Starting phenix.real_space_refine on Fri Mar 14 01:46:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hgo_34744/03_2025/8hgo_34744.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hgo_34744/03_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_34744/03_2025/8hgo_34744.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hgo_34744/03_2025/8hgo_34744.map" model { file = "/net/cci-nas-00/data/ceres_data/8hgo_34744/03_2025/8hgo_34744.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hgo_34744/03_2025/8hgo_34744.cif" } resolution = 3.31 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 7.01, per 1000 atoms: 0.76 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: 2.63 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.14 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: 2.70 Time building geometry restraints manager: 3.03 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: 4.790 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: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 26.040 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.620 ------------------------------------------------------------------------------- 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 9420 Z= 0.239 Angle : 0.711 10.795 12769 Z= 0.397 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.011 0.002 TRP B 452 HIS 0.015 0.001 HIS B 48 PHE 0.019 0.002 PHE A 404 TYR 0.014 0.001 TYR B 554 ARG 0.004 0.000 ARG B 536 *********************** 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 : 1.619 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: 0.2905 time to fit residues: 109.1734 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 : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 0.3980 chunk 87 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 46 optimal weight: 7.9990 chunk 90 optimal weight: 1.9990 chunk 35 optimal weight: 0.0040 chunk 55 optimal weight: 0.9980 chunk 67 optimal weight: 0.4980 chunk 105 optimal weight: 0.0980 overall best weight: 0.3592 ------------------------------------------------------------------------------- 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 = 0.4063 r_free = 0.4063 target = 0.158219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.135664 restraints weight = 13533.017| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 2.82 r_work: 0.3631 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 9420 Z= 0.263 Angle : 0.699 9.966 12769 Z= 0.353 Chirality : 0.050 0.298 1425 Planarity : 0.006 0.048 1679 Dihedral : 8.954 92.432 1433 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 1.56 % Allowed : 7.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.29 (0.22), residues: 1170 helix: -3.53 (0.45), residues: 69 sheet: -2.51 (0.50), residues: 94 loop : -2.29 (0.18), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 452 HIS 0.010 0.001 HIS B 237 PHE 0.024 0.002 PHE A 549 TYR 0.021 0.002 TYR B 409 ARG 0.013 0.001 ARG B 499 *********************** 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 291 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 275 time to evaluate : 1.466 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 30 ASP cc_start: 0.7808 (t70) cc_final: 0.7168 (t70) REVERT: B 89 ASN cc_start: 0.8016 (m-40) cc_final: 0.7718 (m-40) REVERT: B 93 GLN cc_start: 0.7314 (pp30) cc_final: 0.7041 (pp30) REVERT: B 147 GLU cc_start: 0.7221 (tp30) cc_final: 0.6839 (tp30) REVERT: B 156 GLN cc_start: 0.8049 (mt0) cc_final: 0.7808 (mt0) REVERT: B 164 GLN cc_start: 0.7080 (pm20) cc_final: 0.6772 (pm20) REVERT: B 183 LEU cc_start: 0.8396 (mp) cc_final: 0.8019 (tp) REVERT: B 196 SER cc_start: 0.7525 (t) cc_final: 0.7301 (t) REVERT: B 228 LYS cc_start: 0.7868 (mtpt) cc_final: 0.7521 (mtpt) REVERT: B 274 TYR cc_start: 0.8267 (t80) cc_final: 0.7918 (t80) REVERT: B 329 GLN cc_start: 0.7091 (OUTLIER) cc_final: 0.6874 (mt0) REVERT: B 403 LEU cc_start: 0.7047 (tp) cc_final: 0.6776 (tp) REVERT: B 421 ASP cc_start: 0.6385 (p0) cc_final: 0.6151 (p0) REVERT: B 438 ASN cc_start: 0.7754 (m-40) cc_final: 0.7490 (m110) REVERT: B 460 GLU cc_start: 0.7680 (tt0) cc_final: 0.7349 (tt0) REVERT: B 561 LEU cc_start: 0.7323 (mt) cc_final: 0.7054 (mt) REVERT: B 568 GLN cc_start: 0.6826 (tp40) cc_final: 0.6623 (tm-30) REVERT: A 45 GLU cc_start: 0.7706 (mp0) cc_final: 0.7252 (mp0) REVERT: A 46 ASP cc_start: 0.8045 (t70) cc_final: 0.7604 (t0) REVERT: A 80 LYS cc_start: 0.8537 (mttp) cc_final: 0.8292 (mttp) REVERT: A 114 GLU cc_start: 0.6923 (OUTLIER) cc_final: 0.6520 (tm-30) REVERT: A 152 ASN cc_start: 0.7623 (m110) cc_final: 0.7183 (m110) REVERT: A 160 GLU cc_start: 0.7734 (pm20) cc_final: 0.6857 (pm20) REVERT: A 198 SER cc_start: 0.8029 (m) cc_final: 0.7379 (p) REVERT: A 235 GLN cc_start: 0.8036 (mm-40) cc_final: 0.7807 (mm110) REVERT: A 254 PHE cc_start: 0.7847 (m-10) cc_final: 0.7569 (m-10) REVERT: A 255 ARG cc_start: 0.7086 (ttt-90) cc_final: 0.6681 (tmt-80) REVERT: A 268 MET cc_start: 0.6296 (mtm) cc_final: 0.5753 (mtm) REVERT: A 277 MET cc_start: 0.5526 (mtt) cc_final: 0.5134 (mtt) REVERT: A 284 LYS cc_start: 0.8284 (mtmm) cc_final: 0.7934 (mtmm) REVERT: A 292 VAL cc_start: 0.8085 (m) cc_final: 0.7639 (p) REVERT: A 293 LYS cc_start: 0.8093 (mtpp) cc_final: 0.7750 (ptpp) REVERT: A 294 LYS cc_start: 0.8279 (tttt) cc_final: 0.7987 (tttt) REVERT: A 316 TYR cc_start: 0.6520 (t80) cc_final: 0.6117 (t80) REVERT: A 318 MET cc_start: 0.6836 (tpp) cc_final: 0.6538 (tpp) REVERT: A 325 LYS cc_start: 0.7623 (mttt) cc_final: 0.7107 (mtmt) REVERT: A 347 ASP cc_start: 0.7102 (t0) cc_final: 0.6549 (t0) REVERT: A 396 LYS cc_start: 0.8215 (ttmm) cc_final: 0.7905 (mttp) REVERT: A 400 GLU cc_start: 0.7456 (pt0) cc_final: 0.7253 (pt0) REVERT: A 430 THR cc_start: 0.8206 (m) cc_final: 0.7593 (p) REVERT: A 578 ASN cc_start: 0.6859 (m-40) cc_final: 0.6529 (m-40) REVERT: A 593 LYS cc_start: 0.6725 (tptp) cc_final: 0.6504 (tptp) REVERT: C 38 ILE cc_start: 0.8456 (tt) cc_final: 0.8107 (pt) outliers start: 16 outliers final: 9 residues processed: 277 average time/residue: 0.3095 time to fit residues: 111.8733 Evaluate side-chains 273 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 262 time to evaluate : 0.968 ------------------------------------------------------------------------------- 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 114 GLU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 327 LYS Chi-restraints excluded: chain A residue 442 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 94 optimal weight: 0.0970 chunk 80 optimal weight: 0.0970 chunk 89 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 21 optimal weight: 0.0970 chunk 101 optimal weight: 0.2980 chunk 88 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 40 optimal weight: 0.1980 chunk 99 optimal weight: 0.9980 overall best weight: 0.1574 ------------------------------------------------------------------------------- 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 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.157333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.134685 restraints weight = 13636.668| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 2.83 r_work: 0.3622 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9420 Z= 0.174 Angle : 0.605 9.740 12769 Z= 0.307 Chirality : 0.047 0.248 1425 Planarity : 0.005 0.044 1679 Dihedral : 8.120 83.443 1433 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 1.66 % Allowed : 10.05 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.07 (0.22), residues: 1170 helix: -3.22 (0.51), residues: 74 sheet: -2.34 (0.51), residues: 92 loop : -2.12 (0.18), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 49 HIS 0.006 0.001 HIS A 559 PHE 0.019 0.001 PHE A 549 TYR 0.020 0.001 TYR B 163 ARG 0.008 0.001 ARG A 252 *********************** 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 269 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 252 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 30 ASP cc_start: 0.7850 (t70) cc_final: 0.7090 (t0) REVERT: B 64 TYR cc_start: 0.8691 (m-80) cc_final: 0.8162 (m-80) REVERT: B 93 GLN cc_start: 0.7240 (pp30) cc_final: 0.6882 (pp30) REVERT: B 100 ARG cc_start: 0.8245 (tpp80) cc_final: 0.7964 (tpp80) REVERT: B 112 TYR cc_start: 0.7299 (m-80) cc_final: 0.7021 (m-80) REVERT: B 147 GLU cc_start: 0.7275 (tp30) cc_final: 0.6896 (tp30) REVERT: B 156 GLN cc_start: 0.7990 (mt0) cc_final: 0.7694 (mt0) REVERT: B 164 GLN cc_start: 0.7155 (pm20) cc_final: 0.6803 (pm20) REVERT: B 168 LEU cc_start: 0.7938 (tp) cc_final: 0.7729 (tt) REVERT: B 183 LEU cc_start: 0.8408 (mp) cc_final: 0.7909 (tp) REVERT: B 228 LYS cc_start: 0.7852 (mtpt) cc_final: 0.7498 (mtpt) REVERT: B 268 CYS cc_start: 0.6067 (t) cc_final: 0.5797 (t) REVERT: B 274 TYR cc_start: 0.8231 (t80) cc_final: 0.7899 (t80) REVERT: B 284 ASN cc_start: 0.7483 (t0) cc_final: 0.7063 (t0) REVERT: B 403 LEU cc_start: 0.6913 (tp) cc_final: 0.6637 (tp) REVERT: B 405 GLU cc_start: 0.7567 (tt0) cc_final: 0.7305 (tp30) REVERT: B 438 ASN cc_start: 0.7713 (m-40) cc_final: 0.7485 (m110) REVERT: B 441 TYR cc_start: 0.8486 (m-80) cc_final: 0.7804 (m-80) REVERT: B 459 ARG cc_start: 0.7974 (ptt90) cc_final: 0.7714 (ptt90) REVERT: B 460 GLU cc_start: 0.7634 (tt0) cc_final: 0.7318 (tt0) REVERT: B 538 GLN cc_start: 0.6546 (OUTLIER) cc_final: 0.6306 (pm20) REVERT: B 568 GLN cc_start: 0.6936 (tp40) cc_final: 0.6706 (tm-30) REVERT: A 45 GLU cc_start: 0.7680 (mp0) cc_final: 0.7418 (mp0) REVERT: A 46 ASP cc_start: 0.8056 (t70) cc_final: 0.7577 (t0) REVERT: A 152 ASN cc_start: 0.7640 (m110) cc_final: 0.7170 (m110) REVERT: A 160 GLU cc_start: 0.7768 (pm20) cc_final: 0.7545 (pm20) REVERT: A 198 SER cc_start: 0.8065 (m) cc_final: 0.7421 (p) REVERT: A 252 ARG cc_start: 0.7485 (mtp85) cc_final: 0.7100 (mtp85) REVERT: A 254 PHE cc_start: 0.7868 (m-10) cc_final: 0.7581 (m-10) REVERT: A 255 ARG cc_start: 0.6957 (ttt-90) cc_final: 0.6673 (tmt-80) REVERT: A 256 ASP cc_start: 0.7305 (t70) cc_final: 0.6809 (t70) REVERT: A 259 THR cc_start: 0.7930 (p) cc_final: 0.7568 (t) REVERT: A 268 MET cc_start: 0.6340 (mtm) cc_final: 0.5786 (mtm) REVERT: A 277 MET cc_start: 0.5572 (mtt) cc_final: 0.5148 (mtt) REVERT: A 284 LYS cc_start: 0.8244 (mtmm) cc_final: 0.8008 (mtmm) REVERT: A 292 VAL cc_start: 0.8099 (m) cc_final: 0.7682 (p) REVERT: A 294 LYS cc_start: 0.8252 (tttt) cc_final: 0.7998 (tttt) REVERT: A 307 CYS cc_start: 0.7122 (m) cc_final: 0.6807 (m) REVERT: A 316 TYR cc_start: 0.6575 (t80) cc_final: 0.5985 (t80) REVERT: A 318 MET cc_start: 0.6818 (tpp) cc_final: 0.6160 (tpp) REVERT: A 319 GLU cc_start: 0.7278 (pt0) cc_final: 0.7029 (pm20) REVERT: A 325 LYS cc_start: 0.7603 (mttt) cc_final: 0.6985 (mtmt) REVERT: A 347 ASP cc_start: 0.7152 (t0) cc_final: 0.6573 (t0) REVERT: A 391 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7493 (mm-30) REVERT: A 430 THR cc_start: 0.8066 (m) cc_final: 0.7471 (p) REVERT: A 479 LYS cc_start: 0.7840 (pttt) cc_final: 0.7606 (pttm) REVERT: A 489 LYS cc_start: 0.8008 (ttmm) cc_final: 0.7544 (ttmm) REVERT: A 578 ASN cc_start: 0.6832 (m-40) cc_final: 0.6515 (m-40) REVERT: A 593 LYS cc_start: 0.6687 (tptp) cc_final: 0.6455 (tptp) REVERT: C 38 ILE cc_start: 0.8437 (tt) cc_final: 0.8127 (pt) outliers start: 17 outliers final: 8 residues processed: 257 average time/residue: 0.2580 time to fit residues: 87.5306 Evaluate side-chains 248 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 239 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 236 CYS 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 425 ILE Chi-restraints excluded: chain A residue 468 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 63 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 45 optimal weight: 0.3980 chunk 35 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 87 optimal weight: 0.2980 chunk 62 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 49 optimal weight: 0.1980 chunk 55 optimal weight: 4.9990 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 54 GLN B 119 ASN B 260 HIS B 329 GLN ** B 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 559 HIS A 493 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.149660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.126774 restraints weight = 13391.600| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 2.70 r_work: 0.3511 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 9420 Z= 0.326 Angle : 0.687 12.313 12769 Z= 0.347 Chirality : 0.052 0.356 1425 Planarity : 0.005 0.045 1679 Dihedral : 8.085 86.193 1433 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 2.44 % Allowed : 9.95 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.22), residues: 1170 helix: -2.94 (0.57), residues: 59 sheet: -2.27 (0.53), residues: 82 loop : -2.00 (0.18), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 49 HIS 0.008 0.001 HIS A 507 PHE 0.034 0.002 PHE A 549 TYR 0.023 0.002 TYR B 409 ARG 0.006 0.001 ARG B 47 *********************** 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 284 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 259 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 GLN cc_start: 0.8017 (pt0) cc_final: 0.7763 (pt0) REVERT: B 93 GLN cc_start: 0.7301 (pp30) cc_final: 0.6979 (pp30) REVERT: B 112 TYR cc_start: 0.7467 (m-80) cc_final: 0.7185 (m-80) REVERT: B 139 GLU cc_start: 0.6987 (mp0) cc_final: 0.6595 (mp0) REVERT: B 147 GLU cc_start: 0.7265 (tp30) cc_final: 0.6803 (tp30) REVERT: B 164 GLN cc_start: 0.7495 (pm20) cc_final: 0.6907 (pm20) REVERT: B 228 LYS cc_start: 0.7901 (mtpt) cc_final: 0.7546 (mtmm) REVERT: B 261 SER cc_start: 0.7952 (m) cc_final: 0.7602 (p) REVERT: B 268 CYS cc_start: 0.6243 (t) cc_final: 0.5923 (t) REVERT: B 284 ASN cc_start: 0.7877 (t0) cc_final: 0.7503 (t0) REVERT: B 329 GLN cc_start: 0.7158 (OUTLIER) cc_final: 0.6922 (mt0) REVERT: B 405 GLU cc_start: 0.7607 (tt0) cc_final: 0.7256 (tt0) REVERT: B 421 ASP cc_start: 0.7122 (p0) cc_final: 0.6728 (p0) REVERT: B 438 ASN cc_start: 0.7740 (m-40) cc_final: 0.7495 (m110) REVERT: B 441 TYR cc_start: 0.8539 (m-80) cc_final: 0.8251 (m-80) REVERT: B 538 GLN cc_start: 0.6709 (OUTLIER) cc_final: 0.6438 (pm20) REVERT: B 553 GLU cc_start: 0.6268 (mt-10) cc_final: 0.6001 (mt-10) REVERT: B 568 GLN cc_start: 0.7030 (tp40) cc_final: 0.6778 (tm-30) REVERT: A 46 ASP cc_start: 0.7960 (t70) cc_final: 0.7475 (t70) REVERT: A 133 LYS cc_start: 0.7385 (mttt) cc_final: 0.7174 (ttmm) REVERT: A 142 GLU cc_start: 0.7692 (tt0) cc_final: 0.7480 (tt0) REVERT: A 148 VAL cc_start: 0.8524 (t) cc_final: 0.8114 (m) REVERT: A 198 SER cc_start: 0.8153 (m) cc_final: 0.7419 (p) REVERT: A 255 ARG cc_start: 0.6989 (ttt-90) cc_final: 0.6674 (tmt-80) REVERT: A 263 THR cc_start: 0.8080 (m) cc_final: 0.7688 (p) REVERT: A 268 MET cc_start: 0.6540 (mtm) cc_final: 0.6021 (mtm) REVERT: A 277 MET cc_start: 0.5744 (mtt) cc_final: 0.5340 (mtt) REVERT: A 292 VAL cc_start: 0.8230 (m) cc_final: 0.7872 (p) REVERT: A 294 LYS cc_start: 0.8296 (tttt) cc_final: 0.8054 (tttt) REVERT: A 303 ASP cc_start: 0.7497 (p0) cc_final: 0.7230 (p0) REVERT: A 308 VAL cc_start: 0.8231 (OUTLIER) cc_final: 0.8025 (p) REVERT: A 316 TYR cc_start: 0.6799 (t80) cc_final: 0.6385 (t80) REVERT: A 318 MET cc_start: 0.6938 (tpp) cc_final: 0.6668 (tpp) REVERT: A 325 LYS cc_start: 0.7751 (mttt) cc_final: 0.7113 (mtmt) REVERT: A 327 LYS cc_start: 0.7715 (ptpp) cc_final: 0.7232 (ptpp) REVERT: A 347 ASP cc_start: 0.7230 (t0) cc_final: 0.6673 (t0) REVERT: A 357 LYS cc_start: 0.8298 (ptpt) cc_final: 0.7983 (pptt) REVERT: A 430 THR cc_start: 0.8135 (m) cc_final: 0.7542 (p) REVERT: A 455 GLU cc_start: 0.7540 (tt0) cc_final: 0.7140 (tt0) REVERT: A 487 LYS cc_start: 0.7458 (mtmm) cc_final: 0.7159 (mtmm) REVERT: A 489 LYS cc_start: 0.8118 (ttmm) cc_final: 0.7614 (ttmm) REVERT: A 584 HIS cc_start: 0.6142 (m90) cc_final: 0.5862 (m170) REVERT: A 593 LYS cc_start: 0.6799 (tptp) cc_final: 0.6319 (tptp) outliers start: 25 outliers final: 15 residues processed: 265 average time/residue: 0.2533 time to fit residues: 88.1946 Evaluate side-chains 265 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 247 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 54 GLN Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 236 CYS Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 329 GLN Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 538 GLN 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 293 LYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 462 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 61 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 94 optimal weight: 0.2980 chunk 93 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 54 optimal weight: 0.0870 chunk 58 optimal weight: 0.0770 overall best weight: 0.3516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 GLN B 267 HIS ** B 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 491 GLN B 527 GLN ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 GLN A 559 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.149475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.126517 restraints weight = 13411.895| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.79 r_work: 0.3500 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.4348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 9420 Z= 0.247 Angle : 0.646 9.692 12769 Z= 0.329 Chirality : 0.050 0.465 1425 Planarity : 0.004 0.041 1679 Dihedral : 7.730 80.373 1433 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 2.73 % Allowed : 10.93 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.22), residues: 1170 helix: -2.75 (0.58), residues: 59 sheet: -2.31 (0.53), residues: 82 loop : -1.89 (0.18), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 49 HIS 0.006 0.001 HIS A 507 PHE 0.037 0.002 PHE A 549 TYR 0.023 0.002 TYR B 409 ARG 0.007 0.001 ARG B 47 *********************** 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 280 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 252 time to evaluate : 1.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 30 ASP cc_start: 0.8001 (t70) cc_final: 0.7371 (t0) REVERT: B 64 TYR cc_start: 0.8862 (m-80) cc_final: 0.8142 (m-80) REVERT: B 112 TYR cc_start: 0.7446 (m-80) cc_final: 0.7228 (m-80) REVERT: B 138 ARG cc_start: 0.7154 (mmm-85) cc_final: 0.6794 (mmm160) REVERT: B 139 GLU cc_start: 0.7007 (mp0) cc_final: 0.6705 (mp0) REVERT: B 147 GLU cc_start: 0.7309 (tp30) cc_final: 0.6822 (tp30) REVERT: B 228 LYS cc_start: 0.7912 (mtpt) cc_final: 0.7536 (mtmm) REVERT: B 268 CYS cc_start: 0.6347 (t) cc_final: 0.6109 (t) REVERT: B 284 ASN cc_start: 0.7902 (t0) cc_final: 0.7506 (t0) REVERT: B 405 GLU cc_start: 0.7625 (tt0) cc_final: 0.7302 (tt0) REVERT: B 421 ASP cc_start: 0.7039 (p0) cc_final: 0.6667 (p0) REVERT: B 438 ASN cc_start: 0.7701 (m-40) cc_final: 0.7460 (m110) REVERT: B 441 TYR cc_start: 0.8528 (m-80) cc_final: 0.8214 (m-80) REVERT: B 459 ARG cc_start: 0.8059 (ptt90) cc_final: 0.7787 (ptt90) REVERT: B 460 GLU cc_start: 0.7892 (tt0) cc_final: 0.7594 (tp30) REVERT: B 538 GLN cc_start: 0.6708 (OUTLIER) cc_final: 0.6465 (pm20) REVERT: B 553 GLU cc_start: 0.6337 (mt-10) cc_final: 0.6005 (mt-10) REVERT: B 568 GLN cc_start: 0.7001 (tp40) cc_final: 0.6751 (tm-30) REVERT: A 46 ASP cc_start: 0.7981 (t70) cc_final: 0.7425 (t70) REVERT: A 133 LYS cc_start: 0.7277 (mttt) cc_final: 0.7042 (ttmm) REVERT: A 142 GLU cc_start: 0.7714 (tt0) cc_final: 0.7497 (tt0) REVERT: A 148 VAL cc_start: 0.8464 (t) cc_final: 0.8075 (m) REVERT: A 198 SER cc_start: 0.8216 (m) cc_final: 0.7445 (p) REVERT: A 245 GLU cc_start: 0.7669 (tp30) cc_final: 0.7272 (tp30) REVERT: A 284 LYS cc_start: 0.8172 (mtmm) cc_final: 0.7941 (mtmm) REVERT: A 292 VAL cc_start: 0.8140 (m) cc_final: 0.7765 (p) REVERT: A 294 LYS cc_start: 0.8235 (tttt) cc_final: 0.7968 (tttt) REVERT: A 303 ASP cc_start: 0.7489 (p0) cc_final: 0.7258 (p0) REVERT: A 316 TYR cc_start: 0.6847 (t80) cc_final: 0.6434 (t80) REVERT: A 318 MET cc_start: 0.6986 (tpp) cc_final: 0.6687 (tpp) REVERT: A 325 LYS cc_start: 0.7683 (mttt) cc_final: 0.7014 (mtmt) REVERT: A 327 LYS cc_start: 0.7760 (ptpp) cc_final: 0.7310 (ptpp) REVERT: A 347 ASP cc_start: 0.7289 (t0) cc_final: 0.6693 (t0) REVERT: A 358 HIS cc_start: 0.7833 (m90) cc_final: 0.7607 (m170) REVERT: A 430 THR cc_start: 0.8039 (m) cc_final: 0.7467 (p) REVERT: A 455 GLU cc_start: 0.7538 (tt0) cc_final: 0.7017 (tm-30) REVERT: A 479 LYS cc_start: 0.8050 (pttt) cc_final: 0.7783 (pttm) REVERT: A 487 LYS cc_start: 0.7514 (mtmm) cc_final: 0.7188 (mtmm) REVERT: A 489 LYS cc_start: 0.8131 (ttmm) cc_final: 0.7818 (ttmm) REVERT: A 584 HIS cc_start: 0.6128 (m90) cc_final: 0.5837 (m170) REVERT: A 593 LYS cc_start: 0.6793 (tptp) cc_final: 0.6305 (tptp) REVERT: C 38 ILE cc_start: 0.8453 (tt) cc_final: 0.8159 (pt) outliers start: 28 outliers final: 19 residues processed: 263 average time/residue: 0.3051 time to fit residues: 107.6224 Evaluate side-chains 256 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 236 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 54 GLN Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 538 GLN Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 515 CYS Chi-restraints excluded: chain A residue 559 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 18 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 42 optimal weight: 0.0060 chunk 4 optimal weight: 0.3980 chunk 71 optimal weight: 0.8980 chunk 82 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 23 optimal weight: 0.0980 overall best weight: 0.3796 ------------------------------------------------------------------------------- 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 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 329 GLN B 446 GLN ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.147916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.124921 restraints weight = 13512.185| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 2.80 r_work: 0.3475 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.4642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9420 Z= 0.252 Angle : 0.652 9.442 12769 Z= 0.331 Chirality : 0.050 0.437 1425 Planarity : 0.004 0.041 1679 Dihedral : 7.689 80.313 1433 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 2.44 % Allowed : 13.46 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.22), residues: 1170 helix: -2.63 (0.59), residues: 59 sheet: -2.40 (0.52), residues: 82 loop : -1.84 (0.18), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 49 HIS 0.021 0.001 HIS A 559 PHE 0.041 0.002 PHE A 549 TYR 0.025 0.002 TYR B 409 ARG 0.007 0.001 ARG B 47 *********************** 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 275 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 250 time to evaluate : 1.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 30 ASP cc_start: 0.7997 (t70) cc_final: 0.7371 (t0) REVERT: B 75 GLN cc_start: 0.8020 (pt0) cc_final: 0.7627 (pt0) REVERT: B 112 TYR cc_start: 0.7482 (m-80) cc_final: 0.7256 (m-80) REVERT: B 138 ARG cc_start: 0.7282 (mmm-85) cc_final: 0.6886 (mmm160) REVERT: B 139 GLU cc_start: 0.7066 (mp0) cc_final: 0.6753 (mp0) REVERT: B 228 LYS cc_start: 0.7931 (mtpt) cc_final: 0.7648 (mtpt) REVERT: B 261 SER cc_start: 0.7987 (m) cc_final: 0.7636 (p) REVERT: B 268 CYS cc_start: 0.6311 (t) cc_final: 0.6070 (t) REVERT: B 284 ASN cc_start: 0.7987 (t0) cc_final: 0.7459 (t0) REVERT: B 405 GLU cc_start: 0.7648 (tt0) cc_final: 0.7310 (tt0) REVERT: B 421 ASP cc_start: 0.7145 (p0) cc_final: 0.6763 (p0) REVERT: B 438 ASN cc_start: 0.7714 (m-40) cc_final: 0.7464 (m110) REVERT: B 441 TYR cc_start: 0.8517 (m-80) cc_final: 0.8191 (m-80) REVERT: B 459 ARG cc_start: 0.8091 (ptt90) cc_final: 0.7829 (ptt90) REVERT: B 460 GLU cc_start: 0.7926 (tt0) cc_final: 0.7534 (tp30) REVERT: B 538 GLN cc_start: 0.6732 (OUTLIER) cc_final: 0.6495 (pm20) REVERT: B 553 GLU cc_start: 0.6394 (mt-10) cc_final: 0.6035 (mt-10) REVERT: B 568 GLN cc_start: 0.7040 (tp40) cc_final: 0.6757 (tm-30) REVERT: A 46 ASP cc_start: 0.7962 (t70) cc_final: 0.7441 (t70) REVERT: A 133 LYS cc_start: 0.7390 (mttt) cc_final: 0.7010 (mmmm) REVERT: A 142 GLU cc_start: 0.7729 (tt0) cc_final: 0.7499 (tt0) REVERT: A 148 VAL cc_start: 0.8492 (t) cc_final: 0.8107 (m) REVERT: A 198 SER cc_start: 0.8232 (m) cc_final: 0.7474 (p) REVERT: A 245 GLU cc_start: 0.7545 (tp30) cc_final: 0.7084 (tp30) REVERT: A 263 THR cc_start: 0.8052 (m) cc_final: 0.7692 (p) REVERT: A 292 VAL cc_start: 0.8106 (m) cc_final: 0.7706 (p) REVERT: A 294 LYS cc_start: 0.8258 (tttt) cc_final: 0.7939 (ptmm) REVERT: A 308 VAL cc_start: 0.8182 (p) cc_final: 0.7921 (m) REVERT: A 318 MET cc_start: 0.6958 (tpp) cc_final: 0.6712 (tpp) REVERT: A 325 LYS cc_start: 0.7349 (mttt) cc_final: 0.6792 (mtmt) REVERT: A 360 LYS cc_start: 0.8088 (tttt) cc_final: 0.7621 (ttmm) REVERT: A 430 THR cc_start: 0.8067 (m) cc_final: 0.7506 (p) REVERT: A 455 GLU cc_start: 0.7531 (tt0) cc_final: 0.6994 (tm-30) REVERT: A 487 LYS cc_start: 0.7621 (mtmm) cc_final: 0.7270 (mtmm) REVERT: A 524 VAL cc_start: 0.8385 (t) cc_final: 0.8136 (p) REVERT: A 584 HIS cc_start: 0.6172 (m90) cc_final: 0.5876 (m170) REVERT: A 593 LYS cc_start: 0.6800 (tptp) cc_final: 0.6298 (tptp) outliers start: 25 outliers final: 17 residues processed: 261 average time/residue: 0.3349 time to fit residues: 121.3764 Evaluate side-chains 262 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 244 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 538 GLN Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain A residue 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 261 LYS Chi-restraints excluded: chain A residue 311 CYS Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 515 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 19 optimal weight: 0.0980 chunk 52 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 109 optimal weight: 0.0370 chunk 11 optimal weight: 0.7980 chunk 97 optimal weight: 0.3980 chunk 7 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 overall best weight: 0.3658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 329 GLN B 446 GLN ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.146874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.124344 restraints weight = 13440.068| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 2.64 r_work: 0.3478 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.4959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9420 Z= 0.248 Angle : 0.650 9.398 12769 Z= 0.331 Chirality : 0.049 0.429 1425 Planarity : 0.004 0.042 1679 Dihedral : 7.561 79.175 1433 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 2.93 % Allowed : 14.24 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.23), residues: 1170 helix: -2.17 (0.67), residues: 53 sheet: -2.36 (0.53), residues: 82 loop : -1.77 (0.18), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 49 HIS 0.005 0.001 HIS A 507 PHE 0.044 0.002 PHE A 549 TYR 0.026 0.002 TYR B 409 ARG 0.008 0.001 ARG B 47 *********************** 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 285 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 255 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 30 ASP cc_start: 0.7995 (t70) cc_final: 0.7401 (t0) REVERT: B 75 GLN cc_start: 0.7972 (pt0) cc_final: 0.7601 (pt0) REVERT: B 93 GLN cc_start: 0.7420 (pp30) cc_final: 0.7199 (pp30) REVERT: B 112 TYR cc_start: 0.7437 (m-80) cc_final: 0.7199 (m-80) REVERT: B 138 ARG cc_start: 0.7302 (mmm-85) cc_final: 0.6893 (mmm160) REVERT: B 139 GLU cc_start: 0.6992 (mp0) cc_final: 0.6621 (mp0) REVERT: B 147 GLU cc_start: 0.7298 (tp30) cc_final: 0.6992 (tp30) REVERT: B 228 LYS cc_start: 0.7957 (mtpt) cc_final: 0.7657 (mtpt) REVERT: B 261 SER cc_start: 0.8008 (m) cc_final: 0.7672 (p) REVERT: B 268 CYS cc_start: 0.6206 (t) cc_final: 0.5978 (t) REVERT: B 284 ASN cc_start: 0.8164 (t0) cc_final: 0.7761 (t0) REVERT: B 405 GLU cc_start: 0.7585 (tt0) cc_final: 0.7278 (tt0) REVERT: B 421 ASP cc_start: 0.7103 (p0) cc_final: 0.6748 (p0) REVERT: B 438 ASN cc_start: 0.7735 (m-40) cc_final: 0.7448 (m110) REVERT: B 441 TYR cc_start: 0.8484 (m-80) cc_final: 0.8163 (m-80) REVERT: B 459 ARG cc_start: 0.8022 (ptt90) cc_final: 0.7769 (ptt90) REVERT: B 460 GLU cc_start: 0.7875 (tt0) cc_final: 0.7468 (tp30) REVERT: B 538 GLN cc_start: 0.6757 (OUTLIER) cc_final: 0.6504 (pm20) REVERT: B 553 GLU cc_start: 0.6399 (mt-10) cc_final: 0.6054 (mt-10) REVERT: A 46 ASP cc_start: 0.7941 (t70) cc_final: 0.7435 (t70) REVERT: A 133 LYS cc_start: 0.7385 (mttt) cc_final: 0.7167 (ttmm) REVERT: A 142 GLU cc_start: 0.7667 (tt0) cc_final: 0.7415 (tt0) REVERT: A 148 VAL cc_start: 0.8467 (t) cc_final: 0.8108 (m) REVERT: A 245 GLU cc_start: 0.7482 (tp30) cc_final: 0.7064 (tp30) REVERT: A 263 THR cc_start: 0.8047 (m) cc_final: 0.7720 (p) REVERT: A 292 VAL cc_start: 0.8171 (m) cc_final: 0.7825 (p) REVERT: A 294 LYS cc_start: 0.8247 (tttt) cc_final: 0.8002 (tttt) REVERT: A 308 VAL cc_start: 0.8238 (p) cc_final: 0.8000 (m) REVERT: A 325 LYS cc_start: 0.7360 (mttt) cc_final: 0.6820 (mtmt) REVERT: A 357 LYS cc_start: 0.8420 (ptpt) cc_final: 0.8112 (pptt) REVERT: A 430 THR cc_start: 0.8109 (m) cc_final: 0.7578 (p) REVERT: A 455 GLU cc_start: 0.7482 (tt0) cc_final: 0.7181 (tt0) REVERT: A 487 LYS cc_start: 0.7806 (mtmm) cc_final: 0.7507 (mtmm) REVERT: A 489 LYS cc_start: 0.8120 (tttt) cc_final: 0.7585 (ttmm) REVERT: A 584 HIS cc_start: 0.5996 (m90) cc_final: 0.5780 (m170) REVERT: A 593 LYS cc_start: 0.6789 (tptp) cc_final: 0.6261 (tptp) outliers start: 30 outliers final: 22 residues processed: 268 average time/residue: 0.2562 time to fit residues: 91.0503 Evaluate side-chains 270 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 247 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 267 HIS 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 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 293 LYS Chi-restraints excluded: chain A residue 307 CYS 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 515 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 4 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 78 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 59 optimal weight: 0.7980 chunk 39 optimal weight: 0.3980 chunk 45 optimal weight: 0.8980 chunk 86 optimal weight: 0.6980 chunk 97 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 329 GLN B 446 GLN ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 512 HIS B 530 ASN A 153 ASN A 163 GLN A 196 ASN A 233 HIS ** A 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.144459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.121821 restraints weight = 13526.836| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.76 r_work: 0.3430 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.5434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 9420 Z= 0.335 Angle : 0.710 9.352 12769 Z= 0.362 Chirality : 0.052 0.430 1425 Planarity : 0.004 0.044 1679 Dihedral : 7.951 84.306 1433 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 3.02 % Allowed : 15.12 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.23), residues: 1170 helix: -1.98 (0.65), residues: 53 sheet: -2.58 (0.49), residues: 82 loop : -1.78 (0.18), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C 49 HIS 0.008 0.001 HIS A 233 PHE 0.047 0.002 PHE A 549 TYR 0.029 0.002 TYR B 409 ARG 0.009 0.001 ARG B 47 *********************** 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 294 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 263 time to evaluate : 1.054 Fit side-chains revert: symmetry clash REVERT: B 24 GLN cc_start: 0.6737 (pp30) cc_final: 0.6421 (pp30) REVERT: B 30 ASP cc_start: 0.8110 (t70) cc_final: 0.7497 (t0) REVERT: B 93 GLN cc_start: 0.7436 (pp30) cc_final: 0.7214 (pp30) REVERT: B 112 TYR cc_start: 0.7577 (m-80) cc_final: 0.7357 (m-80) REVERT: B 138 ARG cc_start: 0.7346 (mmm-85) cc_final: 0.6958 (mmm160) REVERT: B 139 GLU cc_start: 0.7177 (mp0) cc_final: 0.6767 (mp0) REVERT: B 147 GLU cc_start: 0.7284 (tp30) cc_final: 0.6936 (tp30) REVERT: B 261 SER cc_start: 0.8122 (m) cc_final: 0.7792 (p) REVERT: B 268 CYS cc_start: 0.6330 (t) cc_final: 0.6107 (t) REVERT: B 282 MET cc_start: 0.7651 (mtm) cc_final: 0.7438 (mtm) REVERT: B 284 ASN cc_start: 0.8296 (t0) cc_final: 0.7895 (t0) REVERT: B 297 THR cc_start: 0.8471 (m) cc_final: 0.8199 (p) REVERT: B 405 GLU cc_start: 0.7545 (tt0) cc_final: 0.7186 (tt0) REVERT: B 421 ASP cc_start: 0.7207 (p0) cc_final: 0.6809 (p0) REVERT: B 441 TYR cc_start: 0.8501 (m-80) cc_final: 0.8240 (m-80) REVERT: B 460 GLU cc_start: 0.7911 (tt0) cc_final: 0.7436 (tp30) REVERT: B 533 GLN cc_start: 0.4950 (mp10) cc_final: 0.4509 (pm20) REVERT: B 553 GLU cc_start: 0.6365 (mt-10) cc_final: 0.5986 (mt-10) REVERT: A 46 ASP cc_start: 0.7973 (t70) cc_final: 0.7472 (t70) REVERT: A 142 GLU cc_start: 0.7662 (tt0) cc_final: 0.7292 (tt0) REVERT: A 148 VAL cc_start: 0.8555 (t) cc_final: 0.8171 (m) REVERT: A 158 ASN cc_start: 0.7180 (m110) cc_final: 0.6979 (m110) REVERT: A 166 ASP cc_start: 0.7893 (t70) cc_final: 0.7572 (t0) REVERT: A 198 SER cc_start: 0.8270 (m) cc_final: 0.7460 (p) REVERT: A 212 LYS cc_start: 0.8171 (tttt) cc_final: 0.7928 (tttt) REVERT: A 222 ARG cc_start: 0.7890 (ttm-80) cc_final: 0.7664 (ttm-80) REVERT: A 245 GLU cc_start: 0.7531 (tp30) cc_final: 0.7128 (tp30) REVERT: A 263 THR cc_start: 0.8007 (m) cc_final: 0.7690 (p) REVERT: A 292 VAL cc_start: 0.8127 (m) cc_final: 0.7804 (p) REVERT: A 294 LYS cc_start: 0.8254 (tttt) cc_final: 0.7997 (tttt) REVERT: A 308 VAL cc_start: 0.8238 (p) cc_final: 0.8009 (m) REVERT: A 325 LYS cc_start: 0.7447 (mttt) cc_final: 0.6791 (mtmt) REVERT: A 357 LYS cc_start: 0.8538 (ptpt) cc_final: 0.8182 (pptt) REVERT: A 430 THR cc_start: 0.8137 (m) cc_final: 0.7595 (p) REVERT: A 455 GLU cc_start: 0.7531 (tt0) cc_final: 0.7018 (tm-30) REVERT: A 489 LYS cc_start: 0.8214 (tttt) cc_final: 0.7588 (ttmm) REVERT: A 593 LYS cc_start: 0.6827 (tptp) cc_final: 0.6544 (tptp) outliers start: 31 outliers final: 22 residues processed: 274 average time/residue: 0.2526 time to fit residues: 92.1468 Evaluate side-chains 276 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 254 time to evaluate : 0.985 ------------------------------------------------------------------------------- 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 198 MET Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 538 GLN Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 264 CYS Chi-restraints excluded: chain A residue 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 519 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 14 optimal weight: 0.5980 chunk 112 optimal weight: 0.3980 chunk 106 optimal weight: 0.5980 chunk 95 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 92 optimal weight: 0.4980 chunk 8 optimal weight: 0.0980 chunk 35 optimal weight: 0.0050 chunk 23 optimal weight: 0.8980 chunk 77 optimal weight: 0.0470 overall best weight: 0.2092 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 329 GLN B 446 GLN ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 530 ASN ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 GLN A 196 ASN A 233 HIS A 444 ASN ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.146064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.123891 restraints weight = 13354.428| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 2.75 r_work: 0.3464 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.5435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9420 Z= 0.200 Angle : 0.652 9.415 12769 Z= 0.330 Chirality : 0.048 0.420 1425 Planarity : 0.004 0.043 1679 Dihedral : 7.506 76.972 1433 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 2.24 % Allowed : 16.29 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.23), residues: 1170 helix: -2.18 (0.65), residues: 53 sheet: -2.48 (0.52), residues: 82 loop : -1.68 (0.19), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 49 HIS 0.008 0.001 HIS A 233 PHE 0.041 0.001 PHE A 549 TYR 0.026 0.002 TYR B 409 ARG 0.007 0.001 ARG B 47 *********************** 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 270 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 247 time to evaluate : 1.271 Fit side-chains revert: symmetry clash REVERT: B 24 GLN cc_start: 0.6667 (pp30) cc_final: 0.6310 (pp30) REVERT: B 30 ASP cc_start: 0.8058 (t70) cc_final: 0.7421 (t0) REVERT: B 67 THR cc_start: 0.8541 (m) cc_final: 0.8320 (t) REVERT: B 75 GLN cc_start: 0.8016 (pt0) cc_final: 0.7636 (pt0) REVERT: B 93 GLN cc_start: 0.7380 (pp30) cc_final: 0.7130 (pp30) REVERT: B 138 ARG cc_start: 0.7335 (mmm-85) cc_final: 0.6993 (mmm160) REVERT: B 139 GLU cc_start: 0.7160 (mp0) cc_final: 0.6715 (mp0) REVERT: B 147 GLU cc_start: 0.7257 (tp30) cc_final: 0.6931 (tp30) REVERT: B 268 CYS cc_start: 0.6198 (t) cc_final: 0.5981 (t) REVERT: B 284 ASN cc_start: 0.8309 (t0) cc_final: 0.7903 (t0) REVERT: B 297 THR cc_start: 0.8439 (m) cc_final: 0.8217 (p) REVERT: B 405 GLU cc_start: 0.7598 (tt0) cc_final: 0.7271 (tt0) REVERT: B 421 ASP cc_start: 0.7239 (p0) cc_final: 0.6849 (p0) REVERT: B 441 TYR cc_start: 0.8467 (m-80) cc_final: 0.8150 (m-80) REVERT: B 460 GLU cc_start: 0.7905 (tt0) cc_final: 0.7426 (tp30) REVERT: B 501 GLU cc_start: 0.7066 (mm-30) cc_final: 0.6710 (mm-30) REVERT: B 538 GLN cc_start: 0.6673 (OUTLIER) cc_final: 0.6429 (pm20) REVERT: B 553 GLU cc_start: 0.6307 (mt-10) cc_final: 0.5944 (mt-10) REVERT: B 561 LEU cc_start: 0.7388 (mt) cc_final: 0.7162 (mt) REVERT: A 46 ASP cc_start: 0.7913 (t70) cc_final: 0.7443 (t70) REVERT: A 142 GLU cc_start: 0.7674 (tt0) cc_final: 0.7432 (tt0) REVERT: A 148 VAL cc_start: 0.8453 (t) cc_final: 0.8110 (m) REVERT: A 158 ASN cc_start: 0.7143 (m110) cc_final: 0.6921 (m110) REVERT: A 166 ASP cc_start: 0.7851 (t70) cc_final: 0.7548 (t0) REVERT: A 198 SER cc_start: 0.8356 (m) cc_final: 0.7496 (p) REVERT: A 212 LYS cc_start: 0.7966 (tttt) cc_final: 0.7455 (ttpt) REVERT: A 222 ARG cc_start: 0.7878 (ttm-80) cc_final: 0.7493 (ttm-80) REVERT: A 245 GLU cc_start: 0.7499 (tp30) cc_final: 0.6993 (tp30) REVERT: A 263 THR cc_start: 0.8047 (m) cc_final: 0.7779 (p) REVERT: A 292 VAL cc_start: 0.8091 (m) cc_final: 0.7760 (p) REVERT: A 294 LYS cc_start: 0.8212 (tttt) cc_final: 0.7968 (tttt) REVERT: A 308 VAL cc_start: 0.8148 (p) cc_final: 0.7929 (m) REVERT: A 318 MET cc_start: 0.7148 (tpp) cc_final: 0.6791 (tpp) REVERT: A 325 LYS cc_start: 0.7332 (mttt) cc_final: 0.6828 (mtmt) REVERT: A 430 THR cc_start: 0.8127 (m) cc_final: 0.7590 (p) REVERT: A 455 GLU cc_start: 0.7529 (tt0) cc_final: 0.7004 (tm-30) REVERT: A 489 LYS cc_start: 0.8206 (tttt) cc_final: 0.7582 (ttmm) REVERT: A 593 LYS cc_start: 0.6816 (tptp) cc_final: 0.6505 (tptp) outliers start: 23 outliers final: 17 residues processed: 256 average time/residue: 0.2624 time to fit residues: 89.1181 Evaluate side-chains 254 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 236 time to evaluate : 0.925 ------------------------------------------------------------------------------- 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 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 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 480 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 89 optimal weight: 1.9990 chunk 79 optimal weight: 0.0980 chunk 67 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 63 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 0 optimal weight: 0.9980 chunk 83 optimal weight: 0.0470 chunk 39 optimal weight: 0.8980 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 329 GLN ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 530 ASN A 83 GLN A 433 HIS ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.144394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.121820 restraints weight = 13505.654| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.77 r_work: 0.3428 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.5678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9420 Z= 0.296 Angle : 0.692 9.375 12769 Z= 0.352 Chirality : 0.051 0.418 1425 Planarity : 0.004 0.043 1679 Dihedral : 7.661 78.665 1433 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 2.15 % Allowed : 16.59 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.23), residues: 1170 helix: -2.32 (0.60), residues: 60 sheet: -2.59 (0.53), residues: 72 loop : -1.73 (0.18), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C 49 HIS 0.006 0.001 HIS A 559 PHE 0.023 0.002 PHE A 549 TYR 0.032 0.002 TYR B 112 ARG 0.008 0.001 ARG B 47 ********************** 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 267 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 245 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 24 GLN cc_start: 0.6668 (pp30) cc_final: 0.6357 (pp30) REVERT: B 30 ASP cc_start: 0.8129 (t70) cc_final: 0.7518 (t0) REVERT: B 67 THR cc_start: 0.8598 (m) cc_final: 0.8383 (t) REVERT: B 138 ARG cc_start: 0.7330 (mmm-85) cc_final: 0.6900 (mmm160) REVERT: B 139 GLU cc_start: 0.7187 (mp0) cc_final: 0.6810 (mp0) REVERT: B 147 GLU cc_start: 0.7242 (tp30) cc_final: 0.6934 (tp30) REVERT: B 268 CYS cc_start: 0.6415 (t) cc_final: 0.6186 (t) REVERT: B 284 ASN cc_start: 0.8348 (t0) cc_final: 0.7962 (t0) REVERT: B 297 THR cc_start: 0.8533 (m) cc_final: 0.8294 (p) REVERT: B 321 GLU cc_start: 0.6468 (tt0) cc_final: 0.6173 (tt0) REVERT: B 405 GLU cc_start: 0.7483 (tt0) cc_final: 0.7167 (tt0) REVERT: B 421 ASP cc_start: 0.7218 (p0) cc_final: 0.6805 (p0) REVERT: B 441 TYR cc_start: 0.8479 (m-80) cc_final: 0.8211 (m-80) REVERT: B 460 GLU cc_start: 0.7913 (tt0) cc_final: 0.7414 (tp30) REVERT: B 501 GLU cc_start: 0.7100 (mm-30) cc_final: 0.6763 (mm-30) REVERT: B 533 GLN cc_start: 0.4813 (mp10) cc_final: 0.4273 (pm20) REVERT: B 553 GLU cc_start: 0.6304 (mt-10) cc_final: 0.5941 (mt-10) REVERT: A 28 LYS cc_start: 0.7992 (mmmm) cc_final: 0.7792 (mmtt) REVERT: A 46 ASP cc_start: 0.7912 (t70) cc_final: 0.7424 (t70) REVERT: A 142 GLU cc_start: 0.7653 (tt0) cc_final: 0.7297 (tt0) REVERT: A 148 VAL cc_start: 0.8506 (t) cc_final: 0.8137 (m) REVERT: A 158 ASN cc_start: 0.7114 (m110) cc_final: 0.6729 (m110) REVERT: A 166 ASP cc_start: 0.7882 (t70) cc_final: 0.7554 (t0) REVERT: A 198 SER cc_start: 0.8355 (m) cc_final: 0.7518 (p) REVERT: A 245 GLU cc_start: 0.7505 (tp30) cc_final: 0.7067 (tp30) REVERT: A 263 THR cc_start: 0.8087 (m) cc_final: 0.7835 (p) REVERT: A 292 VAL cc_start: 0.8123 (m) cc_final: 0.7807 (p) REVERT: A 294 LYS cc_start: 0.8200 (tttt) cc_final: 0.7892 (ptmm) REVERT: A 308 VAL cc_start: 0.8174 (p) cc_final: 0.7949 (m) REVERT: A 318 MET cc_start: 0.7173 (tpp) cc_final: 0.6871 (tpp) REVERT: A 325 LYS cc_start: 0.7399 (mttt) cc_final: 0.6906 (mtmt) REVERT: A 399 LYS cc_start: 0.8134 (ttmm) cc_final: 0.7751 (mtpp) REVERT: A 430 THR cc_start: 0.8162 (m) cc_final: 0.7613 (p) REVERT: A 455 GLU cc_start: 0.7522 (tt0) cc_final: 0.7003 (tm-30) REVERT: A 478 LYS cc_start: 0.8390 (mmmt) cc_final: 0.8015 (mmmt) REVERT: A 559 HIS cc_start: 0.6248 (m-70) cc_final: 0.5975 (m-70) REVERT: A 584 HIS cc_start: 0.6015 (m90) cc_final: 0.5751 (m170) REVERT: A 593 LYS cc_start: 0.6842 (tptp) cc_final: 0.6242 (tptp) outliers start: 22 outliers final: 19 residues processed: 252 average time/residue: 0.2447 time to fit residues: 82.8550 Evaluate side-chains 261 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 242 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 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 84 GLU Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 264 CYS Chi-restraints excluded: chain A residue 307 CYS Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 462 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 86 optimal weight: 0.1980 chunk 31 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 39 optimal weight: 0.0070 chunk 43 optimal weight: 0.9990 chunk 110 optimal weight: 0.0060 chunk 42 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 chunk 1 optimal weight: 0.0770 chunk 57 optimal weight: 0.9990 overall best weight: 0.1972 ------------------------------------------------------------------------------- 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 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 530 ASN ** A 486 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 = 0.3903 r_free = 0.3903 target = 0.146090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.123728 restraints weight = 13387.197| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.75 r_work: 0.3460 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.5675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9420 Z= 0.201 Angle : 0.661 9.594 12769 Z= 0.335 Chirality : 0.048 0.412 1425 Planarity : 0.004 0.042 1679 Dihedral : 7.327 71.709 1433 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 2.15 % Allowed : 17.76 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.23), residues: 1170 helix: -2.23 (0.65), residues: 54 sheet: -2.55 (0.55), residues: 70 loop : -1.65 (0.18), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 49 HIS 0.004 0.001 HIS A 559 PHE 0.021 0.001 PHE A 549 TYR 0.026 0.002 TYR B 409 ARG 0.009 0.001 ARG B 47 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5267.80 seconds wall clock time: 92 minutes 55.55 seconds (5575.55 seconds total)