Starting phenix.real_space_refine on Thu Jul 2 17:19:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hgo_34744/07_2026/8hgo_34744.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hgo_34744/07_2026/8hgo_34744.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8hgo_34744/07_2026/8hgo_34744.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hgo_34744/07_2026/8hgo_34744.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hgo_34744/07_2026/8hgo_34744.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hgo_34744/07_2026/8hgo_34744.map" model { file = "/net/cci-nas-00/data/ceres_data/8hgo_34744/07_2026/8hgo_34744.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hgo_34744/07_2026/8hgo_34744.cif" } resolution = 3.31 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= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 109 5.16 5 C 5714 2.51 5 N 1636 2.21 5 O 1768 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 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: 9227 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: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 385 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} 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: 9227 At special positions: 0 Unit cell: (78.11, 131.61, 126.26, 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 109 16.00 O 1768 8.00 N 1636 7.00 C 5714 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=2.02 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=2.03 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 20 " distance=2.03 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS C 31 " distance=2.03 Simple disulfide: pdb=" SG CYS C 33 " - pdb=" SG CYS C 42 " 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: 0.64 Conformation dependent library (CDL) restraints added in 325.4 milliseconds 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2174 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 21 sheets defined 11.9% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'B' and resid 41 through 51 removed outlier: 3.825A pdb=" N GLN B 51 " --> pdb=" O ARG B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 75 removed outlier: 3.965A pdb=" N GLN B 75 " --> pdb=" O SER B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 173 removed outlier: 4.076A pdb=" N ILE B 172 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 212 removed outlier: 3.566A pdb=" N ASP B 211 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N CYS B 212 " --> pdb=" O SER B 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 208 through 212' Processing helix chain 'B' and resid 361 through 365 removed outlier: 3.534A pdb=" N PHE B 364 " --> pdb=" O ILE B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 401 removed outlier: 3.865A pdb=" N VAL B 399 " --> pdb=" O GLN B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 426 removed outlier: 3.601A pdb=" N GLN B 426 " --> pdb=" O SER B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 440 Processing helix chain 'B' and resid 501 through 506 removed outlier: 4.063A pdb=" N GLY B 506 " --> pdb=" O ASP B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.787A pdb=" N GLY B 518 " --> pdb=" O CYS B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 584 removed outlier: 3.586A pdb=" N GLN B 583 " --> pdb=" O GLU B 580 " (cutoff:3.500A) removed outlier: 3.706A 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: 3.798A pdb=" N THR A 81 " --> pdb=" O PHE A 78 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE A 82 " --> pdb=" O LEU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 198 removed outlier: 3.746A pdb=" N GLY A 197 " --> pdb=" O CYS A 194 " (cutoff:3.500A) removed outlier: 3.726A 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 342 through 346 removed outlier: 3.793A pdb=" N PHE A 345 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS A 346 " --> pdb=" O GLY A 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 342 through 346' Processing helix chain 'A' and resid 355 through 360 removed outlier: 3.934A pdb=" N LYS A 360 " --> pdb=" O LYS A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 378 Processing helix chain 'A' and resid 388 through 397 removed outlier: 3.573A pdb=" N LEU A 392 " --> pdb=" O PRO A 389 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASP A 393 " --> pdb=" O GLN A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 421 removed outlier: 3.888A pdb=" N PHE A 420 " --> pdb=" O LEU A 417 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU A 421 " --> pdb=" O HIS A 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 417 through 421' Processing helix chain 'A' and resid 431 through 434 Processing helix chain 'A' and resid 476 through 480 removed outlier: 3.516A pdb=" N LYS A 479 " --> pdb=" O ASN A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 523 removed outlier: 4.427A pdb=" N CYS A 523 " --> pdb=" O PRO A 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 11 Processing sheet with id=AA1, first strand: chain 'B' and resid 25 through 26 removed outlier: 3.743A pdb=" N CYS B 26 " --> pdb=" O VAL B 55 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 60 through 63 removed outlier: 6.411A pdb=" N LEU B 60 " --> pdb=" O LEU B 85 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N ALA B 87 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N LEU B 62 " --> pdb=" O ALA B 87 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU B 114 " --> pdb=" O LEU B 154 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N GLN B 156 " --> pdb=" O LEU B 114 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N VAL B 116 " --> pdb=" O GLN B 156 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 258 through 260 Processing sheet with id=AA4, first strand: chain 'B' and resid 272 through 275 Processing sheet with id=AA5, first strand: chain 'B' and resid 289 through 291 Processing sheet with id=AA6, first strand: chain 'B' and resid 319 through 320 removed outlier: 3.695A pdb=" N GLU B 332 " --> pdb=" O GLN B 320 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 369 through 370 Processing sheet with id=AA8, first strand: chain 'B' and resid 374 through 376 removed outlier: 6.440A pdb=" N LEU B 374 " --> pdb=" O TYR B 411 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N HIS B 469 " --> pdb=" O LEU B 445 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ALA B 466 " --> pdb=" O LEU B 494 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N THR B 496 " --> pdb=" O ALA B 466 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ILE B 468 " --> pdb=" O THR B 496 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 553 through 555 Processing sheet with id=AB1, first strand: chain 'A' and resid 30 through 31 Processing sheet with id=AB2, first strand: chain 'A' and resid 40 through 41 removed outlier: 6.976A pdb=" N GLN A 40 " --> pdb=" O CYS C 33 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 65 through 68 removed outlier: 6.670A pdb=" N LEU A 65 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ALA A 92 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ILE A 67 " --> pdb=" O ALA A 92 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL A 89 " --> pdb=" O ALA A 120 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N LEU A 122 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE A 91 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU A 119 " --> pdb=" O ARG A 149 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N SER A 151 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL A 121 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL A 148 " --> pdb=" O SER A 177 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 236 through 240 removed outlier: 3.574A pdb=" N ALA A 237 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N VAL A 250 " --> pdb=" O ALA A 237 " (cutoff:3.500A) removed outlier: 8.821A pdb=" N GLY A 239 " --> pdb=" O CYS A 248 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N CYS A 248 " --> pdb=" O GLY A 239 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 254 through 256 removed outlier: 3.564A pdb=" N PHE A 254 " --> pdb=" O LYS A 261 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS A 261 " --> pdb=" O PHE A 254 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 300 through 301 Processing sheet with id=AB7, first strand: chain 'A' and resid 316 through 317 Processing sheet with id=AB8, first strand: chain 'A' and resid 364 through 365 Processing sheet with id=AB9, first strand: chain 'A' and resid 369 through 371 removed outlier: 6.569A pdb=" N LEU A 369 " --> pdb=" O LEU A 406 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU A 405 " --> pdb=" O ALA A 439 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N ILE A 462 " --> pdb=" O SER A 437 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ALA A 439 " --> pdb=" O ILE A 462 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL A 461 " --> pdb=" O LYS A 489 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 548 through 549 removed outlier: 3.600A pdb=" N PHE A 549 " --> pdb=" O ILE A 556 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE A 556 " --> pdb=" O PHE A 549 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'A' and resid 585 through 587 Processing sheet with id=AC3, first strand: chain 'C' and resid 37 through 38 97 hydrogen bonds defined for protein. 186 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: 1.07 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3127 1.34 - 1.46: 2001 1.46 - 1.58: 4168 1.58 - 1.70: 0 1.70 - 1.82: 124 Bond restraints: 9420 Sorted by residual: bond pdb=" C5 MAN D 4 " pdb=" O5 MAN D 4 " ideal model delta sigma weight residual 1.418 1.473 -0.055 2.00e-02 2.50e+03 7.67e+00 bond pdb=" C PRO B 593 " pdb=" N PRO B 594 " ideal model delta sigma weight residual 1.334 1.394 -0.060 2.34e-02 1.83e+03 6.51e+00 bond pdb=" C LYS B 336 " pdb=" N PRO B 337 " ideal model delta sigma weight residual 1.334 1.392 -0.058 2.34e-02 1.83e+03 6.17e+00 bond pdb=" C5 BMA D 3 " pdb=" O5 BMA D 3 " ideal model delta sigma weight residual 1.417 1.462 -0.045 2.00e-02 2.50e+03 5.15e+00 bond pdb=" C1 MAN D 4 " pdb=" O5 MAN D 4 " ideal model delta sigma weight residual 1.399 1.443 -0.044 2.00e-02 2.50e+03 4.86e+00 ... (remaining 9415 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 12498 2.16 - 4.32: 242 4.32 - 6.48: 20 6.48 - 8.64: 7 8.64 - 10.79: 2 Bond angle restraints: 12769 Sorted by residual: angle pdb=" N LEU A 509 " pdb=" CA LEU A 509 " pdb=" C LEU A 509 " ideal model delta sigma weight residual 110.80 121.59 -10.79 2.13e+00 2.20e-01 2.57e+01 angle pdb=" N ARG A 334 " pdb=" CA ARG A 334 " pdb=" C ARG A 334 " ideal model delta sigma weight residual 110.97 115.32 -4.35 1.09e+00 8.42e-01 1.59e+01 angle pdb=" C ALA B 324 " pdb=" N GLU B 325 " pdb=" CA GLU B 325 " ideal model delta sigma weight residual 122.08 127.78 -5.70 1.47e+00 4.63e-01 1.50e+01 angle pdb=" C GLU A 204 " pdb=" N GLU A 205 " pdb=" CA GLU A 205 " ideal model delta sigma weight residual 121.54 128.81 -7.27 1.91e+00 2.74e-01 1.45e+01 angle pdb=" N PRO B 593 " pdb=" CA PRO B 593 " pdb=" C PRO B 593 " ideal model delta sigma weight residual 110.70 114.91 -4.21 1.22e+00 6.72e-01 1.19e+01 ... (remaining 12764 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.09: 5559 18.09 - 36.18: 134 36.18 - 54.27: 60 54.27 - 72.36: 5 72.36 - 90.45: 14 Dihedral angle restraints: 5772 sinusoidal: 2390 harmonic: 3382 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 93.00 -176.55 -90.45 1 1.00e+01 1.00e-02 9.67e+01 dihedral pdb=" CB CYS A 219 " pdb=" SG CYS A 219 " pdb=" SG CYS A 231 " pdb=" CB CYS A 231 " ideal model delta sinusoidal sigma weight residual 93.00 -179.51 -87.49 1 1.00e+01 1.00e-02 9.18e+01 dihedral pdb=" CB CYS A 190 " pdb=" SG CYS A 190 " pdb=" SG CYS A 199 " pdb=" CB CYS A 199 " ideal model delta sinusoidal sigma weight residual -86.00 -168.44 82.44 1 1.00e+01 1.00e-02 8.34e+01 ... (remaining 5769 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1224 0.076 - 0.152: 190 0.152 - 0.228: 6 0.228 - 0.304: 2 0.304 - 0.380: 3 Chirality restraints: 1425 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 -2.11 -0.38 2.00e-01 2.50e+01 3.62e+00 chirality pdb=" CA LEU A 509 " pdb=" N LEU A 509 " pdb=" C LEU A 509 " pdb=" CB LEU A 509 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" C1 NAG A 802 " pdb=" ND2 ASN A 175 " pdb=" C2 NAG A 802 " pdb=" O5 NAG A 802 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.55e+00 ... (remaining 1422 not shown) Planarity restraints: 1683 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 519 " 0.035 5.00e-02 4.00e+02 5.27e-02 4.44e+00 pdb=" N PRO A 520 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 520 " 0.027 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 SER A 511 " 0.034 5.00e-02 4.00e+02 5.15e-02 4.25e+00 pdb=" N PRO A 512 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 512 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 512 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 372 " -0.033 5.00e-02 4.00e+02 5.00e-02 3.99e+00 pdb=" N PRO A 373 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 373 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 373 " -0.028 5.00e-02 4.00e+02 ... (remaining 1680 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 2411 2.81 - 3.33: 7501 3.33 - 3.85: 14605 3.85 - 4.38: 16494 4.38 - 4.90: 28622 Nonbonded interactions: 69633 Sorted by model distance: nonbonded pdb=" OH TYR B 163 " pdb=" O HIS B 193 " model vdw 2.284 3.040 nonbonded pdb=" ND1 HIS A 507 " pdb=" O ALA A 508 " model vdw 2.315 3.120 nonbonded pdb=" OG SER B 38 " pdb=" OG1 THR B 41 " model vdw 2.324 3.040 nonbonded pdb=" OE2 GLU A 66 " pdb=" OH TYR A 88 " model vdw 2.349 3.040 nonbonded pdb=" O VAL B 356 " pdb=" OG SER B 380 " model vdw 2.365 3.040 ... (remaining 69628 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 7.250 Find NCS groups from input model: 0.030 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:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6788 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 9475 Z= 0.184 Angle : 0.733 10.795 12887 Z= 0.401 Chirality : 0.054 0.380 1425 Planarity : 0.007 0.053 1679 Dihedral : 7.938 76.743 3457 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.03 % Favored : 91.79 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % 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: -3.74 (0.20), residues: 1170 helix: -3.97 (0.38), residues: 41 sheet: -2.80 (0.49), residues: 91 loop : -2.68 (0.16), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 536 TYR 0.014 0.001 TYR B 554 PHE 0.019 0.002 PHE A 404 TRP 0.011 0.002 TRP B 452 HIS 0.015 0.001 HIS B 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.18 ( 9420) covalent geometry : angle 0.71132 / 0.40 (12769) SS BOND : bond 0.00282 / 0.17 ( 47) SS BOND : angle 1.04892 / 0.65 ( 94) hydrogen bonds : bond 0.23774 / 13.61 ( 97) hydrogen bonds : angle 7.20955 / 4.64 ( 186) link_ALPHA1-3 : bond 0.01436 / 0.76 ( 1) link_ALPHA1-3 : angle 2.81919 / 1.48 ( 3) link_BETA1-3 : bond 0.01341 / 0.71 ( 1) link_BETA1-3 : angle 6.31483 / 3.32 ( 3) link_BETA1-4 : bond 0.00375 / 0.19 ( 2) link_BETA1-4 : angle 1.89672 / 1.34 ( 6) link_NAG-ASN : bond 0.00860 / 0.43 ( 4) link_NAG-ASN : angle 4.09200 / 2.59 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 293 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 30 ASP cc_start: 0.7294 (t70) cc_final: 0.6926 (t70) REVERT: B 89 ASN cc_start: 0.7573 (m-40) cc_final: 0.7250 (m110) REVERT: B 103 ARG cc_start: 0.7732 (mtt-85) cc_final: 0.7373 (mtp85) REVERT: B 112 TYR cc_start: 0.6756 (m-80) cc_final: 0.6533 (m-80) REVERT: B 164 GLN cc_start: 0.6589 (pm20) cc_final: 0.6193 (pm20) REVERT: B 183 LEU cc_start: 0.8231 (mp) cc_final: 0.7844 (tp) REVERT: B 228 LYS cc_start: 0.7510 (mtpt) cc_final: 0.7278 (mtpt) REVERT: B 405 GLU cc_start: 0.6892 (tt0) cc_final: 0.6636 (tt0) REVERT: B 434 ARG cc_start: 0.8286 (mtt90) cc_final: 0.7946 (mtt180) REVERT: B 460 GLU cc_start: 0.6684 (tt0) cc_final: 0.6186 (tt0) REVERT: B 467 LEU cc_start: 0.8448 (tp) cc_final: 0.7784 (tp) REVERT: B 541 VAL cc_start: 0.7565 (m) cc_final: 0.7159 (p) REVERT: B 561 LEU cc_start: 0.7389 (mt) cc_final: 0.7124 (mt) REVERT: A 45 GLU cc_start: 0.7186 (mp0) cc_final: 0.6738 (mp0) REVERT: A 46 ASP cc_start: 0.7642 (t70) cc_final: 0.7218 (t0) REVERT: A 152 ASN cc_start: 0.7274 (m110) cc_final: 0.6942 (m110) REVERT: A 160 GLU cc_start: 0.7180 (pm20) cc_final: 0.6471 (pm20) REVERT: A 234 ASN cc_start: 0.7890 (t0) cc_final: 0.7649 (t0) REVERT: A 268 MET cc_start: 0.5859 (mtm) cc_final: 0.5359 (mtm) REVERT: A 277 MET cc_start: 0.5040 (mtt) cc_final: 0.4820 (mtt) REVERT: A 292 VAL cc_start: 0.7916 (m) cc_final: 0.7545 (p) REVERT: A 293 LYS cc_start: 0.7924 (mtpp) cc_final: 0.7713 (mtpp) REVERT: A 294 LYS cc_start: 0.7981 (tttt) cc_final: 0.7751 (tttt) REVERT: A 325 LYS cc_start: 0.7243 (mttt) cc_final: 0.6891 (mtmm) REVERT: A 360 LYS cc_start: 0.7592 (tttt) cc_final: 0.7361 (tttt) REVERT: A 425 ILE cc_start: 0.8526 (tt) cc_final: 0.7990 (tt) REVERT: A 430 THR cc_start: 0.7999 (m) cc_final: 0.7331 (p) REVERT: A 431 LYS cc_start: 0.8183 (mtmm) cc_final: 0.7855 (mtmm) REVERT: A 593 LYS cc_start: 0.6587 (tptp) cc_final: 0.6324 (tptp) outliers start: 0 outliers final: 0 residues processed: 293 average time/residue: 0.1006 time to fit residues: 38.1784 Evaluate side-chains 231 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.228 ------------------------------------------------------------------------------- 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: 0.6980 chunk 49 optimal weight: 0.4980 chunk 97 optimal weight: 0.3980 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.4980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.2980 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 42 HIS B 81 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 ASN B 329 GLN B 438 ASN A 47 HIS A 64 ASN ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 103 ASN A 110 ASN A 206 ASN A 233 HIS A 235 GLN A 486 GLN A 493 ASN A 559 HIS A 565 GLN A 584 HIS C 16 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.155532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.133176 restraints weight = 13641.043| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 2.73 r_work: 0.3601 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 9475 Z= 0.212 Angle : 0.760 9.985 12887 Z= 0.383 Chirality : 0.052 0.335 1425 Planarity : 0.006 0.048 1679 Dihedral : 5.551 34.580 1269 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 1.56 % Allowed : 7.02 % Favored : 91.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.32 (0.22), residues: 1170 helix: -3.72 (0.42), residues: 75 sheet: -2.53 (0.50), residues: 94 loop : -2.28 (0.18), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 499 TYR 0.024 0.002 TYR B 409 PHE 0.023 0.002 PHE A 549 TRP 0.011 0.002 TRP C 49 HIS 0.015 0.002 HIS B 237 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.21 ( 9420) covalent geometry : angle 0.73369 / 0.37 (12769) SS BOND : bond 0.00550 / 0.30 ( 47) SS BOND : angle 2.02260 / 1.32 ( 94) hydrogen bonds : bond 0.03642 / 2.21 ( 97) hydrogen bonds : angle 6.12805 / 3.92 ( 186) link_ALPHA1-3 : bond 0.00237 / 0.12 ( 1) link_ALPHA1-3 : angle 2.99971 / 1.53 ( 3) link_BETA1-3 : bond 0.00166 / 0.09 ( 1) link_BETA1-3 : angle 4.04930 / 2.09 ( 3) link_BETA1-4 : bond 0.00278 / 0.14 ( 2) link_BETA1-4 : angle 0.69045 / 0.49 ( 6) link_NAG-ASN : bond 0.00335 / 0.16 ( 4) link_NAG-ASN : angle 2.92622 / 1.65 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 272 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 30 ASP cc_start: 0.7819 (t70) cc_final: 0.7201 (t70) REVERT: B 89 ASN cc_start: 0.7997 (m-40) cc_final: 0.7692 (m-40) REVERT: B 98 ARG cc_start: 0.7368 (ttm-80) cc_final: 0.7155 (ttm-80) REVERT: B 147 GLU cc_start: 0.7246 (tp30) cc_final: 0.6845 (tp30) REVERT: B 164 GLN cc_start: 0.7160 (pm20) cc_final: 0.6892 (pm20) REVERT: B 228 LYS cc_start: 0.7854 (mtpt) cc_final: 0.7535 (mtpt) REVERT: B 274 TYR cc_start: 0.8296 (t80) cc_final: 0.8045 (t80) REVERT: B 284 ASN cc_start: 0.7626 (t0) cc_final: 0.7234 (t0) REVERT: B 329 GLN cc_start: 0.7153 (OUTLIER) cc_final: 0.6925 (mt0) REVERT: B 403 LEU cc_start: 0.7134 (tp) cc_final: 0.6866 (tp) REVERT: B 421 ASP cc_start: 0.6472 (p0) cc_final: 0.6222 (p0) REVERT: B 438 ASN cc_start: 0.7783 (m-40) cc_final: 0.7544 (m110) REVERT: B 441 TYR cc_start: 0.8439 (m-80) cc_final: 0.8037 (m-80) REVERT: B 460 GLU cc_start: 0.7653 (tt0) cc_final: 0.7352 (tt0) REVERT: A 45 GLU cc_start: 0.7692 (mp0) cc_final: 0.7322 (mp0) REVERT: A 46 ASP cc_start: 0.8024 (t70) cc_final: 0.7573 (t0) REVERT: A 98 ARG cc_start: 0.8266 (mtp-110) cc_final: 0.8058 (mtp180) REVERT: A 133 LYS cc_start: 0.7282 (mttt) cc_final: 0.6995 (mmmm) REVERT: A 141 GLN cc_start: 0.8419 (mt0) cc_final: 0.8162 (mt0) REVERT: A 152 ASN cc_start: 0.7620 (m110) cc_final: 0.7208 (m110) REVERT: A 160 GLU cc_start: 0.7775 (pm20) cc_final: 0.6912 (pm20) REVERT: A 198 SER cc_start: 0.8043 (m) cc_final: 0.7383 (p) REVERT: A 235 GLN cc_start: 0.8066 (mm-40) cc_final: 0.7837 (mm110) REVERT: A 254 PHE cc_start: 0.7893 (m-10) cc_final: 0.7685 (m-10) REVERT: A 255 ARG cc_start: 0.7072 (ttt-90) cc_final: 0.6651 (tmt-80) REVERT: A 268 MET cc_start: 0.6290 (mtm) cc_final: 0.5757 (mtm) REVERT: A 277 MET cc_start: 0.5501 (mtt) cc_final: 0.5128 (mtt) REVERT: A 284 LYS cc_start: 0.8288 (mtmm) cc_final: 0.7962 (mtmm) REVERT: A 292 VAL cc_start: 0.8156 (m) cc_final: 0.7761 (p) REVERT: A 293 LYS cc_start: 0.8111 (mtpp) cc_final: 0.7819 (ptpp) REVERT: A 294 LYS cc_start: 0.8302 (tttt) cc_final: 0.8022 (tttt) REVERT: A 316 TYR cc_start: 0.6535 (t80) cc_final: 0.6168 (t80) REVERT: A 318 MET cc_start: 0.6811 (tpp) cc_final: 0.6552 (tpp) REVERT: A 325 LYS cc_start: 0.7672 (mttt) cc_final: 0.7158 (mtmt) REVERT: A 430 THR cc_start: 0.8215 (m) cc_final: 0.7607 (p) REVERT: A 578 ASN cc_start: 0.6972 (m-40) cc_final: 0.6742 (m-40) REVERT: A 593 LYS cc_start: 0.6739 (tptp) cc_final: 0.6480 (tptp) REVERT: C 38 ILE cc_start: 0.8520 (tt) cc_final: 0.8166 (pt) outliers start: 16 outliers final: 10 residues processed: 273 average time/residue: 0.1098 time to fit residues: 39.5059 Evaluate side-chains 277 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 266 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 227 CYS Chi-restraints excluded: chain B residue 236 CYS Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 329 GLN Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 515 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 74 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 64 optimal weight: 0.3980 chunk 90 optimal weight: 0.2980 chunk 28 optimal weight: 0.4980 chunk 92 optimal weight: 1.9990 chunk 58 optimal weight: 0.4980 chunk 10 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 87 optimal weight: 0.4980 chunk 75 optimal weight: 0.0870 overall best weight: 0.3558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 329 GLN B 446 GLN B 470 HIS B 559 HIS A 153 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.152333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.129680 restraints weight = 13419.108| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 2.77 r_work: 0.3543 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9475 Z= 0.161 Angle : 0.676 17.183 12887 Z= 0.336 Chirality : 0.050 0.477 1425 Planarity : 0.005 0.044 1679 Dihedral : 5.387 28.463 1269 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 2.15 % Allowed : 9.95 % Favored : 87.90 % 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: -3.00 (0.22), residues: 1170 helix: -3.31 (0.48), residues: 72 sheet: -2.37 (0.50), residues: 92 loop : -2.06 (0.18), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 252 TYR 0.021 0.002 TYR B 163 PHE 0.020 0.002 PHE A 549 TRP 0.014 0.001 TRP C 49 HIS 0.005 0.001 HIS B 237 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 ( 9420) covalent geometry : angle 0.63100 / 0.32 (12769) SS BOND : bond 0.00381 / 0.23 ( 47) SS BOND : angle 1.77498 / 1.11 ( 94) hydrogen bonds : bond 0.03281 / 1.94 ( 97) hydrogen bonds : angle 5.72480 / 3.78 ( 186) link_ALPHA1-3 : bond 0.00906 / 0.48 ( 1) link_ALPHA1-3 : angle 2.02225 / 1.03 ( 3) link_BETA1-3 : bond 0.00391 / 0.21 ( 1) link_BETA1-3 : angle 3.00467 / 1.58 ( 3) link_BETA1-4 : bond 0.00159 / 0.08 ( 2) link_BETA1-4 : angle 1.05618 / 0.60 ( 6) link_NAG-ASN : bond 0.00863 / 0.43 ( 4) link_NAG-ASN : angle 6.15853 / 3.98 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 273 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 30 ASP cc_start: 0.7963 (t70) cc_final: 0.7375 (t0) REVERT: B 75 GLN cc_start: 0.7927 (pt0) cc_final: 0.7652 (pt0) REVERT: B 89 ASN cc_start: 0.7882 (m-40) cc_final: 0.7676 (m-40) REVERT: B 93 GLN cc_start: 0.7296 (pp30) cc_final: 0.6929 (pp30) REVERT: B 112 TYR cc_start: 0.7532 (m-80) cc_final: 0.7312 (m-80) REVERT: B 147 GLU cc_start: 0.7313 (tp30) cc_final: 0.6772 (tp30) REVERT: B 164 GLN cc_start: 0.7391 (pm20) cc_final: 0.7070 (pm20) REVERT: B 228 LYS cc_start: 0.7984 (mtpt) cc_final: 0.7518 (mtpt) REVERT: B 284 ASN cc_start: 0.7810 (t0) cc_final: 0.7410 (t0) REVERT: B 405 GLU cc_start: 0.7628 (tt0) cc_final: 0.7384 (tp30) REVERT: B 421 ASP cc_start: 0.6943 (p0) cc_final: 0.6514 (p0) REVERT: B 438 ASN cc_start: 0.7734 (m-40) cc_final: 0.7500 (m110) REVERT: B 441 TYR cc_start: 0.8539 (m-80) cc_final: 0.8113 (m-80) REVERT: B 459 ARG cc_start: 0.8085 (ptt90) cc_final: 0.7680 (ptt90) REVERT: B 460 GLU cc_start: 0.7740 (tt0) cc_final: 0.7406 (tt0) REVERT: B 538 GLN cc_start: 0.6586 (OUTLIER) cc_final: 0.6350 (pm20) REVERT: B 553 GLU cc_start: 0.6047 (mt-10) cc_final: 0.5821 (tt0) REVERT: A 45 GLU cc_start: 0.7723 (mp0) cc_final: 0.7364 (mp0) REVERT: A 46 ASP cc_start: 0.8035 (t70) cc_final: 0.7577 (t70) REVERT: A 80 LYS cc_start: 0.8564 (mttm) cc_final: 0.8333 (mttp) REVERT: A 97 GLU cc_start: 0.6874 (mp0) cc_final: 0.6377 (mp0) REVERT: A 133 LYS cc_start: 0.7245 (mttt) cc_final: 0.7012 (ttmm) REVERT: A 148 VAL cc_start: 0.8459 (t) cc_final: 0.8048 (m) REVERT: A 198 SER cc_start: 0.8091 (m) cc_final: 0.7428 (p) REVERT: A 252 ARG cc_start: 0.7549 (mtp85) cc_final: 0.7321 (mtp85) REVERT: A 255 ARG cc_start: 0.6964 (ttt-90) cc_final: 0.6628 (tmt-80) REVERT: A 256 ASP cc_start: 0.7446 (t70) cc_final: 0.7135 (t70) REVERT: A 268 MET cc_start: 0.6465 (mtm) cc_final: 0.5891 (mtm) REVERT: A 277 MET cc_start: 0.5744 (mtt) cc_final: 0.5348 (mtt) REVERT: A 292 VAL cc_start: 0.8137 (m) cc_final: 0.7774 (p) REVERT: A 294 LYS cc_start: 0.8259 (tttt) cc_final: 0.8001 (tttt) REVERT: A 307 CYS cc_start: 0.7173 (m) cc_final: 0.6915 (m) REVERT: A 308 VAL cc_start: 0.8205 (OUTLIER) cc_final: 0.8001 (p) REVERT: A 316 TYR cc_start: 0.6696 (t80) cc_final: 0.6036 (t80) REVERT: A 318 MET cc_start: 0.6904 (tpp) cc_final: 0.6490 (tpp) REVERT: A 325 LYS cc_start: 0.7694 (mttt) cc_final: 0.7050 (mtmt) REVERT: A 327 LYS cc_start: 0.7908 (OUTLIER) cc_final: 0.7671 (ptpp) REVERT: A 391 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7433 (mm-30) REVERT: A 430 THR cc_start: 0.8067 (m) cc_final: 0.7422 (p) REVERT: A 479 LYS cc_start: 0.7938 (pttt) cc_final: 0.7714 (pttm) REVERT: A 487 LYS cc_start: 0.7341 (mtmm) cc_final: 0.7071 (mtmm) REVERT: A 489 LYS cc_start: 0.8083 (ttmm) cc_final: 0.7620 (ttmm) REVERT: A 593 LYS cc_start: 0.6720 (tptp) cc_final: 0.6488 (tptp) outliers start: 22 outliers final: 12 residues processed: 278 average time/residue: 0.1129 time to fit residues: 41.1679 Evaluate side-chains 272 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 257 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 236 CYS Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 538 GLN Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 251 CYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 327 LYS Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 425 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 85 optimal weight: 0.4980 chunk 13 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 99 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 114 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 48 HIS B 260 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.146053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.122969 restraints weight = 13543.823| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.78 r_work: 0.3446 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.4634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.110 9475 Z= 0.265 Angle : 0.782 17.837 12887 Z= 0.391 Chirality : 0.054 0.436 1425 Planarity : 0.006 0.083 1679 Dihedral : 5.908 30.208 1269 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 2.93 % Allowed : 10.93 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.88 (0.22), residues: 1170 helix: -3.16 (0.49), residues: 66 sheet: -2.13 (0.52), residues: 84 loop : -2.01 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 47 TYR 0.025 0.002 TYR B 409 PHE 0.041 0.003 PHE A 549 TRP 0.020 0.002 TRP C 49 HIS 0.008 0.002 HIS A 507 Details of bonding type rmsd/Z covalent geometry : bond 0.00602 / 0.27 ( 9420) covalent geometry : angle 0.73431 / 0.38 (12769) SS BOND : bond 0.00534 / 0.32 ( 47) SS BOND : angle 2.05074 / 1.30 ( 94) hydrogen bonds : bond 0.03584 / 2.16 ( 97) hydrogen bonds : angle 6.60914 / 4.37 ( 186) link_ALPHA1-3 : bond 0.00746 / 0.39 ( 1) link_ALPHA1-3 : angle 1.86809 / 0.95 ( 3) link_BETA1-3 : bond 0.00141 / 0.07 ( 1) link_BETA1-3 : angle 2.87793 / 1.50 ( 3) link_BETA1-4 : bond 0.00166 / 0.08 ( 2) link_BETA1-4 : angle 1.01662 / 0.53 ( 6) link_NAG-ASN : bond 0.01496 / 0.75 ( 4) link_NAG-ASN : angle 6.81894 / 4.40 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 291 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: B 30 ASP cc_start: 0.8112 (t70) cc_final: 0.7501 (t0) REVERT: B 75 GLN cc_start: 0.8178 (pt0) cc_final: 0.7976 (pt0) REVERT: B 89 ASN cc_start: 0.8031 (m-40) cc_final: 0.7783 (m-40) REVERT: B 112 TYR cc_start: 0.7802 (m-80) cc_final: 0.7530 (m-80) REVERT: B 138 ARG cc_start: 0.7293 (mmm-85) cc_final: 0.7014 (mmm160) REVERT: B 139 GLU cc_start: 0.7115 (mp0) cc_final: 0.6778 (mp0) REVERT: B 147 GLU cc_start: 0.7269 (tp30) cc_final: 0.6727 (tp30) REVERT: B 164 GLN cc_start: 0.8111 (pm20) cc_final: 0.7669 (pm20) REVERT: B 165 ASP cc_start: 0.7872 (p0) cc_final: 0.7541 (p0) REVERT: B 261 SER cc_start: 0.8038 (m) cc_final: 0.7690 (p) REVERT: B 274 TYR cc_start: 0.8220 (t80) cc_final: 0.7977 (t80) REVERT: B 284 ASN cc_start: 0.8148 (t0) cc_final: 0.7785 (t0) REVERT: B 371 PHE cc_start: 0.7759 (m-10) cc_final: 0.7214 (m-80) REVERT: B 405 GLU cc_start: 0.7528 (tt0) cc_final: 0.7194 (tt0) REVERT: B 421 ASP cc_start: 0.7160 (p0) cc_final: 0.6740 (p0) REVERT: B 438 ASN cc_start: 0.7725 (m-40) cc_final: 0.7508 (m110) REVERT: B 441 TYR cc_start: 0.8589 (m-80) cc_final: 0.8261 (m-80) REVERT: B 446 GLN cc_start: 0.7572 (mt0) cc_final: 0.7227 (mt0) REVERT: B 460 GLU cc_start: 0.7816 (tt0) cc_final: 0.7483 (tt0) REVERT: B 491 GLN cc_start: 0.8140 (mt0) cc_final: 0.7909 (mt0) REVERT: B 553 GLU cc_start: 0.6428 (mt-10) cc_final: 0.6068 (mt-10) REVERT: A 45 GLU cc_start: 0.7779 (mp0) cc_final: 0.7539 (mp0) REVERT: A 46 ASP cc_start: 0.7951 (t70) cc_final: 0.7444 (t70) REVERT: A 97 GLU cc_start: 0.6941 (mp0) cc_final: 0.6480 (mp0) REVERT: A 148 VAL cc_start: 0.8555 (t) cc_final: 0.8178 (m) REVERT: A 222 ARG cc_start: 0.7832 (mtp85) cc_final: 0.7353 (ttm-80) REVERT: A 263 THR cc_start: 0.8037 (m) cc_final: 0.7636 (p) REVERT: A 284 LYS cc_start: 0.8207 (mtmm) cc_final: 0.7959 (mtmm) REVERT: A 292 VAL cc_start: 0.8155 (m) cc_final: 0.7780 (p) REVERT: A 294 LYS cc_start: 0.8255 (tttt) cc_final: 0.7989 (tttt) REVERT: A 303 ASP cc_start: 0.7628 (p0) cc_final: 0.7382 (p0) REVERT: A 325 LYS cc_start: 0.7694 (mttt) cc_final: 0.7070 (mtmt) REVERT: A 357 LYS cc_start: 0.8434 (ptpt) cc_final: 0.8201 (ptpt) REVERT: A 358 HIS cc_start: 0.7977 (m90) cc_final: 0.7741 (m170) REVERT: A 391 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7564 (mm-30) REVERT: A 430 THR cc_start: 0.8129 (m) cc_final: 0.7584 (p) REVERT: A 455 GLU cc_start: 0.7655 (tt0) cc_final: 0.7222 (tt0) REVERT: A 487 LYS cc_start: 0.7742 (mtmm) cc_final: 0.7427 (mtmm) REVERT: A 489 LYS cc_start: 0.8129 (ttmm) cc_final: 0.7810 (ttmm) REVERT: A 524 VAL cc_start: 0.8485 (t) cc_final: 0.8273 (p) REVERT: A 559 HIS cc_start: 0.6631 (OUTLIER) cc_final: 0.6308 (m-70) REVERT: A 584 HIS cc_start: 0.6162 (m90) cc_final: 0.5940 (m170) REVERT: A 593 LYS cc_start: 0.6860 (tptp) cc_final: 0.6352 (tptp) outliers start: 30 outliers final: 21 residues processed: 302 average time/residue: 0.1096 time to fit residues: 44.1694 Evaluate side-chains 298 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 276 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 236 CYS Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 538 GLN Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 251 CYS Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 515 CYS Chi-restraints excluded: chain A residue 559 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 64 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 105 optimal weight: 0.3980 chunk 70 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 99 optimal weight: 0.0470 chunk 6 optimal weight: 0.2980 chunk 74 optimal weight: 0.0980 chunk 25 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 overall best weight: 0.3078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 491 GLN ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 GLN A 444 ASN ** 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 = 0.3913 r_free = 0.3913 target = 0.147104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.124333 restraints weight = 13556.630| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 2.76 r_work: 0.3473 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.4886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 9475 Z= 0.154 Angle : 0.695 17.853 12887 Z= 0.346 Chirality : 0.049 0.400 1425 Planarity : 0.004 0.041 1679 Dihedral : 5.613 26.868 1269 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 2.83 % Allowed : 14.05 % Favored : 83.12 % 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 (0.22), residues: 1170 helix: -2.71 (0.58), residues: 59 sheet: -2.68 (0.46), residues: 92 loop : -1.84 (0.18), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 574 TYR 0.024 0.002 TYR B 409 PHE 0.029 0.002 PHE A 549 TRP 0.011 0.002 TRP C 49 HIS 0.004 0.001 HIS A 507 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 ( 9420) covalent geometry : angle 0.64944 / 0.33 (12769) SS BOND : bond 0.00480 / 0.30 ( 47) SS BOND : angle 1.77349 / 1.13 ( 94) hydrogen bonds : bond 0.02971 / 1.77 ( 97) hydrogen bonds : angle 6.14377 / 4.12 ( 186) link_ALPHA1-3 : bond 0.00998 / 0.53 ( 1) link_ALPHA1-3 : angle 1.90074 / 0.97 ( 3) link_BETA1-3 : bond 0.00569 / 0.30 ( 1) link_BETA1-3 : angle 2.84037 / 1.49 ( 3) link_BETA1-4 : bond 0.00255 / 0.13 ( 2) link_BETA1-4 : angle 1.01269 / 0.57 ( 6) link_NAG-ASN : bond 0.01316 / 0.66 ( 4) link_NAG-ASN : angle 6.41577 / 4.15 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 272 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: B 30 ASP cc_start: 0.7986 (t70) cc_final: 0.7333 (t0) REVERT: B 89 ASN cc_start: 0.8021 (m-40) cc_final: 0.7765 (m-40) REVERT: B 138 ARG cc_start: 0.7346 (mmm-85) cc_final: 0.7009 (mmm160) REVERT: B 139 GLU cc_start: 0.7078 (mp0) cc_final: 0.6754 (mp0) REVERT: B 164 GLN cc_start: 0.7901 (pm20) cc_final: 0.7699 (pm20) REVERT: B 165 ASP cc_start: 0.7858 (p0) cc_final: 0.7528 (p0) REVERT: B 228 LYS cc_start: 0.8142 (mtpt) cc_final: 0.7859 (mtpt) REVERT: B 274 TYR cc_start: 0.8218 (t80) cc_final: 0.7981 (t80) REVERT: B 284 ASN cc_start: 0.8114 (t0) cc_final: 0.7761 (t0) REVERT: B 290 THR cc_start: 0.8002 (m) cc_final: 0.7761 (m) REVERT: B 405 GLU cc_start: 0.7582 (tt0) cc_final: 0.7299 (tt0) REVERT: B 421 ASP cc_start: 0.7181 (p0) cc_final: 0.6799 (p0) REVERT: B 438 ASN cc_start: 0.7728 (m-40) cc_final: 0.7523 (m110) REVERT: B 441 TYR cc_start: 0.8558 (m-80) cc_final: 0.8015 (m-80) REVERT: B 446 GLN cc_start: 0.7510 (mt0) cc_final: 0.7108 (mt0) REVERT: B 460 GLU cc_start: 0.7857 (tt0) cc_final: 0.7576 (tt0) REVERT: B 538 GLN cc_start: 0.6725 (OUTLIER) cc_final: 0.6488 (pm20) REVERT: B 553 GLU cc_start: 0.6489 (mt-10) cc_final: 0.6122 (mt-10) REVERT: B 568 GLN cc_start: 0.6860 (tm-30) cc_final: 0.6458 (tm-30) REVERT: A 46 ASP cc_start: 0.7939 (t70) cc_final: 0.7500 (t0) REVERT: A 80 LYS cc_start: 0.8585 (mttm) cc_final: 0.8313 (mttp) REVERT: A 97 GLU cc_start: 0.6854 (mp0) cc_final: 0.6427 (mp0) REVERT: A 98 ARG cc_start: 0.8365 (mtp-110) cc_final: 0.8125 (mtp180) REVERT: A 148 VAL cc_start: 0.8490 (t) cc_final: 0.8148 (m) REVERT: A 198 SER cc_start: 0.8249 (m) cc_final: 0.7511 (p) REVERT: A 222 ARG cc_start: 0.7656 (mtp85) cc_final: 0.7413 (mtp85) REVERT: A 263 THR cc_start: 0.8040 (m) cc_final: 0.7710 (p) REVERT: A 268 MET cc_start: 0.6768 (mtm) cc_final: 0.6567 (mtm) REVERT: A 284 LYS cc_start: 0.8144 (mtmm) cc_final: 0.7792 (mtmm) REVERT: A 292 VAL cc_start: 0.8112 (m) cc_final: 0.7738 (p) REVERT: A 294 LYS cc_start: 0.8243 (tttt) cc_final: 0.7981 (tttt) REVERT: A 303 ASP cc_start: 0.7583 (p0) cc_final: 0.6914 (p0) REVERT: A 308 VAL cc_start: 0.8254 (p) cc_final: 0.8034 (m) REVERT: A 325 LYS cc_start: 0.7346 (mttt) cc_final: 0.6756 (mtmt) REVERT: A 357 LYS cc_start: 0.8453 (ptpt) cc_final: 0.8224 (ptpt) REVERT: A 391 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7570 (mm-30) REVERT: A 430 THR cc_start: 0.8093 (m) cc_final: 0.7535 (p) REVERT: A 455 GLU cc_start: 0.7575 (tt0) cc_final: 0.7187 (tt0) REVERT: A 487 LYS cc_start: 0.7738 (mtmm) cc_final: 0.7448 (mtmm) REVERT: A 489 LYS cc_start: 0.8122 (ttmm) cc_final: 0.7741 (ttmm) REVERT: A 559 HIS cc_start: 0.6592 (OUTLIER) cc_final: 0.6262 (m-70) REVERT: A 584 HIS cc_start: 0.6106 (m90) cc_final: 0.5858 (m170) REVERT: A 593 LYS cc_start: 0.6815 (tptp) cc_final: 0.6300 (tptp) outliers start: 29 outliers final: 20 residues processed: 285 average time/residue: 0.1105 time to fit residues: 41.8353 Evaluate side-chains 289 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 267 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 236 CYS Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 538 GLN Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 264 CYS Chi-restraints excluded: chain A residue 311 CYS Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 468 ASN Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 559 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 27 optimal weight: 2.9990 chunk 40 optimal weight: 0.1980 chunk 44 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 84 optimal weight: 0.0670 chunk 109 optimal weight: 0.9990 chunk 96 optimal weight: 0.4980 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 512 HIS B 530 ASN ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 ASN ** 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 = 0.3888 r_free = 0.3888 target = 0.145077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.122577 restraints weight = 13500.227| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 2.67 r_work: 0.3448 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.5258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 9475 Z= 0.199 Angle : 0.717 17.531 12887 Z= 0.357 Chirality : 0.050 0.393 1425 Planarity : 0.004 0.042 1679 Dihedral : 5.721 27.593 1269 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 3.22 % Allowed : 14.73 % Favored : 82.05 % 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: -2.73 (0.22), residues: 1170 helix: -2.74 (0.56), residues: 66 sheet: -2.75 (0.46), residues: 92 loop : -1.83 (0.18), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 574 TYR 0.026 0.002 TYR B 409 PHE 0.015 0.002 PHE A 481 TRP 0.026 0.002 TRP C 49 HIS 0.006 0.001 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.20 ( 9420) covalent geometry : angle 0.67323 / 0.34 (12769) SS BOND : bond 0.00402 / 0.25 ( 47) SS BOND : angle 1.81656 / 1.14 ( 94) hydrogen bonds : bond 0.03123 / 1.90 ( 97) hydrogen bonds : angle 6.21250 / 4.14 ( 186) link_ALPHA1-3 : bond 0.01531 / 0.81 ( 1) link_ALPHA1-3 : angle 2.02918 / 1.04 ( 3) link_BETA1-3 : bond 0.00818 / 0.43 ( 1) link_BETA1-3 : angle 2.70994 / 1.42 ( 3) link_BETA1-4 : bond 0.00266 / 0.14 ( 2) link_BETA1-4 : angle 0.86621 / 0.48 ( 6) link_NAG-ASN : bond 0.01289 / 0.65 ( 4) link_NAG-ASN : angle 6.40413 / 4.13 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 274 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 24 GLN cc_start: 0.6867 (pp30) cc_final: 0.6600 (pp30) REVERT: B 30 ASP cc_start: 0.8006 (t70) cc_final: 0.7376 (t0) REVERT: B 75 GLN cc_start: 0.7968 (pt0) cc_final: 0.7604 (pt0) REVERT: B 89 ASN cc_start: 0.8012 (m-40) cc_final: 0.7729 (m-40) REVERT: B 138 ARG cc_start: 0.7339 (mmm-85) cc_final: 0.7014 (mmm160) REVERT: B 139 GLU cc_start: 0.7117 (mp0) cc_final: 0.6763 (mp0) REVERT: B 147 GLU cc_start: 0.7286 (tp30) cc_final: 0.6952 (tp30) REVERT: B 165 ASP cc_start: 0.7857 (p0) cc_final: 0.7505 (p0) REVERT: B 261 SER cc_start: 0.8025 (m) cc_final: 0.7701 (p) REVERT: B 274 TYR cc_start: 0.8245 (t80) cc_final: 0.8039 (t80) REVERT: B 284 ASN cc_start: 0.8161 (t0) cc_final: 0.7803 (t0) REVERT: B 290 THR cc_start: 0.8142 (m) cc_final: 0.7899 (m) REVERT: B 297 THR cc_start: 0.8452 (m) cc_final: 0.8127 (p) REVERT: B 405 GLU cc_start: 0.7482 (tt0) cc_final: 0.7209 (tt0) REVERT: B 421 ASP cc_start: 0.7155 (p0) cc_final: 0.6784 (p0) REVERT: B 438 ASN cc_start: 0.7746 (m-40) cc_final: 0.7513 (m110) REVERT: B 446 GLN cc_start: 0.7519 (mt0) cc_final: 0.7227 (mt0) REVERT: B 460 GLU cc_start: 0.7786 (tt0) cc_final: 0.7516 (tt0) REVERT: B 533 GLN cc_start: 0.4454 (mp10) cc_final: 0.4202 (pm20) REVERT: B 553 GLU cc_start: 0.6504 (mt-10) cc_final: 0.6109 (mt-10) REVERT: A 46 ASP cc_start: 0.7894 (t70) cc_final: 0.7424 (t0) REVERT: A 142 GLU cc_start: 0.7505 (tp30) cc_final: 0.7184 (mm-30) REVERT: A 148 VAL cc_start: 0.8536 (t) cc_final: 0.8180 (m) REVERT: A 160 GLU cc_start: 0.8051 (pm20) cc_final: 0.7641 (pm20) REVERT: A 198 SER cc_start: 0.8306 (m) cc_final: 0.7545 (p) REVERT: A 250 VAL cc_start: 0.8034 (t) cc_final: 0.7754 (m) REVERT: A 263 THR cc_start: 0.7998 (m) cc_final: 0.7689 (p) REVERT: A 268 MET cc_start: 0.6752 (mtm) cc_final: 0.6506 (mtm) REVERT: A 284 LYS cc_start: 0.8180 (mtmm) cc_final: 0.7975 (mtmm) REVERT: A 292 VAL cc_start: 0.8138 (m) cc_final: 0.7767 (p) REVERT: A 294 LYS cc_start: 0.8243 (tttt) cc_final: 0.7996 (tttt) REVERT: A 308 VAL cc_start: 0.8363 (p) cc_final: 0.8107 (m) REVERT: A 319 GLU cc_start: 0.7556 (pt0) cc_final: 0.7198 (tm-30) REVERT: A 325 LYS cc_start: 0.7405 (mttt) cc_final: 0.6813 (mtmt) REVERT: A 357 LYS cc_start: 0.8475 (ptpt) cc_final: 0.8272 (ptpt) REVERT: A 391 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7823 (mm-30) REVERT: A 399 LYS cc_start: 0.8014 (ttmm) cc_final: 0.7666 (mtpp) REVERT: A 430 THR cc_start: 0.8124 (m) cc_final: 0.7609 (p) REVERT: A 455 GLU cc_start: 0.7517 (tt0) cc_final: 0.7122 (tt0) REVERT: A 489 LYS cc_start: 0.8132 (ttmm) cc_final: 0.7677 (ttmm) REVERT: A 559 HIS cc_start: 0.6555 (OUTLIER) cc_final: 0.6253 (m-70) REVERT: A 593 LYS cc_start: 0.6840 (tptp) cc_final: 0.6587 (tptp) outliers start: 33 outliers final: 22 residues processed: 292 average time/residue: 0.1087 time to fit residues: 42.8558 Evaluate side-chains 288 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 265 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 236 CYS Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 538 GLN Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 264 CYS Chi-restraints excluded: chain A residue 307 CYS Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 559 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 16 optimal weight: 0.3980 chunk 12 optimal weight: 0.2980 chunk 95 optimal weight: 0.9980 chunk 94 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 1 optimal weight: 0.0570 chunk 26 optimal weight: 0.3980 chunk 75 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 overall best weight: 0.3498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 329 GLN ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 530 ASN A 444 ASN ** 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 = 0.3893 r_free = 0.3893 target = 0.145196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.122569 restraints weight = 13452.548| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 2.75 r_work: 0.3439 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.5413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9475 Z= 0.161 Angle : 0.694 17.536 12887 Z= 0.346 Chirality : 0.049 0.395 1425 Planarity : 0.004 0.041 1679 Dihedral : 5.608 26.669 1269 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 3.12 % Allowed : 15.41 % Favored : 81.46 % 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: -2.63 (0.22), residues: 1170 helix: -2.24 (0.63), residues: 59 sheet: -2.81 (0.46), residues: 90 loop : -1.79 (0.18), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 499 TYR 0.025 0.002 TYR B 409 PHE 0.011 0.001 PHE B 258 TRP 0.024 0.002 TRP C 49 HIS 0.005 0.001 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 ( 9420) covalent geometry : angle 0.64853 / 0.33 (12769) SS BOND : bond 0.00346 / 0.21 ( 47) SS BOND : angle 1.82588 / 1.13 ( 94) hydrogen bonds : bond 0.02921 / 1.80 ( 97) hydrogen bonds : angle 6.03549 / 4.07 ( 186) link_ALPHA1-3 : bond 0.00969 / 0.51 ( 1) link_ALPHA1-3 : angle 1.79158 / 0.92 ( 3) link_BETA1-3 : bond 0.00704 / 0.37 ( 1) link_BETA1-3 : angle 2.80125 / 1.47 ( 3) link_BETA1-4 : bond 0.00303 / 0.15 ( 2) link_BETA1-4 : angle 0.94256 / 0.54 ( 6) link_NAG-ASN : bond 0.01265 / 0.63 ( 4) link_NAG-ASN : angle 6.31727 / 4.09 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 262 time to evaluate : 0.356 Fit side-chains revert: symmetry clash REVERT: B 24 GLN cc_start: 0.6804 (pp30) cc_final: 0.6514 (pp30) REVERT: B 30 ASP cc_start: 0.8009 (t70) cc_final: 0.7376 (t0) REVERT: B 75 GLN cc_start: 0.8013 (pt0) cc_final: 0.7633 (pt0) REVERT: B 89 ASN cc_start: 0.8039 (m-40) cc_final: 0.7789 (m-40) REVERT: B 138 ARG cc_start: 0.7389 (mmm-85) cc_final: 0.6923 (mmm160) REVERT: B 139 GLU cc_start: 0.7183 (mp0) cc_final: 0.6860 (mp0) REVERT: B 147 GLU cc_start: 0.7292 (tp30) cc_final: 0.6945 (tp30) REVERT: B 165 ASP cc_start: 0.7886 (p0) cc_final: 0.7542 (p0) REVERT: B 248 LYS cc_start: 0.8496 (mmtt) cc_final: 0.8263 (mmpt) REVERT: B 261 SER cc_start: 0.8042 (m) cc_final: 0.7728 (p) REVERT: B 274 TYR cc_start: 0.8223 (t80) cc_final: 0.8019 (t80) REVERT: B 282 MET cc_start: 0.7683 (mtm) cc_final: 0.7378 (mtm) REVERT: B 284 ASN cc_start: 0.8195 (t0) cc_final: 0.7798 (t0) REVERT: B 290 THR cc_start: 0.8082 (m) cc_final: 0.7819 (m) REVERT: B 297 THR cc_start: 0.8440 (m) cc_final: 0.8191 (p) REVERT: B 405 GLU cc_start: 0.7501 (tt0) cc_final: 0.7218 (tt0) REVERT: B 421 ASP cc_start: 0.7249 (p0) cc_final: 0.6858 (p0) REVERT: B 438 ASN cc_start: 0.7692 (m-40) cc_final: 0.7425 (m110) REVERT: B 446 GLN cc_start: 0.7509 (mt0) cc_final: 0.7176 (mt0) REVERT: B 460 GLU cc_start: 0.7874 (tt0) cc_final: 0.7449 (tt0) REVERT: B 553 GLU cc_start: 0.6407 (mt-10) cc_final: 0.6015 (mt-10) REVERT: B 568 GLN cc_start: 0.7028 (tm-30) cc_final: 0.6622 (tm-30) REVERT: A 46 ASP cc_start: 0.7863 (t70) cc_final: 0.7404 (t0) REVERT: A 142 GLU cc_start: 0.7558 (tp30) cc_final: 0.7160 (mm-30) REVERT: A 148 VAL cc_start: 0.8501 (t) cc_final: 0.8148 (m) REVERT: A 160 GLU cc_start: 0.8123 (pm20) cc_final: 0.7699 (pm20) REVERT: A 166 ASP cc_start: 0.7871 (t70) cc_final: 0.7183 (t0) REVERT: A 198 SER cc_start: 0.8280 (m) cc_final: 0.7489 (p) REVERT: A 250 VAL cc_start: 0.7923 (t) cc_final: 0.7663 (m) REVERT: A 263 THR cc_start: 0.8013 (m) cc_final: 0.7692 (p) REVERT: A 268 MET cc_start: 0.6870 (mtm) cc_final: 0.6608 (mtm) REVERT: A 292 VAL cc_start: 0.8055 (m) cc_final: 0.7664 (p) REVERT: A 294 LYS cc_start: 0.8244 (tttt) cc_final: 0.7900 (ptmm) REVERT: A 308 VAL cc_start: 0.8279 (p) cc_final: 0.8032 (m) REVERT: A 325 LYS cc_start: 0.7393 (mttt) cc_final: 0.6743 (mtmt) REVERT: A 327 LYS cc_start: 0.7632 (ptpp) cc_final: 0.7029 (pttm) REVERT: A 338 ASN cc_start: 0.7465 (t0) cc_final: 0.6992 (t0) REVERT: A 344 GLU cc_start: 0.7207 (pm20) cc_final: 0.7004 (pm20) REVERT: A 391 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7872 (mm-30) REVERT: A 399 LYS cc_start: 0.8016 (ttmm) cc_final: 0.7578 (mtpp) REVERT: A 430 THR cc_start: 0.8134 (m) cc_final: 0.7609 (p) REVERT: A 455 GLU cc_start: 0.7606 (tt0) cc_final: 0.7109 (tt0) REVERT: A 551 GLU cc_start: 0.7798 (tm-30) cc_final: 0.7582 (tm-30) REVERT: A 559 HIS cc_start: 0.6639 (OUTLIER) cc_final: 0.6282 (m-70) REVERT: A 593 LYS cc_start: 0.6830 (tptp) cc_final: 0.6537 (tptp) outliers start: 32 outliers final: 20 residues processed: 276 average time/residue: 0.1046 time to fit residues: 39.3745 Evaluate side-chains 274 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 253 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 538 GLN Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 264 CYS Chi-restraints excluded: chain A residue 307 CYS Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 468 ASN Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 559 HIS Chi-restraints excluded: chain A residue 586 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 96 optimal weight: 0.9980 chunk 78 optimal weight: 0.0770 chunk 93 optimal weight: 0.0980 chunk 91 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 86 optimal weight: 0.8980 chunk 114 optimal weight: 0.8980 chunk 63 optimal weight: 0.1980 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 329 GLN ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 530 ASN A 153 ASN ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 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 = 0.3876 r_free = 0.3876 target = 0.144042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.121669 restraints weight = 13381.566| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.61 r_work: 0.3441 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.5611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9475 Z= 0.180 Angle : 0.717 17.194 12887 Z= 0.358 Chirality : 0.050 0.397 1425 Planarity : 0.004 0.040 1679 Dihedral : 5.669 27.861 1269 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 3.22 % Allowed : 15.12 % Favored : 81.66 % 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: -2.59 (0.23), residues: 1170 helix: -1.91 (0.67), residues: 53 sheet: -2.90 (0.46), residues: 90 loop : -1.77 (0.18), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 456 TYR 0.028 0.002 TYR B 409 PHE 0.013 0.001 PHE A 481 TRP 0.035 0.002 TRP C 49 HIS 0.006 0.001 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.18 ( 9420) covalent geometry : angle 0.67164 / 0.34 (12769) SS BOND : bond 0.00367 / 0.23 ( 47) SS BOND : angle 1.97668 / 1.27 ( 94) hydrogen bonds : bond 0.03035 / 1.87 ( 97) hydrogen bonds : angle 5.94830 / 4.00 ( 186) link_ALPHA1-3 : bond 0.00894 / 0.47 ( 1) link_ALPHA1-3 : angle 1.75310 / 0.90 ( 3) link_BETA1-3 : bond 0.00470 / 0.25 ( 1) link_BETA1-3 : angle 2.83172 / 1.48 ( 3) link_BETA1-4 : bond 0.00135 / 0.07 ( 2) link_BETA1-4 : angle 0.91211 / 0.50 ( 6) link_NAG-ASN : bond 0.01265 / 0.63 ( 4) link_NAG-ASN : angle 6.24572 / 4.03 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 257 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 24 GLN cc_start: 0.7034 (pp30) cc_final: 0.6772 (pp30) REVERT: B 30 ASP cc_start: 0.8182 (t70) cc_final: 0.7574 (t0) REVERT: B 75 GLN cc_start: 0.8171 (pt0) cc_final: 0.7796 (pt0) REVERT: B 89 ASN cc_start: 0.8246 (m-40) cc_final: 0.8001 (m-40) REVERT: B 138 ARG cc_start: 0.7634 (mmm-85) cc_final: 0.7234 (mmm160) REVERT: B 139 GLU cc_start: 0.7465 (mp0) cc_final: 0.7104 (mp0) REVERT: B 147 GLU cc_start: 0.7500 (tp30) cc_final: 0.7220 (tp30) REVERT: B 165 ASP cc_start: 0.8076 (p0) cc_final: 0.7723 (p0) REVERT: B 244 CYS cc_start: 0.6483 (p) cc_final: 0.6177 (p) REVERT: B 248 LYS cc_start: 0.8633 (mmtt) cc_final: 0.8411 (mmpt) REVERT: B 282 MET cc_start: 0.7887 (mtm) cc_final: 0.7578 (mtm) REVERT: B 284 ASN cc_start: 0.8297 (t0) cc_final: 0.7983 (t0) REVERT: B 290 THR cc_start: 0.8268 (m) cc_final: 0.8002 (m) REVERT: B 297 THR cc_start: 0.8562 (m) cc_final: 0.8360 (p) REVERT: B 405 GLU cc_start: 0.7750 (tt0) cc_final: 0.7481 (tt0) REVERT: B 411 TYR cc_start: 0.8476 (t80) cc_final: 0.8267 (t80) REVERT: B 421 ASP cc_start: 0.7469 (p0) cc_final: 0.7082 (p0) REVERT: B 438 ASN cc_start: 0.7814 (m-40) cc_final: 0.7565 (m110) REVERT: B 446 GLN cc_start: 0.7721 (mt0) cc_final: 0.7345 (mt0) REVERT: B 460 GLU cc_start: 0.8177 (tt0) cc_final: 0.7900 (tt0) REVERT: B 501 GLU cc_start: 0.7310 (mm-30) cc_final: 0.6908 (mm-30) REVERT: B 533 GLN cc_start: 0.4956 (mp10) cc_final: 0.4361 (pm20) REVERT: B 553 GLU cc_start: 0.6640 (mt-10) cc_final: 0.6278 (mt-10) REVERT: A 46 ASP cc_start: 0.8061 (t70) cc_final: 0.7590 (t0) REVERT: A 142 GLU cc_start: 0.7834 (tp30) cc_final: 0.7448 (mm-30) REVERT: A 148 VAL cc_start: 0.8599 (t) cc_final: 0.8251 (m) REVERT: A 160 GLU cc_start: 0.8293 (pm20) cc_final: 0.7880 (pm20) REVERT: A 198 SER cc_start: 0.8344 (m) cc_final: 0.7569 (p) REVERT: A 217 GLN cc_start: 0.8430 (pt0) cc_final: 0.8123 (pt0) REVERT: A 250 VAL cc_start: 0.8117 (t) cc_final: 0.7870 (m) REVERT: A 263 THR cc_start: 0.8067 (m) cc_final: 0.7768 (p) REVERT: A 268 MET cc_start: 0.6998 (mtm) cc_final: 0.6708 (mtm) REVERT: A 292 VAL cc_start: 0.8123 (m) cc_final: 0.7804 (p) REVERT: A 294 LYS cc_start: 0.8355 (tttt) cc_final: 0.8045 (ptmm) REVERT: A 308 VAL cc_start: 0.8425 (p) cc_final: 0.8176 (m) REVERT: A 325 LYS cc_start: 0.7573 (mttt) cc_final: 0.7012 (mtmt) REVERT: A 344 GLU cc_start: 0.7359 (pm20) cc_final: 0.7089 (pm20) REVERT: A 391 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7937 (mm-30) REVERT: A 399 LYS cc_start: 0.8104 (ttmm) cc_final: 0.7829 (mtpp) REVERT: A 430 THR cc_start: 0.8255 (m) cc_final: 0.7753 (p) REVERT: A 455 GLU cc_start: 0.7863 (tt0) cc_final: 0.7438 (tt0) REVERT: A 551 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7771 (tm-30) REVERT: A 559 HIS cc_start: 0.6836 (OUTLIER) cc_final: 0.6402 (m-70) REVERT: A 593 LYS cc_start: 0.6943 (tptp) cc_final: 0.6617 (tptp) outliers start: 33 outliers final: 25 residues processed: 270 average time/residue: 0.1042 time to fit residues: 38.3660 Evaluate side-chains 274 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 248 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 236 CYS Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 538 GLN Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 264 CYS Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain A residue 307 CYS Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 468 ASN Chi-restraints excluded: chain A residue 510 CYS Chi-restraints excluded: chain A residue 515 CYS Chi-restraints excluded: chain A residue 559 HIS Chi-restraints excluded: chain A residue 586 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 50 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 114 optimal weight: 0.3980 chunk 67 optimal weight: 0.6980 chunk 95 optimal weight: 0.8980 chunk 35 optimal weight: 0.1980 chunk 65 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 78 optimal weight: 0.8980 chunk 105 optimal weight: 0.0370 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 329 GLN ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 530 ASN A 163 GLN A 196 ASN A 433 HIS ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.144107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.121514 restraints weight = 13428.534| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 2.75 r_work: 0.3427 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.5735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9475 Z= 0.178 Angle : 0.720 17.025 12887 Z= 0.359 Chirality : 0.050 0.396 1425 Planarity : 0.004 0.040 1679 Dihedral : 5.701 27.341 1269 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 3.12 % Allowed : 15.51 % Favored : 81.37 % 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: -2.58 (0.23), residues: 1170 helix: -2.12 (0.62), residues: 60 sheet: -2.78 (0.47), residues: 90 loop : -1.76 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 499 TYR 0.028 0.002 TYR B 409 PHE 0.015 0.001 PHE A 481 TRP 0.032 0.002 TRP C 49 HIS 0.005 0.001 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.18 ( 9420) covalent geometry : angle 0.67285 / 0.34 (12769) SS BOND : bond 0.00368 / 0.23 ( 47) SS BOND : angle 2.07499 / 1.35 ( 94) hydrogen bonds : bond 0.03000 / 1.88 ( 97) hydrogen bonds : angle 5.83471 / 3.92 ( 186) link_ALPHA1-3 : bond 0.00923 / 0.49 ( 1) link_ALPHA1-3 : angle 1.76577 / 0.90 ( 3) link_BETA1-3 : bond 0.00466 / 0.25 ( 1) link_BETA1-3 : angle 2.86360 / 1.50 ( 3) link_BETA1-4 : bond 0.00235 / 0.12 ( 2) link_BETA1-4 : angle 0.91426 / 0.51 ( 6) link_NAG-ASN : bond 0.01238 / 0.62 ( 4) link_NAG-ASN : angle 6.18530 / 4.00 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 257 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 24 GLN cc_start: 0.6772 (pp30) cc_final: 0.6485 (pp30) REVERT: B 30 ASP cc_start: 0.8107 (t70) cc_final: 0.7418 (t0) REVERT: B 75 GLN cc_start: 0.8020 (pt0) cc_final: 0.7627 (pt0) REVERT: B 89 ASN cc_start: 0.8010 (m-40) cc_final: 0.7748 (m110) REVERT: B 138 ARG cc_start: 0.7389 (mmm-85) cc_final: 0.7031 (mmm160) REVERT: B 139 GLU cc_start: 0.7247 (mp0) cc_final: 0.6888 (mp0) REVERT: B 147 GLU cc_start: 0.7279 (tp30) cc_final: 0.6944 (tp30) REVERT: B 165 ASP cc_start: 0.7918 (p0) cc_final: 0.7545 (p0) REVERT: B 244 CYS cc_start: 0.5802 (p) cc_final: 0.5513 (p) REVERT: B 261 SER cc_start: 0.8079 (m) cc_final: 0.7789 (p) REVERT: B 282 MET cc_start: 0.7577 (mtm) cc_final: 0.7269 (mtm) REVERT: B 284 ASN cc_start: 0.8223 (t0) cc_final: 0.7686 (t0) REVERT: B 290 THR cc_start: 0.8185 (m) cc_final: 0.7899 (m) REVERT: B 405 GLU cc_start: 0.7430 (tt0) cc_final: 0.7139 (tt0) REVERT: B 411 TYR cc_start: 0.8335 (t80) cc_final: 0.8087 (t80) REVERT: B 421 ASP cc_start: 0.7256 (p0) cc_final: 0.6875 (p0) REVERT: B 438 ASN cc_start: 0.7754 (m-40) cc_final: 0.7487 (m110) REVERT: B 446 GLN cc_start: 0.7472 (mt0) cc_final: 0.7080 (mt0) REVERT: B 460 GLU cc_start: 0.7875 (tt0) cc_final: 0.7539 (tt0) REVERT: B 501 GLU cc_start: 0.7135 (mm-30) cc_final: 0.6766 (mm-30) REVERT: B 514 LEU cc_start: 0.7526 (mp) cc_final: 0.7128 (mt) REVERT: B 533 GLN cc_start: 0.4864 (mp10) cc_final: 0.4020 (pm20) REVERT: B 553 GLU cc_start: 0.6314 (mt-10) cc_final: 0.5957 (mt-10) REVERT: B 568 GLN cc_start: 0.7142 (tm-30) cc_final: 0.6742 (tm-30) REVERT: A 46 ASP cc_start: 0.7877 (t70) cc_final: 0.7378 (t0) REVERT: A 142 GLU cc_start: 0.7571 (tp30) cc_final: 0.7171 (mm-30) REVERT: A 148 VAL cc_start: 0.8475 (t) cc_final: 0.8113 (m) REVERT: A 160 GLU cc_start: 0.8137 (pm20) cc_final: 0.7685 (pm20) REVERT: A 198 SER cc_start: 0.8372 (m) cc_final: 0.7523 (p) REVERT: A 250 VAL cc_start: 0.7915 (t) cc_final: 0.7665 (m) REVERT: A 263 THR cc_start: 0.7974 (m) cc_final: 0.7696 (p) REVERT: A 268 MET cc_start: 0.6964 (mtm) cc_final: 0.6747 (mtm) REVERT: A 292 VAL cc_start: 0.8046 (m) cc_final: 0.7711 (p) REVERT: A 294 LYS cc_start: 0.8214 (tttt) cc_final: 0.7879 (ptmm) REVERT: A 308 VAL cc_start: 0.8316 (p) cc_final: 0.8105 (m) REVERT: A 317 GLU cc_start: 0.7448 (tt0) cc_final: 0.7138 (tm-30) REVERT: A 318 MET cc_start: 0.7176 (OUTLIER) cc_final: 0.6903 (tpp) REVERT: A 325 LYS cc_start: 0.7357 (mttt) cc_final: 0.6758 (mtmt) REVERT: A 344 GLU cc_start: 0.7244 (pm20) cc_final: 0.6955 (pm20) REVERT: A 391 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7932 (mm-30) REVERT: A 399 LYS cc_start: 0.8192 (ttmm) cc_final: 0.7792 (mtpp) REVERT: A 430 THR cc_start: 0.8123 (m) cc_final: 0.7589 (p) REVERT: A 455 GLU cc_start: 0.7614 (tt0) cc_final: 0.7061 (tt0) REVERT: A 478 LYS cc_start: 0.8367 (mmtt) cc_final: 0.8005 (mmmt) REVERT: A 551 GLU cc_start: 0.7825 (tm-30) cc_final: 0.7610 (tm-30) REVERT: A 559 HIS cc_start: 0.6653 (OUTLIER) cc_final: 0.6207 (m-70) REVERT: A 584 HIS cc_start: 0.6046 (m90) cc_final: 0.5773 (m170) REVERT: A 593 LYS cc_start: 0.6869 (tptp) cc_final: 0.6292 (tptp) outliers start: 32 outliers final: 24 residues processed: 270 average time/residue: 0.1087 time to fit residues: 39.6802 Evaluate side-chains 279 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 253 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 228 LYS Chi-restraints excluded: chain B residue 236 CYS Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 538 GLN Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 264 CYS Chi-restraints excluded: chain A residue 307 CYS Chi-restraints excluded: chain A residue 318 MET Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 468 ASN Chi-restraints excluded: chain A residue 510 CYS Chi-restraints excluded: chain A residue 515 CYS Chi-restraints excluded: chain A residue 559 HIS Chi-restraints excluded: chain A residue 586 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 60 optimal weight: 0.0060 chunk 1 optimal weight: 0.0050 chunk 46 optimal weight: 0.4980 chunk 95 optimal weight: 0.9990 chunk 12 optimal weight: 0.1980 chunk 66 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 52 optimal weight: 0.0980 chunk 80 optimal weight: 0.0570 chunk 13 optimal weight: 0.6980 chunk 41 optimal weight: 0.4980 overall best weight: 0.0728 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 329 GLN ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 530 ASN A 145 HIS A 163 GLN A 196 ASN A 422 ASN A 486 GLN ** A 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.146723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.124280 restraints weight = 13552.760| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.81 r_work: 0.3470 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.5649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9475 Z= 0.109 Angle : 0.678 17.225 12887 Z= 0.337 Chirality : 0.047 0.398 1425 Planarity : 0.004 0.038 1679 Dihedral : 5.352 24.637 1269 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.24 % Allowed : 16.20 % Favored : 81.56 % 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: -2.44 (0.23), residues: 1170 helix: -2.28 (0.63), residues: 61 sheet: -2.67 (0.49), residues: 92 loop : -1.63 (0.19), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 100 TYR 0.024 0.001 TYR B 409 PHE 0.014 0.001 PHE A 48 TRP 0.028 0.002 TRP C 49 HIS 0.003 0.001 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 ( 9420) covalent geometry : angle 0.63468 / 0.32 (12769) SS BOND : bond 0.00326 / 0.22 ( 47) SS BOND : angle 1.76919 / 1.13 ( 94) hydrogen bonds : bond 0.02577 / 1.65 ( 97) hydrogen bonds : angle 5.54333 / 3.75 ( 186) link_ALPHA1-3 : bond 0.01081 / 0.57 ( 1) link_ALPHA1-3 : angle 1.73903 / 0.89 ( 3) link_BETA1-3 : bond 0.00689 / 0.36 ( 1) link_BETA1-3 : angle 3.05777 / 1.61 ( 3) link_BETA1-4 : bond 0.00298 / 0.14 ( 2) link_BETA1-4 : angle 1.12831 / 0.64 ( 6) link_NAG-ASN : bond 0.01269 / 0.63 ( 4) link_NAG-ASN : angle 6.09873 / 3.96 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 257 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 24 GLN cc_start: 0.6627 (pp30) cc_final: 0.6354 (pp30) REVERT: B 30 ASP cc_start: 0.8013 (t70) cc_final: 0.7391 (t0) REVERT: B 89 ASN cc_start: 0.8052 (m-40) cc_final: 0.7792 (m110) REVERT: B 138 ARG cc_start: 0.7420 (mmm-85) cc_final: 0.6971 (mmm160) REVERT: B 139 GLU cc_start: 0.7236 (mp0) cc_final: 0.6889 (mp0) REVERT: B 147 GLU cc_start: 0.7288 (tp30) cc_final: 0.6972 (tp30) REVERT: B 165 ASP cc_start: 0.7884 (p0) cc_final: 0.7504 (p0) REVERT: B 251 ASP cc_start: 0.7648 (p0) cc_final: 0.7332 (p0) REVERT: B 284 ASN cc_start: 0.8258 (t0) cc_final: 0.7767 (t0) REVERT: B 290 THR cc_start: 0.8077 (m) cc_final: 0.7770 (m) REVERT: B 405 GLU cc_start: 0.7556 (tt0) cc_final: 0.7260 (tt0) REVERT: B 411 TYR cc_start: 0.8299 (t80) cc_final: 0.8019 (t80) REVERT: B 421 ASP cc_start: 0.7156 (p0) cc_final: 0.6722 (p0) REVERT: B 438 ASN cc_start: 0.7739 (m-40) cc_final: 0.7440 (m110) REVERT: B 446 GLN cc_start: 0.7372 (mt0) cc_final: 0.6964 (mt0) REVERT: B 460 GLU cc_start: 0.7965 (tt0) cc_final: 0.7571 (tt0) REVERT: B 501 GLU cc_start: 0.7089 (mm-30) cc_final: 0.6697 (mm-30) REVERT: B 514 LEU cc_start: 0.7509 (mp) cc_final: 0.7156 (mt) REVERT: B 553 GLU cc_start: 0.6274 (mt-10) cc_final: 0.5932 (mt-10) REVERT: B 568 GLN cc_start: 0.7134 (tm-30) cc_final: 0.6747 (tm-30) REVERT: A 46 ASP cc_start: 0.7901 (t70) cc_final: 0.7388 (t0) REVERT: A 98 ARG cc_start: 0.8308 (mtp-110) cc_final: 0.8089 (mtp180) REVERT: A 142 GLU cc_start: 0.7618 (tp30) cc_final: 0.7278 (mm-30) REVERT: A 148 VAL cc_start: 0.8435 (t) cc_final: 0.8072 (m) REVERT: A 160 GLU cc_start: 0.8037 (pm20) cc_final: 0.7574 (pm20) REVERT: A 198 SER cc_start: 0.8368 (m) cc_final: 0.7568 (p) REVERT: A 250 VAL cc_start: 0.7832 (t) cc_final: 0.7590 (m) REVERT: A 268 MET cc_start: 0.6930 (mtm) cc_final: 0.6723 (mtm) REVERT: A 292 VAL cc_start: 0.7998 (m) cc_final: 0.7655 (p) REVERT: A 294 LYS cc_start: 0.8179 (tttt) cc_final: 0.7892 (ptmm) REVERT: A 308 VAL cc_start: 0.8169 (p) cc_final: 0.7926 (m) REVERT: A 317 GLU cc_start: 0.7413 (tt0) cc_final: 0.7030 (tm-30) REVERT: A 318 MET cc_start: 0.7243 (OUTLIER) cc_final: 0.6830 (tpp) REVERT: A 325 LYS cc_start: 0.7288 (mttt) cc_final: 0.6709 (mtmt) REVERT: A 391 GLU cc_start: 0.8160 (mm-30) cc_final: 0.7515 (mm-30) REVERT: A 399 LYS cc_start: 0.8074 (ttmm) cc_final: 0.7706 (mtpp) REVERT: A 430 THR cc_start: 0.8119 (m) cc_final: 0.7584 (p) REVERT: A 436 PHE cc_start: 0.7790 (m-80) cc_final: 0.7392 (m-80) REVERT: A 471 TYR cc_start: 0.8123 (m-10) cc_final: 0.7777 (m-10) REVERT: A 551 GLU cc_start: 0.7738 (tm-30) cc_final: 0.7275 (tm-30) REVERT: A 559 HIS cc_start: 0.6605 (OUTLIER) cc_final: 0.6273 (m-70) REVERT: A 593 LYS cc_start: 0.6857 (tptp) cc_final: 0.6521 (tptp) outliers start: 23 outliers final: 16 residues processed: 266 average time/residue: 0.1044 time to fit residues: 37.7802 Evaluate side-chains 259 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 241 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 538 GLN Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 264 CYS Chi-restraints excluded: chain A residue 307 CYS Chi-restraints excluded: chain A residue 318 MET Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 468 ASN Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 510 CYS Chi-restraints excluded: chain A residue 519 GLU Chi-restraints excluded: chain A residue 559 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 112 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 90 optimal weight: 0.0980 chunk 73 optimal weight: 0.7980 chunk 52 optimal weight: 0.0010 chunk 26 optimal weight: 0.4980 overall best weight: 0.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 329 GLN ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 530 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.144347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.121830 restraints weight = 13308.969| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 2.73 r_work: 0.3426 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.5834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9475 Z= 0.182 Angle : 0.734 16.577 12887 Z= 0.365 Chirality : 0.051 0.397 1425 Planarity : 0.004 0.040 1679 Dihedral : 5.608 27.660 1269 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 2.05 % Allowed : 17.07 % Favored : 80.88 % 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: -2.53 (0.23), residues: 1170 helix: -2.79 (0.55), residues: 68 sheet: -2.55 (0.50), residues: 90 loop : -1.68 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 456 TYR 0.028 0.002 TYR B 409 PHE 0.017 0.002 PHE A 481 TRP 0.030 0.002 TRP C 49 HIS 0.005 0.001 HIS A 507 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 ( 9420) covalent geometry : angle 0.68966 / 0.35 (12769) SS BOND : bond 0.00379 / 0.23 ( 47) SS BOND : angle 2.05199 / 1.30 ( 94) hydrogen bonds : bond 0.03024 / 1.84 ( 97) hydrogen bonds : angle 5.59418 / 3.77 ( 186) link_ALPHA1-3 : bond 0.01146 / 0.60 ( 1) link_ALPHA1-3 : angle 1.72059 / 0.88 ( 3) link_BETA1-3 : bond 0.00630 / 0.33 ( 1) link_BETA1-3 : angle 2.81673 / 1.47 ( 3) link_BETA1-4 : bond 0.00091 / 0.05 ( 2) link_BETA1-4 : angle 0.88733 / 0.49 ( 6) link_NAG-ASN : bond 0.01196 / 0.60 ( 4) link_NAG-ASN : angle 6.02481 / 3.90 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2464.80 seconds wall clock time: 43 minutes 2.55 seconds (2582.55 seconds total)