Starting phenix.real_space_refine on Sun Jun 8 09:00:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hgo_34744/06_2025/8hgo_34744.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hgo_34744/06_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_34744/06_2025/8hgo_34744.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hgo_34744/06_2025/8hgo_34744.map" model { file = "/net/cci-nas-00/data/ceres_data/8hgo_34744/06_2025/8hgo_34744.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hgo_34744/06_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 6.42, per 1000 atoms: 0.70 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: 2.40 Conformation dependent library (CDL) restraints added in 1.2 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: 1.16 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: 2.43 Time building geometry restraints manager: 2.81 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: 4.410 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 24.250 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6544 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 9475 Z= 0.184 Angle : 0.733 10.795 12887 Z= 0.401 Chirality : 0.054 0.380 1425 Planarity : 0.007 0.053 1679 Dihedral : 10.134 112.989 3621 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.03 % Favored : 91.79 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 Details of bonding type rmsd link_NAG-ASN : bond 0.00860 ( 4) link_NAG-ASN : angle 4.09200 ( 12) link_BETA1-4 : bond 0.00375 ( 2) link_BETA1-4 : angle 1.89672 ( 6) link_ALPHA1-3 : bond 0.01436 ( 1) link_ALPHA1-3 : angle 2.81919 ( 3) hydrogen bonds : bond 0.23774 ( 97) hydrogen bonds : angle 7.20955 ( 186) SS BOND : bond 0.00282 ( 47) SS BOND : angle 1.04892 ( 94) link_BETA1-3 : bond 0.01341 ( 1) link_BETA1-3 : angle 6.31483 ( 3) covalent geometry : bond 0.00354 ( 9420) covalent geometry : angle 0.71132 (12769) *********************** 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 : 1.314 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: 0.2906 time to fit residues: 109.0408 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 : 1.021 ------------------------------------------------------------------------------- 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 9475 Z= 0.174 Angle : 0.726 9.966 12887 Z= 0.362 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00254 ( 4) link_NAG-ASN : angle 2.85217 ( 12) link_BETA1-4 : bond 0.00091 ( 2) link_BETA1-4 : angle 1.08976 ( 6) link_ALPHA1-3 : bond 0.01587 ( 1) link_ALPHA1-3 : angle 2.44807 ( 3) hydrogen bonds : bond 0.03647 ( 97) hydrogen bonds : angle 6.05467 ( 186) SS BOND : bond 0.00341 ( 47) SS BOND : angle 1.95766 ( 94) link_BETA1-3 : bond 0.00552 ( 1) link_BETA1-3 : angle 4.57470 ( 3) covalent geometry : bond 0.00394 ( 9420) covalent geometry : angle 0.69901 (12769) *********************** 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 : 1.080 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: 0.2868 time to fit residues: 105.3513 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 : 1.034 ------------------------------------------------------------------------------- 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 9475 Z= 0.113 Angle : 0.628 9.740 12887 Z= 0.315 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00398 ( 4) link_NAG-ASN : angle 2.45953 ( 12) link_BETA1-4 : bond 0.00214 ( 2) link_BETA1-4 : angle 1.11935 ( 6) link_ALPHA1-3 : bond 0.01844 ( 1) link_ALPHA1-3 : angle 2.26336 ( 3) hydrogen bonds : bond 0.02997 ( 97) hydrogen bonds : angle 5.72331 ( 186) SS BOND : bond 0.00281 ( 47) SS BOND : angle 1.69345 ( 94) link_BETA1-3 : bond 0.00712 ( 1) link_BETA1-3 : angle 3.58495 ( 3) covalent geometry : bond 0.00260 ( 9420) covalent geometry : angle 0.60533 (12769) *********************** 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 : 0.947 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: 0.2636 time to fit residues: 89.9698 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 : 0.934 ------------------------------------------------------------------------------- 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: 0.3980 chunk 62 optimal weight: 0.8980 chunk 90 optimal weight: 0.1980 chunk 49 optimal weight: 0.1980 chunk 55 optimal weight: 4.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- 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 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 559 HIS A 493 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.150520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.127459 restraints weight = 13383.184| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.78 r_work: 0.3520 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.3927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9475 Z= 0.187 Angle : 0.701 15.072 12887 Z= 0.346 Chirality : 0.054 0.656 1425 Planarity : 0.005 0.045 1679 Dihedral : 7.818 80.275 1433 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 2.44 % Allowed : 9.37 % Favored : 88.20 % 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: -2.80 (0.22), residues: 1170 helix: -2.82 (0.58), residues: 59 sheet: -2.26 (0.53), residues: 82 loop : -1.96 (0.18), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 49 HIS 0.008 0.001 HIS A 507 PHE 0.036 0.002 PHE A 549 TYR 0.027 0.002 TYR B 163 ARG 0.006 0.001 ARG B 545 Details of bonding type rmsd link_NAG-ASN : bond 0.00862 ( 4) link_NAG-ASN : angle 5.34596 ( 12) link_BETA1-4 : bond 0.00310 ( 2) link_BETA1-4 : angle 1.02587 ( 6) link_ALPHA1-3 : bond 0.01994 ( 1) link_ALPHA1-3 : angle 2.64959 ( 3) hydrogen bonds : bond 0.03266 ( 97) hydrogen bonds : angle 5.83380 ( 186) SS BOND : bond 0.00381 ( 47) SS BOND : angle 1.56623 ( 94) link_BETA1-3 : bond 0.00575 ( 1) link_BETA1-3 : angle 3.04764 ( 3) covalent geometry : bond 0.00419 ( 9420) covalent geometry : angle 0.66820 (12769) *********************** 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 283 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 258 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 GLN cc_start: 0.8033 (pt0) cc_final: 0.7741 (pt0) REVERT: B 93 GLN cc_start: 0.7309 (pp30) cc_final: 0.6955 (pp30) REVERT: B 112 TYR cc_start: 0.7440 (m-80) cc_final: 0.7160 (m-80) REVERT: B 139 GLU cc_start: 0.7004 (mp0) cc_final: 0.6606 (mp0) REVERT: B 147 GLU cc_start: 0.7283 (tp30) cc_final: 0.6791 (tp30) REVERT: B 164 GLN cc_start: 0.7467 (pm20) cc_final: 0.6837 (pm20) REVERT: B 228 LYS cc_start: 0.7898 (mtpt) cc_final: 0.7513 (mtmm) REVERT: B 268 CYS cc_start: 0.6152 (t) cc_final: 0.5831 (t) REVERT: B 284 ASN cc_start: 0.7870 (t0) cc_final: 0.7462 (t0) REVERT: B 405 GLU cc_start: 0.7625 (tt0) cc_final: 0.7268 (tt0) REVERT: B 411 TYR cc_start: 0.8307 (t80) cc_final: 0.8068 (t80) REVERT: B 421 ASP cc_start: 0.7236 (p0) cc_final: 0.6832 (p0) REVERT: B 438 ASN cc_start: 0.7708 (m-40) cc_final: 0.7456 (m110) REVERT: B 441 TYR cc_start: 0.8530 (m-80) cc_final: 0.8246 (m-80) REVERT: B 460 GLU cc_start: 0.7679 (tt0) cc_final: 0.7348 (tt0) REVERT: B 538 GLN cc_start: 0.6680 (OUTLIER) cc_final: 0.6428 (pm20) REVERT: B 553 GLU cc_start: 0.6236 (mt-10) cc_final: 0.5955 (mt-10) REVERT: B 568 GLN cc_start: 0.7016 (tp40) cc_final: 0.6767 (tm-30) REVERT: A 46 ASP cc_start: 0.7995 (t70) cc_final: 0.7509 (t70) REVERT: A 133 LYS cc_start: 0.7338 (mttt) cc_final: 0.7098 (ttmm) REVERT: A 148 VAL cc_start: 0.8476 (t) cc_final: 0.8066 (m) REVERT: A 198 SER cc_start: 0.8160 (m) cc_final: 0.7438 (p) REVERT: A 255 ARG cc_start: 0.6979 (ttt-90) cc_final: 0.6648 (tmt-80) REVERT: A 263 THR cc_start: 0.8060 (m) cc_final: 0.7665 (p) REVERT: A 268 MET cc_start: 0.6568 (mtm) cc_final: 0.6044 (mtm) REVERT: A 277 MET cc_start: 0.5765 (mtt) cc_final: 0.5360 (mtt) REVERT: A 292 VAL cc_start: 0.8196 (m) cc_final: 0.7823 (p) REVERT: A 294 LYS cc_start: 0.8300 (tttt) cc_final: 0.8051 (tttt) REVERT: A 303 ASP cc_start: 0.7530 (p0) cc_final: 0.7268 (p0) REVERT: A 316 TYR cc_start: 0.6800 (t80) cc_final: 0.6423 (t80) REVERT: A 318 MET cc_start: 0.6875 (tpp) cc_final: 0.6554 (tpp) REVERT: A 325 LYS cc_start: 0.7727 (mttt) cc_final: 0.7054 (mtmt) REVERT: A 327 LYS cc_start: 0.7739 (ptpp) cc_final: 0.7178 (ptpp) REVERT: A 347 ASP cc_start: 0.7269 (t0) cc_final: 0.6688 (t0) REVERT: A 357 LYS cc_start: 0.8334 (ptpt) cc_final: 0.7981 (pptt) REVERT: A 391 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7641 (mm-30) REVERT: A 430 THR cc_start: 0.8114 (m) cc_final: 0.7507 (p) REVERT: A 455 GLU cc_start: 0.7608 (tt0) cc_final: 0.7182 (tt0) REVERT: A 487 LYS cc_start: 0.7469 (mtmm) cc_final: 0.7158 (mtmm) REVERT: A 489 LYS cc_start: 0.8120 (ttmm) cc_final: 0.7598 (ttmm) REVERT: A 549 PHE cc_start: 0.7135 (p90) cc_final: 0.6836 (p90) REVERT: A 559 HIS cc_start: 0.6242 (OUTLIER) cc_final: 0.5790 (m-70) REVERT: A 584 HIS cc_start: 0.6269 (m90) cc_final: 0.5922 (m170) REVERT: A 593 LYS cc_start: 0.6787 (tptp) cc_final: 0.6302 (tptp) outliers start: 25 outliers final: 16 residues processed: 265 average time/residue: 0.2549 time to fit residues: 88.8361 Evaluate side-chains 261 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 243 time to evaluate : 1.091 ------------------------------------------------------------------------------- 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 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 425 ILE Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 515 CYS Chi-restraints excluded: chain A residue 559 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 61 optimal weight: 0.3980 chunk 6 optimal weight: 0.3980 chunk 18 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 93 optimal weight: 0.6980 chunk 73 optimal weight: 0.7980 chunk 97 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 54 optimal weight: 0.4980 chunk 58 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 267 HIS B 329 GLN ** B 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 491 GLN ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 233 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.148228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.125305 restraints weight = 13416.947| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 2.77 r_work: 0.3477 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.4478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9475 Z= 0.203 Angle : 0.708 17.440 12887 Z= 0.352 Chirality : 0.051 0.464 1425 Planarity : 0.004 0.042 1679 Dihedral : 7.715 79.366 1433 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 2.83 % Allowed : 11.12 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.69 (0.22), residues: 1170 helix: -2.77 (0.57), residues: 59 sheet: -2.33 (0.53), residues: 82 loop : -1.86 (0.18), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 49 HIS 0.006 0.001 HIS A 507 PHE 0.027 0.002 PHE A 549 TYR 0.020 0.002 TYR B 163 ARG 0.007 0.001 ARG B 47 Details of bonding type rmsd link_NAG-ASN : bond 0.01413 ( 4) link_NAG-ASN : angle 6.37478 ( 12) link_BETA1-4 : bond 0.00093 ( 2) link_BETA1-4 : angle 0.81358 ( 6) link_ALPHA1-3 : bond 0.01557 ( 1) link_ALPHA1-3 : angle 2.50202 ( 3) hydrogen bonds : bond 0.03269 ( 97) hydrogen bonds : angle 6.04167 ( 186) SS BOND : bond 0.00438 ( 47) SS BOND : angle 1.78475 ( 94) link_BETA1-3 : bond 0.00478 ( 1) link_BETA1-3 : angle 2.80959 ( 3) covalent geometry : bond 0.00458 ( 9420) covalent geometry : angle 0.66361 (12769) *********************** 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 290 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 261 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 30 ASP cc_start: 0.8006 (t70) cc_final: 0.7376 (t0) REVERT: B 75 GLN cc_start: 0.8129 (pt0) cc_final: 0.7552 (pt0) REVERT: B 112 TYR cc_start: 0.7494 (m-80) cc_final: 0.7277 (m-80) REVERT: B 138 ARG cc_start: 0.7254 (mmm-85) cc_final: 0.6905 (mmm160) REVERT: B 139 GLU cc_start: 0.7049 (mp0) cc_final: 0.6751 (mp0) REVERT: B 147 GLU cc_start: 0.7308 (tp30) cc_final: 0.6808 (tp30) REVERT: B 228 LYS cc_start: 0.7960 (mtpt) cc_final: 0.7677 (mtpt) REVERT: B 261 SER cc_start: 0.7981 (m) cc_final: 0.7631 (p) REVERT: B 268 CYS cc_start: 0.6442 (t) cc_final: 0.6206 (t) REVERT: B 284 ASN cc_start: 0.7981 (t0) cc_final: 0.7592 (t0) REVERT: B 405 GLU cc_start: 0.7663 (tt0) cc_final: 0.7321 (tt0) REVERT: B 421 ASP cc_start: 0.7034 (p0) cc_final: 0.6666 (p0) REVERT: B 438 ASN cc_start: 0.7709 (m-40) cc_final: 0.7471 (m110) REVERT: B 441 TYR cc_start: 0.8537 (m-80) cc_final: 0.8239 (m-80) REVERT: B 460 GLU cc_start: 0.7732 (tt0) cc_final: 0.7509 (tt0) REVERT: B 538 GLN cc_start: 0.6736 (OUTLIER) cc_final: 0.6484 (pm20) REVERT: B 553 GLU cc_start: 0.6368 (mt-10) cc_final: 0.6015 (mt-10) REVERT: B 568 GLN cc_start: 0.7045 (tp40) cc_final: 0.6775 (tm-30) REVERT: A 46 ASP cc_start: 0.7965 (t70) cc_final: 0.7463 (t70) REVERT: A 133 LYS cc_start: 0.7426 (mttt) cc_final: 0.7206 (ttmm) REVERT: A 142 GLU cc_start: 0.7705 (tt0) cc_final: 0.7184 (tp30) REVERT: A 148 VAL cc_start: 0.8484 (t) cc_final: 0.8108 (m) REVERT: A 198 SER cc_start: 0.8213 (m) cc_final: 0.7458 (p) REVERT: A 222 ARG cc_start: 0.7815 (ttm-80) cc_final: 0.7557 (ttm170) REVERT: A 263 THR cc_start: 0.8117 (m) cc_final: 0.7696 (p) REVERT: A 292 VAL cc_start: 0.8137 (m) cc_final: 0.7753 (p) REVERT: A 294 LYS cc_start: 0.8263 (tttt) cc_final: 0.7995 (tttt) REVERT: A 303 ASP cc_start: 0.7532 (p0) cc_final: 0.7300 (p0) REVERT: A 308 VAL cc_start: 0.8145 (p) cc_final: 0.7877 (m) REVERT: A 316 TYR cc_start: 0.6856 (t80) cc_final: 0.6495 (t80) REVERT: A 318 MET cc_start: 0.7020 (tpp) cc_final: 0.6727 (tpp) REVERT: A 325 LYS cc_start: 0.7714 (mttt) cc_final: 0.7027 (mtmt) REVERT: A 327 LYS cc_start: 0.7736 (ptpp) cc_final: 0.7304 (ptpp) REVERT: A 338 ASN cc_start: 0.7598 (m-40) cc_final: 0.7360 (t0) REVERT: A 347 ASP cc_start: 0.7320 (t0) cc_final: 0.6747 (t0) REVERT: A 358 HIS cc_start: 0.7909 (m90) cc_final: 0.7619 (m170) REVERT: A 391 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7644 (mm-30) REVERT: A 430 THR cc_start: 0.8054 (m) cc_final: 0.7487 (p) REVERT: A 455 GLU cc_start: 0.7543 (tt0) cc_final: 0.7032 (tm-30) REVERT: A 487 LYS cc_start: 0.7658 (mtmm) cc_final: 0.7374 (mtmm) REVERT: A 489 LYS cc_start: 0.8142 (ttmm) cc_final: 0.7631 (ttmm) REVERT: A 549 PHE cc_start: 0.7230 (p90) cc_final: 0.6919 (p90) REVERT: A 559 HIS cc_start: 0.6150 (OUTLIER) cc_final: 0.5708 (m-70) REVERT: A 584 HIS cc_start: 0.6188 (m90) cc_final: 0.5883 (m170) REVERT: A 593 LYS cc_start: 0.6821 (tptp) cc_final: 0.6338 (tptp) outliers start: 29 outliers final: 18 residues processed: 272 average time/residue: 0.2797 time to fit residues: 102.1509 Evaluate side-chains 267 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 247 time to evaluate : 1.262 ------------------------------------------------------------------------------- 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 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 293 LYS Chi-restraints excluded: chain A residue 336 VAL 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 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: 0.6980 chunk 101 optimal weight: 0.5980 chunk 68 optimal weight: 0.4980 chunk 33 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 48 HIS ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 329 GLN ** B 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 512 HIS B 527 GLN A 233 HIS A 444 ASN ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.144286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.121909 restraints weight = 13441.787| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.70 r_work: 0.3435 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.5174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 9475 Z= 0.254 Angle : 0.758 16.212 12887 Z= 0.379 Chirality : 0.053 0.438 1425 Planarity : 0.005 0.046 1679 Dihedral : 8.176 88.517 1433 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 3.32 % Allowed : 12.98 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -2.67 (0.22), residues: 1170 helix: -2.77 (0.57), residues: 59 sheet: -2.24 (0.56), residues: 74 loop : -1.87 (0.18), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 49 HIS 0.007 0.001 HIS A 507 PHE 0.027 0.002 PHE A 549 TYR 0.028 0.002 TYR B 409 ARG 0.008 0.001 ARG B 47 Details of bonding type rmsd link_NAG-ASN : bond 0.01178 ( 4) link_NAG-ASN : angle 6.01652 ( 12) link_BETA1-4 : bond 0.00098 ( 2) link_BETA1-4 : angle 0.75865 ( 6) link_ALPHA1-3 : bond 0.01319 ( 1) link_ALPHA1-3 : angle 2.50587 ( 3) hydrogen bonds : bond 0.03395 ( 97) hydrogen bonds : angle 6.28724 ( 186) SS BOND : bond 0.00477 ( 47) SS BOND : angle 1.88103 ( 94) link_BETA1-3 : bond 0.00296 ( 1) link_BETA1-3 : angle 2.67643 ( 3) covalent geometry : bond 0.00571 ( 9420) covalent geometry : angle 0.71859 (12769) *********************** 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 311 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 277 time to evaluate : 1.146 Fit side-chains revert: symmetry clash REVERT: B 24 GLN cc_start: 0.6793 (pp30) cc_final: 0.6441 (pp30) REVERT: B 30 ASP cc_start: 0.8070 (t70) cc_final: 0.7465 (t0) REVERT: B 54 GLN cc_start: 0.8025 (mm-40) cc_final: 0.7813 (mt0) REVERT: B 112 TYR cc_start: 0.7665 (m-80) cc_final: 0.7358 (m-80) REVERT: B 138 ARG cc_start: 0.7313 (mmm-85) cc_final: 0.6816 (mmm160) REVERT: B 139 GLU cc_start: 0.7099 (mp0) cc_final: 0.6739 (mp0) REVERT: B 228 LYS cc_start: 0.7991 (mtpt) cc_final: 0.7672 (mtpt) REVERT: B 261 SER cc_start: 0.8117 (m) cc_final: 0.7788 (p) REVERT: B 268 CYS cc_start: 0.6361 (t) cc_final: 0.6148 (t) REVERT: B 284 ASN cc_start: 0.8106 (t0) cc_final: 0.7598 (t0) REVERT: B 405 GLU cc_start: 0.7543 (tt0) cc_final: 0.7165 (tt0) REVERT: B 421 ASP cc_start: 0.7247 (p0) cc_final: 0.6842 (p0) REVERT: B 438 ASN cc_start: 0.7743 (m-40) cc_final: 0.7534 (m110) REVERT: B 441 TYR cc_start: 0.8519 (m-80) cc_final: 0.8248 (m-80) REVERT: B 450 ILE cc_start: 0.8292 (tt) cc_final: 0.8000 (pt) REVERT: B 460 GLU cc_start: 0.7823 (tt0) cc_final: 0.7455 (tt0) REVERT: B 553 GLU cc_start: 0.6427 (mt-10) cc_final: 0.6053 (mt-10) REVERT: B 568 GLN cc_start: 0.7191 (tp40) cc_final: 0.6969 (tm-30) REVERT: A 45 GLU cc_start: 0.7742 (mp0) cc_final: 0.7440 (mp0) REVERT: A 46 ASP cc_start: 0.7900 (t70) cc_final: 0.7391 (t70) REVERT: A 74 TYR cc_start: 0.8572 (m-10) cc_final: 0.8310 (m-80) REVERT: A 142 GLU cc_start: 0.7618 (tt0) cc_final: 0.7259 (tp30) REVERT: A 148 VAL cc_start: 0.8559 (t) cc_final: 0.8203 (m) REVERT: A 160 GLU cc_start: 0.8229 (pm20) cc_final: 0.7857 (pm20) REVERT: A 166 ASP cc_start: 0.7953 (t70) cc_final: 0.7402 (t0) REVERT: A 263 THR cc_start: 0.7998 (m) cc_final: 0.7686 (p) REVERT: A 268 MET cc_start: 0.6792 (mtm) cc_final: 0.6581 (mtm) REVERT: A 292 VAL cc_start: 0.8132 (m) cc_final: 0.7810 (p) REVERT: A 294 LYS cc_start: 0.8275 (tttt) cc_final: 0.8017 (tttt) REVERT: A 319 GLU cc_start: 0.7743 (pt0) cc_final: 0.7272 (tm-30) REVERT: A 325 LYS cc_start: 0.7310 (mttt) cc_final: 0.6750 (mtmt) REVERT: A 357 LYS cc_start: 0.8506 (ptpt) cc_final: 0.8305 (ptpt) REVERT: A 391 GLU cc_start: 0.8192 (mm-30) cc_final: 0.7898 (mm-30) REVERT: A 430 THR cc_start: 0.8133 (m) cc_final: 0.7644 (p) REVERT: A 455 GLU cc_start: 0.7527 (tt0) cc_final: 0.7048 (tm-30) REVERT: A 551 GLU cc_start: 0.7660 (tm-30) cc_final: 0.7072 (tm-30) REVERT: A 593 LYS cc_start: 0.6832 (tptp) cc_final: 0.6604 (tptp) outliers start: 34 outliers final: 24 residues processed: 293 average time/residue: 0.3114 time to fit residues: 120.5536 Evaluate side-chains 285 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 261 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 538 GLN Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 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 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 488 THR 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: 0.0170 chunk 52 optimal weight: 0.0980 chunk 47 optimal weight: 0.1980 chunk 109 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 32 optimal weight: 0.2980 chunk 75 optimal weight: 0.7980 overall best weight: 0.2418 ------------------------------------------------------------------------------- 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 233 HIS A 444 ASN ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 16 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.146055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.123516 restraints weight = 13389.371| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 2.75 r_work: 0.3460 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.5258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9475 Z= 0.142 Angle : 0.688 16.770 12887 Z= 0.342 Chirality : 0.049 0.429 1425 Planarity : 0.004 0.041 1679 Dihedral : 7.757 83.359 1433 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 2.54 % Allowed : 16.39 % Favored : 81.07 % 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: -2.56 (0.23), residues: 1170 helix: -2.35 (0.60), residues: 59 sheet: -2.54 (0.51), residues: 82 loop : -1.77 (0.18), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C 49 HIS 0.007 0.001 HIS A 233 PHE 0.009 0.001 PHE A 404 TYR 0.026 0.002 TYR B 409 ARG 0.007 0.001 ARG B 47 Details of bonding type rmsd link_NAG-ASN : bond 0.01270 ( 4) link_NAG-ASN : angle 6.04070 ( 12) link_BETA1-4 : bond 0.00193 ( 2) link_BETA1-4 : angle 0.84855 ( 6) link_ALPHA1-3 : bond 0.01733 ( 1) link_ALPHA1-3 : angle 2.44698 ( 3) hydrogen bonds : bond 0.02840 ( 97) hydrogen bonds : angle 5.88191 ( 186) SS BOND : bond 0.00416 ( 47) SS BOND : angle 1.67615 ( 94) link_BETA1-3 : bond 0.00733 ( 1) link_BETA1-3 : angle 2.63142 ( 3) covalent geometry : bond 0.00326 ( 9420) covalent geometry : angle 0.64780 (12769) *********************** 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 286 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 260 time to evaluate : 0.975 Fit side-chains revert: symmetry clash REVERT: B 30 ASP cc_start: 0.8006 (t70) cc_final: 0.7362 (t0) REVERT: B 75 GLN cc_start: 0.8047 (pt0) cc_final: 0.7687 (pt0) REVERT: B 112 TYR cc_start: 0.7485 (m-80) cc_final: 0.7207 (m-80) REVERT: B 138 ARG cc_start: 0.7318 (mmm-85) cc_final: 0.6975 (mmm160) REVERT: B 139 GLU cc_start: 0.7115 (mp0) cc_final: 0.6720 (mp0) REVERT: B 147 GLU cc_start: 0.7302 (tp30) cc_final: 0.6935 (tp30) REVERT: B 261 SER cc_start: 0.8070 (m) cc_final: 0.7745 (p) REVERT: B 268 CYS cc_start: 0.6208 (t) cc_final: 0.5995 (t) REVERT: B 284 ASN cc_start: 0.8190 (t0) cc_final: 0.7756 (t0) REVERT: B 405 GLU cc_start: 0.7586 (tt0) cc_final: 0.7241 (tt0) REVERT: B 421 ASP cc_start: 0.7190 (p0) cc_final: 0.6787 (p0) REVERT: B 438 ASN cc_start: 0.7736 (m-40) cc_final: 0.7461 (m110) REVERT: B 441 TYR cc_start: 0.8480 (m-80) cc_final: 0.8159 (m-80) REVERT: B 460 GLU cc_start: 0.7868 (tt0) cc_final: 0.7518 (tt0) REVERT: B 533 GLN cc_start: 0.5122 (mp10) cc_final: 0.4892 (pm20) REVERT: B 538 GLN cc_start: 0.6704 (OUTLIER) cc_final: 0.6500 (pm20) REVERT: B 553 GLU cc_start: 0.6342 (mt-10) cc_final: 0.5967 (mt-10) REVERT: B 561 LEU cc_start: 0.7431 (mt) cc_final: 0.7205 (mt) REVERT: B 568 GLN cc_start: 0.7202 (tp40) cc_final: 0.6992 (tm-30) REVERT: A 45 GLU cc_start: 0.7716 (mp0) cc_final: 0.7424 (mp0) REVERT: A 46 ASP cc_start: 0.7908 (t70) cc_final: 0.7402 (t70) REVERT: A 74 TYR cc_start: 0.8618 (m-10) cc_final: 0.8383 (m-80) REVERT: A 142 GLU cc_start: 0.7666 (tt0) cc_final: 0.7307 (tp30) REVERT: A 148 VAL cc_start: 0.8494 (t) cc_final: 0.8131 (m) REVERT: A 160 GLU cc_start: 0.8211 (pm20) cc_final: 0.7772 (pm20) REVERT: A 166 ASP cc_start: 0.7964 (t70) cc_final: 0.7340 (t0) REVERT: A 245 GLU cc_start: 0.7571 (mm-30) cc_final: 0.7334 (mm-30) REVERT: A 263 THR cc_start: 0.8044 (m) cc_final: 0.7771 (p) REVERT: A 268 MET cc_start: 0.6761 (mtm) cc_final: 0.6514 (mtm) REVERT: A 292 VAL cc_start: 0.8094 (m) cc_final: 0.7756 (p) REVERT: A 294 LYS cc_start: 0.8254 (tttt) cc_final: 0.7996 (tttt) REVERT: A 318 MET cc_start: 0.6878 (tpp) cc_final: 0.6420 (tpp) REVERT: A 325 LYS cc_start: 0.7341 (mttt) cc_final: 0.6753 (mtmt) REVERT: A 338 ASN cc_start: 0.7575 (t0) cc_final: 0.7143 (t0) REVERT: A 357 LYS cc_start: 0.8508 (ptpt) cc_final: 0.8163 (pptt) REVERT: A 391 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7894 (mm-30) REVERT: A 399 LYS cc_start: 0.8026 (ttmm) cc_final: 0.7597 (mtpp) REVERT: A 430 THR cc_start: 0.8099 (m) cc_final: 0.7536 (p) REVERT: A 455 GLU cc_start: 0.7543 (tt0) cc_final: 0.7034 (tm-30) REVERT: A 489 LYS cc_start: 0.8115 (ttmm) cc_final: 0.7534 (ttmm) REVERT: A 551 GLU cc_start: 0.7650 (tm-30) cc_final: 0.7064 (tm-30) REVERT: A 593 LYS cc_start: 0.6801 (tptp) cc_final: 0.6544 (tptp) outliers start: 26 outliers final: 16 residues processed: 271 average time/residue: 0.3024 time to fit residues: 110.8924 Evaluate side-chains 273 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 256 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 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 261 LYS Chi-restraints excluded: chain A residue 307 CYS Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 515 CYS Chi-restraints excluded: chain A residue 519 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 4 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 21 optimal weight: 0.1980 chunk 65 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 59 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 97 optimal weight: 0.0050 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 530 ASN A 153 ASN ** A 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 16 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.144369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.121604 restraints weight = 13503.842| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.76 r_work: 0.3431 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.5524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9475 Z= 0.183 Angle : 0.705 16.266 12887 Z= 0.352 Chirality : 0.050 0.424 1425 Planarity : 0.004 0.043 1679 Dihedral : 7.808 85.131 1433 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 2.73 % Allowed : 16.29 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (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: -2.53 (0.23), residues: 1170 helix: -2.35 (0.60), residues: 59 sheet: -2.53 (0.57), residues: 67 loop : -1.76 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 49 HIS 0.005 0.001 HIS A 304 PHE 0.015 0.002 PHE A 481 TYR 0.028 0.002 TYR B 409 ARG 0.007 0.001 ARG B 47 Details of bonding type rmsd link_NAG-ASN : bond 0.01200 ( 4) link_NAG-ASN : angle 5.94427 ( 12) link_BETA1-4 : bond 0.00146 ( 2) link_BETA1-4 : angle 0.75244 ( 6) link_ALPHA1-3 : bond 0.01705 ( 1) link_ALPHA1-3 : angle 2.54794 ( 3) hydrogen bonds : bond 0.02958 ( 97) hydrogen bonds : angle 5.84109 ( 186) SS BOND : bond 0.00363 ( 47) SS BOND : angle 1.73744 ( 94) link_BETA1-3 : bond 0.00288 ( 1) link_BETA1-3 : angle 2.74569 ( 3) covalent geometry : bond 0.00418 ( 9420) covalent geometry : angle 0.66576 (12769) *********************** 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 284 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 256 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 30 ASP cc_start: 0.8086 (t70) cc_final: 0.7461 (t0) REVERT: B 67 THR cc_start: 0.8578 (m) cc_final: 0.8363 (t) REVERT: B 112 TYR cc_start: 0.7556 (m-80) cc_final: 0.7260 (m-80) REVERT: B 138 ARG cc_start: 0.7349 (mmm-85) cc_final: 0.7026 (mmm160) REVERT: B 139 GLU cc_start: 0.7191 (mp0) cc_final: 0.6776 (mp0) REVERT: B 147 GLU cc_start: 0.7288 (tp30) cc_final: 0.6915 (tp30) REVERT: B 261 SER cc_start: 0.8099 (m) cc_final: 0.7781 (p) REVERT: B 268 CYS cc_start: 0.6318 (t) cc_final: 0.6101 (t) REVERT: B 284 ASN cc_start: 0.8281 (t0) cc_final: 0.7868 (t0) REVERT: B 297 THR cc_start: 0.8461 (m) cc_final: 0.8185 (p) REVERT: B 405 GLU cc_start: 0.7468 (tt0) cc_final: 0.7126 (tt0) REVERT: B 421 ASP cc_start: 0.7232 (p0) cc_final: 0.6831 (p0) REVERT: B 441 TYR cc_start: 0.8492 (m-80) cc_final: 0.8237 (m-80) REVERT: B 460 GLU cc_start: 0.7879 (tt0) cc_final: 0.7514 (tt0) REVERT: B 533 GLN cc_start: 0.5415 (mp10) cc_final: 0.5214 (pm20) REVERT: B 538 GLN cc_start: 0.6695 (OUTLIER) cc_final: 0.6467 (pm20) REVERT: B 553 GLU cc_start: 0.6354 (mt-10) cc_final: 0.5998 (mt-10) REVERT: A 46 ASP cc_start: 0.7900 (t70) cc_final: 0.7422 (t0) REVERT: A 74 TYR cc_start: 0.8679 (m-10) cc_final: 0.8435 (m-80) REVERT: A 97 GLU cc_start: 0.6919 (mp0) cc_final: 0.6713 (mp0) REVERT: A 142 GLU cc_start: 0.7686 (tt0) cc_final: 0.7344 (tp30) REVERT: A 148 VAL cc_start: 0.8529 (t) cc_final: 0.8143 (m) REVERT: A 166 ASP cc_start: 0.7990 (t70) cc_final: 0.7540 (t70) REVERT: A 198 SER cc_start: 0.8285 (m) cc_final: 0.7510 (p) REVERT: A 261 LYS cc_start: 0.7881 (OUTLIER) cc_final: 0.7653 (pttt) REVERT: A 263 THR cc_start: 0.8093 (m) cc_final: 0.7816 (p) REVERT: A 268 MET cc_start: 0.6875 (mtm) cc_final: 0.6606 (mtm) REVERT: A 292 VAL cc_start: 0.8099 (m) cc_final: 0.7759 (p) REVERT: A 294 LYS cc_start: 0.8260 (tttt) cc_final: 0.7942 (ptmm) REVERT: A 325 LYS cc_start: 0.7378 (mttt) cc_final: 0.6842 (mtmt) REVERT: A 338 ASN cc_start: 0.7608 (t0) cc_final: 0.7160 (t0) REVERT: A 391 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7622 (mm-30) REVERT: A 399 LYS cc_start: 0.8065 (ttmm) cc_final: 0.7706 (mtpp) REVERT: A 421 GLU cc_start: 0.7266 (mt-10) cc_final: 0.6887 (mt-10) REVERT: A 430 THR cc_start: 0.8167 (m) cc_final: 0.7611 (p) REVERT: A 489 LYS cc_start: 0.8157 (ttmm) cc_final: 0.7955 (tttp) REVERT: A 551 GLU cc_start: 0.7769 (tm-30) cc_final: 0.7029 (tm-30) REVERT: A 593 LYS cc_start: 0.6836 (tptp) cc_final: 0.6536 (tptp) outliers start: 28 outliers final: 21 residues processed: 267 average time/residue: 0.2340 time to fit residues: 83.9321 Evaluate side-chains 274 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 251 time to evaluate : 1.534 ------------------------------------------------------------------------------- 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 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 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 416 ASP Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 515 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 14 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 95 optimal weight: 0.3980 chunk 66 optimal weight: 0.0050 chunk 0 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 530 ASN ** A 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 16 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.143286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.120881 restraints weight = 13302.695| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.74 r_work: 0.3408 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.5852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 9475 Z= 0.219 Angle : 0.744 16.038 12887 Z= 0.374 Chirality : 0.052 0.423 1425 Planarity : 0.004 0.042 1679 Dihedral : 8.090 89.472 1433 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 3.12 % Allowed : 15.90 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (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: -2.16 (0.63), residues: 54 sheet: -2.91 (0.48), residues: 86 loop : -1.73 (0.18), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP C 49 HIS 0.006 0.001 HIS A 304 PHE 0.017 0.002 PHE A 481 TYR 0.029 0.002 TYR B 409 ARG 0.007 0.001 ARG B 499 Details of bonding type rmsd link_NAG-ASN : bond 0.01165 ( 4) link_NAG-ASN : angle 5.87467 ( 12) link_BETA1-4 : bond 0.00105 ( 2) link_BETA1-4 : angle 0.76472 ( 6) link_ALPHA1-3 : bond 0.01508 ( 1) link_ALPHA1-3 : angle 2.45291 ( 3) hydrogen bonds : bond 0.03279 ( 97) hydrogen bonds : angle 5.84180 ( 186) SS BOND : bond 0.00408 ( 47) SS BOND : angle 1.83071 ( 94) link_BETA1-3 : bond 0.00410 ( 1) link_BETA1-3 : angle 2.59384 ( 3) covalent geometry : bond 0.00496 ( 9420) covalent geometry : angle 0.70543 (12769) *********************** 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 295 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 263 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 24 GLN cc_start: 0.6387 (pp30) cc_final: 0.6069 (pp30) REVERT: B 30 ASP cc_start: 0.8098 (t70) cc_final: 0.7450 (t0) REVERT: B 67 THR cc_start: 0.8601 (m) cc_final: 0.8390 (t) REVERT: B 138 ARG cc_start: 0.7414 (mmm-85) cc_final: 0.6939 (mmm160) REVERT: B 139 GLU cc_start: 0.7276 (mp0) cc_final: 0.6919 (mp0) REVERT: B 147 GLU cc_start: 0.7267 (tp30) cc_final: 0.6907 (tp30) REVERT: B 261 SER cc_start: 0.8174 (m) cc_final: 0.7881 (p) REVERT: B 268 CYS cc_start: 0.6387 (t) cc_final: 0.6169 (t) REVERT: B 284 ASN cc_start: 0.8387 (t0) cc_final: 0.7992 (t0) REVERT: B 297 THR cc_start: 0.8556 (m) cc_final: 0.8269 (p) REVERT: B 321 GLU cc_start: 0.6436 (tt0) cc_final: 0.6119 (tt0) REVERT: B 405 GLU cc_start: 0.7449 (tt0) cc_final: 0.7124 (tt0) REVERT: B 421 ASP cc_start: 0.7300 (p0) cc_final: 0.6863 (p0) REVERT: B 438 ASN cc_start: 0.7714 (m-40) cc_final: 0.7482 (m110) REVERT: B 441 TYR cc_start: 0.8483 (m-80) cc_final: 0.8182 (m-80) REVERT: B 460 GLU cc_start: 0.7922 (tt0) cc_final: 0.7459 (tt0) REVERT: B 501 GLU cc_start: 0.7122 (mm-30) cc_final: 0.6806 (mm-30) REVERT: B 514 LEU cc_start: 0.7489 (mp) cc_final: 0.7162 (mt) REVERT: B 533 GLN cc_start: 0.5273 (mp10) cc_final: 0.5043 (pm20) REVERT: B 553 GLU cc_start: 0.6391 (mt-10) cc_final: 0.6024 (mt-10) REVERT: B 568 GLN cc_start: 0.7286 (tp40) cc_final: 0.7055 (tm-30) REVERT: A 46 ASP cc_start: 0.7920 (t70) cc_final: 0.7398 (t70) REVERT: A 74 TYR cc_start: 0.8727 (m-10) cc_final: 0.8467 (m-80) REVERT: A 148 VAL cc_start: 0.8504 (t) cc_final: 0.8143 (m) REVERT: A 160 GLU cc_start: 0.8264 (pm20) cc_final: 0.7830 (pm20) REVERT: A 166 ASP cc_start: 0.7914 (t70) cc_final: 0.7582 (t70) REVERT: A 198 SER cc_start: 0.8361 (m) cc_final: 0.7551 (p) REVERT: A 245 GLU cc_start: 0.7473 (mm-30) cc_final: 0.7213 (mm-30) REVERT: A 263 THR cc_start: 0.8034 (m) cc_final: 0.7793 (p) REVERT: A 268 MET cc_start: 0.7117 (mtm) cc_final: 0.6852 (mtm) REVERT: A 292 VAL cc_start: 0.8085 (m) cc_final: 0.7726 (p) REVERT: A 294 LYS cc_start: 0.8272 (tttt) cc_final: 0.7960 (ptmm) REVERT: A 325 LYS cc_start: 0.7417 (mttt) cc_final: 0.6890 (mtmt) REVERT: A 338 ASN cc_start: 0.7751 (t0) cc_final: 0.7154 (t0) REVERT: A 391 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7885 (mm-30) REVERT: A 399 LYS cc_start: 0.8113 (ttmm) cc_final: 0.7750 (mtpp) REVERT: A 421 GLU cc_start: 0.7271 (mt-10) cc_final: 0.6884 (mt-10) REVERT: A 430 THR cc_start: 0.8123 (m) cc_final: 0.7550 (p) REVERT: A 455 GLU cc_start: 0.7564 (tt0) cc_final: 0.7181 (tt0) REVERT: A 478 LYS cc_start: 0.8404 (mmtt) cc_final: 0.8051 (mmmt) REVERT: A 489 LYS cc_start: 0.8185 (ttmm) cc_final: 0.7880 (tttp) REVERT: A 551 GLU cc_start: 0.7781 (tm-30) cc_final: 0.7108 (tm-30) REVERT: A 584 HIS cc_start: 0.6046 (m90) cc_final: 0.5702 (m90) REVERT: A 593 LYS cc_start: 0.6859 (tptp) cc_final: 0.6285 (tptp) outliers start: 32 outliers final: 25 residues processed: 275 average time/residue: 0.2699 time to fit residues: 100.1482 Evaluate side-chains 283 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 258 time to evaluate : 1.271 ------------------------------------------------------------------------------- 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 77 ILE Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 228 LYS Chi-restraints excluded: chain B residue 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 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 311 CYS Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 515 CYS Chi-restraints excluded: chain A residue 519 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 89 optimal weight: 0.1980 chunk 79 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 63 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 50 optimal weight: 0.0370 chunk 0 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.4258 ------------------------------------------------------------------------------- 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 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN A 433 HIS ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 16 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.143219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.120886 restraints weight = 13510.290| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.74 r_work: 0.3415 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.5937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9475 Z= 0.189 Angle : 0.740 15.959 12887 Z= 0.371 Chirality : 0.051 0.421 1425 Planarity : 0.004 0.041 1679 Dihedral : 8.005 88.469 1433 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 2.15 % Allowed : 17.17 % Favored : 80.68 % 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: -2.50 (0.23), residues: 1170 helix: -2.07 (0.64), residues: 54 sheet: -2.82 (0.50), residues: 86 loop : -1.70 (0.19), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 49 HIS 0.006 0.001 HIS A 304 PHE 0.014 0.002 PHE A 481 TYR 0.031 0.002 TYR B 409 ARG 0.013 0.001 ARG A 222 Details of bonding type rmsd link_NAG-ASN : bond 0.01173 ( 4) link_NAG-ASN : angle 5.81642 ( 12) link_BETA1-4 : bond 0.00135 ( 2) link_BETA1-4 : angle 0.81457 ( 6) link_ALPHA1-3 : bond 0.01400 ( 1) link_ALPHA1-3 : angle 2.34724 ( 3) hydrogen bonds : bond 0.02991 ( 97) hydrogen bonds : angle 5.69264 ( 186) SS BOND : bond 0.00363 ( 47) SS BOND : angle 1.77663 ( 94) link_BETA1-3 : bond 0.00642 ( 1) link_BETA1-3 : angle 2.62099 ( 3) covalent geometry : bond 0.00435 ( 9420) covalent geometry : angle 0.70263 (12769) ********************** 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 270 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 248 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 30 ASP cc_start: 0.8184 (t70) cc_final: 0.7528 (t0) REVERT: B 67 THR cc_start: 0.8639 (m) cc_final: 0.8432 (t) REVERT: B 138 ARG cc_start: 0.7390 (mmm-85) cc_final: 0.6952 (mmm160) REVERT: B 139 GLU cc_start: 0.7264 (mp0) cc_final: 0.6904 (mp0) REVERT: B 147 GLU cc_start: 0.7245 (tp30) cc_final: 0.6911 (tp30) REVERT: B 268 CYS cc_start: 0.6363 (t) cc_final: 0.6157 (t) REVERT: B 284 ASN cc_start: 0.8401 (t0) cc_final: 0.8030 (t0) REVERT: B 297 THR cc_start: 0.8536 (m) cc_final: 0.8281 (p) REVERT: B 321 GLU cc_start: 0.6456 (tt0) cc_final: 0.6134 (tt0) REVERT: B 405 GLU cc_start: 0.7433 (tt0) cc_final: 0.7116 (tt0) REVERT: B 421 ASP cc_start: 0.7280 (p0) cc_final: 0.6848 (p0) REVERT: B 438 ASN cc_start: 0.7778 (m-40) cc_final: 0.7507 (m110) REVERT: B 441 TYR cc_start: 0.8482 (m-80) cc_final: 0.8177 (m-80) REVERT: B 460 GLU cc_start: 0.7911 (tt0) cc_final: 0.7441 (tt0) REVERT: B 501 GLU cc_start: 0.7131 (mm-30) cc_final: 0.6814 (mm-30) REVERT: B 514 LEU cc_start: 0.7459 (mp) cc_final: 0.7077 (mt) REVERT: B 533 GLN cc_start: 0.5433 (mp10) cc_final: 0.5197 (mm-40) REVERT: B 553 GLU cc_start: 0.6351 (mt-10) cc_final: 0.5983 (mt-10) REVERT: A 46 ASP cc_start: 0.7882 (t70) cc_final: 0.7377 (t70) REVERT: A 148 VAL cc_start: 0.8494 (t) cc_final: 0.8130 (m) REVERT: A 160 GLU cc_start: 0.8218 (pm20) cc_final: 0.7779 (pm20) REVERT: A 166 ASP cc_start: 0.7954 (t70) cc_final: 0.7390 (t0) REVERT: A 198 SER cc_start: 0.8355 (m) cc_final: 0.7502 (p) REVERT: A 263 THR cc_start: 0.8066 (m) cc_final: 0.7806 (p) REVERT: A 268 MET cc_start: 0.7135 (mtm) cc_final: 0.6868 (mtm) REVERT: A 292 VAL cc_start: 0.8052 (m) cc_final: 0.7710 (p) REVERT: A 294 LYS cc_start: 0.8258 (tttt) cc_final: 0.7948 (ptmm) REVERT: A 318 MET cc_start: 0.7194 (tpp) cc_final: 0.6843 (tpp) REVERT: A 325 LYS cc_start: 0.7346 (mttt) cc_final: 0.6857 (mtmt) REVERT: A 391 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7873 (mm-30) REVERT: A 399 LYS cc_start: 0.8124 (ttmm) cc_final: 0.7717 (mtpp) REVERT: A 421 GLU cc_start: 0.7249 (mt-10) cc_final: 0.6872 (mt-10) REVERT: A 430 THR cc_start: 0.8133 (m) cc_final: 0.7561 (p) REVERT: A 455 GLU cc_start: 0.7552 (tt0) cc_final: 0.7164 (tt0) REVERT: A 478 LYS cc_start: 0.8417 (mmtt) cc_final: 0.8069 (mmmt) REVERT: A 551 GLU cc_start: 0.7791 (tm-30) cc_final: 0.7085 (tm-30) REVERT: A 559 HIS cc_start: 0.6504 (m-70) cc_final: 0.6128 (m-70) REVERT: A 584 HIS cc_start: 0.6145 (m90) cc_final: 0.5771 (m90) REVERT: A 593 LYS cc_start: 0.6858 (tptp) cc_final: 0.6322 (tptp) outliers start: 22 outliers final: 19 residues processed: 257 average time/residue: 0.2443 time to fit residues: 84.6642 Evaluate side-chains 267 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 248 time to evaluate : 1.026 ------------------------------------------------------------------------------- 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 397 LEU Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 538 GLN Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 84 GLU 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 416 ASP Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 492 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 86 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 110 optimal weight: 0.0670 chunk 42 optimal weight: 0.7980 chunk 55 optimal weight: 0.0980 chunk 1 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.4518 ------------------------------------------------------------------------------- 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 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 16 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.142480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.120224 restraints weight = 13418.295| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.71 r_work: 0.3414 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.6074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9475 Z= 0.196 Angle : 0.739 15.728 12887 Z= 0.371 Chirality : 0.051 0.417 1425 Planarity : 0.004 0.040 1679 Dihedral : 7.970 89.392 1433 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 2.54 % Allowed : 17.37 % Favored : 80.10 % 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: -2.46 (0.23), residues: 1170 helix: -2.12 (0.64), residues: 54 sheet: -2.63 (0.47), residues: 102 loop : -1.65 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP C 49 HIS 0.009 0.001 HIS A 233 PHE 0.017 0.002 PHE A 48 TYR 0.030 0.002 TYR B 409 ARG 0.010 0.001 ARG A 222 Details of bonding type rmsd link_NAG-ASN : bond 0.01136 ( 4) link_NAG-ASN : angle 5.74324 ( 12) link_BETA1-4 : bond 0.00132 ( 2) link_BETA1-4 : angle 0.82136 ( 6) link_ALPHA1-3 : bond 0.01477 ( 1) link_ALPHA1-3 : angle 2.38186 ( 3) hydrogen bonds : bond 0.02971 ( 97) hydrogen bonds : angle 5.66167 ( 186) SS BOND : bond 0.00385 ( 47) SS BOND : angle 1.78306 ( 94) link_BETA1-3 : bond 0.00485 ( 1) link_BETA1-3 : angle 2.68271 ( 3) covalent geometry : bond 0.00450 ( 9420) covalent geometry : angle 0.70241 (12769) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5129.56 seconds wall clock time: 91 minutes 13.89 seconds (5473.89 seconds total)