Starting phenix.real_space_refine on Sat Aug 23 03:30:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hgo_34744/08_2025/8hgo_34744.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hgo_34744/08_2025/8hgo_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8hgo_34744/08_2025/8hgo_34744.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hgo_34744/08_2025/8hgo_34744.map" model { file = "/net/cci-nas-00/data/ceres_data/8hgo_34744/08_2025/8hgo_34744.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hgo_34744/08_2025/8hgo_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-2.0-5787/lib/python3.9/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 dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Residues with excluded nonbonded symmetry interactions: 9 residue: pdb=" N ASN A 182 " occ=0.00 ... (6 atoms not shown) pdb=" ND2 ASN A 182 " occ=0.00 residue: pdb=" N HIS A 183 " occ=0.00 ... (8 atoms not shown) pdb=" NE2 HIS A 183 " occ=0.00 residue: pdb=" N LEU A 184 " occ=0.00 ... (6 atoms not shown) pdb=" CD2 LEU A 184 " occ=0.00 residue: pdb=" N GLY A 203 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY A 203 " occ=0.00 residue: pdb=" N CYS A 329 " occ=0.00 ... (4 atoms not shown) pdb=" SG CYS A 329 " occ=0.00 residue: pdb=" N GLU A 330 " occ=0.00 ... (7 atoms not shown) pdb=" OE2 GLU A 330 " occ=0.00 residue: pdb=" N GLY A 331 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY A 331 " occ=0.00 residue: pdb=" N PRO A 332 " occ=0.00 ... (5 atoms not shown) pdb=" CD PRO A 332 " occ=0.00 residue: pdb=" N CYS A 333 " occ=0.00 ... (4 atoms not shown) pdb=" SG CYS A 333 " occ=0.00 Time building chain proxies: 2.25, per 1000 atoms: 0.24 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: 0.91 Conformation dependent library (CDL) restraints added in 375.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.28 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: 1.22 Time building geometry restraints manager: 1.19 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 - 22.60: 5723 22.60 - 45.20: 152 45.20 - 67.79: 35 67.79 - 90.39: 18 90.39 - 112.99: 8 Dihedral angle restraints: 5936 sinusoidal: 2554 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 5933 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: 3.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 9.720 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6544 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 : 10.134 112.989 3621 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 aren 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 covalent geometry : bond 0.00354 ( 9420) covalent geometry : angle 0.71132 (12769) SS BOND : bond 0.00282 ( 47) SS BOND : angle 1.04892 ( 94) hydrogen bonds : bond 0.23774 ( 97) hydrogen bonds : angle 7.20955 ( 186) link_ALPHA1-3 : bond 0.01436 ( 1) link_ALPHA1-3 : angle 2.81919 ( 3) link_BETA1-3 : bond 0.01341 ( 1) link_BETA1-3 : angle 6.31483 ( 3) link_BETA1-4 : bond 0.00375 ( 2) link_BETA1-4 : angle 1.89672 ( 6) link_NAG-ASN : bond 0.00860 ( 4) link_NAG-ASN : angle 4.09200 ( 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 : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 30 ASP cc_start: 0.7294 (t70) cc_final: 0.6925 (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: 0.7945 (mtt180) REVERT: B 460 GLU cc_start: 0.6684 (tt0) cc_final: 0.6187 (tt0) REVERT: B 467 LEU cc_start: 0.8448 (tp) cc_final: 0.7783 (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: 0.5860 (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: 0.1291 time to fit residues: 48.7024 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 : 0.263 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 559 HIS A 565 GLN A 584 HIS C 16 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.155609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.132868 restraints weight = 13640.669| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.81 r_work: 0.3593 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 9475 Z= 0.207 Angle : 0.754 10.012 12887 Z= 0.378 Chirality : 0.052 0.353 1425 Planarity : 0.006 0.047 1679 Dihedral : 9.084 94.403 1433 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 1.66 % Allowed : 7.12 % Favored : 91.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.29 (0.22), residues: 1170 helix: -3.58 (0.44), residues: 69 sheet: -2.54 (0.50), residues: 94 loop : -2.27 (0.18), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 499 TYR 0.023 0.002 TYR B 409 PHE 0.024 0.002 PHE A 549 TRP 0.011 0.002 TRP C 49 HIS 0.010 0.001 HIS B 237 Details of bonding type rmsd covalent geometry : bond 0.00460 ( 9420) covalent geometry : angle 0.72848 (12769) SS BOND : bond 0.00394 ( 47) SS BOND : angle 1.92169 ( 94) hydrogen bonds : bond 0.03809 ( 97) hydrogen bonds : angle 6.06862 ( 186) link_ALPHA1-3 : bond 0.01072 ( 1) link_ALPHA1-3 : angle 2.52826 ( 3) link_BETA1-3 : bond 0.00267 ( 1) link_BETA1-3 : angle 4.66309 ( 3) link_BETA1-4 : bond 0.00428 ( 2) link_BETA1-4 : angle 1.04895 ( 6) link_NAG-ASN : bond 0.00273 ( 4) link_NAG-ASN : angle 2.98129 ( 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 292 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 275 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 30 ASP cc_start: 0.7832 (t70) cc_final: 0.7214 (t70) REVERT: B 89 ASN cc_start: 0.8029 (m-40) cc_final: 0.7740 (m-40) REVERT: B 93 GLN cc_start: 0.7346 (pp30) cc_final: 0.7086 (pp30) REVERT: B 147 GLU cc_start: 0.7261 (tp30) cc_final: 0.6850 (tp30) REVERT: B 164 GLN cc_start: 0.7163 (pm20) cc_final: 0.6862 (pm20) REVERT: B 228 LYS cc_start: 0.7907 (mtpt) cc_final: 0.7518 (mtpt) REVERT: B 274 TYR cc_start: 0.8284 (t80) cc_final: 0.8052 (t80) REVERT: B 284 ASN cc_start: 0.7693 (t0) cc_final: 0.7303 (t0) REVERT: B 329 GLN cc_start: 0.7131 (OUTLIER) cc_final: 0.6900 (mt0) REVERT: B 403 LEU cc_start: 0.7111 (tp) cc_final: 0.6851 (tp) REVERT: B 421 ASP cc_start: 0.6494 (p0) cc_final: 0.6254 (p0) REVERT: B 438 ASN cc_start: 0.7769 (m-40) cc_final: 0.7531 (m110) REVERT: B 441 TYR cc_start: 0.8450 (m-80) cc_final: 0.8019 (m-80) REVERT: B 460 GLU cc_start: 0.7680 (tt0) cc_final: 0.7360 (tt0) REVERT: B 568 GLN cc_start: 0.6882 (tp40) cc_final: 0.6671 (tm-30) REVERT: A 45 GLU cc_start: 0.7725 (mp0) cc_final: 0.7342 (mp0) REVERT: A 46 ASP cc_start: 0.8044 (t70) cc_final: 0.7581 (t70) REVERT: A 80 LYS cc_start: 0.8555 (mttp) cc_final: 0.8311 (mttp) REVERT: A 98 ARG cc_start: 0.8290 (mtp-110) cc_final: 0.8076 (mtp180) REVERT: A 133 LYS cc_start: 0.7269 (mttt) cc_final: 0.6961 (mmmm) REVERT: A 152 ASN cc_start: 0.7630 (m110) cc_final: 0.7198 (m110) REVERT: A 160 GLU cc_start: 0.7811 (pm20) cc_final: 0.6923 (pm20) REVERT: A 198 SER cc_start: 0.8065 (m) cc_final: 0.7420 (p) REVERT: A 235 GLN cc_start: 0.8046 (mm-40) cc_final: 0.7806 (mm110) REVERT: A 255 ARG cc_start: 0.7065 (ttt-90) cc_final: 0.6671 (tmt-80) REVERT: A 256 ASP cc_start: 0.7124 (t70) cc_final: 0.6735 (t70) REVERT: A 268 MET cc_start: 0.6319 (mtm) cc_final: 0.5781 (mtm) REVERT: A 277 MET cc_start: 0.5556 (mtt) cc_final: 0.5162 (mtt) REVERT: A 284 LYS cc_start: 0.8303 (mtmm) cc_final: 0.7991 (mtmm) REVERT: A 292 VAL cc_start: 0.8117 (m) cc_final: 0.7700 (p) REVERT: A 293 LYS cc_start: 0.8117 (mtpp) cc_final: 0.7797 (ptpp) REVERT: A 294 LYS cc_start: 0.8301 (tttt) cc_final: 0.8013 (tttt) REVERT: A 316 TYR cc_start: 0.6555 (t80) cc_final: 0.6156 (t80) REVERT: A 318 MET cc_start: 0.6846 (tpp) cc_final: 0.6567 (tpp) REVERT: A 325 LYS cc_start: 0.7658 (mttt) cc_final: 0.7116 (mtmt) REVERT: A 430 THR cc_start: 0.8205 (m) cc_final: 0.7586 (p) REVERT: A 578 ASN cc_start: 0.6985 (m-40) cc_final: 0.6646 (m-40) REVERT: A 593 LYS cc_start: 0.6736 (tptp) cc_final: 0.6478 (tptp) REVERT: C 38 ILE cc_start: 0.8495 (tt) cc_final: 0.8144 (pt) outliers start: 17 outliers final: 10 residues processed: 277 average time/residue: 0.1253 time to fit residues: 45.4784 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 : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 193 HIS 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 462 ILE 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: 0.1980 chunk 53 optimal weight: 1.9990 chunk 64 optimal weight: 0.4980 chunk 90 optimal weight: 0.0070 chunk 28 optimal weight: 0.0060 chunk 92 optimal weight: 0.9980 chunk 58 optimal weight: 0.4980 chunk 10 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 87 optimal weight: 0.3980 chunk 75 optimal weight: 0.4980 overall best weight: 0.2214 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 GLN B 470 HIS ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 153 ASN ** A 493 ASN ** 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 = 0.4022 r_free = 0.4022 target = 0.155049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.132432 restraints weight = 13499.156| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 2.80 r_work: 0.3587 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9475 Z= 0.127 Angle : 0.668 16.494 12887 Z= 0.329 Chirality : 0.048 0.479 1425 Planarity : 0.005 0.042 1679 Dihedral : 8.368 87.506 1433 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 1.76 % Allowed : 10.44 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.09 (0.22), residues: 1170 helix: -3.41 (0.46), residues: 81 sheet: -2.37 (0.51), residues: 92 loop : -2.10 (0.18), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 47 TYR 0.020 0.002 TYR B 163 PHE 0.022 0.001 PHE A 549 TRP 0.012 0.001 TRP C 49 HIS 0.005 0.001 HIS A 507 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 9420) covalent geometry : angle 0.62629 (12769) SS BOND : bond 0.00374 ( 47) SS BOND : angle 1.66573 ( 94) hydrogen bonds : bond 0.03113 ( 97) hydrogen bonds : angle 5.74347 ( 186) link_ALPHA1-3 : bond 0.01602 ( 1) link_ALPHA1-3 : angle 2.28973 ( 3) link_BETA1-3 : bond 0.00912 ( 1) link_BETA1-3 : angle 3.48262 ( 3) link_BETA1-4 : bond 0.00142 ( 2) link_BETA1-4 : angle 1.12507 ( 6) link_NAG-ASN : bond 0.01508 ( 4) link_NAG-ASN : angle 5.94170 ( 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 283 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 265 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 30 ASP cc_start: 0.7911 (t70) cc_final: 0.7315 (t0) REVERT: B 89 ASN cc_start: 0.7887 (m-40) cc_final: 0.7668 (m-40) REVERT: B 93 GLN cc_start: 0.7279 (pp30) cc_final: 0.6899 (pp30) REVERT: B 100 ARG cc_start: 0.8267 (tpp80) cc_final: 0.8006 (tpp80) REVERT: B 112 TYR cc_start: 0.7461 (m-80) cc_final: 0.7216 (m-80) REVERT: B 147 GLU cc_start: 0.7250 (tp30) cc_final: 0.6852 (tp30) REVERT: B 156 GLN cc_start: 0.7954 (mt0) cc_final: 0.7662 (mt0) REVERT: B 164 GLN cc_start: 0.7257 (pm20) cc_final: 0.6900 (pm20) REVERT: B 183 LEU cc_start: 0.8378 (mp) cc_final: 0.7965 (tp) REVERT: B 228 LYS cc_start: 0.7904 (mtpt) cc_final: 0.7488 (mtpt) REVERT: B 268 CYS cc_start: 0.6201 (t) cc_final: 0.5934 (t) REVERT: B 274 TYR cc_start: 0.8248 (t80) cc_final: 0.7991 (t80) REVERT: B 284 ASN cc_start: 0.7714 (t0) cc_final: 0.7333 (t0) REVERT: B 403 LEU cc_start: 0.6983 (tp) cc_final: 0.6752 (tp) REVERT: B 421 ASP cc_start: 0.6824 (p0) cc_final: 0.6407 (p0) REVERT: B 438 ASN cc_start: 0.7718 (m-40) cc_final: 0.7457 (m110) REVERT: B 441 TYR cc_start: 0.8522 (m-80) cc_final: 0.8065 (m-80) REVERT: B 460 GLU cc_start: 0.7718 (tt0) cc_final: 0.7427 (tt0) REVERT: B 538 GLN cc_start: 0.6586 (OUTLIER) cc_final: 0.6323 (pm20) REVERT: A 45 GLU cc_start: 0.7700 (mp0) cc_final: 0.7329 (mp0) REVERT: A 46 ASP cc_start: 0.8032 (t70) cc_final: 0.7576 (t70) REVERT: A 80 LYS cc_start: 0.8565 (mttp) cc_final: 0.8320 (mttp) REVERT: A 97 GLU cc_start: 0.6848 (mp0) cc_final: 0.6366 (mp0) REVERT: A 98 ARG cc_start: 0.8307 (mtp-110) cc_final: 0.8099 (mtp180) REVERT: A 133 LYS cc_start: 0.7199 (mttt) cc_final: 0.6830 (mmmm) REVERT: A 148 VAL cc_start: 0.8412 (t) cc_final: 0.7997 (m) REVERT: A 198 SER cc_start: 0.8108 (m) cc_final: 0.7449 (p) REVERT: A 252 ARG cc_start: 0.7558 (mtp85) cc_final: 0.7271 (mtp85) REVERT: A 255 ARG cc_start: 0.6960 (ttt-90) cc_final: 0.6656 (tmt-80) REVERT: A 256 ASP cc_start: 0.7404 (t70) cc_final: 0.7112 (t70) REVERT: A 268 MET cc_start: 0.6430 (mtm) cc_final: 0.5871 (mtm) REVERT: A 277 MET cc_start: 0.5600 (mtt) cc_final: 0.5193 (mtt) REVERT: A 284 LYS cc_start: 0.8227 (mtmm) cc_final: 0.8009 (mtmm) REVERT: A 292 VAL cc_start: 0.8107 (m) cc_final: 0.7705 (p) REVERT: A 294 LYS cc_start: 0.8259 (tttt) cc_final: 0.8001 (tttt) REVERT: A 307 CYS cc_start: 0.7182 (m) cc_final: 0.6864 (m) REVERT: A 316 TYR cc_start: 0.6654 (t80) cc_final: 0.6023 (t80) REVERT: A 318 MET cc_start: 0.6800 (tpp) cc_final: 0.6386 (tpp) REVERT: A 325 LYS cc_start: 0.7654 (mttt) cc_final: 0.7044 (mtmt) REVERT: A 327 LYS cc_start: 0.7915 (OUTLIER) cc_final: 0.7677 (ptpp) REVERT: A 391 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7274 (mm-30) REVERT: A 430 THR cc_start: 0.8151 (m) cc_final: 0.7499 (p) REVERT: A 487 LYS cc_start: 0.7165 (mtmm) cc_final: 0.6895 (mtmm) REVERT: A 489 LYS cc_start: 0.8049 (ttmm) cc_final: 0.7592 (ttmm) REVERT: A 578 ASN cc_start: 0.6996 (m-40) cc_final: 0.6640 (m-40) REVERT: A 593 LYS cc_start: 0.6707 (tptp) cc_final: 0.6475 (tptp) outliers start: 18 outliers final: 10 residues processed: 270 average time/residue: 0.1050 time to fit residues: 37.8366 Evaluate side-chains 272 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 260 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 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 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 425 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 85 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 7 optimal weight: 0.4980 chunk 99 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 114 optimal weight: 0.3980 chunk 56 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 48 HIS B 54 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 HIS B 533 GLN B 559 HIS A 57 ASN A 493 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.147024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.124021 restraints weight = 13457.579| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.80 r_work: 0.3460 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.4500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 9475 Z= 0.237 Angle : 0.759 16.528 12887 Z= 0.377 Chirality : 0.054 0.450 1425 Planarity : 0.005 0.045 1679 Dihedral : 8.374 91.776 1433 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 2.93 % Allowed : 10.83 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.87 (0.22), residues: 1170 helix: -3.08 (0.51), residues: 66 sheet: -2.30 (0.52), residues: 82 loop : -1.99 (0.18), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 47 TYR 0.025 0.002 TYR B 163 PHE 0.025 0.003 PHE A 481 TRP 0.021 0.002 TRP C 49 HIS 0.008 0.002 HIS A 507 Details of bonding type rmsd covalent geometry : bond 0.00531 ( 9420) covalent geometry : angle 0.71966 (12769) SS BOND : bond 0.00462 ( 47) SS BOND : angle 1.73166 ( 94) hydrogen bonds : bond 0.03522 ( 97) hydrogen bonds : angle 6.05973 ( 186) link_ALPHA1-3 : bond 0.01116 ( 1) link_ALPHA1-3 : angle 2.38290 ( 3) link_BETA1-3 : bond 0.00241 ( 1) link_BETA1-3 : angle 2.98692 ( 3) link_BETA1-4 : bond 0.00371 ( 2) link_BETA1-4 : angle 0.87339 ( 6) link_NAG-ASN : bond 0.01428 ( 4) link_NAG-ASN : angle 6.37257 ( 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 312 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 282 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: B 30 ASP cc_start: 0.8091 (t70) cc_final: 0.7492 (t0) REVERT: B 75 GLN cc_start: 0.8108 (pt0) cc_final: 0.7516 (pt0) REVERT: B 89 ASN cc_start: 0.8017 (m-40) cc_final: 0.7774 (m-40) REVERT: B 93 GLN cc_start: 0.7381 (pp30) cc_final: 0.7050 (pp30) REVERT: B 112 TYR cc_start: 0.7774 (m-80) cc_final: 0.7511 (m-80) REVERT: B 138 ARG cc_start: 0.7180 (mmm-85) cc_final: 0.6800 (mmm160) REVERT: B 139 GLU cc_start: 0.7079 (mp0) cc_final: 0.6786 (mp0) REVERT: B 147 GLU cc_start: 0.7253 (tp30) cc_final: 0.6703 (tp30) REVERT: B 228 LYS cc_start: 0.8025 (mtpt) cc_final: 0.7742 (mtpt) REVERT: B 261 SER cc_start: 0.8033 (m) cc_final: 0.7689 (p) REVERT: B 268 CYS cc_start: 0.6467 (t) cc_final: 0.6205 (t) REVERT: B 284 ASN cc_start: 0.8051 (t0) cc_final: 0.7693 (t0) REVERT: B 405 GLU cc_start: 0.7550 (tt0) cc_final: 0.7189 (tt0) REVERT: B 421 ASP cc_start: 0.7158 (p0) cc_final: 0.6731 (p0) REVERT: B 438 ASN cc_start: 0.7742 (m-40) cc_final: 0.7520 (m110) REVERT: B 441 TYR cc_start: 0.8604 (m-80) cc_final: 0.8272 (m-80) REVERT: B 446 GLN cc_start: 0.7549 (mt0) cc_final: 0.7189 (mt0) REVERT: B 460 GLU cc_start: 0.7692 (tt0) cc_final: 0.7257 (tt0) REVERT: B 538 GLN cc_start: 0.6774 (OUTLIER) cc_final: 0.6506 (pm20) REVERT: B 553 GLU cc_start: 0.6277 (tt0) cc_final: 0.5713 (mt-10) REVERT: B 568 GLN cc_start: 0.6902 (tm-30) cc_final: 0.6427 (tm-30) REVERT: A 45 GLU cc_start: 0.7780 (mp0) cc_final: 0.7542 (mp0) REVERT: A 46 ASP cc_start: 0.7955 (t70) cc_final: 0.7439 (t70) REVERT: A 148 VAL cc_start: 0.8546 (t) cc_final: 0.8168 (m) REVERT: A 255 ARG cc_start: 0.7052 (ttt-90) cc_final: 0.6734 (tmt-80) REVERT: A 263 THR cc_start: 0.8062 (m) cc_final: 0.7713 (p) REVERT: A 292 VAL cc_start: 0.8188 (m) cc_final: 0.7820 (p) REVERT: A 294 LYS cc_start: 0.8260 (tttt) cc_final: 0.8005 (tttt) REVERT: A 303 ASP cc_start: 0.7622 (p0) cc_final: 0.7381 (p0) REVERT: A 316 TYR cc_start: 0.6903 (t80) cc_final: 0.6638 (t80) REVERT: A 325 LYS cc_start: 0.7720 (mttt) cc_final: 0.7109 (mtmt) REVERT: A 357 LYS cc_start: 0.8392 (ptpt) cc_final: 0.8063 (pptt) REVERT: A 360 LYS cc_start: 0.8120 (tttt) cc_final: 0.7760 (tttt) REVERT: A 430 THR cc_start: 0.8142 (m) cc_final: 0.7593 (p) REVERT: A 455 GLU cc_start: 0.7586 (tt0) cc_final: 0.7181 (tt0) REVERT: A 487 LYS cc_start: 0.7716 (mtmm) cc_final: 0.7375 (mtmm) REVERT: A 489 LYS cc_start: 0.8116 (ttmm) cc_final: 0.7612 (ttmm) REVERT: A 524 VAL cc_start: 0.8441 (t) cc_final: 0.8198 (p) REVERT: A 559 HIS cc_start: 0.6305 (OUTLIER) cc_final: 0.6097 (m-70) REVERT: A 584 HIS cc_start: 0.6188 (m90) cc_final: 0.5891 (m170) REVERT: A 593 LYS cc_start: 0.6852 (tptp) cc_final: 0.6357 (tptp) outliers start: 30 outliers final: 18 residues processed: 290 average time/residue: 0.1039 time to fit residues: 39.8595 Evaluate side-chains 286 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 266 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 CYS Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 54 GLN 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 293 LYS Chi-restraints excluded: chain A residue 351 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: 0.8980 chunk 109 optimal weight: 1.9990 chunk 105 optimal weight: 0.2980 chunk 70 optimal weight: 0.0030 chunk 1 optimal weight: 0.0070 chunk 99 optimal weight: 0.0020 chunk 6 optimal weight: 0.2980 chunk 74 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 overall best weight: 0.1216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 GLN ** 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 ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 GLN ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.149548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.126827 restraints weight = 13541.638| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 2.83 r_work: 0.3504 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.4624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 9475 Z= 0.120 Angle : 0.673 16.640 12887 Z= 0.333 Chirality : 0.048 0.424 1425 Planarity : 0.004 0.041 1679 Dihedral : 7.832 83.870 1433 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 2.34 % Allowed : 13.37 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.69 (0.22), residues: 1170 helix: -2.69 (0.59), residues: 59 sheet: -2.49 (0.48), residues: 94 loop : -1.84 (0.18), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 222 TYR 0.021 0.002 TYR B 409 PHE 0.010 0.001 PHE A 481 TRP 0.010 0.001 TRP C 49 HIS 0.004 0.001 HIS A 559 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 9420) covalent geometry : angle 0.63205 (12769) SS BOND : bond 0.00382 ( 47) SS BOND : angle 1.68433 ( 94) hydrogen bonds : bond 0.02820 ( 97) hydrogen bonds : angle 6.07139 ( 186) link_ALPHA1-3 : bond 0.01765 ( 1) link_ALPHA1-3 : angle 2.41750 ( 3) link_BETA1-3 : bond 0.00851 ( 1) link_BETA1-3 : angle 2.91865 ( 3) link_BETA1-4 : bond 0.00201 ( 2) link_BETA1-4 : angle 0.98489 ( 6) link_NAG-ASN : bond 0.01292 ( 4) link_NAG-ASN : angle 5.95817 ( 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 297 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 273 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 30 ASP cc_start: 0.7964 (t70) cc_final: 0.7320 (t0) REVERT: B 112 TYR cc_start: 0.7529 (m-80) cc_final: 0.7282 (m-80) REVERT: B 138 ARG cc_start: 0.7259 (mmm-85) cc_final: 0.6909 (mmm160) REVERT: B 139 GLU cc_start: 0.6961 (mp0) cc_final: 0.6653 (mp0) REVERT: B 147 GLU cc_start: 0.7304 (tp30) cc_final: 0.6786 (tp30) REVERT: B 166 THR cc_start: 0.8670 (p) cc_final: 0.8458 (p) REVERT: B 228 LYS cc_start: 0.7968 (mtpt) cc_final: 0.7568 (mtmm) REVERT: B 261 SER cc_start: 0.7948 (m) cc_final: 0.7600 (p) REVERT: B 268 CYS cc_start: 0.6321 (t) cc_final: 0.6097 (t) REVERT: B 284 ASN cc_start: 0.7981 (t0) cc_final: 0.7572 (t0) REVERT: B 405 GLU cc_start: 0.7597 (tt0) cc_final: 0.7333 (tt0) REVERT: B 421 ASP cc_start: 0.7097 (p0) cc_final: 0.6724 (p0) REVERT: B 438 ASN cc_start: 0.7673 (m-40) cc_final: 0.7461 (m110) REVERT: B 441 TYR cc_start: 0.8510 (m-80) cc_final: 0.7977 (m-80) REVERT: B 446 GLN cc_start: 0.7411 (mt0) cc_final: 0.7047 (mt0) REVERT: B 459 ARG cc_start: 0.7997 (ptt90) cc_final: 0.7771 (ptt90) REVERT: B 460 GLU cc_start: 0.7786 (tt0) cc_final: 0.7401 (tt0) REVERT: B 538 GLN cc_start: 0.6700 (OUTLIER) cc_final: 0.6495 (pm20) REVERT: B 553 GLU cc_start: 0.6266 (tt0) cc_final: 0.5716 (mt-10) REVERT: A 45 GLU cc_start: 0.7742 (mp0) cc_final: 0.7440 (mp0) REVERT: A 46 ASP cc_start: 0.7955 (t70) cc_final: 0.7450 (t70) REVERT: A 98 ARG cc_start: 0.8379 (mtp-110) cc_final: 0.8168 (mtp180) REVERT: A 142 GLU cc_start: 0.7709 (tt0) cc_final: 0.7318 (tp30) REVERT: A 148 VAL cc_start: 0.8489 (t) cc_final: 0.8118 (m) REVERT: A 160 GLU cc_start: 0.8096 (pm20) cc_final: 0.7687 (pm20) REVERT: A 198 SER cc_start: 0.8218 (m) cc_final: 0.7474 (p) REVERT: A 263 THR cc_start: 0.8041 (m) cc_final: 0.7636 (p) REVERT: A 292 VAL cc_start: 0.8143 (m) cc_final: 0.7737 (p) REVERT: A 294 LYS cc_start: 0.8226 (tttt) cc_final: 0.7976 (tttt) REVERT: A 303 ASP cc_start: 0.7530 (p0) cc_final: 0.7150 (p0) REVERT: A 308 VAL cc_start: 0.8173 (p) cc_final: 0.7889 (m) REVERT: A 316 TYR cc_start: 0.6748 (t80) cc_final: 0.6449 (t80) REVERT: A 318 MET cc_start: 0.6923 (tpp) cc_final: 0.6534 (tpp) REVERT: A 325 LYS cc_start: 0.7312 (mttt) cc_final: 0.6766 (mtmt) REVERT: A 347 ASP cc_start: 0.7319 (t0) cc_final: 0.6741 (t0) REVERT: A 391 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7725 (mm-30) REVERT: A 400 GLU cc_start: 0.7565 (pt0) cc_final: 0.7352 (pt0) REVERT: A 430 THR cc_start: 0.8049 (m) cc_final: 0.7483 (p) REVERT: A 455 GLU cc_start: 0.7564 (tt0) cc_final: 0.7111 (tt0) REVERT: A 487 LYS cc_start: 0.7508 (mtmm) cc_final: 0.7228 (mtmm) REVERT: A 489 LYS cc_start: 0.8136 (ttmm) cc_final: 0.7639 (ttmm) REVERT: A 551 GLU cc_start: 0.7539 (tm-30) cc_final: 0.7102 (tm-30) REVERT: A 559 HIS cc_start: 0.6145 (OUTLIER) cc_final: 0.5944 (m-70) REVERT: A 584 HIS cc_start: 0.6160 (m90) cc_final: 0.5881 (m170) REVERT: A 593 LYS cc_start: 0.6802 (tptp) cc_final: 0.6328 (tptp) outliers start: 24 outliers final: 16 residues processed: 282 average time/residue: 0.0958 time to fit residues: 35.9936 Evaluate side-chains 278 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 260 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 227 CYS Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 329 GLN 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 311 CYS 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 468 ASN Chi-restraints excluded: chain A residue 519 GLU 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: 0.9990 chunk 40 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 95 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 109 optimal weight: 4.9990 chunk 96 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 512 HIS ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.143736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.121398 restraints weight = 13524.396| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 2.59 r_work: 0.3433 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.5312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.082 9475 Z= 0.301 Angle : 0.806 16.059 12887 Z= 0.402 Chirality : 0.055 0.429 1425 Planarity : 0.005 0.051 1679 Dihedral : 8.383 96.304 1433 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer: Outliers : 3.41 % Allowed : 14.05 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.74 (0.22), residues: 1170 helix: -2.64 (0.55), residues: 66 sheet: -2.61 (0.51), residues: 82 loop : -1.89 (0.18), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 222 TYR 0.030 0.002 TYR B 409 PHE 0.045 0.003 PHE A 549 TRP 0.016 0.002 TRP C 49 HIS 0.008 0.002 HIS A 507 Details of bonding type rmsd covalent geometry : bond 0.00675 ( 9420) covalent geometry : angle 0.76468 (12769) SS BOND : bond 0.00506 ( 47) SS BOND : angle 2.10653 ( 94) hydrogen bonds : bond 0.03680 ( 97) hydrogen bonds : angle 6.36391 ( 186) link_ALPHA1-3 : bond 0.00940 ( 1) link_ALPHA1-3 : angle 2.47082 ( 3) link_BETA1-3 : bond 0.00036 ( 1) link_BETA1-3 : angle 2.73800 ( 3) link_BETA1-4 : bond 0.00113 ( 2) link_BETA1-4 : angle 0.95735 ( 6) link_NAG-ASN : bond 0.01187 ( 4) link_NAG-ASN : angle 6.02129 ( 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 304 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 269 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: B 24 GLN cc_start: 0.7026 (pp30) cc_final: 0.6765 (pp30) REVERT: B 30 ASP cc_start: 0.8251 (t70) cc_final: 0.7654 (t0) REVERT: B 92 ARG cc_start: 0.8336 (mtt90) cc_final: 0.7698 (mmt-90) REVERT: B 93 GLN cc_start: 0.7693 (pp30) cc_final: 0.7481 (pp30) REVERT: B 138 ARG cc_start: 0.7584 (mmm-85) cc_final: 0.6926 (mmm160) REVERT: B 139 GLU cc_start: 0.7440 (mp0) cc_final: 0.7099 (mp0) REVERT: B 261 SER cc_start: 0.8241 (m) cc_final: 0.7925 (p) REVERT: B 284 ASN cc_start: 0.8227 (t0) cc_final: 0.7900 (t0) REVERT: B 297 THR cc_start: 0.8544 (m) cc_final: 0.8295 (p) REVERT: B 405 GLU cc_start: 0.7858 (tt0) cc_final: 0.7550 (tt0) REVERT: B 421 ASP cc_start: 0.7472 (p0) cc_final: 0.7036 (p0) REVERT: B 438 ASN cc_start: 0.7851 (m-40) cc_final: 0.7637 (m110) REVERT: B 441 TYR cc_start: 0.8673 (m-80) cc_final: 0.8424 (m-80) REVERT: B 446 GLN cc_start: 0.7769 (mt0) cc_final: 0.7428 (mt0) REVERT: B 450 ILE cc_start: 0.8438 (tt) cc_final: 0.8133 (pt) REVERT: B 460 GLU cc_start: 0.8097 (tt0) cc_final: 0.7730 (tt0) REVERT: B 499 ARG cc_start: 0.7688 (ttt-90) cc_final: 0.7475 (ttt-90) REVERT: B 553 GLU cc_start: 0.6528 (tt0) cc_final: 0.6265 (mt-10) REVERT: B 568 GLN cc_start: 0.6987 (tm-30) cc_final: 0.6602 (tm-30) REVERT: A 46 ASP cc_start: 0.8120 (t70) cc_final: 0.7647 (t0) REVERT: A 74 TYR cc_start: 0.8562 (m-10) cc_final: 0.8272 (m-80) REVERT: A 142 GLU cc_start: 0.7877 (tt0) cc_final: 0.7372 (tp30) REVERT: A 148 VAL cc_start: 0.8646 (t) cc_final: 0.8275 (m) REVERT: A 245 GLU cc_start: 0.8051 (pt0) cc_final: 0.7486 (tp30) REVERT: A 263 THR cc_start: 0.8049 (m) cc_final: 0.7832 (p) REVERT: A 292 VAL cc_start: 0.8194 (m) cc_final: 0.7832 (p) REVERT: A 294 LYS cc_start: 0.8356 (tttt) cc_final: 0.8057 (ptmm) REVERT: A 308 VAL cc_start: 0.8418 (p) cc_final: 0.8144 (m) REVERT: A 325 LYS cc_start: 0.7557 (mttt) cc_final: 0.7024 (mtmt) REVERT: A 360 LYS cc_start: 0.8187 (tttt) cc_final: 0.7676 (ttmm) REVERT: A 430 THR cc_start: 0.8256 (m) cc_final: 0.7737 (p) REVERT: A 455 GLU cc_start: 0.7817 (tt0) cc_final: 0.7317 (tt0) REVERT: A 487 LYS cc_start: 0.8113 (mtmm) cc_final: 0.7912 (mtmm) REVERT: A 559 HIS cc_start: 0.6803 (OUTLIER) cc_final: 0.6537 (m-70) REVERT: A 593 LYS cc_start: 0.6961 (tptp) cc_final: 0.6718 (tptp) outliers start: 35 outliers final: 25 residues processed: 284 average time/residue: 0.1071 time to fit residues: 40.8423 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 : 0.370 ------------------------------------------------------------------------------- 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 238 GLU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 526 THR 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 84 GLU 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 293 LYS Chi-restraints excluded: chain A residue 307 CYS 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 488 THR Chi-restraints excluded: chain A residue 515 CYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 559 HIS Chi-restraints excluded: chain C residue 50 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 16 optimal weight: 0.2980 chunk 12 optimal weight: 0.5980 chunk 95 optimal weight: 0.0980 chunk 94 optimal weight: 0.3980 chunk 7 optimal weight: 0.6980 chunk 59 optimal weight: 0.5980 chunk 55 optimal weight: 0.0370 chunk 1 optimal weight: 0.0370 chunk 26 optimal weight: 0.5980 chunk 75 optimal weight: 0.5980 chunk 72 optimal weight: 0.9980 overall best weight: 0.1736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 ASN ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 557 GLN C 16 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.146694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.124488 restraints weight = 13561.925| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.63 r_work: 0.3481 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.5310 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= 0.128 Angle : 0.704 16.386 12887 Z= 0.349 Chirality : 0.048 0.422 1425 Planarity : 0.004 0.041 1679 Dihedral : 7.851 89.093 1433 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 2.05 % Allowed : 16.20 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.56 (0.23), residues: 1170 helix: -2.22 (0.66), residues: 54 sheet: -2.88 (0.44), residues: 102 loop : -1.70 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 222 TYR 0.020 0.002 TYR B 409 PHE 0.037 0.001 PHE A 549 TRP 0.029 0.002 TRP C 49 HIS 0.005 0.001 HIS A 304 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 9420) covalent geometry : angle 0.66223 (12769) SS BOND : bond 0.00308 ( 47) SS BOND : angle 1.88339 ( 94) hydrogen bonds : bond 0.02733 ( 97) hydrogen bonds : angle 6.01090 ( 186) link_ALPHA1-3 : bond 0.01652 ( 1) link_ALPHA1-3 : angle 2.29950 ( 3) link_BETA1-3 : bond 0.00777 ( 1) link_BETA1-3 : angle 2.73888 ( 3) link_BETA1-4 : bond 0.00258 ( 2) link_BETA1-4 : angle 1.01466 ( 6) link_NAG-ASN : bond 0.01254 ( 4) link_NAG-ASN : angle 5.84594 ( 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 276 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 255 time to evaluate : 0.303 Fit side-chains REVERT: B 24 GLN cc_start: 0.7013 (pp30) cc_final: 0.6727 (pp30) REVERT: B 30 ASP cc_start: 0.8159 (t70) cc_final: 0.7486 (t0) REVERT: B 67 THR cc_start: 0.8547 (m) cc_final: 0.8301 (t) REVERT: B 75 GLN cc_start: 0.8137 (pt0) cc_final: 0.7780 (pt0) REVERT: B 92 ARG cc_start: 0.8311 (mtt90) cc_final: 0.7721 (mmt-90) REVERT: B 93 GLN cc_start: 0.7644 (pp30) cc_final: 0.7412 (pp30) REVERT: B 138 ARG cc_start: 0.7524 (mmm-85) cc_final: 0.7108 (mmm160) REVERT: B 139 GLU cc_start: 0.7326 (mp0) cc_final: 0.6954 (mp0) REVERT: B 147 GLU cc_start: 0.7599 (tp30) cc_final: 0.7070 (tp30) REVERT: B 261 SER cc_start: 0.8147 (m) cc_final: 0.7833 (p) REVERT: B 284 ASN cc_start: 0.8193 (t0) cc_final: 0.7836 (t0) REVERT: B 297 THR cc_start: 0.8520 (m) cc_final: 0.8317 (p) REVERT: B 405 GLU cc_start: 0.7809 (tt0) cc_final: 0.7518 (tt0) REVERT: B 421 ASP cc_start: 0.7405 (p0) cc_final: 0.7014 (p0) REVERT: B 438 ASN cc_start: 0.7820 (m-40) cc_final: 0.7544 (m110) REVERT: B 446 GLN cc_start: 0.7633 (mt0) cc_final: 0.7319 (mt0) REVERT: B 460 GLU cc_start: 0.8113 (tt0) cc_final: 0.7836 (tt0) REVERT: B 530 ASN cc_start: 0.7271 (t0) cc_final: 0.6922 (t0) REVERT: B 538 GLN cc_start: 0.6869 (OUTLIER) cc_final: 0.6647 (pm20) REVERT: B 553 GLU cc_start: 0.6440 (tt0) cc_final: 0.6192 (mt-10) REVERT: B 568 GLN cc_start: 0.6954 (tm-30) cc_final: 0.6531 (tm-30) REVERT: A 46 ASP cc_start: 0.8069 (t70) cc_final: 0.7616 (t0) REVERT: A 74 TYR cc_start: 0.8551 (m-10) cc_final: 0.8331 (m-80) REVERT: A 98 ARG cc_start: 0.8557 (mtp-110) cc_final: 0.8350 (mtp180) REVERT: A 142 GLU cc_start: 0.7900 (tt0) cc_final: 0.7419 (tp30) REVERT: A 148 VAL cc_start: 0.8595 (t) cc_final: 0.8246 (m) REVERT: A 263 THR cc_start: 0.8110 (m) cc_final: 0.7827 (p) REVERT: A 292 VAL cc_start: 0.8156 (m) cc_final: 0.7810 (p) REVERT: A 294 LYS cc_start: 0.8323 (tttt) cc_final: 0.8011 (ptmm) REVERT: A 308 VAL cc_start: 0.8340 (p) cc_final: 0.8082 (m) REVERT: A 325 LYS cc_start: 0.7437 (mttt) cc_final: 0.6839 (mtmt) REVERT: A 338 ASN cc_start: 0.7712 (t0) cc_final: 0.7257 (t0) REVERT: A 391 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7801 (mm-30) REVERT: A 399 LYS cc_start: 0.8073 (ttmm) cc_final: 0.7646 (mtpp) REVERT: A 430 THR cc_start: 0.8174 (m) cc_final: 0.7675 (p) REVERT: A 455 GLU cc_start: 0.7764 (tt0) cc_final: 0.7313 (tt0) REVERT: A 559 HIS cc_start: 0.6590 (OUTLIER) cc_final: 0.6106 (m-70) REVERT: A 593 LYS cc_start: 0.6901 (tptp) cc_final: 0.6642 (tptp) outliers start: 21 outliers final: 14 residues processed: 263 average time/residue: 0.1101 time to fit residues: 38.6709 Evaluate side-chains 265 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 249 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 329 GLN 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 84 GLU 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 425 ILE Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 559 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 96 optimal weight: 0.7980 chunk 78 optimal weight: 0.9980 chunk 93 optimal weight: 0.2980 chunk 91 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 81 optimal weight: 0.4980 chunk 64 optimal weight: 0.4980 chunk 25 optimal weight: 0.6980 chunk 86 optimal weight: 6.9990 chunk 114 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 16 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.143617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.120952 restraints weight = 13364.793| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.73 r_work: 0.3416 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.5656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 9475 Z= 0.227 Angle : 0.759 15.824 12887 Z= 0.379 Chirality : 0.052 0.418 1425 Planarity : 0.005 0.046 1679 Dihedral : 8.071 94.780 1433 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.63 % Favored : 91.37 % Rotamer: Outliers : 3.51 % Allowed : 15.22 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.57 (0.23), residues: 1170 helix: -2.38 (0.63), residues: 54 sheet: -2.91 (0.45), residues: 92 loop : -1.72 (0.18), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 47 TYR 0.029 0.002 TYR B 409 PHE 0.015 0.002 PHE A 481 TRP 0.033 0.002 TRP C 49 HIS 0.006 0.001 HIS A 304 Details of bonding type rmsd covalent geometry : bond 0.00515 ( 9420) covalent geometry : angle 0.71845 (12769) SS BOND : bond 0.00444 ( 47) SS BOND : angle 2.04272 ( 94) hydrogen bonds : bond 0.03186 ( 97) hydrogen bonds : angle 6.10458 ( 186) link_ALPHA1-3 : bond 0.01437 ( 1) link_ALPHA1-3 : angle 2.32598 ( 3) link_BETA1-3 : bond 0.00286 ( 1) link_BETA1-3 : angle 2.72883 ( 3) link_BETA1-4 : bond 0.00090 ( 2) link_BETA1-4 : angle 0.92372 ( 6) link_NAG-ASN : bond 0.01177 ( 4) link_NAG-ASN : angle 5.77707 ( 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 289 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 253 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: B 24 GLN cc_start: 0.6764 (pp30) cc_final: 0.6469 (pp30) REVERT: B 30 ASP cc_start: 0.8134 (t70) cc_final: 0.7518 (t0) REVERT: B 67 THR cc_start: 0.8626 (m) cc_final: 0.8379 (t) REVERT: B 71 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7684 (mt) REVERT: B 92 ARG cc_start: 0.8224 (mtt90) cc_final: 0.7604 (mmt-90) REVERT: B 93 GLN cc_start: 0.7422 (pp30) cc_final: 0.7199 (pp30) REVERT: B 138 ARG cc_start: 0.7370 (mmm-85) cc_final: 0.6939 (mmm160) REVERT: B 139 GLU cc_start: 0.7196 (mp0) cc_final: 0.6823 (mp0) REVERT: B 147 GLU cc_start: 0.7357 (tp30) cc_final: 0.6996 (tp30) REVERT: B 261 SER cc_start: 0.8149 (m) cc_final: 0.7841 (p) REVERT: B 284 ASN cc_start: 0.8185 (t0) cc_final: 0.7624 (t0) REVERT: B 297 THR cc_start: 0.8475 (m) cc_final: 0.8255 (p) REVERT: B 405 GLU cc_start: 0.7479 (tt0) cc_final: 0.7175 (tt0) REVERT: B 421 ASP cc_start: 0.7252 (p0) cc_final: 0.6832 (p0) REVERT: B 438 ASN cc_start: 0.7710 (m-40) cc_final: 0.7457 (m110) REVERT: B 441 TYR cc_start: 0.8534 (m-80) cc_final: 0.8191 (m-80) REVERT: B 446 GLN cc_start: 0.7486 (mt0) cc_final: 0.7157 (mt0) REVERT: B 460 GLU cc_start: 0.7864 (tt0) cc_final: 0.7537 (tt0) REVERT: B 530 ASN cc_start: 0.7170 (t0) cc_final: 0.6966 (t0) REVERT: B 538 GLN cc_start: 0.6727 (OUTLIER) cc_final: 0.6527 (pm20) REVERT: B 553 GLU cc_start: 0.6147 (tt0) cc_final: 0.5881 (mt-10) REVERT: A 46 ASP cc_start: 0.7877 (t70) cc_final: 0.7392 (t0) REVERT: A 74 TYR cc_start: 0.8523 (m-10) cc_final: 0.8320 (m-80) REVERT: A 142 GLU cc_start: 0.7611 (tt0) cc_final: 0.7077 (tp30) REVERT: A 148 VAL cc_start: 0.8499 (t) cc_final: 0.8127 (m) REVERT: A 198 SER cc_start: 0.8346 (m) cc_final: 0.7542 (p) REVERT: A 263 THR cc_start: 0.8048 (m) cc_final: 0.7830 (p) REVERT: A 292 VAL cc_start: 0.8123 (m) cc_final: 0.7774 (p) REVERT: A 294 LYS cc_start: 0.8257 (tttt) cc_final: 0.7953 (ptmm) REVERT: A 325 LYS cc_start: 0.7396 (mttt) cc_final: 0.6760 (mtmt) REVERT: A 338 ASN cc_start: 0.7615 (t0) cc_final: 0.7083 (t0) REVERT: A 344 GLU cc_start: 0.7292 (pm20) cc_final: 0.7060 (pm20) REVERT: A 360 LYS cc_start: 0.8142 (tttt) cc_final: 0.7712 (ttmm) REVERT: A 399 LYS cc_start: 0.8070 (ttmm) cc_final: 0.7732 (mtpp) REVERT: A 430 THR cc_start: 0.8141 (m) cc_final: 0.7605 (p) REVERT: A 455 GLU cc_start: 0.7612 (tt0) cc_final: 0.7003 (tm-30) REVERT: A 489 LYS cc_start: 0.8241 (tttt) cc_final: 0.7930 (tttp) REVERT: A 534 GLU cc_start: 0.7097 (pt0) cc_final: 0.6817 (pm20) REVERT: A 559 HIS cc_start: 0.6674 (OUTLIER) cc_final: 0.6095 (m-70) REVERT: A 584 HIS cc_start: 0.6169 (m90) cc_final: 0.5899 (m90) REVERT: A 593 LYS cc_start: 0.6850 (tptp) cc_final: 0.6296 (tptp) outliers start: 36 outliers final: 24 residues processed: 269 average time/residue: 0.1017 time to fit residues: 36.9788 Evaluate side-chains 278 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 251 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 CYS Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 329 GLN 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 82 ILE Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain A residue 122 LEU 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 425 ILE Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 559 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 50 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 34 optimal weight: 0.0980 chunk 114 optimal weight: 0.6980 chunk 67 optimal weight: 0.5980 chunk 95 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 60 optimal weight: 0.5980 chunk 78 optimal weight: 0.7980 chunk 105 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 153 ASN A 433 HIS ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 16 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.143156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.120999 restraints weight = 13366.972| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.58 r_work: 0.3429 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.5861 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= 0.211 Angle : 0.752 15.844 12887 Z= 0.376 Chirality : 0.051 0.421 1425 Planarity : 0.004 0.042 1679 Dihedral : 8.130 95.887 1433 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 3.32 % Allowed : 15.71 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.60 (0.23), residues: 1170 helix: -2.28 (0.62), residues: 55 sheet: -2.97 (0.46), residues: 92 loop : -1.75 (0.18), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 222 TYR 0.028 0.002 TYR B 409 PHE 0.012 0.002 PHE A 254 TRP 0.031 0.002 TRP C 49 HIS 0.006 0.001 HIS A 304 Details of bonding type rmsd covalent geometry : bond 0.00483 ( 9420) covalent geometry : angle 0.71044 (12769) SS BOND : bond 0.00420 ( 47) SS BOND : angle 2.08554 ( 94) hydrogen bonds : bond 0.03056 ( 97) hydrogen bonds : angle 5.90798 ( 186) link_ALPHA1-3 : bond 0.01477 ( 1) link_ALPHA1-3 : angle 2.22116 ( 3) link_BETA1-3 : bond 0.00464 ( 1) link_BETA1-3 : angle 2.62905 ( 3) link_BETA1-4 : bond 0.00160 ( 2) link_BETA1-4 : angle 0.99486 ( 6) link_NAG-ASN : bond 0.01160 ( 4) link_NAG-ASN : angle 5.69969 ( 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 283 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 249 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: B 24 GLN cc_start: 0.6993 (pp30) cc_final: 0.6700 (pp30) REVERT: B 30 ASP cc_start: 0.8241 (t70) cc_final: 0.7666 (t0) REVERT: B 67 THR cc_start: 0.8655 (m) cc_final: 0.8428 (t) REVERT: B 71 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7702 (mt) REVERT: B 92 ARG cc_start: 0.8352 (mtt90) cc_final: 0.7721 (mmt-90) REVERT: B 93 GLN cc_start: 0.7682 (pp30) cc_final: 0.7451 (pp30) REVERT: B 138 ARG cc_start: 0.7627 (mmm-85) cc_final: 0.7267 (tpp80) REVERT: B 139 GLU cc_start: 0.7488 (mp0) cc_final: 0.7048 (mp0) REVERT: B 147 GLU cc_start: 0.7624 (tp30) cc_final: 0.7343 (tp30) REVERT: B 284 ASN cc_start: 0.8442 (t0) cc_final: 0.7957 (t0) REVERT: B 351 ARG cc_start: 0.7179 (mmm-85) cc_final: 0.6775 (mmm-85) REVERT: B 405 GLU cc_start: 0.7749 (tt0) cc_final: 0.7433 (tt0) REVERT: B 421 ASP cc_start: 0.7503 (p0) cc_final: 0.7107 (p0) REVERT: B 438 ASN cc_start: 0.7865 (m-40) cc_final: 0.7585 (m110) REVERT: B 441 TYR cc_start: 0.8636 (m-80) cc_final: 0.8330 (m-80) REVERT: B 446 GLN cc_start: 0.7690 (mt0) cc_final: 0.7393 (mt0) REVERT: B 460 GLU cc_start: 0.8146 (tt0) cc_final: 0.7837 (tt0) REVERT: B 501 GLU cc_start: 0.7289 (mm-30) cc_final: 0.6939 (mm-30) REVERT: B 530 ASN cc_start: 0.7290 (t0) cc_final: 0.6963 (t0) REVERT: B 538 GLN cc_start: 0.6888 (OUTLIER) cc_final: 0.6665 (pm20) REVERT: B 553 GLU cc_start: 0.6462 (tt0) cc_final: 0.6214 (mt-10) REVERT: B 568 GLN cc_start: 0.7150 (tm-30) cc_final: 0.6754 (tm-30) REVERT: A 46 ASP cc_start: 0.8037 (t70) cc_final: 0.7571 (t0) REVERT: A 142 GLU cc_start: 0.7944 (tt0) cc_final: 0.7496 (tp30) REVERT: A 148 VAL cc_start: 0.8555 (t) cc_final: 0.8229 (m) REVERT: A 198 SER cc_start: 0.8313 (m) cc_final: 0.7490 (p) REVERT: A 263 THR cc_start: 0.8145 (m) cc_final: 0.7938 (p) REVERT: A 292 VAL cc_start: 0.8176 (m) cc_final: 0.7833 (p) REVERT: A 294 LYS cc_start: 0.8351 (tttt) cc_final: 0.8033 (ptmm) REVERT: A 325 LYS cc_start: 0.7569 (mttt) cc_final: 0.7093 (mtmt) REVERT: A 399 LYS cc_start: 0.8381 (ttmm) cc_final: 0.8024 (mtpp) REVERT: A 430 THR cc_start: 0.8256 (m) cc_final: 0.7751 (p) REVERT: A 534 GLU cc_start: 0.7191 (pt0) cc_final: 0.6881 (pm20) REVERT: A 559 HIS cc_start: 0.6759 (OUTLIER) cc_final: 0.6183 (m-70) REVERT: A 584 HIS cc_start: 0.6247 (m90) cc_final: 0.5854 (m90) REVERT: A 593 LYS cc_start: 0.6965 (tptp) cc_final: 0.6390 (tptp) outliers start: 34 outliers final: 25 residues processed: 266 average time/residue: 0.0792 time to fit residues: 28.4717 Evaluate side-chains 271 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 243 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 CYS Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 244 CYS 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 82 ILE Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain A residue 122 LEU 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 340 ILE 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 487 LYS Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 510 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: 0.3980 chunk 1 optimal weight: 0.0000 chunk 46 optimal weight: 0.5980 chunk 95 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 66 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 overall best weight: 0.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 GLN A 196 ASN ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 16 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.142834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.120634 restraints weight = 13505.874| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.73 r_work: 0.3416 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.5980 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= 0.192 Angle : 0.746 15.498 12887 Z= 0.372 Chirality : 0.051 0.411 1425 Planarity : 0.004 0.041 1679 Dihedral : 8.049 95.754 1433 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 3.12 % Allowed : 16.10 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.53 (0.23), residues: 1170 helix: -2.29 (0.62), residues: 55 sheet: -3.01 (0.50), residues: 82 loop : -1.70 (0.18), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 222 TYR 0.030 0.002 TYR B 409 PHE 0.015 0.002 PHE A 481 TRP 0.031 0.002 TRP C 49 HIS 0.006 0.001 HIS A 304 Details of bonding type rmsd covalent geometry : bond 0.00443 ( 9420) covalent geometry : angle 0.70723 (12769) SS BOND : bond 0.00415 ( 47) SS BOND : angle 1.95924 ( 94) hydrogen bonds : bond 0.03072 ( 97) hydrogen bonds : angle 5.78442 ( 186) link_ALPHA1-3 : bond 0.01468 ( 1) link_ALPHA1-3 : angle 2.21793 ( 3) link_BETA1-3 : bond 0.00538 ( 1) link_BETA1-3 : angle 2.70121 ( 3) link_BETA1-4 : bond 0.00175 ( 2) link_BETA1-4 : angle 0.97378 ( 6) link_NAG-ASN : bond 0.01154 ( 4) link_NAG-ASN : angle 5.59202 ( 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 276 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 244 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 24 GLN cc_start: 0.6688 (pp30) cc_final: 0.6352 (pp30) REVERT: B 30 ASP cc_start: 0.8154 (t70) cc_final: 0.7536 (t0) REVERT: B 67 THR cc_start: 0.8648 (m) cc_final: 0.8406 (t) REVERT: B 71 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7631 (mt) REVERT: B 92 ARG cc_start: 0.8235 (mtt90) cc_final: 0.7634 (mmt-90) REVERT: B 93 GLN cc_start: 0.7378 (pp30) cc_final: 0.7155 (pp30) REVERT: B 138 ARG cc_start: 0.7331 (mmm-85) cc_final: 0.6702 (mmm-85) REVERT: B 139 GLU cc_start: 0.7243 (mp0) cc_final: 0.6828 (mp0) REVERT: B 147 GLU cc_start: 0.7360 (tp30) cc_final: 0.7027 (tp30) REVERT: B 284 ASN cc_start: 0.8360 (t0) cc_final: 0.8012 (t0) REVERT: B 351 ARG cc_start: 0.7159 (mmm-85) cc_final: 0.6820 (mmm-85) REVERT: B 405 GLU cc_start: 0.7492 (tt0) cc_final: 0.7138 (tt0) REVERT: B 421 ASP cc_start: 0.7354 (p0) cc_final: 0.6893 (p0) REVERT: B 438 ASN cc_start: 0.7751 (m-40) cc_final: 0.7465 (m110) REVERT: B 441 TYR cc_start: 0.8514 (m-80) cc_final: 0.8156 (m-80) REVERT: B 446 GLN cc_start: 0.7469 (mt0) cc_final: 0.7120 (mt0) REVERT: B 460 GLU cc_start: 0.7840 (tt0) cc_final: 0.7478 (tt0) REVERT: B 499 ARG cc_start: 0.7579 (ttt-90) cc_final: 0.7349 (ttt90) REVERT: B 501 GLU cc_start: 0.7104 (mm-30) cc_final: 0.6818 (mm-30) REVERT: B 514 LEU cc_start: 0.7559 (mp) cc_final: 0.7188 (mt) REVERT: B 530 ASN cc_start: 0.7007 (t0) cc_final: 0.6689 (t0) REVERT: B 538 GLN cc_start: 0.6671 (OUTLIER) cc_final: 0.6468 (pm20) REVERT: B 553 GLU cc_start: 0.6118 (tt0) cc_final: 0.5885 (mt-10) REVERT: B 568 GLN cc_start: 0.7072 (tm-30) cc_final: 0.6667 (tm-30) REVERT: A 46 ASP cc_start: 0.7838 (t70) cc_final: 0.7335 (t0) REVERT: A 142 GLU cc_start: 0.7698 (tt0) cc_final: 0.7183 (tp30) REVERT: A 148 VAL cc_start: 0.8452 (t) cc_final: 0.8097 (m) REVERT: A 198 SER cc_start: 0.8324 (m) cc_final: 0.7541 (p) REVERT: A 263 THR cc_start: 0.8071 (m) cc_final: 0.7862 (p) REVERT: A 292 VAL cc_start: 0.8109 (m) cc_final: 0.7749 (p) REVERT: A 294 LYS cc_start: 0.8234 (tttt) cc_final: 0.7908 (ptmm) REVERT: A 325 LYS cc_start: 0.7454 (mttt) cc_final: 0.6948 (mtmt) REVERT: A 399 LYS cc_start: 0.8258 (ttmm) cc_final: 0.7892 (mtpp) REVERT: A 430 THR cc_start: 0.8132 (m) cc_final: 0.7590 (p) REVERT: A 436 PHE cc_start: 0.7897 (m-80) cc_final: 0.7433 (m-80) REVERT: A 455 GLU cc_start: 0.7559 (tt0) cc_final: 0.7250 (tt0) REVERT: A 534 GLU cc_start: 0.7075 (pt0) cc_final: 0.6752 (pm20) REVERT: A 559 HIS cc_start: 0.6506 (OUTLIER) cc_final: 0.5932 (m-70) REVERT: A 584 HIS cc_start: 0.6178 (m90) cc_final: 0.5771 (m90) REVERT: A 593 LYS cc_start: 0.6862 (tptp) cc_final: 0.6300 (tptp) outliers start: 32 outliers final: 26 residues processed: 259 average time/residue: 0.0813 time to fit residues: 28.4939 Evaluate side-chains 267 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 238 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 CYS Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 472 THR 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 84 GLU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 264 CYS Chi-restraints excluded: chain A residue 307 CYS Chi-restraints excluded: chain A residue 340 ILE 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 487 LYS Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 510 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 84 optimal weight: 1.9990 chunk 96 optimal weight: 0.2980 chunk 32 optimal weight: 0.6980 chunk 112 optimal weight: 0.4980 chunk 106 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 chunk 73 optimal weight: 0.9980 chunk 52 optimal weight: 0.0980 chunk 26 optimal weight: 0.0770 overall best weight: 0.3338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 486 GLN C 16 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.143777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.121636 restraints weight = 13341.296| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.64 r_work: 0.3434 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.6032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 9475 Z= 0.166 Angle : 0.733 15.386 12887 Z= 0.366 Chirality : 0.050 0.412 1425 Planarity : 0.004 0.042 1679 Dihedral : 7.945 93.831 1433 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 2.34 % Allowed : 17.37 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.48 (0.23), residues: 1170 helix: -2.22 (0.63), residues: 55 sheet: -2.82 (0.50), residues: 80 loop : -1.68 (0.18), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 222 TYR 0.028 0.002 TYR B 409 PHE 0.016 0.002 PHE A 180 TRP 0.034 0.002 TRP C 49 HIS 0.005 0.001 HIS A 304 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 9420) covalent geometry : angle 0.69516 (12769) SS BOND : bond 0.00427 ( 47) SS BOND : angle 1.89998 ( 94) hydrogen bonds : bond 0.02860 ( 97) hydrogen bonds : angle 5.71855 ( 186) link_ALPHA1-3 : bond 0.01593 ( 1) link_ALPHA1-3 : angle 2.29702 ( 3) link_BETA1-3 : bond 0.00643 ( 1) link_BETA1-3 : angle 2.75593 ( 3) link_BETA1-4 : bond 0.00187 ( 2) link_BETA1-4 : angle 1.06196 ( 6) link_NAG-ASN : bond 0.01132 ( 4) link_NAG-ASN : angle 5.52821 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2323.38 seconds wall clock time: 40 minutes 22.07 seconds (2422.07 seconds total)