Starting phenix.real_space_refine on Wed Mar 4 15:21:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8evc_28626/03_2026/8evc_28626_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8evc_28626/03_2026/8evc_28626.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8evc_28626/03_2026/8evc_28626.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8evc_28626/03_2026/8evc_28626.map" model { file = "/net/cci-nas-00/data/ceres_data/8evc_28626/03_2026/8evc_28626_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8evc_28626/03_2026/8evc_28626_neut.cif" } resolution = 3.33 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.034 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 65 5.16 5 C 9470 2.51 5 N 2369 2.21 5 O 2623 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 166 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14531 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3632 Classifications: {'peptide': 446} Link IDs: {'PTRANS': 14, 'TRANS': 431} Chain breaks: 1 Chain: "B" Number of atoms: 3565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3565 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 13, 'TRANS': 422} Chain breaks: 2 Chain: "C" Number of atoms: 3598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3598 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 14, 'TRANS': 426} Chain breaks: 1 Chain: "D" Number of atoms: 3602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3602 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 13, 'TRANS': 427} Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {'NAG': 1, 'PCG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {'NAG': 1, 'PCG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {'NAG': 1, 'PCG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'PCG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.24, per 1000 atoms: 0.22 Number of scatterers: 14531 At special positions: 0 Unit cell: (104.58, 108.73, 124.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 65 16.00 P 4 15.00 O 2623 8.00 N 2369 7.00 C 9470 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 NAG-ASN " NAG A 801 " - " ASN A 339 " " NAG B 801 " - " ASN B 339 " " NAG C 801 " - " ASN C 339 " Time building additional restraints: 1.06 Conformation dependent library (CDL) restraints added in 613.0 milliseconds 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3340 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 13 sheets defined 65.7% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 166 through 192 Proline residue: A 178 - end of helix removed outlier: 5.453A pdb=" N ILE A 187 " --> pdb=" O TRP A 183 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N CYS A 188 " --> pdb=" O TYR A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 198 removed outlier: 3.971A pdb=" N GLN A 196 " --> pdb=" O PHE A 192 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER A 197 " --> pdb=" O ASP A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 222 Processing helix chain 'A' and resid 235 through 246 removed outlier: 4.197A pdb=" N THR A 246 " --> pdb=" O HIS A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 255 Processing helix chain 'A' and resid 271 through 278 removed outlier: 3.688A pdb=" N PHE A 275 " --> pdb=" O GLU A 272 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ASN A 276 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG A 277 " --> pdb=" O ARG A 274 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU A 278 " --> pdb=" O PHE A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 295 Processing helix chain 'A' and resid 297 through 329 Processing helix chain 'A' and resid 347 through 364 Processing helix chain 'A' and resid 374 through 428 removed outlier: 4.099A pdb=" N MET A 406 " --> pdb=" O MET A 402 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASN A 407 " --> pdb=" O ILE A 403 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N SER A 409 " --> pdb=" O ASN A 405 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ARG A 410 " --> pdb=" O MET A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 447 Processing helix chain 'A' and resid 452 through 457 Processing helix chain 'A' and resid 461 through 473 Processing helix chain 'A' and resid 473 through 478 Processing helix chain 'A' and resid 487 through 498 Processing helix chain 'A' and resid 548 through 553 Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 591 through 609 removed outlier: 3.862A pdb=" N LYS A 595 " --> pdb=" O TYR A 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 193 Proline residue: B 178 - end of helix Processing helix chain 'B' and resid 194 through 199 Processing helix chain 'B' and resid 199 through 223 removed outlier: 3.947A pdb=" N TRP B 203 " --> pdb=" O TYR B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 245 Processing helix chain 'B' and resid 246 through 255 Processing helix chain 'B' and resid 273 through 279 removed outlier: 3.884A pdb=" N ASN B 276 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU B 278 " --> pdb=" O PHE B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 295 removed outlier: 4.259A pdb=" N LEU B 284 " --> pdb=" O LYS B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 329 Processing helix chain 'B' and resid 347 through 364 Processing helix chain 'B' and resid 374 through 406 Processing helix chain 'B' and resid 408 through 427 Processing helix chain 'B' and resid 430 through 447 Processing helix chain 'B' and resid 452 through 457 Processing helix chain 'B' and resid 461 through 478 removed outlier: 5.756A pdb=" N ASP B 475 " --> pdb=" O ASN B 471 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N THR B 476 " --> pdb=" O VAL B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 496 removed outlier: 3.985A pdb=" N VAL B 495 " --> pdb=" O LEU B 491 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LEU B 496 " --> pdb=" O VAL B 492 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 491 through 496' Processing helix chain 'B' and resid 581 through 587 Processing helix chain 'B' and resid 591 through 610 removed outlier: 4.214A pdb=" N LYS B 595 " --> pdb=" O TYR B 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 190 Proline residue: C 178 - end of helix Processing helix chain 'C' and resid 192 through 199 removed outlier: 3.982A pdb=" N GLN C 196 " --> pdb=" O PHE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 223 Processing helix chain 'C' and resid 235 through 245 Processing helix chain 'C' and resid 247 through 255 Processing helix chain 'C' and resid 274 through 279 removed outlier: 3.842A pdb=" N LEU C 278 " --> pdb=" O PHE C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 295 Processing helix chain 'C' and resid 297 through 329 Processing helix chain 'C' and resid 347 through 364 Processing helix chain 'C' and resid 374 through 427 removed outlier: 5.240A pdb=" N SER C 409 " --> pdb=" O ASN C 405 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N ARG C 410 " --> pdb=" O MET C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 447 Processing helix chain 'C' and resid 453 through 460 Processing helix chain 'C' and resid 461 through 479 removed outlier: 5.107A pdb=" N ASP C 475 " --> pdb=" O ASN C 471 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N THR C 476 " --> pdb=" O VAL C 472 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS C 479 " --> pdb=" O ASP C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 497 Processing helix chain 'C' and resid 580 through 588 Processing helix chain 'C' and resid 592 through 607 Processing helix chain 'D' and resid 215 through 242 removed outlier: 3.522A pdb=" N ALA D 228 " --> pdb=" O LEU D 224 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N TRP D 231 " --> pdb=" O LEU D 227 " (cutoff:3.500A) Proline residue: D 237 - end of helix Processing helix chain 'D' and resid 249 through 272 Processing helix chain 'D' and resid 273 through 275 No H-bonds generated for 'chain 'D' and resid 273 through 275' Processing helix chain 'D' and resid 286 through 296 Processing helix chain 'D' and resid 298 through 307 Processing helix chain 'D' and resid 310 through 318 removed outlier: 4.163A pdb=" N LEU D 315 " --> pdb=" O ASP D 311 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE D 316 " --> pdb=" O ILE D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 345 Processing helix chain 'D' and resid 347 through 379 removed outlier: 4.353A pdb=" N TYR D 351 " --> pdb=" O LYS D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 406 removed outlier: 3.805A pdb=" N TRP D 400 " --> pdb=" O ARG D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 449 removed outlier: 4.072A pdb=" N THR D 449 " --> pdb=" O ILE D 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 469 Processing helix chain 'D' and resid 472 through 490 Processing helix chain 'D' and resid 494 through 499 removed outlier: 3.850A pdb=" N LEU D 498 " --> pdb=" O ASP D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 522 Processing helix chain 'D' and resid 529 through 540 Processing helix chain 'D' and resid 592 through 600 removed outlier: 4.044A pdb=" N LEU D 595 " --> pdb=" O GLU D 592 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU D 596 " --> pdb=" O ILE D 593 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ALA D 597 " --> pdb=" O SER D 594 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ALA D 598 " --> pdb=" O LEU D 595 " (cutoff:3.500A) Processing helix chain 'D' and resid 620 through 629 Processing helix chain 'D' and resid 631 through 646 Processing sheet with id=AA1, first strand: chain 'A' and resid 227 through 228 removed outlier: 3.597A pdb=" N LEU A 231 " --> pdb=" O GLU A 228 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 499 through 503 Processing sheet with id=AA3, first strand: chain 'A' and resid 507 through 510 removed outlier: 3.949A pdb=" N ASP A 507 " --> pdb=" O SER A 570 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ILE A 568 " --> pdb=" O ILE A 509 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASN A 567 " --> pdb=" O VAL A 530 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 227 through 228 Processing sheet with id=AA5, first strand: chain 'B' and resid 499 through 503 Processing sheet with id=AA6, first strand: chain 'B' and resid 507 through 508 removed outlier: 3.579A pdb=" N ASP B 507 " --> pdb=" O SER B 570 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 227 through 228 Processing sheet with id=AA8, first strand: chain 'C' and resid 501 through 503 Processing sheet with id=AA9, first strand: chain 'C' and resid 508 through 510 removed outlier: 6.882A pdb=" N TYR C 508 " --> pdb=" O SER C 570 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N SER C 570 " --> pdb=" O TYR C 508 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N CYS C 510 " --> pdb=" O ILE C 568 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASN C 567 " --> pdb=" O VAL C 530 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 520 through 521 Processing sheet with id=AB2, first strand: chain 'D' and resid 277 through 279 removed outlier: 4.014A pdb=" N PHE D 277 " --> pdb=" O ILE D 284 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP D 282 " --> pdb=" O ARG D 279 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 541 through 545 removed outlier: 3.555A pdb=" N SER D 588 " --> pdb=" O ILE D 564 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 550 through 552 removed outlier: 6.934A pdb=" N VAL D 608 " --> pdb=" O VAL D 551 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N VAL D 582 " --> pdb=" O VAL D 571 " (cutoff:3.500A) 908 hydrogen bonds defined for protein. 2652 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: 2.32 Time building geometry restraints manager: 1.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4302 1.34 - 1.46: 3330 1.46 - 1.58: 7142 1.58 - 1.70: 0 1.70 - 1.82: 104 Bond restraints: 14878 Sorted by residual: bond pdb=" O5' PCG D 901 " pdb=" PA PCG D 901 " ideal model delta sigma weight residual 1.606 1.489 0.117 2.00e-02 2.50e+03 3.42e+01 bond pdb=" O5' PCG C 802 " pdb=" PA PCG C 802 " ideal model delta sigma weight residual 1.606 1.489 0.117 2.00e-02 2.50e+03 3.40e+01 bond pdb=" O5' PCG B 802 " pdb=" PA PCG B 802 " ideal model delta sigma weight residual 1.606 1.490 0.116 2.00e-02 2.50e+03 3.37e+01 bond pdb=" O5' PCG A 802 " pdb=" PA PCG A 802 " ideal model delta sigma weight residual 1.606 1.490 0.116 2.00e-02 2.50e+03 3.35e+01 bond pdb=" O3' PCG B 802 " pdb=" PA PCG B 802 " ideal model delta sigma weight residual 1.617 1.513 0.104 2.00e-02 2.50e+03 2.69e+01 ... (remaining 14873 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.66: 19963 3.66 - 7.31: 167 7.31 - 10.97: 48 10.97 - 14.62: 4 14.62 - 18.28: 12 Bond angle restraints: 20194 Sorted by residual: angle pdb=" C3' PCG B 802 " pdb=" C4' PCG B 802 " pdb=" C5' PCG B 802 " ideal model delta sigma weight residual 109.85 128.13 -18.28 3.00e+00 1.11e-01 3.71e+01 angle pdb=" C3' PCG D 901 " pdb=" C4' PCG D 901 " pdb=" C5' PCG D 901 " ideal model delta sigma weight residual 109.85 128.12 -18.27 3.00e+00 1.11e-01 3.71e+01 angle pdb=" C3' PCG C 802 " pdb=" C4' PCG C 802 " pdb=" C5' PCG C 802 " ideal model delta sigma weight residual 109.85 128.11 -18.26 3.00e+00 1.11e-01 3.71e+01 angle pdb=" C3' PCG A 802 " pdb=" C4' PCG A 802 " pdb=" C5' PCG A 802 " ideal model delta sigma weight residual 109.85 128.07 -18.22 3.00e+00 1.11e-01 3.69e+01 angle pdb=" O1A PCG C 802 " pdb=" PA PCG C 802 " pdb=" O5' PCG C 802 " ideal model delta sigma weight residual 102.28 117.92 -15.64 3.00e+00 1.11e-01 2.72e+01 ... (remaining 20189 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.94: 8383 25.94 - 51.88: 461 51.88 - 77.81: 33 77.81 - 103.75: 13 103.75 - 129.69: 16 Dihedral angle restraints: 8906 sinusoidal: 3709 harmonic: 5197 Sorted by residual: dihedral pdb=" CA THR A 245 " pdb=" C THR A 245 " pdb=" N THR A 246 " pdb=" CA THR A 246 " ideal model delta harmonic sigma weight residual -180.00 -151.91 -28.09 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" N SER C 558 " pdb=" C SER C 558 " pdb=" CA SER C 558 " pdb=" CB SER C 558 " ideal model delta harmonic sigma weight residual 122.80 135.17 -12.37 0 2.50e+00 1.60e-01 2.45e+01 dihedral pdb=" C THR B 536 " pdb=" N THR B 536 " pdb=" CA THR B 536 " pdb=" CB THR B 536 " ideal model delta harmonic sigma weight residual -122.00 -133.71 11.71 0 2.50e+00 1.60e-01 2.20e+01 ... (remaining 8903 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.356: 2289 0.356 - 0.712: 4 0.712 - 1.069: 0 1.069 - 1.425: 0 1.425 - 1.781: 4 Chirality restraints: 2297 Sorted by residual: chirality pdb=" C4' PCG C 802 " pdb=" C3' PCG C 802 " pdb=" C5' PCG C 802 " pdb=" O4' PCG C 802 " both_signs ideal model delta sigma weight residual False -2.50 -0.72 -1.78 2.00e-01 2.50e+01 7.93e+01 chirality pdb=" C4' PCG D 901 " pdb=" C3' PCG D 901 " pdb=" C5' PCG D 901 " pdb=" O4' PCG D 901 " both_signs ideal model delta sigma weight residual False -2.50 -0.72 -1.78 2.00e-01 2.50e+01 7.92e+01 chirality pdb=" C4' PCG B 802 " pdb=" C3' PCG B 802 " pdb=" C5' PCG B 802 " pdb=" O4' PCG B 802 " both_signs ideal model delta sigma weight residual False -2.50 -0.72 -1.78 2.00e-01 2.50e+01 7.90e+01 ... (remaining 2294 not shown) Planarity restraints: 2483 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 389 " -0.016 2.00e-02 2.50e+03 3.16e-02 9.96e+00 pdb=" C VAL A 389 " 0.055 2.00e-02 2.50e+03 pdb=" O VAL A 389 " -0.021 2.00e-02 2.50e+03 pdb=" N LEU A 390 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 512 " -0.015 2.00e-02 2.50e+03 3.03e-02 9.20e+00 pdb=" C ILE D 512 " 0.052 2.00e-02 2.50e+03 pdb=" O ILE D 512 " -0.019 2.00e-02 2.50e+03 pdb=" N ASP D 513 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET D 268 " -0.015 2.00e-02 2.50e+03 3.01e-02 9.07e+00 pdb=" C MET D 268 " 0.052 2.00e-02 2.50e+03 pdb=" O MET D 268 " -0.020 2.00e-02 2.50e+03 pdb=" N LEU D 269 " -0.018 2.00e-02 2.50e+03 ... (remaining 2480 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2073 2.76 - 3.30: 13460 3.30 - 3.83: 24620 3.83 - 4.37: 27484 4.37 - 4.90: 48265 Nonbonded interactions: 115902 Sorted by model distance: nonbonded pdb=" NZ LYS B 512 " pdb=" O THR B 565 " model vdw 2.228 3.120 nonbonded pdb=" O THR C 360 " pdb=" OG1 THR C 364 " model vdw 2.267 3.040 nonbonded pdb=" NH1 ARG B 564 " pdb=" O2A PCG B 802 " model vdw 2.304 3.120 nonbonded pdb=" OG1 THR A 476 " pdb=" OD1 ASN A 523 " model vdw 2.306 3.040 nonbonded pdb=" O TYR D 294 " pdb=" OG SER D 297 " model vdw 2.331 3.040 ... (remaining 115897 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 159 through 257 or resid 269 through 483 or resid 489 thro \ ugh 607 or resid 801 through 802)) selection = (chain 'B' and (resid 159 through 607 or resid 801 through 802)) selection = (chain 'C' and (resid 159 through 257 or resid 269 through 483 or resid 489 thro \ ugh 802)) } 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=1.00 max=1.00 mean=1.00 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: 2.030 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 13.300 Find NCS groups from input model: 0.270 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 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 : 0.006 0.117 14881 Z= 0.316 Angle : 1.073 18.281 20203 Z= 0.538 Chirality : 0.094 1.781 2297 Planarity : 0.008 0.069 2480 Dihedral : 16.450 129.691 5566 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.95 % Allowed : 4.29 % Favored : 94.76 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.28 (0.14), residues: 1748 helix: -2.78 (0.10), residues: 1115 sheet: -2.84 (0.48), residues: 74 loop : -2.49 (0.22), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 324 TYR 0.039 0.002 TYR D 314 PHE 0.043 0.002 PHE D 427 TRP 0.033 0.002 TRP C 240 HIS 0.007 0.002 HIS B 473 Details of bonding type rmsd covalent geometry : bond 0.00649 (14878) covalent geometry : angle 1.07134 (20194) hydrogen bonds : bond 0.10910 ( 908) hydrogen bonds : angle 6.34087 ( 2652) link_NAG-ASN : bond 0.00435 ( 3) link_NAG-ASN : angle 2.72301 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 238 time to evaluate : 0.559 Fit side-chains revert: symmetry clash REVERT: A 175 ILE cc_start: 0.8563 (tp) cc_final: 0.8358 (tp) REVERT: B 175 ILE cc_start: 0.8695 (tp) cc_final: 0.8349 (tp) REVERT: B 445 TRP cc_start: 0.8669 (t-100) cc_final: 0.8377 (t-100) REVERT: B 526 LYS cc_start: 0.8232 (mmmt) cc_final: 0.7898 (mmtm) REVERT: C 184 TYR cc_start: 0.7581 (m-80) cc_final: 0.7081 (m-80) REVERT: C 407 ASN cc_start: 0.7542 (t0) cc_final: 0.6957 (t0) REVERT: D 532 MET cc_start: 0.4701 (tmm) cc_final: 0.4248 (ppp) REVERT: D 608 VAL cc_start: 0.7484 (OUTLIER) cc_final: 0.7236 (p) REVERT: D 639 MET cc_start: 0.6085 (mmp) cc_final: 0.4717 (mtt) outliers start: 15 outliers final: 3 residues processed: 253 average time/residue: 0.1259 time to fit residues: 46.0851 Evaluate side-chains 158 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 154 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 LYS Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain D residue 608 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.2980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN ** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 GLN B 407 ASN ** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 537 GLN C 229 GLN C 317 ASN C 414 GLN C 425 GLN D 340 HIS D 367 ASN D 423 GLN D 426 ASN D 468 ASN D 607 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.162288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.122129 restraints weight = 19620.243| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.08 r_work: 0.3359 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 14881 Z= 0.159 Angle : 0.572 8.076 20203 Z= 0.305 Chirality : 0.041 0.274 2297 Planarity : 0.005 0.052 2480 Dihedral : 13.157 150.336 2144 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.64 % Allowed : 8.90 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.18), residues: 1748 helix: -0.50 (0.14), residues: 1117 sheet: -2.56 (0.50), residues: 73 loop : -2.02 (0.24), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 439 TYR 0.014 0.001 TYR D 387 PHE 0.015 0.001 PHE C 547 TRP 0.016 0.001 TRP C 171 HIS 0.005 0.001 HIS A 315 Details of bonding type rmsd covalent geometry : bond 0.00353 (14878) covalent geometry : angle 0.56944 (20194) hydrogen bonds : bond 0.04625 ( 908) hydrogen bonds : angle 4.76406 ( 2652) link_NAG-ASN : bond 0.00267 ( 3) link_NAG-ASN : angle 2.81448 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 171 time to evaluate : 0.537 Fit side-chains REVERT: A 175 ILE cc_start: 0.8649 (tp) cc_final: 0.8437 (tp) REVERT: B 175 ILE cc_start: 0.8847 (tp) cc_final: 0.8561 (tp) REVERT: B 193 ASP cc_start: 0.8580 (t0) cc_final: 0.8368 (t0) REVERT: B 418 ASP cc_start: 0.8427 (t0) cc_final: 0.8080 (m-30) REVERT: C 184 TYR cc_start: 0.7973 (m-80) cc_final: 0.7495 (m-80) REVERT: C 237 ASN cc_start: 0.7998 (m-40) cc_final: 0.7779 (t0) REVERT: C 274 ARG cc_start: 0.7634 (mmt-90) cc_final: 0.6819 (mpt180) REVERT: C 604 GLN cc_start: 0.7746 (OUTLIER) cc_final: 0.6569 (mp10) REVERT: D 270 PHE cc_start: 0.8078 (m-10) cc_final: 0.7849 (m-10) REVERT: D 322 MET cc_start: 0.6534 (ttt) cc_final: 0.5218 (tmm) REVERT: D 532 MET cc_start: 0.4702 (tmm) cc_final: 0.4355 (ppp) outliers start: 26 outliers final: 16 residues processed: 192 average time/residue: 0.0936 time to fit residues: 28.3337 Evaluate side-chains 175 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 158 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 562 ASN Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 604 GLN Chi-restraints excluded: chain D residue 313 CYS Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 608 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 153 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 172 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 161 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 chunk 110 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 317 ASN B 345 HIS B 407 ASN ** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN D 272 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.159080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.119247 restraints weight = 19579.749| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.05 r_work: 0.3339 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 14881 Z= 0.170 Angle : 0.547 7.136 20203 Z= 0.290 Chirality : 0.042 0.235 2297 Planarity : 0.004 0.046 2480 Dihedral : 12.940 156.431 2140 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.40 % Allowed : 11.11 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.20), residues: 1748 helix: 0.52 (0.15), residues: 1111 sheet: -2.18 (0.55), residues: 67 loop : -1.83 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 439 TYR 0.017 0.001 TYR B 297 PHE 0.021 0.001 PHE C 392 TRP 0.015 0.001 TRP A 171 HIS 0.003 0.001 HIS A 315 Details of bonding type rmsd covalent geometry : bond 0.00396 (14878) covalent geometry : angle 0.54402 (20194) hydrogen bonds : bond 0.04458 ( 908) hydrogen bonds : angle 4.53964 ( 2652) link_NAG-ASN : bond 0.00159 ( 3) link_NAG-ASN : angle 2.61665 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 165 time to evaluate : 0.574 Fit side-chains REVERT: A 421 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7774 (mtmt) REVERT: A 493 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6524 (tm-30) REVERT: A 524 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7300 (tt0) REVERT: B 199 TYR cc_start: 0.8062 (OUTLIER) cc_final: 0.7319 (p90) REVERT: B 418 ASP cc_start: 0.8447 (t0) cc_final: 0.8058 (m-30) REVERT: C 184 TYR cc_start: 0.7941 (m-80) cc_final: 0.7508 (m-80) REVERT: C 274 ARG cc_start: 0.7680 (mmt-90) cc_final: 0.7003 (mpt180) REVERT: C 511 LYS cc_start: 0.7243 (mmmt) cc_final: 0.6558 (tppt) REVERT: C 546 TYR cc_start: 0.8015 (p90) cc_final: 0.7509 (p90) REVERT: C 604 GLN cc_start: 0.7751 (OUTLIER) cc_final: 0.6680 (mp10) REVERT: D 322 MET cc_start: 0.6653 (ttt) cc_final: 0.5378 (tmm) REVERT: D 532 MET cc_start: 0.4648 (tmm) cc_final: 0.4372 (ppp) outliers start: 38 outliers final: 24 residues processed: 194 average time/residue: 0.0962 time to fit residues: 29.8623 Evaluate side-chains 178 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 150 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 LYS Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 562 ASN Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 462 ASP Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 604 GLN Chi-restraints excluded: chain D residue 313 CYS Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 608 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 166 optimal weight: 0.9980 chunk 137 optimal weight: 5.9990 chunk 65 optimal weight: 0.5980 chunk 154 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 153 optimal weight: 0.9980 chunk 136 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 GLN B 407 ASN ** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN C 425 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.160313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.120467 restraints weight = 19442.881| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.05 r_work: 0.3349 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 14881 Z= 0.133 Angle : 0.507 7.351 20203 Z= 0.268 Chirality : 0.040 0.193 2297 Planarity : 0.004 0.042 2480 Dihedral : 12.776 154.180 2140 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.40 % Allowed : 12.75 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.20), residues: 1748 helix: 1.06 (0.15), residues: 1104 sheet: -1.85 (0.54), residues: 72 loop : -1.70 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 569 TYR 0.010 0.001 TYR D 399 PHE 0.015 0.001 PHE C 180 TRP 0.014 0.001 TRP C 171 HIS 0.002 0.001 HIS D 251 Details of bonding type rmsd covalent geometry : bond 0.00299 (14878) covalent geometry : angle 0.50402 (20194) hydrogen bonds : bond 0.04100 ( 908) hydrogen bonds : angle 4.38990 ( 2652) link_NAG-ASN : bond 0.00152 ( 3) link_NAG-ASN : angle 2.57122 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 165 time to evaluate : 0.493 Fit side-chains REVERT: A 421 LYS cc_start: 0.8089 (OUTLIER) cc_final: 0.7784 (mtmt) REVERT: A 493 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.6538 (tm-30) REVERT: A 524 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7237 (tt0) REVERT: B 175 ILE cc_start: 0.8824 (tp) cc_final: 0.8529 (tp) REVERT: B 199 TYR cc_start: 0.8133 (OUTLIER) cc_final: 0.7439 (p90) REVERT: B 418 ASP cc_start: 0.8381 (t0) cc_final: 0.8015 (m-30) REVERT: B 514 ASP cc_start: 0.8229 (t0) cc_final: 0.7708 (t0) REVERT: C 184 TYR cc_start: 0.7858 (m-80) cc_final: 0.7405 (m-80) REVERT: C 274 ARG cc_start: 0.7584 (mmt-90) cc_final: 0.6924 (mpt180) REVERT: C 511 LYS cc_start: 0.7170 (mmmt) cc_final: 0.6953 (mmmt) REVERT: C 546 TYR cc_start: 0.8126 (p90) cc_final: 0.7542 (p90) REVERT: D 322 MET cc_start: 0.6671 (ttt) cc_final: 0.5430 (tmm) REVERT: D 377 TYR cc_start: 0.8859 (t80) cc_final: 0.8648 (t80) REVERT: D 532 MET cc_start: 0.4597 (tmm) cc_final: 0.4316 (ppp) outliers start: 38 outliers final: 22 residues processed: 195 average time/residue: 0.0942 time to fit residues: 29.4414 Evaluate side-chains 177 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 152 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 421 LYS Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 562 ASN Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 462 ASP Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 608 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 25 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 146 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 86 optimal weight: 10.0000 chunk 155 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 407 ASN ** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 537 GLN C 414 GLN C 425 GLN ** C 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.160624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.119789 restraints weight = 19748.204| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.10 r_work: 0.3326 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 14881 Z= 0.160 Angle : 0.524 7.539 20203 Z= 0.276 Chirality : 0.041 0.184 2297 Planarity : 0.004 0.040 2480 Dihedral : 12.736 154.511 2140 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.97 % Allowed : 12.94 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.20), residues: 1748 helix: 1.19 (0.15), residues: 1103 sheet: -1.77 (0.55), residues: 72 loop : -1.60 (0.26), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 569 TYR 0.013 0.001 TYR B 297 PHE 0.014 0.001 PHE C 180 TRP 0.015 0.001 TRP A 171 HIS 0.004 0.001 HIS C 473 Details of bonding type rmsd covalent geometry : bond 0.00373 (14878) covalent geometry : angle 0.52171 (20194) hydrogen bonds : bond 0.04282 ( 908) hydrogen bonds : angle 4.39588 ( 2652) link_NAG-ASN : bond 0.00177 ( 3) link_NAG-ASN : angle 2.48861 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 160 time to evaluate : 0.572 Fit side-chains REVERT: A 254 LEU cc_start: 0.8353 (mp) cc_final: 0.8121 (mp) REVERT: A 421 LYS cc_start: 0.8113 (OUTLIER) cc_final: 0.7850 (mtmt) REVERT: A 427 ARG cc_start: 0.7366 (mtt180) cc_final: 0.6965 (mtt180) REVERT: A 493 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.6596 (tm-30) REVERT: A 524 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7279 (tt0) REVERT: B 199 TYR cc_start: 0.8218 (OUTLIER) cc_final: 0.7441 (p90) REVERT: B 418 ASP cc_start: 0.8370 (t0) cc_final: 0.8011 (m-30) REVERT: B 514 ASP cc_start: 0.8236 (t0) cc_final: 0.7666 (t0) REVERT: C 184 TYR cc_start: 0.7898 (m-80) cc_final: 0.7485 (m-80) REVERT: C 274 ARG cc_start: 0.7650 (mmt-90) cc_final: 0.6992 (mpt180) REVERT: C 394 THR cc_start: 0.8564 (OUTLIER) cc_final: 0.7974 (m) REVERT: C 546 TYR cc_start: 0.8184 (p90) cc_final: 0.7653 (p90) REVERT: D 310 PHE cc_start: 0.6099 (m-80) cc_final: 0.5890 (m-80) REVERT: D 322 MET cc_start: 0.6792 (ttt) cc_final: 0.5529 (tmm) REVERT: D 377 TYR cc_start: 0.8889 (t80) cc_final: 0.8669 (t80) REVERT: D 492 MET cc_start: 0.8815 (OUTLIER) cc_final: 0.8440 (ptp) REVERT: D 532 MET cc_start: 0.4679 (tmm) cc_final: 0.4395 (ppp) REVERT: D 556 GLU cc_start: 0.8365 (pt0) cc_final: 0.8095 (pm20) outliers start: 47 outliers final: 33 residues processed: 197 average time/residue: 0.0971 time to fit residues: 30.5275 Evaluate side-chains 189 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 151 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 421 LYS Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 462 ASP Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain C residue 300 MET Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 313 CYS Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 492 MET Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 608 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 159 optimal weight: 3.9990 chunk 59 optimal weight: 0.0980 chunk 72 optimal weight: 0.1980 chunk 90 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 167 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 chunk 2 optimal weight: 0.6980 chunk 29 optimal weight: 5.9990 chunk 100 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 407 ASN ** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN C 425 GLN D 367 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.163236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.123299 restraints weight = 19301.228| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.06 r_work: 0.3382 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.097 14881 Z= 0.104 Angle : 0.473 5.801 20203 Z= 0.252 Chirality : 0.039 0.167 2297 Planarity : 0.003 0.041 2480 Dihedral : 12.530 152.553 2138 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.96 % Allowed : 14.46 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.20), residues: 1748 helix: 1.51 (0.16), residues: 1110 sheet: -1.74 (0.59), residues: 62 loop : -1.44 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 569 TYR 0.012 0.001 TYR A 297 PHE 0.016 0.001 PHE B 192 TRP 0.014 0.001 TRP A 171 HIS 0.004 0.001 HIS C 473 Details of bonding type rmsd covalent geometry : bond 0.00224 (14878) covalent geometry : angle 0.47051 (20194) hydrogen bonds : bond 0.03766 ( 908) hydrogen bonds : angle 4.22416 ( 2652) link_NAG-ASN : bond 0.00051 ( 3) link_NAG-ASN : angle 2.45221 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 179 time to evaluate : 0.572 Fit side-chains REVERT: A 254 LEU cc_start: 0.8317 (mp) cc_final: 0.8065 (mp) REVERT: A 421 LYS cc_start: 0.8017 (OUTLIER) cc_final: 0.7608 (mtmt) REVERT: A 427 ARG cc_start: 0.7297 (mtt180) cc_final: 0.6920 (mtt180) REVERT: A 493 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.6558 (tm-30) REVERT: A 524 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7099 (tt0) REVERT: B 418 ASP cc_start: 0.8364 (t0) cc_final: 0.8027 (m-30) REVERT: B 425 GLN cc_start: 0.8387 (tp40) cc_final: 0.7629 (mp10) REVERT: B 514 ASP cc_start: 0.8201 (t0) cc_final: 0.7726 (t0) REVERT: C 184 TYR cc_start: 0.7783 (m-80) cc_final: 0.7408 (m-80) REVERT: C 274 ARG cc_start: 0.7552 (mmt-90) cc_final: 0.6762 (mpt180) REVERT: C 352 TYR cc_start: 0.8325 (t80) cc_final: 0.8091 (t80) REVERT: C 414 GLN cc_start: 0.8309 (tp40) cc_final: 0.7836 (tp40) REVERT: C 511 LYS cc_start: 0.6874 (mmmt) cc_final: 0.6318 (tppt) REVERT: C 519 MET cc_start: 0.7823 (mtp) cc_final: 0.7560 (ttm) REVERT: C 546 TYR cc_start: 0.8106 (p90) cc_final: 0.7547 (p90) REVERT: C 604 GLN cc_start: 0.7698 (OUTLIER) cc_final: 0.7193 (mp10) REVERT: D 322 MET cc_start: 0.6641 (ttt) cc_final: 0.5470 (tmm) REVERT: D 377 TYR cc_start: 0.8776 (t80) cc_final: 0.8429 (t80) REVERT: D 532 MET cc_start: 0.4526 (tmm) cc_final: 0.4320 (ppp) outliers start: 31 outliers final: 17 residues processed: 203 average time/residue: 0.1004 time to fit residues: 32.0821 Evaluate side-chains 184 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 164 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 421 LYS Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 562 ASN Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 462 ASP Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain C residue 300 MET Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 604 GLN Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 608 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 51 optimal weight: 0.5980 chunk 172 optimal weight: 1.9990 chunk 42 optimal weight: 0.4980 chunk 96 optimal weight: 0.4980 chunk 7 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 162 optimal weight: 0.0070 chunk 89 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 GLN B 407 ASN ** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.162503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.124233 restraints weight = 19120.294| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 1.93 r_work: 0.3403 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.106 14881 Z= 0.105 Angle : 0.484 7.289 20203 Z= 0.255 Chirality : 0.039 0.143 2297 Planarity : 0.003 0.040 2480 Dihedral : 12.460 153.104 2137 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.83 % Allowed : 14.77 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.21), residues: 1748 helix: 1.68 (0.16), residues: 1110 sheet: -1.50 (0.61), residues: 62 loop : -1.31 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 563 TYR 0.014 0.001 TYR B 297 PHE 0.012 0.001 PHE C 180 TRP 0.013 0.001 TRP A 171 HIS 0.003 0.001 HIS C 473 Details of bonding type rmsd covalent geometry : bond 0.00230 (14878) covalent geometry : angle 0.48176 (20194) hydrogen bonds : bond 0.03723 ( 908) hydrogen bonds : angle 4.15104 ( 2652) link_NAG-ASN : bond 0.00090 ( 3) link_NAG-ASN : angle 2.34925 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 174 time to evaluate : 0.600 Fit side-chains REVERT: A 254 LEU cc_start: 0.8322 (mp) cc_final: 0.8062 (mp) REVERT: A 421 LYS cc_start: 0.8041 (OUTLIER) cc_final: 0.7652 (mtmt) REVERT: A 427 ARG cc_start: 0.7262 (mtt180) cc_final: 0.6970 (mtt180) REVERT: A 524 GLU cc_start: 0.7693 (mm-30) cc_final: 0.6984 (mm-30) REVERT: A 569 ARG cc_start: 0.8319 (ttm-80) cc_final: 0.8102 (ttm-80) REVERT: A 607 MET cc_start: 0.7564 (mmp) cc_final: 0.7304 (mmp) REVERT: B 337 TYR cc_start: 0.8601 (t80) cc_final: 0.8299 (t80) REVERT: B 418 ASP cc_start: 0.8305 (t0) cc_final: 0.8057 (m-30) REVERT: B 514 ASP cc_start: 0.8177 (t0) cc_final: 0.7778 (t0) REVERT: C 184 TYR cc_start: 0.7725 (m-80) cc_final: 0.7391 (m-80) REVERT: C 274 ARG cc_start: 0.7525 (mmt-90) cc_final: 0.6770 (mpt180) REVERT: C 414 GLN cc_start: 0.8341 (tp40) cc_final: 0.7951 (tp40) REVERT: C 519 MET cc_start: 0.7836 (mtp) cc_final: 0.7593 (ttm) REVERT: C 546 TYR cc_start: 0.8071 (p90) cc_final: 0.7578 (p90) REVERT: C 604 GLN cc_start: 0.7738 (OUTLIER) cc_final: 0.7123 (mp10) REVERT: D 322 MET cc_start: 0.6692 (ttt) cc_final: 0.5534 (tmm) REVERT: D 377 TYR cc_start: 0.8760 (t80) cc_final: 0.8429 (t80) REVERT: D 556 GLU cc_start: 0.8246 (pt0) cc_final: 0.8031 (pm20) REVERT: D 639 MET cc_start: 0.6228 (mmp) cc_final: 0.4709 (mtt) outliers start: 29 outliers final: 23 residues processed: 193 average time/residue: 0.0988 time to fit residues: 29.9406 Evaluate side-chains 188 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 163 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 421 LYS Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 407 ASN Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 462 ASP Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 604 GLN Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 644 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 80 optimal weight: 9.9990 chunk 129 optimal weight: 9.9990 chunk 67 optimal weight: 0.0170 chunk 46 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 28 optimal weight: 0.0970 chunk 119 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 151 optimal weight: 0.9980 overall best weight: 0.6016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 GLN ** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 GLN D 531 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.162287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.126666 restraints weight = 19244.061| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 1.91 r_work: 0.3403 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.094 14881 Z= 0.110 Angle : 0.490 8.385 20203 Z= 0.257 Chirality : 0.039 0.149 2297 Planarity : 0.003 0.040 2480 Dihedral : 12.427 153.584 2137 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.15 % Allowed : 15.09 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.21), residues: 1748 helix: 1.68 (0.16), residues: 1118 sheet: -1.39 (0.61), residues: 62 loop : -1.38 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 569 TYR 0.011 0.001 TYR C 243 PHE 0.013 0.001 PHE C 180 TRP 0.012 0.001 TRP A 171 HIS 0.003 0.001 HIS D 251 Details of bonding type rmsd covalent geometry : bond 0.00246 (14878) covalent geometry : angle 0.48765 (20194) hydrogen bonds : bond 0.03682 ( 908) hydrogen bonds : angle 4.13875 ( 2652) link_NAG-ASN : bond 0.00068 ( 3) link_NAG-ASN : angle 2.30427 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 174 time to evaluate : 0.563 Fit side-chains REVERT: A 219 LEU cc_start: 0.8549 (mp) cc_final: 0.8200 (tt) REVERT: A 254 LEU cc_start: 0.8326 (mp) cc_final: 0.8062 (mp) REVERT: A 427 ARG cc_start: 0.7201 (mtt180) cc_final: 0.6907 (mtt180) REVERT: A 493 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.6575 (tm-30) REVERT: A 524 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7000 (mm-30) REVERT: A 569 ARG cc_start: 0.8330 (ttm-80) cc_final: 0.8126 (ttm-80) REVERT: A 607 MET cc_start: 0.7559 (mmp) cc_final: 0.7304 (mmp) REVERT: B 337 TYR cc_start: 0.8597 (t80) cc_final: 0.8323 (t80) REVERT: B 418 ASP cc_start: 0.8302 (t0) cc_final: 0.8064 (m-30) REVERT: B 425 GLN cc_start: 0.8403 (tp40) cc_final: 0.7621 (mp10) REVERT: B 514 ASP cc_start: 0.8178 (t0) cc_final: 0.7779 (t0) REVERT: C 184 TYR cc_start: 0.7702 (m-80) cc_final: 0.7344 (m-80) REVERT: C 274 ARG cc_start: 0.7531 (mmt-90) cc_final: 0.6800 (mpt180) REVERT: C 414 GLN cc_start: 0.8334 (tp40) cc_final: 0.7935 (tp40) REVERT: C 546 TYR cc_start: 0.8085 (p90) cc_final: 0.7683 (p90) REVERT: C 604 GLN cc_start: 0.7725 (OUTLIER) cc_final: 0.7152 (mp10) REVERT: D 322 MET cc_start: 0.6700 (ttt) cc_final: 0.5576 (tmm) REVERT: D 377 TYR cc_start: 0.8769 (t80) cc_final: 0.8429 (t80) REVERT: D 532 MET cc_start: 0.4330 (ppp) cc_final: 0.3595 (ttp) REVERT: D 639 MET cc_start: 0.6274 (mmp) cc_final: 0.4748 (mtt) outliers start: 34 outliers final: 26 residues processed: 197 average time/residue: 0.0954 time to fit residues: 29.8964 Evaluate side-chains 194 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 166 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 462 ASP Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 604 GLN Chi-restraints excluded: chain D residue 428 PHE Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 644 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 125 optimal weight: 9.9990 chunk 25 optimal weight: 0.6980 chunk 162 optimal weight: 10.0000 chunk 165 optimal weight: 0.4980 chunk 157 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 170 optimal weight: 8.9990 chunk 67 optimal weight: 4.9990 chunk 79 optimal weight: 9.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.163200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.122800 restraints weight = 19626.666| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.08 r_work: 0.3361 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 14881 Z= 0.128 Angle : 0.509 8.097 20203 Z= 0.266 Chirality : 0.040 0.147 2297 Planarity : 0.003 0.039 2480 Dihedral : 12.426 154.190 2137 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.21 % Allowed : 15.34 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.21), residues: 1748 helix: 1.66 (0.16), residues: 1118 sheet: -1.25 (0.62), residues: 62 loop : -1.37 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 569 TYR 0.014 0.001 TYR B 297 PHE 0.014 0.001 PHE C 180 TRP 0.011 0.001 TRP A 171 HIS 0.003 0.001 HIS D 251 Details of bonding type rmsd covalent geometry : bond 0.00296 (14878) covalent geometry : angle 0.50744 (20194) hydrogen bonds : bond 0.03829 ( 908) hydrogen bonds : angle 4.17582 ( 2652) link_NAG-ASN : bond 0.00084 ( 3) link_NAG-ASN : angle 2.21839 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 167 time to evaluate : 0.356 Fit side-chains REVERT: A 219 LEU cc_start: 0.8562 (mp) cc_final: 0.8181 (tt) REVERT: A 254 LEU cc_start: 0.8313 (mp) cc_final: 0.8045 (mp) REVERT: A 427 ARG cc_start: 0.7224 (mtt180) cc_final: 0.6915 (mtt180) REVERT: A 491 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8344 (tp) REVERT: A 493 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.6623 (tm-30) REVERT: A 524 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7175 (tt0) REVERT: B 418 ASP cc_start: 0.8344 (t0) cc_final: 0.8059 (m-30) REVERT: B 514 ASP cc_start: 0.8184 (t0) cc_final: 0.7733 (t0) REVERT: B 519 MET cc_start: 0.8186 (ttt) cc_final: 0.7874 (ttt) REVERT: C 184 TYR cc_start: 0.7784 (m-80) cc_final: 0.7492 (m-80) REVERT: C 274 ARG cc_start: 0.7598 (mmt-90) cc_final: 0.6922 (mpt180) REVERT: C 342 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7864 (tp) REVERT: C 352 TYR cc_start: 0.8382 (t80) cc_final: 0.8177 (t80) REVERT: C 384 ASP cc_start: 0.9144 (OUTLIER) cc_final: 0.8591 (t0) REVERT: C 414 GLN cc_start: 0.8345 (tp40) cc_final: 0.7910 (tp40) REVERT: C 546 TYR cc_start: 0.8066 (p90) cc_final: 0.7652 (p90) REVERT: C 604 GLN cc_start: 0.7590 (OUTLIER) cc_final: 0.7309 (mp10) REVERT: D 310 PHE cc_start: 0.5977 (m-10) cc_final: 0.5751 (m-80) REVERT: D 322 MET cc_start: 0.6730 (ttt) cc_final: 0.5569 (tmm) REVERT: D 377 TYR cc_start: 0.8814 (t80) cc_final: 0.8443 (t80) REVERT: D 532 MET cc_start: 0.4275 (ppp) cc_final: 0.3617 (ttp) REVERT: D 556 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7589 (pm20) outliers start: 35 outliers final: 24 residues processed: 192 average time/residue: 0.0969 time to fit residues: 29.1656 Evaluate side-chains 190 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 160 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 604 GLN Chi-restraints excluded: chain D residue 313 CYS Chi-restraints excluded: chain D residue 556 GLU Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 644 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 157 optimal weight: 0.8980 chunk 141 optimal weight: 0.9980 chunk 28 optimal weight: 0.0970 chunk 40 optimal weight: 8.9990 chunk 44 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 167 optimal weight: 4.9990 chunk 133 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 43 optimal weight: 10.0000 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 GLN ** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.161748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.123496 restraints weight = 19284.889| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 1.92 r_work: 0.3400 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 14881 Z= 0.117 Angle : 0.508 8.309 20203 Z= 0.266 Chirality : 0.040 0.169 2297 Planarity : 0.003 0.039 2480 Dihedral : 12.398 154.021 2137 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.96 % Allowed : 15.78 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.21), residues: 1748 helix: 1.69 (0.16), residues: 1122 sheet: -1.06 (0.64), residues: 62 loop : -1.30 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 569 TYR 0.011 0.001 TYR C 243 PHE 0.017 0.001 PHE C 547 TRP 0.017 0.001 TRP C 203 HIS 0.002 0.001 HIS D 251 Details of bonding type rmsd covalent geometry : bond 0.00264 (14878) covalent geometry : angle 0.50594 (20194) hydrogen bonds : bond 0.03752 ( 908) hydrogen bonds : angle 4.15545 ( 2652) link_NAG-ASN : bond 0.00063 ( 3) link_NAG-ASN : angle 2.19577 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 166 time to evaluate : 0.546 Fit side-chains REVERT: A 219 LEU cc_start: 0.8536 (mp) cc_final: 0.8196 (tt) REVERT: A 254 LEU cc_start: 0.8327 (mp) cc_final: 0.8057 (mp) REVERT: A 427 ARG cc_start: 0.7205 (mtt180) cc_final: 0.6907 (mtt180) REVERT: A 493 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.6586 (tm-30) REVERT: A 524 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7225 (tt0) REVERT: B 337 TYR cc_start: 0.8611 (t80) cc_final: 0.8343 (t80) REVERT: B 418 ASP cc_start: 0.8325 (t0) cc_final: 0.8091 (m-30) REVERT: B 425 GLN cc_start: 0.8412 (tp40) cc_final: 0.7601 (mp10) REVERT: B 514 ASP cc_start: 0.8127 (t0) cc_final: 0.7721 (t0) REVERT: B 519 MET cc_start: 0.8175 (ttt) cc_final: 0.7880 (ttt) REVERT: C 184 TYR cc_start: 0.7748 (m-80) cc_final: 0.7351 (m-80) REVERT: C 274 ARG cc_start: 0.7595 (mmt-90) cc_final: 0.6818 (mpt180) REVERT: C 342 ILE cc_start: 0.8153 (OUTLIER) cc_final: 0.7904 (tp) REVERT: C 352 TYR cc_start: 0.8358 (t80) cc_final: 0.8121 (t80) REVERT: C 384 ASP cc_start: 0.9104 (OUTLIER) cc_final: 0.8586 (t0) REVERT: C 414 GLN cc_start: 0.8365 (tp40) cc_final: 0.7974 (tp40) REVERT: C 546 TYR cc_start: 0.8072 (p90) cc_final: 0.7686 (p90) REVERT: C 604 GLN cc_start: 0.7603 (OUTLIER) cc_final: 0.7296 (mp10) REVERT: D 322 MET cc_start: 0.6706 (ttt) cc_final: 0.5631 (tmm) REVERT: D 377 TYR cc_start: 0.8784 (t80) cc_final: 0.8445 (t80) REVERT: D 532 MET cc_start: 0.4339 (ppp) cc_final: 0.3653 (ttp) outliers start: 31 outliers final: 24 residues processed: 189 average time/residue: 0.0943 time to fit residues: 28.6441 Evaluate side-chains 189 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 161 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 604 GLN Chi-restraints excluded: chain D residue 313 CYS Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 644 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 112 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 171 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 125 optimal weight: 6.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.160801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.122539 restraints weight = 19089.212| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.89 r_work: 0.3385 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 14881 Z= 0.125 Angle : 0.515 8.135 20203 Z= 0.269 Chirality : 0.040 0.163 2297 Planarity : 0.003 0.039 2480 Dihedral : 12.406 154.484 2137 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.21 % Allowed : 15.85 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.21), residues: 1748 helix: 1.72 (0.16), residues: 1120 sheet: -0.96 (0.64), residues: 62 loop : -1.33 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 410 TYR 0.020 0.001 TYR B 297 PHE 0.014 0.001 PHE C 180 TRP 0.013 0.001 TRP A 171 HIS 0.002 0.001 HIS D 251 Details of bonding type rmsd covalent geometry : bond 0.00286 (14878) covalent geometry : angle 0.51333 (20194) hydrogen bonds : bond 0.03800 ( 908) hydrogen bonds : angle 4.15889 ( 2652) link_NAG-ASN : bond 0.00076 ( 3) link_NAG-ASN : angle 2.16531 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3712.84 seconds wall clock time: 64 minutes 13.57 seconds (3853.57 seconds total)