0.7916 (m-80) REVERT: B 374 LEU cc_start: 0.7284 (mt) cc_final: 0.7077 (mp) REVERT: B 398 GLN cc_start: 0.8241 (mm-40) cc_final: 0.7955 (mm-40) REVERT: B 407 THR cc_start: 0.7899 (p) cc_final: 0.7453 (m) REVERT: B 411 TYR cc_start: 0.7438 (t80) cc_final: 0.6573 (t80) REVERT: B 426 GLN cc_start: 0.8017 (pt0) cc_final: 0.7317 (pp30) REVERT: B 436 LEU cc_start: 0.7926 (mt) cc_final: 0.7628 (mp) REVERT: B 444 THR cc_start: 0.7580 (m) cc_final: 0.7195 (m) REVERT: B 451 SER cc_start: 0.8130 (p) cc_final: 0.7651 (m) REVERT: B 452 TRP cc_start: 0.7943 (p90) cc_final: 0.7544 (p90) REVERT: B 467 LEU cc_start: 0.7324 (tp) cc_final: 0.7103 (tp) REVERT: B 481 PRO cc_start: 0.8108 (Cg_endo) cc_final: 0.7622 (Cg_exo) REVERT: B 483 ASP cc_start: 0.8434 (m-30) cc_final: 0.7703 (t0) REVERT: B 484 GLN cc_start: 0.8808 (mt0) cc_final: 0.8603 (mt0) REVERT: B 487 ARG cc_start: 0.7835 (mmt90) cc_final: 0.7302 (mtt90) REVERT: B 488 ASN cc_start: 0.7942 (t0) cc_final: 0.6965 (t0) REVERT: B 491 GLN cc_start: 0.6168 (mt0) cc_final: 0.5679 (mt0) REVERT: B 493 LEU cc_start: 0.8003 (tp) cc_final: 0.7503 (tp) REVERT: B 494 LEU cc_start: 0.8672 (mt) cc_final: 0.8446 (mt) REVERT: B 527 GLN cc_start: 0.7040 (pm20) cc_final: 0.6136 (pm20) REVERT: B 556 ASN cc_start: 0.8210 (t0) cc_final: 0.7544 (t0) REVERT: B 566 GLU cc_start: 0.7755 (mm-30) cc_final: 0.6514 (tm-30) REVERT: B 577 PHE cc_start: 0.8291 (m-80) cc_final: 0.7983 (m-80) REVERT: B 580 GLU cc_start: 0.8413 (tp30) cc_final: 0.7999 (tp30) REVERT: A 29 LYS cc_start: 0.8015 (pttm) cc_final: 0.7407 (pttm) REVERT: A 44 PHE cc_start: 0.8138 (m-80) cc_final: 0.7891 (m-80) REVERT: A 46 ASP cc_start: 0.7174 (t70) cc_final: 0.6499 (t70) REVERT: A 47 HIS cc_start: 0.7995 (t70) cc_final: 0.6886 (t70) REVERT: A 51 LEU cc_start: 0.8930 (tp) cc_final: 0.8683 (tp) REVERT: A 61 VAL cc_start: 0.8362 (m) cc_final: 0.8072 (p) REVERT: A 67 ILE cc_start: 0.8338 (mt) cc_final: 0.8108 (mm) REVERT: A 71 GLN cc_start: 0.6935 (mm110) cc_final: 0.6723 (mm110) REVERT: A 74 TYR cc_start: 0.8074 (m-80) cc_final: 0.7078 (m-80) REVERT: A 83 GLN cc_start: 0.7912 (mm110) cc_final: 0.7695 (mm110) REVERT: A 98 ARG cc_start: 0.7469 (ttt90) cc_final: 0.7147 (tpp80) REVERT: A 112 TYR cc_start: 0.7357 (m-80) cc_final: 0.6590 (m-10) REVERT: A 122 LEU cc_start: 0.7962 (mp) cc_final: 0.7473 (mm) REVERT: A 138 ARG cc_start: 0.8369 (mtt180) cc_final: 0.8050 (mtt-85) REVERT: A 176 MET cc_start: 0.8449 (ptp) cc_final: 0.8107 (ptt) REVERT: A 209 LYS cc_start: 0.8267 (mttt) cc_final: 0.7725 (mtmm) REVERT: A 217 GLN cc_start: 0.8217 (pt0) cc_final: 0.8002 (pm20) REVERT: A 229 SER cc_start: 0.7989 (p) cc_final: 0.7681 (t) REVERT: A 252 ARG cc_start: 0.7556 (mtp85) cc_final: 0.7177 (ttp-110) REVERT: A 257 GLU cc_start: 0.8507 (mm-30) cc_final: 0.8042 (mm-30) REVERT: A 261 LYS cc_start: 0.7253 (ptmt) cc_final: 0.6852 (ptmt) REVERT: A 268 MET cc_start: 0.6147 (mtm) cc_final: 0.4859 (mtm) REVERT: A 277 MET cc_start: 0.6343 (mtt) cc_final: 0.5152 (mtt) REVERT: A 293 LYS cc_start: 0.7840 (mtpp) cc_final: 0.6869 (mtpp) REVERT: A 338 ASN cc_start: 0.7335 (p0) cc_final: 0.7086 (p0) REVERT: A 340 ILE cc_start: 0.7437 (mp) cc_final: 0.7191 (mp) REVERT: A 351 ILE cc_start: 0.7696 (tt) cc_final: 0.7103 (mp) REVERT: A 358 HIS cc_start: 0.8491 (m90) cc_final: 0.8288 (m-70) REVERT: A 360 LYS cc_start: 0.8697 (tttt) cc_final: 0.8393 (tttt) REVERT: A 368 ASP cc_start: 0.5204 (m-30) cc_final: 0.4630 (m-30) REVERT: A 371 ILE cc_start: 0.7910 (mm) cc_final: 0.7116 (mm) REVERT: A 396 LYS cc_start: 0.8426 (tppp) cc_final: 0.7927 (tppp) REVERT: A 404 PHE cc_start: 0.7596 (p90) cc_final: 0.6358 (p90) REVERT: A 416 ASP cc_start: 0.7151 (p0) cc_final: 0.6854 (p0) REVERT: A 417 LEU cc_start: 0.7527 (mt) cc_final: 0.7228 (mp) REVERT: A 421 GLU cc_start: 0.8668 (tt0) cc_final: 0.7610 (tt0) REVERT: A 436 PHE cc_start: 0.8111 (m-80) cc_final: 0.7849 (m-80) REVERT: A 445 ILE cc_start: 0.7790 (pt) cc_final: 0.7501 (pt) REVERT: A 457 SER cc_start: 0.8143 (m) cc_final: 0.7860 (m) REVERT: A 463 ILE cc_start: 0.6920 (mt) cc_final: 0.6619 (mp) REVERT: A 476 ASN cc_start: 0.7820 (t0) cc_final: 0.7397 (t0) REVERT: A 487 LYS cc_start: 0.7792 (mtmm) cc_final: 0.7555 (mtmm) REVERT: A 489 LYS cc_start: 0.7742 (ttmm) cc_final: 0.7530 (mmmm) REVERT: A 496 GLU cc_start: 0.7511 (mp0) cc_final: 0.7181 (mp0) REVERT: A 551 GLU cc_start: 0.8689 (pt0) cc_final: 0.8262 (pm20) REVERT: A 559 HIS cc_start: 0.7598 (t70) cc_final: 0.7214 (t-170) REVERT: C 18 GLN cc_start: 0.8039 (tt0) cc_final: 0.6969 (tt0) REVERT: C 25 MET cc_start: 0.7907 (mmp) cc_final: 0.7405 (mmp) outliers start: 1 outliers final: 0 residues processed: 379 average time/residue: 0.0967 time to fit residues: 48.8817 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 : 0.307 ------------------------------------------------------------------------------- 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: 0.7980 chunk 49 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 113 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 88 optimal weight: 0.2980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 158 ASN ** 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 A 163 GLN A 280 ASN A 584 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.126333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.100619 restraints weight = 16614.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.106027 restraints weight = 9389.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.109913 restraints weight = 5942.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.112637 restraints weight = 4049.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.114689 restraints weight = 2927.738| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6710 moved from start: 0.4765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9413 Z= 0.193 Angle : 0.674 9.395 12798 Z= 0.345 Chirality : 0.048 0.271 1417 Planarity : 0.005 0.081 1669 Dihedral : 5.272 22.328 1262 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.65 % Favored : 89.35 % Rotamer: Outliers : 0.10 % Allowed : 1.18 % Favored : 98.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.61 (0.23), residues: 1164 helix: -2.11 (0.65), residues: 54 sheet: -1.70 (0.74), residues: 52 loop : -1.93 (0.18), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 100 TYR 0.019 0.002 TYR A 117 PHE 0.011 0.002 PHE B 108 TRP 0.016 0.002 TRP A 200 HIS 0.009 0.001 HIS A 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.19 ( 9358) covalent geometry : angle 0.65463 / 0.34 (12680) SS BOND : bond 0.00312 / 0.21 ( 47) SS BOND : angle 1.53201 / 0.96 ( 94) hydrogen bonds : bond 0.03737 / 2.41 ( 81) hydrogen bonds : angle 5.96705 / 3.76 ( 174) link_ALPHA1-3 : bond 0.01414 / 0.74 ( 1) link_ALPHA1-3 : angle 2.31864 / 1.20 ( 3) link_BETA1-3 : bond 0.00517 / 0.27 ( 1) link_BETA1-3 : angle 3.43843 / 1.81 ( 3) link_BETA1-4 : bond 0.00153 / 0.08 ( 2) link_BETA1-4 : angle 1.25854 / 0.77 ( 6) link_NAG-ASN : bond 0.00395 / 0.21 ( 4) link_NAG-ASN : angle 2.98154 / 1.60 ( 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 393 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 392 time to evaluate : 0.326 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: 0.7271 (pp30) cc_final: 0.5566 (tm-30) REVERT: B 31 MET cc_start: 0.7535 (mtp) cc_final: 0.6729 (ptp) REVERT: B 32 LYS cc_start: 0.8278 (mmtm) cc_final: 0.7881 (mmtt) REVERT: B 44 ASP cc_start: 0.7384 (t0) cc_final: 0.6656 (t0) REVERT: B 45 MET cc_start: 0.8356 (tmm) cc_final: 0.8111 (tmm) REVERT: B 46 LEU cc_start: 0.8793 (mt) cc_final: 0.8262 (mt) REVERT: B 47 ARG cc_start: 0.8039 (ttp80) cc_final: 0.7496 (ttp80) REVERT: B 54 GLN cc_start: 0.7297 (mt0) cc_final: 0.6968 (mp-120) REVERT: B 55 VAL cc_start: 0.7702 (t) cc_final: 0.7020 (p) REVERT: B 61 GLU cc_start: 0.6940 (tm-30) cc_final: 0.3715 (tm-30) REVERT: B 75 GLN cc_start: 0.7970 (pt0) cc_final: 0.7645 (pt0) REVERT: B 81 GLN cc_start: 0.6646 (mt0) cc_final: 0.6220 (mt0) REVERT: B 103 ARG cc_start: 0.7360 (mtt90) cc_final: 0.6955 (ttm110) REVERT: B 105 THR cc_start: 0.8061 (p) cc_final: 0.7677 (t) REVERT: B 106 GLN cc_start: 0.7844 (mt0) cc_final: 0.7412 (mp-120) REVERT: B 112 TYR cc_start: 0.7351 (m-80) cc_final: 0.7009 (m-80) REVERT: B 143 ARG cc_start: 0.7761 (mtt180) cc_final: 0.7472 (mtt180) REVERT: B 148 ILE cc_start: 0.7669 (mt) cc_final: 0.7453 (mm) REVERT: B 185 ASP cc_start: 0.7309 (t0) cc_final: 0.6952 (t0) REVERT: B 208 SER cc_start: 0.7909 (m) cc_final: 0.7641 (t) REVERT: B 211 ASP cc_start: 0.7946 (m-30) cc_final: 0.7403 (m-30) REVERT: B 213 GLN cc_start: 0.8155 (tm-30) cc_final: 0.7871 (tm-30) REVERT: B 237 HIS cc_start: 0.7413 (t-90) cc_final: 0.7136 (t70) REVERT: B 248 LYS cc_start: 0.8754 (mmtt) cc_final: 0.8050 (mmtt) REVERT: B 253 LEU cc_start: 0.7760 (mt) cc_final: 0.7533 (mt) REVERT: B 267 HIS cc_start: 0.7520 (m170) cc_final: 0.7232 (m170) REVERT: B 271 LEU cc_start: 0.8610 (mt) cc_final: 0.8391 (pt) REVERT: B 274 TYR cc_start: 0.6835 (t80) cc_final: 0.5794 (t80) REVERT: B 282 MET cc_start: 0.8167 (mtp) cc_final: 0.7866 (mtp) REVERT: B 286 GLU cc_start: 0.8359 (pp20) cc_final: 0.7565 (tm-30) REVERT: B 288 ARG cc_start: 0.7935 (mmt-90) cc_final: 0.7576 (mmt-90) REVERT: B 303 TYR cc_start: 0.8014 (m-80) cc_final: 0.7664 (m-80) REVERT: B 311 CYS cc_start: 0.4202 (p) cc_final: 0.3504 (m) REVERT: B 320 GLN cc_start: 0.6739 (mt0) cc_final: 0.6043 (mt0) REVERT: B 332 GLU cc_start: 0.7363 (mt-10) cc_final: 0.6982 (mt-10) REVERT: B 364 PHE cc_start: 0.8682 (m-80) cc_final: 0.7976 (m-80) REVERT: B 398 GLN cc_start: 0.8201 (mm-40) cc_final: 0.7930 (mm-40) REVERT: B 405 GLU cc_start: 0.6206 (tp30) cc_final: 0.5589 (tp30) REVERT: B 407 THR cc_start: 0.7893 (p) cc_final: 0.7440 (m) REVERT: B 411 TYR cc_start: 0.7314 (t80) cc_final: 0.6533 (t80) REVERT: B 426 GLN cc_start: 0.7963 (pt0) cc_final: 0.7200 (pp30) REVERT: B 430 VAL cc_start: 0.7827 (t) cc_final: 0.7000 (p) REVERT: B 436 LEU cc_start: 0.7970 (mt) cc_final: 0.7649 (mp) REVERT: B 444 THR cc_start: 0.7566 (m) cc_final: 0.7189 (m) REVERT: B 451 SER cc_start: 0.8214 (p) cc_final: 0.7717 (m) REVERT: B 452 TRP cc_start: 0.7943 (p90) cc_final: 0.7533 (p90) REVERT: B 481 PRO cc_start: 0.8097 (Cg_endo) cc_final: 0.7672 (Cg_exo) REVERT: B 484 GLN cc_start: 0.8805 (mt0) cc_final: 0.8449 (mm-40) REVERT: B 486 PHE cc_start: 0.8370 (m-10) cc_final: 0.8060 (m-10) REVERT: B 487 ARG cc_start: 0.7842 (mmt90) cc_final: 0.7357 (mmt90) REVERT: B 488 ASN cc_start: 0.7966 (t0) cc_final: 0.7432 (t0) REVERT: B 491 GLN cc_start: 0.6174 (mt0) cc_final: 0.5377 (mt0) REVERT: B 493 LEU cc_start: 0.8114 (tp) cc_final: 0.7785 (tp) REVERT: B 494 LEU cc_start: 0.8628 (mt) cc_final: 0.8385 (mt) REVERT: B 527 GLN cc_start: 0.7210 (pm20) cc_final: 0.6595 (pm20) REVERT: B 556 ASN cc_start: 0.8272 (t0) cc_final: 0.7597 (t0) REVERT: B 577 PHE cc_start: 0.8344 (m-80) cc_final: 0.7988 (m-80) REVERT: B 580 GLU cc_start: 0.8354 (tp30) cc_final: 0.7986 (tp30) REVERT: A 29 LYS cc_start: 0.8015 (pttm) cc_final: 0.7435 (pttm) REVERT: A 36 ASN cc_start: 0.8460 (p0) cc_final: 0.8083 (p0) REVERT: A 46 ASP cc_start: 0.7181 (t70) cc_final: 0.6558 (t70) REVERT: A 47 HIS cc_start: 0.8033 (t70) cc_final: 0.6948 (t70) REVERT: A 51 LEU cc_start: 0.8939 (tp) cc_final: 0.8637 (tp) REVERT: A 55 PHE cc_start: 0.7916 (m-10) cc_final: 0.7515 (m-10) REVERT: A 61 VAL cc_start: 0.8332 (m) cc_final: 0.8016 (p) REVERT: A 74 TYR cc_start: 0.8126 (m-80) cc_final: 0.7136 (m-80) REVERT: A 78 PHE cc_start: 0.8676 (p90) cc_final: 0.8224 (p90) REVERT: A 80 LYS cc_start: 0.8482 (mtmm) cc_final: 0.8174 (mtmm) REVERT: A 107 ILE cc_start: 0.8568 (mm) cc_final: 0.8245 (mm) REVERT: A 112 TYR cc_start: 0.7355 (m-80) cc_final: 0.6951 (m-80) REVERT: A 119 LEU cc_start: 0.7553 (tp) cc_final: 0.6946 (tp) REVERT: A 143 ILE cc_start: 0.8971 (mt) cc_final: 0.8539 (mm) REVERT: A 163 GLN cc_start: 0.8463 (tt0) cc_final: 0.7992 (tt0) REVERT: A 166 ASP cc_start: 0.8398 (p0) cc_final: 0.7923 (p0) REVERT: A 176 MET cc_start: 0.8579 (ptp) cc_final: 0.7944 (ptp) REVERT: A 209 LYS cc_start: 0.8275 (mttt) cc_final: 0.7747 (mtmt) REVERT: A 229 SER cc_start: 0.7994 (p) cc_final: 0.7642 (t) REVERT: A 230 ASP cc_start: 0.8200 (m-30) cc_final: 0.7172 (p0) REVERT: A 252 ARG cc_start: 0.7516 (mtp85) cc_final: 0.7081 (mtp85) REVERT: A 253 LYS cc_start: 0.8081 (tptm) cc_final: 0.7242 (tptm) REVERT: A 257 GLU cc_start: 0.8435 (mm-30) cc_final: 0.8003 (mm-30) REVERT: A 261 LYS cc_start: 0.7475 (ptmt) cc_final: 0.6890 (ptmt) REVERT: A 262 ASP cc_start: 0.8322 (t0) cc_final: 0.7674 (t70) REVERT: A 268 MET cc_start: 0.6244 (mtm) cc_final: 0.4940 (mtm) REVERT: A 277 MET cc_start: 0.6428 (mtt) cc_final: 0.5201 (mtt) REVERT: A 293 LYS cc_start: 0.7892 (mtpp) cc_final: 0.6968 (mtpp) REVERT: A 338 ASN cc_start: 0.7411 (p0) cc_final: 0.7082 (p0) REVERT: A 360 LYS cc_start: 0.8703 (tttt) cc_final: 0.8388 (tttt) REVERT: A 396 LYS cc_start: 0.8432 (tppp) cc_final: 0.7891 (tppp) REVERT: A 404 PHE cc_start: 0.7514 (p90) cc_final: 0.6816 (p90) REVERT: A 417 LEU cc_start: 0.7621 (mt) cc_final: 0.7242 (mp) REVERT: A 421 GLU cc_start: 0.8528 (tt0) cc_final: 0.7993 (tt0) REVERT: A 424 GLU cc_start: 0.7642 (mt-10) cc_final: 0.7439 (mt-10) REVERT: A 429 ARG cc_start: 0.8174 (mtt180) cc_final: 0.7603 (mtt-85) REVERT: A 436 PHE cc_start: 0.8091 (m-80) cc_final: 0.7609 (m-80) REVERT: A 445 ILE cc_start: 0.7935 (pt) cc_final: 0.7635 (pt) REVERT: A 454 LYS cc_start: 0.8704 (mmtt) cc_final: 0.8186 (mmtt) REVERT: A 456 ILE cc_start: 0.8624 (mm) cc_final: 0.8080 (pt) REVERT: A 457 SER cc_start: 0.8247 (m) cc_final: 0.7872 (m) REVERT: A 463 ILE cc_start: 0.7087 (mt) cc_final: 0.6841 (mt) REVERT: A 476 ASN cc_start: 0.7798 (t0) cc_final: 0.7346 (t0) REVERT: A 487 LYS cc_start: 0.7838 (mtmm) cc_final: 0.7630 (mtmm) REVERT: A 489 LYS cc_start: 0.7751 (ttmm) cc_final: 0.7517 (mtpp) REVERT: A 496 GLU cc_start: 0.7458 (mp0) cc_final: 0.7118 (mp0) REVERT: A 551 GLU cc_start: 0.8663 (pt0) cc_final: 0.8252 (pm20) REVERT: A 559 HIS cc_start: 0.7639 (t70) cc_final: 0.7232 (t-170) REVERT: C 18 GLN cc_start: 0.7983 (tt0) cc_final: 0.7295 (tt0) REVERT: C 25 MET cc_start: 0.7799 (mmp) cc_final: 0.7460 (mmp) outliers start: 1 outliers final: 0 residues processed: 392 average time/residue: 0.1062 time to fit residues: 55.1196 Evaluate side-chains 362 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 362 time to evaluate : 0.227 ------------------------------------------------------------------------------- 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: 0.5980 chunk 64 optimal weight: 0.2980 chunk 47 optimal weight: 0.0980 chunk 16 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 80 optimal weight: 0.5980 chunk 35 optimal weight: 0.0270 chunk 1 optimal weight: 0.1980 chunk 108 optimal weight: 0.4980 overall best weight: 0.2238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 ASN ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 GLN A 435 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.128805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.102991 restraints weight = 16518.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.108459 restraints weight = 9365.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.112396 restraints weight = 5943.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.115183 restraints weight = 4052.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.117273 restraints weight = 2922.267| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6668 moved from start: 0.4848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9413 Z= 0.108 Angle : 0.626 10.089 12798 Z= 0.312 Chirality : 0.046 0.270 1417 Planarity : 0.004 0.069 1669 Dihedral : 4.897 23.804 1262 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % 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 are not related in a simple way. whole: -2.41 (0.24), residues: 1164 helix: -1.69 (0.74), residues: 48 sheet: -1.06 (0.63), residues: 79 loop : -1.84 (0.19), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 224 TYR 0.017 0.001 TYR A 113 PHE 0.022 0.001 PHE B 73 TRP 0.011 0.001 TRP A 164 HIS 0.005 0.001 HIS B 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 ( 9358) covalent geometry : angle 0.60972 / 0.31 (12680) SS BOND : bond 0.00249 / 0.17 ( 47) SS BOND : angle 1.37888 / 0.85 ( 94) hydrogen bonds : bond 0.03468 / 2.17 ( 81) hydrogen bonds : angle 5.44121 / 3.46 ( 174) link_ALPHA1-3 : bond 0.00889 / 0.47 ( 1) link_ALPHA1-3 : angle 1.75619 / 0.90 ( 3) link_BETA1-3 : bond 0.00750 / 0.39 ( 1) link_BETA1-3 : angle 3.81241 / 2.01 ( 3) link_BETA1-4 : bond 0.00399 / 0.21 ( 2) link_BETA1-4 : angle 1.29310 / 0.77 ( 6) link_NAG-ASN : bond 0.00348 / 0.17 ( 4) link_NAG-ASN : angle 2.31915 / 1.31 ( 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 386 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 385 time to evaluate : 0.479 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: B 24 GLN cc_start: 0.7347 (pp30) cc_final: 0.6381 (tm-30) REVERT: B 31 MET cc_start: 0.7462 (mtp) cc_final: 0.6602 (ptp) REVERT: B 44 ASP cc_start: 0.7406 (t0) cc_final: 0.6533 (t0) REVERT: B 45 MET cc_start: 0.8150 (tmm) cc_final: 0.7940 (tmm) REVERT: B 46 LEU cc_start: 0.8549 (mt) cc_final: 0.8179 (mt) REVERT: B 47 ARG cc_start: 0.7855 (ttp80) cc_final: 0.7333 (ttp80) REVERT: B 55 VAL cc_start: 0.7818 (t) cc_final: 0.7153 (p) REVERT: B 59 ASN cc_start: 0.7381 (m-40) cc_final: 0.6923 (m-40) REVERT: B 61 GLU cc_start: 0.6920 (tm-30) cc_final: 0.3505 (tm-30) REVERT: B 75 GLN cc_start: 0.7875 (pt0) cc_final: 0.7557 (pt0) REVERT: B 81 GLN cc_start: 0.6481 (mt0) cc_final: 0.6165 (mt0) REVERT: B 105 THR cc_start: 0.7946 (p) cc_final: 0.7567 (t) REVERT: B 106 GLN cc_start: 0.7834 (mt0) cc_final: 0.7379 (mp10) REVERT: B 109 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7605 (mm-30) REVERT: B 112 TYR cc_start: 0.7301 (m-80) cc_final: 0.6762 (m-80) REVERT: B 143 ARG cc_start: 0.7632 (mtt180) cc_final: 0.7415 (mtt180) REVERT: B 148 ILE cc_start: 0.7618 (mt) cc_final: 0.7372 (mm) REVERT: B 208 SER cc_start: 0.7882 (m) cc_final: 0.7647 (t) REVERT: B 211 ASP cc_start: 0.7830 (m-30) cc_final: 0.7345 (m-30) REVERT: B 213 GLN cc_start: 0.8122 (tm-30) cc_final: 0.7537 (tm-30) REVERT: B 248 LYS cc_start: 0.8746 (mmtt) cc_final: 0.8065 (mmtt) REVERT: B 250 SER cc_start: 0.8316 (p) cc_final: 0.8116 (p) REVERT: B 265 GLU cc_start: 0.6914 (pm20) cc_final: 0.6184 (pm20) REVERT: B 267 HIS cc_start: 0.7570 (m170) cc_final: 0.7058 (m170) REVERT: B 271 LEU cc_start: 0.8633 (mt) cc_final: 0.8399 (mt) REVERT: B 274 TYR cc_start: 0.6780 (t80) cc_final: 0.6219 (t80) REVERT: B 275 ASN cc_start: 0.7978 (t0) cc_final: 0.7711 (t0) REVERT: B 286 GLU cc_start: 0.8367 (pp20) cc_final: 0.7515 (tm-30) REVERT: B 303 TYR cc_start: 0.7937 (m-80) cc_final: 0.7494 (m-80) REVERT: B 313 LEU cc_start: 0.8220 (mt) cc_final: 0.7949 (pt) REVERT: B 320 GLN cc_start: 0.6671 (mt0) cc_final: 0.5891 (mt0) REVERT: B 332 GLU cc_start: 0.7224 (mt-10) cc_final: 0.6931 (mt-10) REVERT: B 364 PHE cc_start: 0.8646 (m-80) cc_final: 0.7986 (m-80) REVERT: B 398 GLN cc_start: 0.8131 (mm-40) cc_final: 0.7765 (mm-40) REVERT: B 411 TYR cc_start: 0.7214 (t80) cc_final: 0.6481 (t80) REVERT: B 426 GLN cc_start: 0.7975 (pt0) cc_final: 0.7097 (pp30) REVERT: B 436 LEU cc_start: 0.8007 (mt) cc_final: 0.7610 (mp) REVERT: B 444 THR cc_start: 0.7444 (m) cc_final: 0.6936 (m) REVERT: B 451 SER cc_start: 0.8230 (p) cc_final: 0.7691 (m) REVERT: B 452 TRP cc_start: 0.7862 (p90) cc_final: 0.7424 (p90) REVERT: B 481 PRO cc_start: 0.8065 (Cg_endo) cc_final: 0.7654 (Cg_exo) REVERT: B 483 ASP cc_start: 0.8342 (m-30) cc_final: 0.7295 (t0) REVERT: B 484 GLN cc_start: 0.8729 (mt0) cc_final: 0.8041 (mp-120) REVERT: B 486 PHE cc_start: 0.8209 (m-10) cc_final: 0.7960 (m-10) REVERT: B 487 ARG cc_start: 0.7885 (mmt90) cc_final: 0.7301 (ttm-80) REVERT: B 488 ASN cc_start: 0.8105 (t0) cc_final: 0.7101 (t0) REVERT: B 491 GLN cc_start: 0.6319 (mt0) cc_final: 0.5632 (mt0) REVERT: B 493 LEU cc_start: 0.8026 (tp) cc_final: 0.7704 (tp) REVERT: B 494 LEU cc_start: 0.8656 (mt) cc_final: 0.8424 (mt) REVERT: B 527 GLN cc_start: 0.7262 (pm20) cc_final: 0.6517 (pm20) REVERT: B 556 ASN cc_start: 0.8281 (t0) cc_final: 0.7657 (t0) REVERT: B 577 PHE cc_start: 0.8329 (m-80) cc_final: 0.7988 (m-80) REVERT: B 580 GLU cc_start: 0.8364 (tp30) cc_final: 0.7947 (tp30) REVERT: A 29 LYS cc_start: 0.7769 (pttm) cc_final: 0.7391 (pttm) REVERT: A 45 GLU cc_start: 0.8338 (mp0) cc_final: 0.7987 (mp0) REVERT: A 46 ASP cc_start: 0.7296 (t70) cc_final: 0.6739 (t70) REVERT: A 47 HIS cc_start: 0.7798 (t70) cc_final: 0.6749 (t70) REVERT: A 51 LEU cc_start: 0.8795 (tp) cc_final: 0.8457 (tp) REVERT: A 61 VAL cc_start: 0.8330 (m) cc_final: 0.8040 (p) REVERT: A 74 TYR cc_start: 0.8044 (m-80) cc_final: 0.7118 (m-80) REVERT: A 80 LYS cc_start: 0.8522 (mtmm) cc_final: 0.8128 (mtmm) REVERT: A 98 ARG cc_start: 0.7436 (tpp80) cc_final: 0.7085 (tpp80) REVERT: A 107 ILE cc_start: 0.8597 (mm) cc_final: 0.8205 (mm) REVERT: A 112 TYR cc_start: 0.7369 (m-80) cc_final: 0.7023 (m-80) REVERT: A 114 GLU cc_start: 0.7152 (tt0) cc_final: 0.6479 (tt0) REVERT: A 119 LEU cc_start: 0.7767 (tp) cc_final: 0.7273 (tp) REVERT: A 143 ILE cc_start: 0.8967 (mt) cc_final: 0.8527 (mm) REVERT: A 163 GLN cc_start: 0.8522 (tt0) cc_final: 0.7995 (tt0) REVERT: A 176 MET cc_start: 0.8442 (ptp) cc_final: 0.8115 (ptt) REVERT: A 196 ASN cc_start: 0.8872 (m-40) cc_final: 0.8613 (m110) REVERT: A 209 LYS cc_start: 0.8151 (mttt) cc_final: 0.7679 (mtmt) REVERT: A 229 SER cc_start: 0.7772 (p) cc_final: 0.7451 (t) REVERT: A 230 ASP cc_start: 0.8001 (m-30) cc_final: 0.7125 (p0) REVERT: A 252 ARG cc_start: 0.7512 (mtp85) cc_final: 0.7018 (mtm110) REVERT: A 257 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8116 (mm-30) REVERT: A 261 LYS cc_start: 0.7496 (ptmt) cc_final: 0.6961 (ptmt) REVERT: A 262 ASP cc_start: 0.8330 (t0) cc_final: 0.7316 (t0) REVERT: A 268 MET cc_start: 0.6108 (mtm) cc_final: 0.4723 (mtm) REVERT: A 277 MET cc_start: 0.6223 (mtt) cc_final: 0.5020 (mtt) REVERT: A 293 LYS cc_start: 0.7854 (mtpp) cc_final: 0.6922 (mtpp) REVERT: A 338 ASN cc_start: 0.7436 (p0) cc_final: 0.7119 (p0) REVERT: A 360 LYS cc_start: 0.8651 (tttt) cc_final: 0.8342 (tttt) REVERT: A 368 ASP cc_start: 0.5081 (m-30) cc_final: 0.4699 (m-30) REVERT: A 388 ASP cc_start: 0.8475 (t70) cc_final: 0.7702 (t0) REVERT: A 391 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7489 (mm-30) REVERT: A 396 LYS cc_start: 0.8409 (tppp) cc_final: 0.7838 (tppp) REVERT: A 404 PHE cc_start: 0.7593 (p90) cc_final: 0.6266 (p90) REVERT: A 421 GLU cc_start: 0.8560 (tt0) cc_final: 0.7954 (tt0) REVERT: A 454 LYS cc_start: 0.8695 (mmtt) cc_final: 0.8127 (mmtt) REVERT: A 456 ILE cc_start: 0.8632 (mm) cc_final: 0.8057 (pt) REVERT: A 457 SER cc_start: 0.8137 (m) cc_final: 0.7724 (m) REVERT: A 476 ASN cc_start: 0.7737 (t0) cc_final: 0.6765 (t0) REVERT: A 479 LYS cc_start: 0.7825 (mtpt) cc_final: 0.6924 (mtpt) REVERT: A 486 GLN cc_start: 0.6777 (tm-30) cc_final: 0.6532 (tm-30) REVERT: A 487 LYS cc_start: 0.7788 (mtmm) cc_final: 0.7499 (mtmm) REVERT: A 496 GLU cc_start: 0.7364 (mp0) cc_final: 0.7006 (mp0) REVERT: A 551 GLU cc_start: 0.8633 (pt0) cc_final: 0.8223 (pm20) REVERT: A 559 HIS cc_start: 0.7538 (t70) cc_final: 0.7177 (t-170) REVERT: A 567 MET cc_start: 0.7290 (tmm) cc_final: 0.7015 (tmm) REVERT: C 18 GLN cc_start: 0.8036 (tt0) cc_final: 0.6978 (tt0) REVERT: C 25 MET cc_start: 0.7837 (mmp) cc_final: 0.7346 (mmp) outliers start: 1 outliers final: 0 residues processed: 385 average time/residue: 0.0992 time to fit residues: 51.3396 Evaluate side-chains 353 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 353 time to evaluate : 0.348 ------------------------------------------------------------------------------- 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: 1.9990 chunk 81 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 114 optimal weight: 0.0470 chunk 113 optimal weight: 0.6980 chunk 84 optimal weight: 0.2980 chunk 9 optimal weight: 0.5980 chunk 77 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN B 237 HIS B 239 GLN B 257 HIS ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 83 GLN A 280 ASN ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 GLN A 435 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.126647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.100713 restraints weight = 16500.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.106112 restraints weight = 9340.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.109992 restraints weight = 5919.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.112716 restraints weight = 4043.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.114758 restraints weight = 2923.489| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6717 moved from start: 0.5272 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= 0.163 Angle : 0.670 9.385 12798 Z= 0.337 Chirality : 0.047 0.269 1417 Planarity : 0.005 0.064 1669 Dihedral : 5.154 20.675 1262 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.91 % Favored : 89.09 % Rotamer: Outliers : 0.10 % Allowed : 0.98 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.42 (0.24), residues: 1164 helix: -2.23 (0.63), residues: 60 sheet: -1.04 (0.74), residues: 52 loop : -1.79 (0.19), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 103 TYR 0.019 0.002 TYR A 117 PHE 0.023 0.001 PHE B 73 TRP 0.041 0.003 TRP A 200 HIS 0.007 0.001 HIS A 507 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.16 ( 9358) covalent geometry : angle 0.65315 / 0.33 (12680) SS BOND : bond 0.00263 / 0.18 ( 47) SS BOND : angle 1.38541 / 0.88 ( 94) hydrogen bonds : bond 0.03634 / 2.33 ( 81) hydrogen bonds : angle 5.66169 / 3.58 ( 174) link_ALPHA1-3 : bond 0.01287 / 0.68 ( 1) link_ALPHA1-3 : angle 2.24797 / 1.16 ( 3) link_BETA1-3 : bond 0.00551 / 0.29 ( 1) link_BETA1-3 : angle 3.45606 / 1.82 ( 3) link_BETA1-4 : bond 0.00244 / 0.13 ( 2) link_BETA1-4 : angle 1.23034 / 0.73 ( 6) link_NAG-ASN : bond 0.00331 / 0.17 ( 4) link_NAG-ASN : angle 2.71998 / 1.47 ( 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 368 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 367 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 GLN cc_start: 0.7332 (pp30) cc_final: 0.6167 (mm-40) REVERT: B 31 MET cc_start: 0.7767 (mtp) cc_final: 0.6664 (ptp) REVERT: B 44 ASP cc_start: 0.7489 (t0) cc_final: 0.6612 (t0) REVERT: B 45 MET cc_start: 0.8315 (tmm) cc_final: 0.8054 (tmm) REVERT: B 46 LEU cc_start: 0.8596 (mt) cc_final: 0.8182 (mt) REVERT: B 47 ARG cc_start: 0.7884 (ttp80) cc_final: 0.7399 (ttp80) REVERT: B 55 VAL cc_start: 0.7740 (t) cc_final: 0.7469 (p) REVERT: B 61 GLU cc_start: 0.6959 (tm-30) cc_final: 0.3602 (tm-30) REVERT: B 81 GLN cc_start: 0.6496 (mt0) cc_final: 0.6159 (mt0) REVERT: B 105 THR cc_start: 0.7932 (p) cc_final: 0.7604 (t) REVERT: B 106 GLN cc_start: 0.7811 (mt0) cc_final: 0.7408 (mp10) REVERT: B 109 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7592 (mm-30) REVERT: B 112 TYR cc_start: 0.7474 (m-80) cc_final: 0.6871 (m-80) REVERT: B 139 GLU cc_start: 0.7233 (mp0) cc_final: 0.6935 (mp0) REVERT: B 143 ARG cc_start: 0.7730 (mtt180) cc_final: 0.7350 (ttm110) REVERT: B 208 SER cc_start: 0.7888 (m) cc_final: 0.7628 (t) REVERT: B 211 ASP cc_start: 0.7898 (m-30) cc_final: 0.7667 (m-30) REVERT: B 213 GLN cc_start: 0.8051 (tm-30) cc_final: 0.7419 (tm-30) REVERT: B 237 HIS cc_start: 0.7333 (t-90) cc_final: 0.6806 (t70) REVERT: B 239 GLN cc_start: 0.7864 (mm-40) cc_final: 0.7419 (mp10) REVERT: B 248 LYS cc_start: 0.8791 (mmtt) cc_final: 0.8081 (mmtt) REVERT: B 250 SER cc_start: 0.8463 (p) cc_final: 0.8262 (p) REVERT: B 265 GLU cc_start: 0.7079 (pm20) cc_final: 0.6275 (pm20) REVERT: B 271 LEU cc_start: 0.8653 (mt) cc_final: 0.8346 (pt) REVERT: B 274 TYR cc_start: 0.6623 (t80) cc_final: 0.6205 (t80) REVERT: B 286 GLU cc_start: 0.8392 (pp20) cc_final: 0.7579 (tm-30) REVERT: B 288 ARG cc_start: 0.7930 (mpt-90) cc_final: 0.7474 (mmt-90) REVERT: B 303 TYR cc_start: 0.8041 (m-80) cc_final: 0.7533 (m-80) REVERT: B 320 GLN cc_start: 0.6621 (mt0) cc_final: 0.5992 (mt0) REVERT: B 332 GLU cc_start: 0.7252 (mt-10) cc_final: 0.6970 (mt-10) REVERT: B 364 PHE cc_start: 0.8732 (m-80) cc_final: 0.8044 (m-80) REVERT: B 393 GLN cc_start: 0.8049 (mm-40) cc_final: 0.7805 (mm-40) REVERT: B 398 GLN cc_start: 0.8182 (mm-40) cc_final: 0.7769 (mm-40) REVERT: B 411 TYR cc_start: 0.7241 (t80) cc_final: 0.6543 (t80) REVERT: B 426 GLN cc_start: 0.7946 (pt0) cc_final: 0.7287 (pp30) REVERT: B 430 VAL cc_start: 0.7588 (t) cc_final: 0.7323 (p) REVERT: B 436 LEU cc_start: 0.7978 (mt) cc_final: 0.7644 (mp) REVERT: B 444 THR cc_start: 0.7543 (m) cc_final: 0.6093 (m) REVERT: B 451 SER cc_start: 0.8249 (p) cc_final: 0.7791 (m) REVERT: B 452 TRP cc_start: 0.7943 (p90) cc_final: 0.7515 (p90) REVERT: B 467 LEU cc_start: 0.7298 (tp) cc_final: 0.6393 (pp) REVERT: B 481 PRO cc_start: 0.8030 (Cg_endo) cc_final: 0.7554 (Cg_exo) REVERT: B 482 TRP cc_start: 0.8407 (m100) cc_final: 0.7937 (m100) REVERT: B 483 ASP cc_start: 0.8472 (m-30) cc_final: 0.7631 (t0) REVERT: B 484 GLN cc_start: 0.8771 (mt0) cc_final: 0.8230 (mm-40) REVERT: B 486 PHE cc_start: 0.8324 (m-10) cc_final: 0.7582 (m-10) REVERT: B 493 LEU cc_start: 0.8190 (tp) cc_final: 0.7495 (tp) REVERT: B 527 GLN cc_start: 0.7224 (pm20) cc_final: 0.6560 (pm20) REVERT: B 556 ASN cc_start: 0.8309 (t0) cc_final: 0.7810 (t0) REVERT: B 577 PHE cc_start: 0.8360 (m-80) cc_final: 0.8017 (m-80) REVERT: B 580 GLU cc_start: 0.8382 (tp30) cc_final: 0.7997 (tp30) REVERT: A 28 LYS cc_start: 0.7899 (mtmm) cc_final: 0.7228 (ptpp) REVERT: A 45 GLU cc_start: 0.8389 (mp0) cc_final: 0.8025 (mp0) REVERT: A 46 ASP cc_start: 0.7212 (t70) cc_final: 0.6782 (t70) REVERT: A 47 HIS cc_start: 0.7923 (t70) cc_final: 0.6860 (t70) REVERT: A 51 LEU cc_start: 0.8955 (tp) cc_final: 0.8555 (tp) REVERT: A 55 PHE cc_start: 0.7939 (m-10) cc_final: 0.7655 (m-10) REVERT: A 61 VAL cc_start: 0.8304 (m) cc_final: 0.8014 (p) REVERT: A 65 LEU cc_start: 0.7832 (tp) cc_final: 0.6971 (pp) REVERT: A 74 TYR cc_start: 0.8052 (m-80) cc_final: 0.7190 (m-80) REVERT: A 75 ASP cc_start: 0.7807 (t70) cc_final: 0.7422 (t0) REVERT: A 76 LEU cc_start: 0.8380 (mt) cc_final: 0.7975 (mt) REVERT: A 78 PHE cc_start: 0.8684 (p90) cc_final: 0.8176 (p90) REVERT: A 80 LYS cc_start: 0.8411 (mtmm) cc_final: 0.7962 (mtmm) REVERT: A 90 LEU cc_start: 0.8142 (tp) cc_final: 0.7870 (tp) REVERT: A 102 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7207 (mt-10) REVERT: A 107 ILE cc_start: 0.8513 (mm) cc_final: 0.8161 (mm) REVERT: A 112 TYR cc_start: 0.7459 (m-80) cc_final: 0.6998 (m-80) REVERT: A 119 LEU cc_start: 0.7698 (tp) cc_final: 0.7085 (tp) REVERT: A 137 MET cc_start: 0.8164 (mtm) cc_final: 0.7860 (mtm) REVERT: A 143 ILE cc_start: 0.8973 (mt) cc_final: 0.8554 (mm) REVERT: A 165 ARG cc_start: 0.7353 (mtp-110) cc_final: 0.7050 (mtp-110) REVERT: A 166 ASP cc_start: 0.8075 (p0) cc_final: 0.7809 (p0) REVERT: A 172 PHE cc_start: 0.8329 (m-80) cc_final: 0.7956 (m-80) REVERT: A 173 LEU cc_start: 0.8091 (mt) cc_final: 0.7706 (mm) REVERT: A 176 MET cc_start: 0.8581 (ptp) cc_final: 0.8053 (ptp) REVERT: A 196 ASN cc_start: 0.8899 (m-40) cc_final: 0.8616 (m110) REVERT: A 209 LYS cc_start: 0.8191 (mttt) cc_final: 0.7683 (mtmm) REVERT: A 212 LYS cc_start: 0.7301 (ttmm) cc_final: 0.7022 (ttmm) REVERT: A 252 ARG cc_start: 0.7480 (mtp85) cc_final: 0.7187 (mtp85) REVERT: A 261 LYS cc_start: 0.7616 (ptmt) cc_final: 0.6978 (ptmt) REVERT: A 262 ASP cc_start: 0.8311 (t0) cc_final: 0.7965 (t70) REVERT: A 268 MET cc_start: 0.6247 (mtm) cc_final: 0.4907 (mtm) REVERT: A 277 MET cc_start: 0.6394 (mtt) cc_final: 0.5099 (mtt) REVERT: A 293 LYS cc_start: 0.7945 (mtpp) cc_final: 0.7028 (mtpp) REVERT: A 316 TYR cc_start: 0.7467 (t80) cc_final: 0.7183 (t80) REVERT: A 360 LYS cc_start: 0.8678 (tttt) cc_final: 0.8349 (tttt) REVERT: A 396 LYS cc_start: 0.8440 (tppp) cc_final: 0.7854 (tppp) REVERT: A 404 PHE cc_start: 0.7333 (p90) cc_final: 0.6067 (p90) REVERT: A 421 GLU cc_start: 0.8592 (tt0) cc_final: 0.7928 (tt0) REVERT: A 431 LYS cc_start: 0.8042 (mtmm) cc_final: 0.7602 (mtpt) REVERT: A 433 HIS cc_start: 0.8050 (m90) cc_final: 0.7838 (m90) REVERT: A 454 LYS cc_start: 0.8718 (mmtt) cc_final: 0.8196 (mmtt) REVERT: A 456 ILE cc_start: 0.8654 (mm) cc_final: 0.8086 (pt) REVERT: A 457 SER cc_start: 0.8195 (m) cc_final: 0.7848 (m) REVERT: A 476 ASN cc_start: 0.7849 (t0) cc_final: 0.7386 (t0) REVERT: A 487 LYS cc_start: 0.7754 (mtmm) cc_final: 0.7466 (mtmm) REVERT: A 496 GLU cc_start: 0.7499 (mp0) cc_final: 0.7240 (mp0) REVERT: A 551 GLU cc_start: 0.8630 (pt0) cc_final: 0.8190 (pm20) REVERT: A 559 HIS cc_start: 0.7616 (t70) cc_final: 0.7225 (t-170) REVERT: C 18 GLN cc_start: 0.8086 (tt0) cc_final: 0.7628 (tt0) REVERT: C 25 MET cc_start: 0.7891 (mmp) cc_final: 0.7410 (mmp) REVERT: C 31 ARG cc_start: 0.6955 (ttp-170) cc_final: 0.6554 (ttm170) outliers start: 1 outliers final: 0 residues processed: 367 average time/residue: 0.1018 time to fit residues: 49.9211 Evaluate side-chains 351 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 351 time to evaluate : 0.414 ------------------------------------------------------------------------------- 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: 0.6980 chunk 12 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 55 optimal weight: 0.0470 chunk 110 optimal weight: 0.0670 chunk 105 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 27 optimal weight: 0.4980 chunk 114 optimal weight: 1.9990 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN B 302 ASN B 329 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 280 ASN A 370 HIS ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.124931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.099466 restraints weight = 16609.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.104748 restraints weight = 9469.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.108565 restraints weight = 6026.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.111303 restraints weight = 4107.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.113304 restraints weight = 2962.862| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6707 moved from start: 0.5406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9413 Z= 0.138 Angle : 0.675 9.390 12798 Z= 0.338 Chirality : 0.047 0.266 1417 Planarity : 0.005 0.062 1669 Dihedral : 5.088 20.620 1262 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.36 % Favored : 90.64 % 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 are not related in a simple way. whole: -2.41 (0.24), residues: 1164 helix: -2.18 (0.64), residues: 60 sheet: -1.51 (0.64), residues: 66 loop : -1.75 (0.19), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 103 TYR 0.017 0.002 TYR A 125 PHE 0.020 0.001 PHE B 73 TRP 0.034 0.002 TRP A 200 HIS 0.005 0.001 HIS B 237 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 9358) covalent geometry : angle 0.66012 / 0.33 (12680) SS BOND : bond 0.00318 / 0.21 ( 47) SS BOND : angle 1.36744 / 0.81 ( 94) hydrogen bonds : bond 0.03512 / 2.22 ( 81) hydrogen bonds : angle 5.47709 / 3.52 ( 174) link_ALPHA1-3 : bond 0.01185 / 0.62 ( 1) link_ALPHA1-3 : angle 1.98834 / 1.03 ( 3) link_BETA1-3 : bond 0.00804 / 0.42 ( 1) link_BETA1-3 : angle 3.61562 / 1.90 ( 3) link_BETA1-4 : bond 0.00270 / 0.14 ( 2) link_BETA1-4 : angle 1.32288 / 0.78 ( 6) link_NAG-ASN : bond 0.00312 / 0.16 ( 4) link_NAG-ASN : angle 2.50990 / 1.38 ( 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 367 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 366 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 GLN cc_start: 0.7198 (pp30) cc_final: 0.6250 (mm-40) REVERT: B 31 MET cc_start: 0.7842 (mtp) cc_final: 0.6693 (ptp) REVERT: B 44 ASP cc_start: 0.7344 (t0) cc_final: 0.6481 (t0) REVERT: B 45 MET cc_start: 0.8263 (tmm) cc_final: 0.8021 (tmm) REVERT: B 46 LEU cc_start: 0.8638 (mt) cc_final: 0.8237 (mt) REVERT: B 47 ARG cc_start: 0.7840 (ttp80) cc_final: 0.7375 (ttp80) REVERT: B 55 VAL cc_start: 0.7833 (t) cc_final: 0.7442 (p) REVERT: B 59 ASN cc_start: 0.7415 (m-40) cc_final: 0.6946 (m-40) REVERT: B 61 GLU cc_start: 0.6973 (tm-30) cc_final: 0.3737 (tm-30) REVERT: B 75 GLN cc_start: 0.7954 (pt0) cc_final: 0.7679 (pt0) REVERT: B 81 GLN cc_start: 0.6513 (mt0) cc_final: 0.6257 (mt0) REVERT: B 106 GLN cc_start: 0.7784 (mt0) cc_final: 0.7430 (mp10) REVERT: B 109 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7605 (mm-30) REVERT: B 139 GLU cc_start: 0.7281 (mp0) cc_final: 0.7070 (mp0) REVERT: B 164 GLN cc_start: 0.7730 (pm20) cc_final: 0.7361 (pm20) REVERT: B 193 HIS cc_start: 0.7829 (m90) cc_final: 0.7348 (m90) REVERT: B 208 SER cc_start: 0.7887 (m) cc_final: 0.7664 (t) REVERT: B 211 ASP cc_start: 0.7879 (m-30) cc_final: 0.7586 (m-30) REVERT: B 213 GLN cc_start: 0.8074 (tm-30) cc_final: 0.7571 (tm-30) REVERT: B 248 LYS cc_start: 0.8713 (mmtt) cc_final: 0.8052 (mmtt) REVERT: B 265 GLU cc_start: 0.7147 (pm20) cc_final: 0.6318 (pm20) REVERT: B 271 LEU cc_start: 0.8652 (mt) cc_final: 0.8370 (pt) REVERT: B 274 TYR cc_start: 0.6645 (t80) cc_final: 0.6271 (t80) REVERT: B 286 GLU cc_start: 0.8386 (pp20) cc_final: 0.7574 (tm-30) REVERT: B 303 TYR cc_start: 0.7991 (m-80) cc_final: 0.7548 (m-80) REVERT: B 320 GLN cc_start: 0.6553 (mt0) cc_final: 0.5894 (mt0) REVERT: B 332 GLU cc_start: 0.7259 (mt-10) cc_final: 0.6954 (mt-10) REVERT: B 364 PHE cc_start: 0.8728 (m-80) cc_final: 0.8097 (m-80) REVERT: B 398 GLN cc_start: 0.8177 (mm-40) cc_final: 0.7841 (mm-40) REVERT: B 409 TYR cc_start: 0.7135 (p90) cc_final: 0.6903 (p90) REVERT: B 411 TYR cc_start: 0.7215 (t80) cc_final: 0.6516 (t80) REVERT: B 426 GLN cc_start: 0.7940 (pt0) cc_final: 0.7291 (pp30) REVERT: B 430 VAL cc_start: 0.7550 (t) cc_final: 0.7318 (p) REVERT: B 432 ARG cc_start: 0.7313 (mmt-90) cc_final: 0.7005 (mmt-90) REVERT: B 444 THR cc_start: 0.7490 (m) cc_final: 0.6258 (m) REVERT: B 451 SER cc_start: 0.8233 (p) cc_final: 0.7770 (m) REVERT: B 452 TRP cc_start: 0.7950 (p90) cc_final: 0.7530 (p90) REVERT: B 467 LEU cc_start: 0.7259 (tp) cc_final: 0.6402 (pp) REVERT: B 481 PRO cc_start: 0.8046 (Cg_endo) cc_final: 0.7557 (Cg_exo) REVERT: B 483 ASP cc_start: 0.8428 (m-30) cc_final: 0.7755 (t0) REVERT: B 484 GLN cc_start: 0.8754 (mt0) cc_final: 0.8529 (mt0) REVERT: B 487 ARG cc_start: 0.7965 (mmt90) cc_final: 0.6923 (ttm-80) REVERT: B 488 ASN cc_start: 0.8440 (t0) cc_final: 0.8016 (t0) REVERT: B 527 GLN cc_start: 0.7229 (pm20) cc_final: 0.6562 (pm20) REVERT: B 539 GLU cc_start: 0.7785 (tp30) cc_final: 0.7567 (tp30) REVERT: B 556 ASN cc_start: 0.8332 (t0) cc_final: 0.7700 (t0) REVERT: B 577 PHE cc_start: 0.8438 (m-80) cc_final: 0.8057 (m-80) REVERT: B 580 GLU cc_start: 0.8332 (tp30) cc_final: 0.8016 (tp30) REVERT: A 45 GLU cc_start: 0.8406 (mp0) cc_final: 0.8051 (mp0) REVERT: A 46 ASP cc_start: 0.7188 (t70) cc_final: 0.6762 (t70) REVERT: A 47 HIS cc_start: 0.7820 (t70) cc_final: 0.6866 (t70) REVERT: A 51 LEU cc_start: 0.8984 (tp) cc_final: 0.8589 (tp) REVERT: A 55 PHE cc_start: 0.7967 (m-10) cc_final: 0.7591 (m-10) REVERT: A 61 VAL cc_start: 0.8282 (m) cc_final: 0.7953 (p) REVERT: A 74 TYR cc_start: 0.8070 (m-80) cc_final: 0.7123 (m-80) REVERT: A 76 LEU cc_start: 0.8372 (mt) cc_final: 0.8149 (mt) REVERT: A 78 PHE cc_start: 0.8634 (p90) cc_final: 0.8114 (p90) REVERT: A 90 LEU cc_start: 0.8160 (tp) cc_final: 0.7755 (tp) REVERT: A 102 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7101 (mt-10) REVERT: A 107 ILE cc_start: 0.8515 (mm) cc_final: 0.8153 (mm) REVERT: A 112 TYR cc_start: 0.7481 (m-80) cc_final: 0.6992 (m-80) REVERT: A 119 LEU cc_start: 0.7735 (tp) cc_final: 0.7139 (tp) REVERT: A 137 MET cc_start: 0.8050 (mtm) cc_final: 0.7793 (mtm) REVERT: A 143 ILE cc_start: 0.8978 (mt) cc_final: 0.8555 (mm) REVERT: A 165 ARG cc_start: 0.7312 (mtp-110) cc_final: 0.7034 (mtp-110) REVERT: A 166 ASP cc_start: 0.8023 (p0) cc_final: 0.7778 (p0) REVERT: A 172 PHE cc_start: 0.8303 (m-80) cc_final: 0.7955 (m-80) REVERT: A 176 MET cc_start: 0.8523 (ptp) cc_final: 0.7974 (ptp) REVERT: A 196 ASN cc_start: 0.8884 (m-40) cc_final: 0.8590 (m110) REVERT: A 209 LYS cc_start: 0.8121 (mttt) cc_final: 0.7630 (mtmt) REVERT: A 212 LYS cc_start: 0.7190 (ttmm) cc_final: 0.6933 (ttmm) REVERT: A 252 ARG cc_start: 0.7443 (mtp85) cc_final: 0.7149 (mtp85) REVERT: A 261 LYS cc_start: 0.7618 (ptmt) cc_final: 0.7019 (ptmt) REVERT: A 262 ASP cc_start: 0.8259 (t0) cc_final: 0.7328 (t0) REVERT: A 268 MET cc_start: 0.6252 (mtm) cc_final: 0.4860 (mtm) REVERT: A 277 MET cc_start: 0.6351 (mtt) cc_final: 0.5107 (mtt) REVERT: A 293 LYS cc_start: 0.8004 (mtpp) cc_final: 0.7126 (mtpp) REVERT: A 316 TYR cc_start: 0.7454 (t80) cc_final: 0.7168 (t80) REVERT: A 360 LYS cc_start: 0.8616 (tttt) cc_final: 0.8302 (tttt) REVERT: A 370 HIS cc_start: 0.7999 (m90) cc_final: 0.7776 (m90) REVERT: A 396 LYS cc_start: 0.8446 (tppp) cc_final: 0.7812 (tppp) REVERT: A 404 PHE cc_start: 0.7336 (p90) cc_final: 0.6453 (p90) REVERT: A 417 LEU cc_start: 0.7696 (mt) cc_final: 0.7356 (mt) REVERT: A 421 GLU cc_start: 0.8602 (tt0) cc_final: 0.8067 (tt0) REVERT: A 433 HIS cc_start: 0.8111 (m90) cc_final: 0.7855 (m90) REVERT: A 454 LYS cc_start: 0.8723 (mmtt) cc_final: 0.8198 (mmtt) REVERT: A 456 ILE cc_start: 0.8650 (mm) cc_final: 0.8095 (pt) REVERT: A 457 SER cc_start: 0.8140 (m) cc_final: 0.7771 (m) REVERT: A 476 ASN cc_start: 0.7840 (t0) cc_final: 0.7443 (t0) REVERT: A 487 LYS cc_start: 0.7760 (mtmm) cc_final: 0.7464 (mtmm) REVERT: A 496 GLU cc_start: 0.7494 (mp0) cc_final: 0.7138 (mp0) REVERT: A 551 GLU cc_start: 0.8547 (pt0) cc_final: 0.8111 (pm20) REVERT: A 559 HIS cc_start: 0.7578 (t70) cc_final: 0.7195 (t-170) REVERT: C 18 GLN cc_start: 0.7996 (tt0) cc_final: 0.7573 (tt0) REVERT: C 25 MET cc_start: 0.7794 (mmp) cc_final: 0.7194 (mmp) REVERT: C 31 ARG cc_start: 0.7055 (ttp-170) cc_final: 0.6606 (ttm170) outliers start: 1 outliers final: 0 residues processed: 366 average time/residue: 0.1145 time to fit residues: 55.7094 Evaluate side-chains 336 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 336 time to evaluate : 0.329 ------------------------------------------------------------------------------- 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: 0.6980 chunk 22 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 91 optimal weight: 0.0270 chunk 80 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN ** B 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 329 GLN ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 568 GLN A 32 GLN A 280 ASN A 432 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.125313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.099879 restraints weight = 16444.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.105069 restraints weight = 9390.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.108753 restraints weight = 6001.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.111472 restraints weight = 4128.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.113416 restraints weight = 2997.979| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6746 moved from start: 0.5742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9413 Z= 0.181 Angle : 0.713 9.943 12798 Z= 0.358 Chirality : 0.049 0.279 1417 Planarity : 0.005 0.061 1669 Dihedral : 5.415 21.196 1262 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.77 % Favored : 88.23 % Rotamer: Outliers : 0.10 % Allowed : 0.10 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.48 (0.23), residues: 1164 helix: -2.63 (0.57), residues: 66 sheet: -1.55 (0.58), residues: 81 loop : -1.76 (0.19), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 103 TYR 0.021 0.002 TYR A 117 PHE 0.018 0.002 PHE B 73 TRP 0.032 0.003 TRP A 200 HIS 0.008 0.001 HIS A 507 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.18 ( 9358) covalent geometry : angle 0.69769 / 0.35 (12680) SS BOND : bond 0.00296 / 0.19 ( 47) SS BOND : angle 1.35982 / 0.82 ( 94) hydrogen bonds : bond 0.03649 / 2.32 ( 81) hydrogen bonds : angle 5.70260 / 3.67 ( 174) link_ALPHA1-3 : bond 0.01232 / 0.65 ( 1) link_ALPHA1-3 : angle 2.32726 / 1.20 ( 3) link_BETA1-3 : bond 0.00614 / 0.32 ( 1) link_BETA1-3 : angle 3.52341 / 1.86 ( 3) link_BETA1-4 : bond 0.00300 / 0.16 ( 2) link_BETA1-4 : angle 1.21178 / 0.71 ( 6) link_NAG-ASN : bond 0.00372 / 0.19 ( 4) link_NAG-ASN : angle 2.83265 / 1.53 ( 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 373 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 372 time to evaluate : 0.336 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: B 24 GLN cc_start: 0.7072 (pp30) cc_final: 0.6558 (mm-40) REVERT: B 31 MET cc_start: 0.7903 (mtp) cc_final: 0.6876 (ptp) REVERT: B 44 ASP cc_start: 0.7455 (t0) cc_final: 0.6616 (t0) REVERT: B 45 MET cc_start: 0.8321 (tmm) cc_final: 0.8044 (tmm) REVERT: B 46 LEU cc_start: 0.8679 (mt) cc_final: 0.8231 (mt) REVERT: B 47 ARG cc_start: 0.7906 (ttp80) cc_final: 0.7437 (ttp80) REVERT: B 55 VAL cc_start: 0.7916 (t) cc_final: 0.6926 (p) REVERT: B 59 ASN cc_start: 0.7430 (m-40) cc_final: 0.6952 (m-40) REVERT: B 61 GLU cc_start: 0.7017 (tm-30) cc_final: 0.3801 (tm-30) REVERT: B 75 GLN cc_start: 0.8023 (pt0) cc_final: 0.7740 (pt0) REVERT: B 100 ARG cc_start: 0.7725 (mmm-85) cc_final: 0.7502 (mmm-85) REVERT: B 106 GLN cc_start: 0.7830 (mt0) cc_final: 0.7497 (mp-120) REVERT: B 109 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7629 (mm-30) REVERT: B 143 ARG cc_start: 0.7683 (mtt180) cc_final: 0.7179 (mtt180) REVERT: B 164 GLN cc_start: 0.7831 (pm20) cc_final: 0.7167 (pm20) REVERT: B 193 HIS cc_start: 0.7822 (m90) cc_final: 0.7342 (m90) REVERT: B 233 THR cc_start: 0.7822 (m) cc_final: 0.7590 (t) REVERT: B 248 LYS cc_start: 0.8724 (mmtt) cc_final: 0.8071 (mmtt) REVERT: B 265 GLU cc_start: 0.7131 (pm20) cc_final: 0.6282 (pm20) REVERT: B 267 HIS cc_start: 0.7750 (m170) cc_final: 0.7385 (m170) REVERT: B 271 LEU cc_start: 0.8754 (mt) cc_final: 0.8457 (pt) REVERT: B 274 TYR cc_start: 0.6536 (t80) cc_final: 0.6164 (t80) REVERT: B 286 GLU cc_start: 0.8377 (pp20) cc_final: 0.7647 (tm-30) REVERT: B 303 TYR cc_start: 0.8049 (m-80) cc_final: 0.7596 (m-80) REVERT: B 319 ASN cc_start: 0.7879 (m-40) cc_final: 0.7651 (m-40) REVERT: B 320 GLN cc_start: 0.6627 (mt0) cc_final: 0.5936 (mt0) REVERT: B 332 GLU cc_start: 0.7265 (mt-10) cc_final: 0.6953 (mt-10) REVERT: B 364 PHE cc_start: 0.8722 (m-80) cc_final: 0.8127 (m-80) REVERT: B 398 GLN cc_start: 0.8254 (mm-40) cc_final: 0.7891 (mm-40) REVERT: B 411 TYR cc_start: 0.7231 (t80) cc_final: 0.6507 (t80) REVERT: B 426 GLN cc_start: 0.8035 (pt0) cc_final: 0.7431 (pp30) REVERT: B 432 ARG cc_start: 0.7367 (mmt-90) cc_final: 0.6536 (tpp-160) REVERT: B 436 LEU cc_start: 0.7966 (mt) cc_final: 0.7375 (mp) REVERT: B 444 THR cc_start: 0.7553 (m) cc_final: 0.6635 (m) REVERT: B 451 SER cc_start: 0.8239 (p) cc_final: 0.7728 (m) REVERT: B 452 TRP cc_start: 0.7984 (p90) cc_final: 0.7570 (p90) REVERT: B 467 LEU cc_start: 0.7301 (tp) cc_final: 0.6594 (pp) REVERT: B 481 PRO cc_start: 0.7991 (Cg_endo) cc_final: 0.7507 (Cg_exo) REVERT: B 483 ASP cc_start: 0.8451 (m-30) cc_final: 0.7708 (t0) REVERT: B 484 GLN cc_start: 0.8853 (mt0) cc_final: 0.8624 (mt0) REVERT: B 487 ARG cc_start: 0.7913 (mmt90) cc_final: 0.6907 (ttm-80) REVERT: B 488 ASN cc_start: 0.8399 (t0) cc_final: 0.8020 (t0) REVERT: B 520 CYS cc_start: 0.4587 (t) cc_final: 0.3919 (m) REVERT: B 527 GLN cc_start: 0.7019 (pm20) cc_final: 0.6277 (pm20) REVERT: B 539 GLU cc_start: 0.7807 (tp30) cc_final: 0.7524 (tp30) REVERT: B 577 PHE cc_start: 0.8463 (m-80) cc_final: 0.8082 (m-80) REVERT: B 580 GLU cc_start: 0.8339 (tp30) cc_final: 0.8004 (tp30) REVERT: A 45 GLU cc_start: 0.8427 (mp0) cc_final: 0.8059 (mp0) REVERT: A 46 ASP cc_start: 0.7214 (t70) cc_final: 0.6779 (t70) REVERT: A 47 HIS cc_start: 0.7900 (t70) cc_final: 0.6765 (t70) REVERT: A 51 LEU cc_start: 0.8990 (tp) cc_final: 0.8576 (tp) REVERT: A 54 MET cc_start: 0.8162 (tpt) cc_final: 0.7901 (tpt) REVERT: A 55 PHE cc_start: 0.7931 (m-10) cc_final: 0.7668 (m-10) REVERT: A 61 VAL cc_start: 0.8303 (m) cc_final: 0.7966 (p) REVERT: A 74 TYR cc_start: 0.8101 (m-80) cc_final: 0.7128 (m-80) REVERT: A 90 LEU cc_start: 0.8087 (tp) cc_final: 0.7722 (tp) REVERT: A 102 GLU cc_start: 0.7725 (mt-10) cc_final: 0.6982 (mt-10) REVERT: A 107 ILE cc_start: 0.8535 (mm) cc_final: 0.8158 (mm) REVERT: A 112 TYR cc_start: 0.7539 (m-80) cc_final: 0.7040 (m-80) REVERT: A 119 LEU cc_start: 0.7632 (tp) cc_final: 0.7162 (tp) REVERT: A 125 TYR cc_start: 0.6915 (p90) cc_final: 0.6509 (p90) REVERT: A 137 MET cc_start: 0.8264 (mtm) cc_final: 0.7939 (mtm) REVERT: A 143 ILE cc_start: 0.8985 (mt) cc_final: 0.8571 (mm) REVERT: A 163 GLN cc_start: 0.8440 (tt0) cc_final: 0.7981 (tt0) REVERT: A 165 ARG cc_start: 0.7411 (mtp-110) cc_final: 0.7075 (ttm-80) REVERT: A 166 ASP cc_start: 0.8094 (p0) cc_final: 0.7751 (p0) REVERT: A 172 PHE cc_start: 0.8259 (m-80) cc_final: 0.7999 (m-80) REVERT: A 176 MET cc_start: 0.8458 (ptp) cc_final: 0.7980 (ptp) REVERT: A 196 ASN cc_start: 0.8865 (m-40) cc_final: 0.8602 (m110) REVERT: A 209 LYS cc_start: 0.8145 (mttt) cc_final: 0.7660 (mtmm) REVERT: A 212 LYS cc_start: 0.7230 (ttmm) cc_final: 0.6995 (ttmm) REVERT: A 252 ARG cc_start: 0.7434 (mtp85) cc_final: 0.7059 (mtm110) REVERT: A 261 LYS cc_start: 0.7713 (ptmt) cc_final: 0.7055 (ptmt) REVERT: A 262 ASP cc_start: 0.8415 (t0) cc_final: 0.8055 (t70) REVERT: A 268 MET cc_start: 0.6312 (mtm) cc_final: 0.4914 (mtm) REVERT: A 277 MET cc_start: 0.6439 (mtt) cc_final: 0.5180 (mtt) REVERT: A 316 TYR cc_start: 0.7383 (t80) cc_final: 0.7116 (t80) REVERT: A 344 GLU cc_start: 0.7225 (tt0) cc_final: 0.7020 (tt0) REVERT: A 360 LYS cc_start: 0.8602 (tttt) cc_final: 0.8308 (tttt) REVERT: A 370 HIS cc_start: 0.7959 (m90) cc_final: 0.7402 (m170) REVERT: A 377 ARG cc_start: 0.7649 (ptm-80) cc_final: 0.7326 (ptp-110) REVERT: A 396 LYS cc_start: 0.8472 (tppp) cc_final: 0.7835 (tppp) REVERT: A 404 PHE cc_start: 0.7419 (p90) cc_final: 0.6306 (p90) REVERT: A 420 PHE cc_start: 0.8468 (m-80) cc_final: 0.8233 (m-80) REVERT: A 421 GLU cc_start: 0.8656 (tt0) cc_final: 0.8076 (tt0) REVERT: A 431 LYS cc_start: 0.8043 (mtmm) cc_final: 0.7498 (mtmm) REVERT: A 432 GLN cc_start: 0.8641 (tm130) cc_final: 0.8227 (tm-30) REVERT: A 433 HIS cc_start: 0.8120 (m90) cc_final: 0.7630 (m90) REVERT: A 445 ILE cc_start: 0.7923 (pt) cc_final: 0.7613 (pt) REVERT: A 451 ARG cc_start: 0.7739 (ptp-110) cc_final: 0.7500 (ptp-170) REVERT: A 454 LYS cc_start: 0.8743 (mmtt) cc_final: 0.8229 (mmtt) REVERT: A 456 ILE cc_start: 0.8686 (mm) cc_final: 0.8136 (pt) REVERT: A 457 SER cc_start: 0.8157 (m) cc_final: 0.7784 (m) REVERT: A 476 ASN cc_start: 0.7893 (t0) cc_final: 0.7470 (t0) REVERT: A 496 GLU cc_start: 0.7490 (mp0) cc_final: 0.7085 (mp0) REVERT: A 548 GLU cc_start: 0.7187 (mp0) cc_final: 0.6949 (mp0) REVERT: A 551 GLU cc_start: 0.8549 (pt0) cc_final: 0.8069 (pm20) REVERT: A 554 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8256 (mt-10) REVERT: A 559 HIS cc_start: 0.7633 (t70) cc_final: 0.7230 (t-170) REVERT: C 18 GLN cc_start: 0.8000 (tt0) cc_final: 0.7363 (tt0) REVERT: C 25 MET cc_start: 0.7811 (mmp) cc_final: 0.7236 (mmp) REVERT: C 31 ARG cc_start: 0.7126 (ttp-170) cc_final: 0.6746 (ttp-110) outliers start: 1 outliers final: 0 residues processed: 372 average time/residue: 0.1126 time to fit residues: 55.6767 Evaluate side-chains 348 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 348 time to evaluate : 0.362 ------------------------------------------------------------------------------- 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: 0.9990 chunk 33 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 56 optimal weight: 0.5980 chunk 79 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 89 optimal weight: 0.0570 chunk 112 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 57 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN ** B 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 329 GLN ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 GLN A 435 GLN ** 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 = 0.3722 r_free = 0.3722 target = 0.123908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.098534 restraints weight = 16384.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.103554 restraints weight = 9408.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.107145 restraints weight = 6066.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.109788 restraints weight = 4206.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.111664 restraints weight = 3076.983| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6762 moved from start: 0.6033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9413 Z= 0.191 Angle : 0.734 9.316 12798 Z= 0.372 Chirality : 0.050 0.273 1417 Planarity : 0.005 0.081 1669 Dihedral : 5.567 24.274 1262 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.17 % Favored : 88.83 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.56 (0.23), residues: 1164 helix: -2.65 (0.57), residues: 66 sheet: -1.66 (0.58), residues: 81 loop : -1.82 (0.19), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG B 143 TYR 0.020 0.002 TYR C 29 PHE 0.019 0.002 PHE B 73 TRP 0.026 0.003 TRP A 200 HIS 0.007 0.001 HIS A 507 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.19 ( 9358) covalent geometry : angle 0.71741 / 0.37 (12680) SS BOND : bond 0.00296 / 0.19 ( 47) SS BOND : angle 1.46372 / 0.91 ( 94) hydrogen bonds : bond 0.04012 / 2.50 ( 81) hydrogen bonds : angle 5.58733 / 3.69 ( 174) link_ALPHA1-3 : bond 0.01142 / 0.60 ( 1) link_ALPHA1-3 : angle 2.28485 / 1.18 ( 3) link_BETA1-3 : bond 0.00733 / 0.39 ( 1) link_BETA1-3 : angle 3.56524 / 1.88 ( 3) link_BETA1-4 : bond 0.00220 / 0.11 ( 2) link_BETA1-4 : angle 1.34453 / 0.81 ( 6) link_NAG-ASN : bond 0.00394 / 0.20 ( 4) link_NAG-ASN : angle 2.83863 / 1.53 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1820.52 seconds wall clock time: 32 minutes 2.76 seconds (1922.76 seconds total)