Starting phenix.real_space_refine on Wed Mar 4 15:46:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eu3_28603/03_2026/8eu3_28603_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eu3_28603/03_2026/8eu3_28603.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8eu3_28603/03_2026/8eu3_28603_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eu3_28603/03_2026/8eu3_28603_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8eu3_28603/03_2026/8eu3_28603.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eu3_28603/03_2026/8eu3_28603.map" } resolution = 3.62 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= 0.003 sd= 0.072 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 66 5.16 5 C 9511 2.51 5 N 2378 2.21 5 O 2637 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 155 residue(s): 0.01s 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: 14596 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3631 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 444, 3623 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 14, 'TRANS': 429} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 444, 3623 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 14, 'TRANS': 429} Chain breaks: 1 bond proxies already assigned to first conformer: 3695 Chain: "B" Number of atoms: 3616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3616 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 14, 'TRANS': 428} Chain breaks: 1 Chain: "C" Number of atoms: 3624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3624 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 14, 'TRANS': 430} Chain breaks: 1 Chain: "D" Number of atoms: 3591 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 438, 3583 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 12, 'TRANS': 425} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 438, 3583 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 12, 'TRANS': 425} Chain breaks: 1 bond proxies already assigned to first conformer: 3663 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: 4.10, per 1000 atoms: 0.28 Number of scatterers: 14596 At special positions: 0 Unit cell: (132.25, 108.974, 106.858, 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 66 16.00 P 4 15.00 O 2637 8.00 N 2378 7.00 C 9511 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: 1.12 Conformation dependent library (CDL) restraints added in 817.8 milliseconds 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3358 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 12 sheets defined 67.9% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 166 through 193 Proline residue: A 178 - end of helix removed outlier: 3.708A pdb=" N ASP A 193 " --> pdb=" O ARG A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 199 removed outlier: 3.671A pdb=" N SER A 197 " --> pdb=" O ASP A 193 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR A 199 " --> pdb=" O LEU A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 222 Processing helix chain 'A' and resid 235 through 245 Processing helix chain 'A' and resid 246 through 255 removed outlier: 3.860A pdb=" N LYS A 250 " --> pdb=" O THR A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.696A pdb=" N VAL A 273 " --> pdb=" O TYR A 270 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG A 274 " --> pdb=" O PRO A 271 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ASN A 276 " --> pdb=" O VAL A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 295 removed outlier: 4.342A pdb=" N LEU A 284 " --> pdb=" O LYS A 280 " (cutoff:3.500A) 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 427 removed outlier: 4.806A pdb=" N SER A 409 " --> pdb=" O ASN A 405 " (cutoff:3.500A) removed outlier: 5.346A 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 458 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 554 Processing helix chain 'A' and resid 581 through 589 removed outlier: 3.825A pdb=" N ALA A 587 " --> pdb=" O ASP A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 609 removed outlier: 4.026A pdb=" N LYS A 595 " --> pdb=" O TYR A 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 193 removed outlier: 3.876A pdb=" N TYR B 169 " --> pdb=" O SER B 165 " (cutoff:3.500A) Proline residue: B 178 - end of helix removed outlier: 4.022A pdb=" N ASP B 193 " --> pdb=" O ARG B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 199 Processing helix chain 'B' and resid 199 through 223 Processing helix chain 'B' and resid 235 through 245 Processing helix chain 'B' and resid 246 through 256 removed outlier: 4.040A pdb=" N LYS B 250 " --> pdb=" O THR B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 279 removed outlier: 4.107A pdb=" N VAL B 273 " --> pdb=" O TYR B 270 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG B 274 " --> pdb=" O PRO B 271 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE B 275 " --> pdb=" O GLU B 272 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ASN B 276 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU B 278 " --> pdb=" O PHE B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 295 removed outlier: 4.049A 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 407 through 427 Processing helix chain 'B' and resid 430 through 448 Processing helix chain 'B' and resid 452 through 457 Processing helix chain 'B' and resid 461 through 478 removed outlier: 5.044A pdb=" N ASP B 475 " --> pdb=" O ASN B 471 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N THR B 476 " --> pdb=" O VAL B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 498 Processing helix chain 'B' and resid 580 through 588 Processing helix chain 'B' and resid 591 through 610 Processing helix chain 'C' and resid 166 through 193 Proline residue: C 178 - end of helix removed outlier: 3.939A pdb=" N ASP C 193 " --> pdb=" O ARG C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 199 Processing helix chain 'C' and resid 199 through 222 Processing helix chain 'C' and resid 235 through 245 Processing helix chain 'C' and resid 247 through 256 Processing helix chain 'C' and resid 270 through 279 removed outlier: 4.184A pdb=" N VAL C 273 " --> pdb=" O TYR C 270 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE C 275 " --> pdb=" O GLU C 272 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ASN C 276 " --> pdb=" O VAL C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 295 removed outlier: 3.965A pdb=" N LEU C 284 " --> pdb=" O LYS C 280 " (cutoff:3.500A) 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 407 removed outlier: 3.818A pdb=" N ASN C 407 " --> pdb=" O ILE C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 428 Processing helix chain 'C' and resid 430 through 447 Processing helix chain 'C' and resid 452 through 458 Processing helix chain 'C' and resid 461 through 478 removed outlier: 5.422A pdb=" N ASP C 475 " --> pdb=" O ASN C 471 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N THR C 476 " --> pdb=" O VAL C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 498 Processing helix chain 'C' and resid 581 through 589 Processing helix chain 'C' and resid 591 through 609 Processing helix chain 'D' and resid 215 through 242 Proline residue: D 237 - end of helix Processing helix chain 'D' and resid 249 through 270 Processing helix chain 'D' and resid 271 through 275 removed outlier: 3.910A pdb=" N LEU D 275 " --> pdb=" O GLN D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 296 Processing helix chain 'D' and resid 297 through 307 removed outlier: 3.940A pdb=" N GLN D 301 " --> pdb=" O SER D 297 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU D 302 " --> pdb=" O THR D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 312 removed outlier: 3.707A pdb=" N ILE D 312 " --> pdb=" O PRO D 309 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 309 through 312' Processing helix chain 'D' and resid 313 through 318 Processing helix chain 'D' and resid 320 through 329 removed outlier: 4.284A pdb=" N ASN D 326 " --> pdb=" O PHE D 323 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU D 329 " --> pdb=" O ASN D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 345 removed outlier: 3.606A pdb=" N PHE D 337 " --> pdb=" O SER D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 379 removed outlier: 4.018A pdb=" N TYR D 351 " --> pdb=" O LYS D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 406 Processing helix chain 'D' and resid 416 through 449 Processing helix chain 'D' and resid 449 through 469 Processing helix chain 'D' and resid 472 through 491 Processing helix chain 'D' and resid 495 through 500 Processing helix chain 'D' and resid 503 through 521 removed outlier: 3.596A pdb=" N VAL D 514 " --> pdb=" O LEU D 510 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N SER D 517 " --> pdb=" O ASP D 513 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N ILE D 518 " --> pdb=" O VAL D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 527 removed outlier: 3.955A pdb=" N LYS D 526 " --> pdb=" O ASP D 523 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLY D 527 " --> pdb=" O LEU D 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 523 through 527' Processing helix chain 'D' and resid 529 through 539 Processing helix chain 'D' and resid 592 through 597 removed outlier: 3.724A pdb=" N LEU D 596 " --> pdb=" O GLU D 592 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ALA D 597 " --> pdb=" O ILE D 593 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 592 through 597' Processing helix chain 'D' and resid 621 through 629 Processing helix chain 'D' and resid 631 through 646 Processing sheet with id=AA1, first strand: chain 'A' and resid 226 through 228 removed outlier: 4.143A pdb=" N PHE A 226 " --> pdb=" O VAL A 233 " (cutoff:3.500A) removed outlier: 3.776A 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 500 Processing sheet with id=AA3, first strand: chain 'A' and resid 540 through 541 removed outlier: 3.902A 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 520 through 521 Processing sheet with id=AA7, first strand: chain 'B' and resid 529 through 530 Processing sheet with id=AA8, first strand: chain 'C' and resid 227 through 228 Processing sheet with id=AA9, first strand: chain 'C' and resid 499 through 502 Processing sheet with id=AB1, first strand: chain 'C' and resid 508 through 510 removed outlier: 6.735A pdb=" N ILE C 568 " --> pdb=" O ILE C 509 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL C 539 " --> pdb=" O VAL C 529 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 541 through 542 Processing sheet with id=AB3, first strand: chain 'D' and resid 550 through 552 removed outlier: 6.741A pdb=" N PHE D 550 " --> pdb=" O ALA D 610 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ALA D 610 " --> pdb=" O PHE D 550 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N CYS D 552 " --> pdb=" O VAL D 608 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N VAL D 569 " --> pdb=" O THR D 583 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N THR D 583 " --> pdb=" O VAL D 569 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL D 571 " --> pdb=" O LEU D 581 " (cutoff:3.500A) 918 hydrogen bonds defined for protein. 2668 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: 2.40 Time building geometry restraints manager: 1.45 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: 4341 1.34 - 1.46: 2764 1.46 - 1.57: 7736 1.57 - 1.69: 0 1.69 - 1.81: 105 Bond restraints: 14946 Sorted by residual: bond pdb=" O5' PCG B 802 " pdb=" PA PCG B 802 " ideal model delta sigma weight residual 1.606 1.488 0.118 2.00e-02 2.50e+03 3.47e+01 bond pdb=" O5' PCG C 802 " pdb=" PA PCG C 802 " ideal model delta sigma weight residual 1.606 1.488 0.118 2.00e-02 2.50e+03 3.47e+01 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 3.43e+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 3.38e+01 bond pdb=" O3' PCG C 802 " pdb=" PA PCG C 802 " ideal model delta sigma weight residual 1.617 1.513 0.104 2.00e-02 2.50e+03 2.72e+01 ... (remaining 14941 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.68: 20066 3.68 - 7.36: 165 7.36 - 11.04: 42 11.04 - 14.72: 5 14.72 - 18.40: 10 Bond angle restraints: 20288 Sorted by residual: angle pdb=" C3' PCG C 802 " pdb=" C4' PCG C 802 " pdb=" C5' PCG C 802 " ideal model delta sigma weight residual 109.85 128.25 -18.40 3.00e+00 1.11e-01 3.76e+01 angle pdb=" C3' PCG B 802 " pdb=" C4' PCG B 802 " pdb=" C5' PCG B 802 " ideal model delta sigma weight residual 109.85 127.96 -18.11 3.00e+00 1.11e-01 3.64e+01 angle pdb=" C3' PCG A 802 " pdb=" C4' PCG A 802 " pdb=" C5' PCG A 802 " ideal model delta sigma weight residual 109.85 127.89 -18.04 3.00e+00 1.11e-01 3.62e+01 angle pdb=" C3' PCG D 901 " pdb=" C4' PCG D 901 " pdb=" C5' PCG D 901 " ideal model delta sigma weight residual 109.85 127.88 -18.03 3.00e+00 1.11e-01 3.61e+01 angle pdb=" O1A PCG D 901 " pdb=" PA PCG D 901 " pdb=" O5' PCG D 901 " ideal model delta sigma weight residual 102.28 118.01 -15.73 3.00e+00 1.11e-01 2.75e+01 ... (remaining 20283 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.12: 8710 35.12 - 70.25: 214 70.25 - 105.37: 27 105.37 - 140.50: 0 140.50 - 175.62: 4 Dihedral angle restraints: 8955 sinusoidal: 3730 harmonic: 5225 Sorted by residual: dihedral pdb=" CA LEU B 588 " pdb=" C LEU B 588 " pdb=" N THR B 589 " pdb=" CA THR B 589 " ideal model delta harmonic sigma weight residual 180.00 153.32 26.68 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" CA VAL A 480 " pdb=" C VAL A 480 " pdb=" N ARG A 481 " pdb=" CA ARG A 481 " ideal model delta harmonic sigma weight residual -180.00 -155.87 -24.13 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA ASP C 193 " pdb=" C ASP C 193 " pdb=" N GLU C 194 " pdb=" CA GLU C 194 " ideal model delta harmonic sigma weight residual 180.00 156.70 23.30 0 5.00e+00 4.00e-02 2.17e+01 ... (remaining 8952 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.347: 2303 0.347 - 0.693: 0 0.693 - 1.040: 0 1.040 - 1.386: 0 1.386 - 1.733: 4 Chirality restraints: 2307 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 -0.77 -1.73 2.00e-01 2.50e+01 7.50e+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 -0.79 -1.71 2.00e-01 2.50e+01 7.33e+01 chirality pdb=" C4' PCG A 802 " pdb=" C3' PCG A 802 " pdb=" C5' PCG A 802 " pdb=" O4' PCG A 802 " both_signs ideal model delta sigma weight residual False -2.50 -0.83 -1.67 2.00e-01 2.50e+01 6.94e+01 ... (remaining 2304 not shown) Planarity restraints: 2496 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 392 " 0.056 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" O PHE A 392 " -0.020 2.00e-02 2.50e+03 pdb=" CA APHE A 392 " -0.016 2.00e-02 2.50e+03 pdb=" N ALA A 393 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN D 272 " 0.052 5.00e-02 4.00e+02 7.86e-02 9.87e+00 pdb=" N PRO D 273 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO D 273 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO D 273 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 236 " -0.048 5.00e-02 4.00e+02 7.27e-02 8.46e+00 pdb=" N PRO D 237 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO D 237 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO D 237 " -0.041 5.00e-02 4.00e+02 ... (remaining 2493 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1946 2.75 - 3.29: 14265 3.29 - 3.82: 24992 3.82 - 4.36: 27235 4.36 - 4.90: 47520 Nonbonded interactions: 115958 Sorted by model distance: nonbonded pdb=" OG SER A 580 " pdb=" OD1 ASP A 582 " model vdw 2.211 3.040 nonbonded pdb=" O ASP A 162 " pdb=" OG SER A 165 " model vdw 2.289 3.040 nonbonded pdb=" O THR A 360 " pdb=" OG1 THR A 364 " model vdw 2.290 3.040 nonbonded pdb=" O TYR D 294 " pdb=" OG SER D 297 " model vdw 2.302 3.040 nonbonded pdb=" OG SER D 594 " pdb=" O ASN D 602 " model vdw 2.308 3.040 ... (remaining 115953 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 259 or resid 270 through 391 or resid 393 thro \ ugh 802)) selection = (chain 'B' and (resid 159 through 259 or resid 270 through 391 or resid 393 thro \ ugh 609 or resid 801 through 802)) selection = (chain 'C' and (resid 159 through 259 or resid 270 through 391 or resid 393 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=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.850 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.130 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 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 : 0.007 0.118 14949 Z= 0.324 Angle : 1.020 18.401 20297 Z= 0.500 Chirality : 0.088 1.733 2307 Planarity : 0.007 0.079 2493 Dihedral : 16.537 175.619 5597 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.19 % Allowed : 4.90 % Favored : 94.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.46 (0.15), residues: 1756 helix: -1.94 (0.11), residues: 1151 sheet: -2.82 (0.62), residues: 59 loop : -2.64 (0.22), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 539 TYR 0.023 0.002 TYR A 184 PHE 0.043 0.002 PHE A 385 TRP 0.017 0.002 TRP D 400 HIS 0.006 0.001 HIS D 293 Details of bonding type rmsd covalent geometry : bond 0.00709 (14946) covalent geometry : angle 1.01839 (20288) hydrogen bonds : bond 0.11448 ( 918) hydrogen bonds : angle 4.90246 ( 2668) link_NAG-ASN : bond 0.00317 ( 3) link_NAG-ASN : angle 2.53023 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 311 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 219 LEU cc_start: 0.8562 (tt) cc_final: 0.8358 (tt) REVERT: A 232 MET cc_start: 0.8156 (tpp) cc_final: 0.7843 (tpp) REVERT: A 241 GLN cc_start: 0.8433 (mm-40) cc_final: 0.8040 (mp10) REVERT: A 300 MET cc_start: 0.7112 (mmm) cc_final: 0.6861 (tpt) REVERT: A 439 ARG cc_start: 0.8556 (ttt90) cc_final: 0.8245 (mtp85) REVERT: A 467 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7494 (mm-30) REVERT: A 478 LYS cc_start: 0.7527 (ptmt) cc_final: 0.7249 (tptp) REVERT: B 240 TRP cc_start: 0.8482 (t-100) cc_final: 0.8199 (t60) REVERT: B 254 LEU cc_start: 0.8782 (tp) cc_final: 0.8545 (tp) REVERT: B 289 ASP cc_start: 0.7464 (t0) cc_final: 0.7217 (t70) REVERT: B 314 ILE cc_start: 0.8738 (mm) cc_final: 0.8536 (mt) REVERT: B 410 ARG cc_start: 0.8068 (tpm170) cc_final: 0.7732 (tpm170) REVERT: B 414 GLN cc_start: 0.8704 (tp-100) cc_final: 0.8354 (tp40) REVERT: B 546 TYR cc_start: 0.7618 (p90) cc_final: 0.7377 (p90) REVERT: C 200 LEU cc_start: 0.9116 (tp) cc_final: 0.8810 (tp) REVERT: C 241 GLN cc_start: 0.8618 (mm110) cc_final: 0.8368 (mm-40) REVERT: C 406 MET cc_start: 0.7798 (ttp) cc_final: 0.7547 (mtp) REVERT: C 604 GLN cc_start: 0.9081 (mt0) cc_final: 0.8800 (pp30) REVERT: D 248 ASP cc_start: 0.5907 (t0) cc_final: 0.5346 (t0) REVERT: D 250 ILE cc_start: 0.8790 (mt) cc_final: 0.8560 (mt) REVERT: D 291 ARG cc_start: 0.8182 (ttm-80) cc_final: 0.7955 (ttp-170) REVERT: D 327 ARG cc_start: 0.7620 (mpt180) cc_final: 0.7336 (mpt-90) REVERT: D 635 GLU cc_start: 0.8007 (tm-30) cc_final: 0.7704 (tm-30) outliers start: 3 outliers final: 0 residues processed: 312 average time/residue: 0.1232 time to fit residues: 54.7644 Evaluate side-chains 221 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 345 HIS ** A 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 405 ASN A 425 GLN A 471 ASN ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 GLN B 229 GLN B 305 ASN ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 537 GLN B 554 ASN B 604 GLN ** C 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 554 ASN D 245 GLN ** D 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 288 ASN D 340 HIS D 365 HIS D 570 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.180622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.150811 restraints weight = 24192.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.154268 restraints weight = 47008.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.155144 restraints weight = 23573.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.155387 restraints weight = 17554.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.156038 restraints weight = 14550.847| |-----------------------------------------------------------------------------| r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3811 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3811 r_free = 0.3811 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3810 r_free = 0.3810 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3810 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14949 Z= 0.148 Angle : 0.627 8.722 20297 Z= 0.325 Chirality : 0.042 0.166 2307 Planarity : 0.005 0.063 2493 Dihedral : 11.217 179.638 2147 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.70 % Allowed : 11.18 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.18), residues: 1756 helix: -0.11 (0.14), residues: 1155 sheet: -2.70 (0.65), residues: 49 loop : -2.04 (0.24), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 384 TYR 0.025 0.001 TYR C 184 PHE 0.028 0.002 PHE D 310 TRP 0.013 0.001 TRP D 373 HIS 0.010 0.001 HIS C 242 Details of bonding type rmsd covalent geometry : bond 0.00319 (14946) covalent geometry : angle 0.62593 (20288) hydrogen bonds : bond 0.04574 ( 918) hydrogen bonds : angle 4.31509 ( 2668) link_NAG-ASN : bond 0.00062 ( 3) link_NAG-ASN : angle 2.16074 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 255 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 MET cc_start: 0.6761 (mmm) cc_final: 0.6518 (tpt) REVERT: A 410 ARG cc_start: 0.7161 (tpm170) cc_final: 0.6723 (tpp-160) REVERT: A 473 HIS cc_start: 0.6537 (OUTLIER) cc_final: 0.5278 (t-90) REVERT: A 478 LYS cc_start: 0.6659 (ptmt) cc_final: 0.6317 (tppt) REVERT: B 254 LEU cc_start: 0.8538 (tp) cc_final: 0.8245 (tp) REVERT: C 422 GLN cc_start: 0.8424 (tp40) cc_final: 0.8172 (tp40) REVERT: D 248 ASP cc_start: 0.5274 (t0) cc_final: 0.5033 (t0) outliers start: 27 outliers final: 15 residues processed: 268 average time/residue: 0.1095 time to fit residues: 43.5831 Evaluate side-chains 242 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 226 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 473 HIS Chi-restraints excluded: chain A residue 546 TYR Chi-restraints excluded: chain A residue 581 LYS Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 462 ASP Chi-restraints excluded: chain C residue 486 CYS Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain D residue 572 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 6 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 128 optimal weight: 8.9990 chunk 83 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 140 optimal weight: 0.9980 chunk 168 optimal weight: 9.9990 chunk 130 optimal weight: 6.9990 chunk 171 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 105 optimal weight: 0.0770 overall best weight: 0.7738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 GLN B 425 GLN B 473 HIS B 604 GLN C 242 HIS ** C 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 288 ASN D 340 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.180399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.155998 restraints weight = 34846.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.157813 restraints weight = 54902.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.158926 restraints weight = 19845.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.160665 restraints weight = 13398.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.160681 restraints weight = 9071.877| |-----------------------------------------------------------------------------| r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3851 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3851 r_free = 0.3851 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3851 r_free = 0.3851 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3851 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14949 Z= 0.139 Angle : 0.595 9.695 20297 Z= 0.307 Chirality : 0.041 0.170 2307 Planarity : 0.004 0.057 2493 Dihedral : 10.794 172.099 2147 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.88 % Allowed : 13.19 % Favored : 84.92 % 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: -0.26 (0.20), residues: 1756 helix: 0.67 (0.15), residues: 1157 sheet: -1.86 (0.64), residues: 64 loop : -1.75 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 384 TYR 0.025 0.001 TYR C 591 PHE 0.029 0.001 PHE D 310 TRP 0.012 0.001 TRP D 373 HIS 0.013 0.001 HIS C 242 Details of bonding type rmsd covalent geometry : bond 0.00307 (14946) covalent geometry : angle 0.59400 (20288) hydrogen bonds : bond 0.04278 ( 918) hydrogen bonds : angle 4.14719 ( 2668) link_NAG-ASN : bond 0.00036 ( 3) link_NAG-ASN : angle 2.02327 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 238 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 LEU cc_start: 0.8752 (tp) cc_final: 0.8489 (tp) REVERT: A 410 ARG cc_start: 0.7135 (tpm170) cc_final: 0.6687 (tpp-160) REVERT: A 478 LYS cc_start: 0.6829 (ptmt) cc_final: 0.6390 (tppt) REVERT: B 175 ILE cc_start: 0.9038 (tp) cc_final: 0.8681 (tp) REVERT: B 254 LEU cc_start: 0.8465 (tp) cc_final: 0.8165 (tp) REVERT: B 425 GLN cc_start: 0.8209 (tp40) cc_final: 0.7832 (tp-100) REVERT: B 552 ILE cc_start: 0.8128 (OUTLIER) cc_final: 0.7915 (pt) REVERT: C 200 LEU cc_start: 0.9032 (tp) cc_final: 0.8753 (tp) REVERT: C 232 MET cc_start: 0.8195 (tpp) cc_final: 0.7724 (tpp) REVERT: C 422 GLN cc_start: 0.8562 (tp40) cc_final: 0.8285 (tp40) REVERT: C 462 ASP cc_start: 0.7870 (OUTLIER) cc_final: 0.7598 (t0) REVERT: D 210 ILE cc_start: 0.8240 (mm) cc_final: 0.7984 (mm) REVERT: D 248 ASP cc_start: 0.5226 (t0) cc_final: 0.4997 (t0) REVERT: D 249 ASN cc_start: 0.6469 (t0) cc_final: 0.6245 (t0) outliers start: 30 outliers final: 18 residues processed: 256 average time/residue: 0.1095 time to fit residues: 41.8662 Evaluate side-chains 243 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 223 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 473 HIS Chi-restraints excluded: chain A residue 581 LYS Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 552 ILE Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 462 ASP Chi-restraints excluded: chain C residue 486 CYS Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain D residue 350 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 152 optimal weight: 0.8980 chunk 145 optimal weight: 3.9990 chunk 53 optimal weight: 0.2980 chunk 64 optimal weight: 0.0050 chunk 127 optimal weight: 8.9990 chunk 4 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 129 optimal weight: 0.6980 chunk 125 optimal weight: 10.0000 overall best weight: 0.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 523 ASN ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 GLN ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 567 ASN B 604 GLN ** C 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.176067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.139283 restraints weight = 20418.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.138942 restraints weight = 31869.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.140228 restraints weight = 31186.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.140880 restraints weight = 19426.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.141505 restraints weight = 17318.017| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3660 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3660 r_free = 0.3660 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3660 r_free = 0.3660 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3660 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14949 Z= 0.137 Angle : 0.572 10.950 20297 Z= 0.297 Chirality : 0.040 0.168 2307 Planarity : 0.004 0.055 2493 Dihedral : 10.600 174.904 2147 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.63 % Allowed : 14.76 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.13 (0.20), residues: 1756 helix: 1.00 (0.15), residues: 1160 sheet: -1.79 (0.62), residues: 69 loop : -1.65 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 603 TYR 0.016 0.001 TYR A 184 PHE 0.022 0.001 PHE D 310 TRP 0.011 0.001 TRP D 373 HIS 0.012 0.001 HIS C 242 Details of bonding type rmsd covalent geometry : bond 0.00305 (14946) covalent geometry : angle 0.57056 (20288) hydrogen bonds : bond 0.04142 ( 918) hydrogen bonds : angle 4.09627 ( 2668) link_NAG-ASN : bond 0.00042 ( 3) link_NAG-ASN : angle 1.95367 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 245 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 ASP cc_start: 0.7876 (OUTLIER) cc_final: 0.7666 (m-30) REVERT: A 256 LEU cc_start: 0.8833 (tp) cc_final: 0.8605 (tp) REVERT: A 410 ARG cc_start: 0.7032 (tpm170) cc_final: 0.6685 (tpp-160) REVERT: A 478 LYS cc_start: 0.6858 (ptmt) cc_final: 0.6515 (tppt) REVERT: B 175 ILE cc_start: 0.9032 (tp) cc_final: 0.8690 (tp) REVERT: B 254 LEU cc_start: 0.8551 (tp) cc_final: 0.8217 (tp) REVERT: B 425 GLN cc_start: 0.8490 (tp40) cc_final: 0.8028 (tp-100) REVERT: C 232 MET cc_start: 0.8284 (tpp) cc_final: 0.7808 (tpp) REVERT: C 462 ASP cc_start: 0.7980 (OUTLIER) cc_final: 0.7773 (t0) REVERT: C 546 TYR cc_start: 0.7624 (p90) cc_final: 0.7344 (p90) REVERT: D 210 ILE cc_start: 0.8360 (mm) cc_final: 0.8120 (mm) REVERT: D 248 ASP cc_start: 0.5587 (t0) cc_final: 0.5214 (t0) REVERT: D 249 ASN cc_start: 0.6501 (t0) cc_final: 0.6244 (t0) REVERT: D 398 TYR cc_start: 0.8182 (t80) cc_final: 0.7476 (t80) outliers start: 26 outliers final: 18 residues processed: 261 average time/residue: 0.1058 time to fit residues: 41.0729 Evaluate side-chains 245 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 225 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 581 LYS Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 462 ASP Chi-restraints excluded: chain C residue 486 CYS Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 573 TYR Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 506 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 49 optimal weight: 0.2980 chunk 55 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 154 optimal weight: 0.5980 chunk 160 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 104 optimal weight: 0.0980 chunk 139 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 GLN B 523 ASN B 604 GLN C 317 ASN C 471 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.176482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.143865 restraints weight = 23971.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.146772 restraints weight = 47737.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.148350 restraints weight = 25771.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.148716 restraints weight = 17618.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.149692 restraints weight = 15138.775| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3740 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3740 r_free = 0.3740 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3740 r_free = 0.3740 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3740 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14949 Z= 0.126 Angle : 0.569 10.468 20297 Z= 0.295 Chirality : 0.040 0.163 2307 Planarity : 0.004 0.053 2493 Dihedral : 10.458 174.126 2147 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.95 % Allowed : 15.64 % Favored : 82.41 % 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: 0.44 (0.20), residues: 1756 helix: 1.26 (0.15), residues: 1154 sheet: -1.74 (0.62), residues: 69 loop : -1.55 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 603 TYR 0.023 0.001 TYR C 591 PHE 0.020 0.001 PHE D 310 TRP 0.010 0.001 TRP D 373 HIS 0.010 0.001 HIS C 242 Details of bonding type rmsd covalent geometry : bond 0.00280 (14946) covalent geometry : angle 0.56733 (20288) hydrogen bonds : bond 0.04010 ( 918) hydrogen bonds : angle 4.03439 ( 2668) link_NAG-ASN : bond 0.00043 ( 3) link_NAG-ASN : angle 1.88941 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 235 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 ASP cc_start: 0.7750 (OUTLIER) cc_final: 0.7548 (m-30) REVERT: A 256 LEU cc_start: 0.8752 (tp) cc_final: 0.8541 (tp) REVERT: A 410 ARG cc_start: 0.6980 (tpm170) cc_final: 0.6640 (tpp-160) REVERT: A 473 HIS cc_start: 0.6187 (OUTLIER) cc_final: 0.5732 (t-90) REVERT: A 478 LYS cc_start: 0.6825 (ptmt) cc_final: 0.6447 (tppt) REVERT: B 254 LEU cc_start: 0.8408 (tp) cc_final: 0.8096 (tp) REVERT: B 425 GLN cc_start: 0.8309 (tp40) cc_final: 0.7928 (tp-100) REVERT: C 200 LEU cc_start: 0.9014 (tp) cc_final: 0.8718 (tp) REVERT: C 232 MET cc_start: 0.8210 (tpp) cc_final: 0.7718 (tpp) REVERT: C 509 ILE cc_start: 0.8261 (mm) cc_final: 0.7881 (mt) REVERT: C 580 SER cc_start: 0.8186 (OUTLIER) cc_final: 0.7901 (p) REVERT: D 210 ILE cc_start: 0.8225 (mm) cc_final: 0.8008 (mm) REVERT: D 248 ASP cc_start: 0.5548 (t0) cc_final: 0.5224 (t0) outliers start: 31 outliers final: 20 residues processed: 252 average time/residue: 0.1050 time to fit residues: 40.0484 Evaluate side-chains 244 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 221 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 473 HIS Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 581 LYS Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 486 CYS Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 580 SER Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 469 TYR Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 582 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 2 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 145 optimal weight: 0.6980 chunk 30 optimal weight: 4.9990 chunk 151 optimal weight: 0.3980 chunk 110 optimal weight: 1.9990 chunk 128 optimal weight: 8.9990 chunk 7 optimal weight: 6.9990 chunk 100 optimal weight: 0.7980 chunk 43 optimal weight: 9.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 GLN ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.176264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.142240 restraints weight = 28815.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.136862 restraints weight = 36564.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.135470 restraints weight = 34817.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.136361 restraints weight = 29276.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.136982 restraints weight = 24237.038| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3603 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3603 r_free = 0.3603 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3603 r_free = 0.3603 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3603 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14949 Z= 0.135 Angle : 0.566 10.168 20297 Z= 0.294 Chirality : 0.040 0.163 2307 Planarity : 0.004 0.054 2493 Dihedral : 10.320 173.250 2147 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.88 % Allowed : 16.39 % Favored : 81.72 % 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: 0.61 (0.20), residues: 1756 helix: 1.37 (0.15), residues: 1154 sheet: -1.62 (0.63), residues: 69 loop : -1.45 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 410 TYR 0.027 0.001 TYR C 573 PHE 0.020 0.001 PHE C 226 TRP 0.010 0.001 TRP D 253 HIS 0.010 0.001 HIS C 242 Details of bonding type rmsd covalent geometry : bond 0.00303 (14946) covalent geometry : angle 0.56508 (20288) hydrogen bonds : bond 0.03999 ( 918) hydrogen bonds : angle 4.03288 ( 2668) link_NAG-ASN : bond 0.00035 ( 3) link_NAG-ASN : angle 1.84494 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 237 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 410 ARG cc_start: 0.7018 (tpm170) cc_final: 0.6664 (tpp-160) REVERT: A 478 LYS cc_start: 0.6970 (ptmt) cc_final: 0.6526 (tppt) REVERT: B 175 ILE cc_start: 0.9041 (tp) cc_final: 0.8707 (tp) REVERT: B 254 LEU cc_start: 0.8499 (tp) cc_final: 0.8154 (tp) REVERT: B 425 GLN cc_start: 0.8500 (tp40) cc_final: 0.8142 (tp-100) REVERT: C 200 LEU cc_start: 0.9041 (tp) cc_final: 0.8736 (tp) REVERT: C 490 LEU cc_start: 0.7429 (OUTLIER) cc_final: 0.6866 (mm) REVERT: C 509 ILE cc_start: 0.8253 (mm) cc_final: 0.7949 (mt) REVERT: C 519 MET cc_start: 0.8247 (tpt) cc_final: 0.7746 (tpt) REVERT: C 580 SER cc_start: 0.8223 (OUTLIER) cc_final: 0.7930 (p) REVERT: D 210 ILE cc_start: 0.8401 (mm) cc_final: 0.8192 (mm) REVERT: D 248 ASP cc_start: 0.5336 (t0) cc_final: 0.5049 (t0) outliers start: 30 outliers final: 19 residues processed: 254 average time/residue: 0.1060 time to fit residues: 40.6771 Evaluate side-chains 240 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 219 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 581 LYS Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 462 ASP Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 580 SER Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 561 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 34 optimal weight: 0.7980 chunk 149 optimal weight: 1.9990 chunk 137 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 104 optimal weight: 0.0470 chunk 128 optimal weight: 3.9990 chunk 42 optimal weight: 7.9990 chunk 94 optimal weight: 6.9990 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 GLN ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 604 GLN C 604 GLN D 272 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.176708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.143779 restraints weight = 23524.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.143078 restraints weight = 40105.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.145941 restraints weight = 27956.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.146300 restraints weight = 16994.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.149942 restraints weight = 13847.175| |-----------------------------------------------------------------------------| r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3715 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3715 r_free = 0.3715 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3715 r_free = 0.3715 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3715 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14949 Z= 0.134 Angle : 0.584 15.345 20297 Z= 0.301 Chirality : 0.040 0.164 2307 Planarity : 0.004 0.056 2493 Dihedral : 10.258 173.021 2147 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.01 % Allowed : 16.65 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.66 (0.20), residues: 1756 helix: 1.40 (0.15), residues: 1155 sheet: -1.70 (0.62), residues: 69 loop : -1.37 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 279 TYR 0.029 0.001 TYR C 573 PHE 0.036 0.001 PHE C 226 TRP 0.009 0.001 TRP D 373 HIS 0.007 0.001 HIS C 242 Details of bonding type rmsd covalent geometry : bond 0.00300 (14946) covalent geometry : angle 0.58300 (20288) hydrogen bonds : bond 0.04016 ( 918) hydrogen bonds : angle 4.01922 ( 2668) link_NAG-ASN : bond 0.00035 ( 3) link_NAG-ASN : angle 1.81351 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 229 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 410 ARG cc_start: 0.7121 (tpm170) cc_final: 0.6891 (mmm160) REVERT: A 473 HIS cc_start: 0.6719 (OUTLIER) cc_final: 0.6313 (t-90) REVERT: B 175 ILE cc_start: 0.8981 (tp) cc_final: 0.8622 (tp) REVERT: B 254 LEU cc_start: 0.8579 (tp) cc_final: 0.8221 (tp) REVERT: B 425 GLN cc_start: 0.8787 (tp40) cc_final: 0.8438 (tp-100) REVERT: B 464 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7841 (mm) REVERT: C 200 LEU cc_start: 0.9037 (tp) cc_final: 0.8771 (tp) REVERT: C 519 MET cc_start: 0.8427 (tpt) cc_final: 0.7821 (tpt) REVERT: C 580 SER cc_start: 0.8212 (OUTLIER) cc_final: 0.7837 (p) REVERT: C 599 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7627 (tp30) REVERT: D 210 ILE cc_start: 0.8651 (mm) cc_final: 0.8425 (mm) REVERT: D 248 ASP cc_start: 0.5512 (t0) cc_final: 0.5137 (t0) outliers start: 32 outliers final: 17 residues processed: 249 average time/residue: 0.1084 time to fit residues: 40.6960 Evaluate side-chains 240 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 220 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 473 HIS Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 581 LYS Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 283 ARG Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 462 ASP Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 580 SER Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 506 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 51 optimal weight: 0.0670 chunk 33 optimal weight: 3.9990 chunk 137 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 142 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 GLN ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.177433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.143128 restraints weight = 35133.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.140144 restraints weight = 40494.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.137178 restraints weight = 31664.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.138408 restraints weight = 28866.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.138916 restraints weight = 21396.905| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3626 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3626 r_free = 0.3626 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3626 r_free = 0.3626 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3626 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14949 Z= 0.127 Angle : 0.584 9.916 20297 Z= 0.300 Chirality : 0.040 0.162 2307 Planarity : 0.004 0.056 2493 Dihedral : 10.153 172.606 2147 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.57 % Allowed : 17.09 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.80 (0.21), residues: 1756 helix: 1.50 (0.15), residues: 1155 sheet: -1.68 (0.62), residues: 69 loop : -1.30 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 216 TYR 0.027 0.001 TYR D 294 PHE 0.028 0.001 PHE C 226 TRP 0.014 0.001 TRP A 171 HIS 0.007 0.001 HIS A 473 Details of bonding type rmsd covalent geometry : bond 0.00283 (14946) covalent geometry : angle 0.58247 (20288) hydrogen bonds : bond 0.03899 ( 918) hydrogen bonds : angle 3.98058 ( 2668) link_NAG-ASN : bond 0.00042 ( 3) link_NAG-ASN : angle 1.77770 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 227 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 410 ARG cc_start: 0.7049 (tpm170) cc_final: 0.6829 (mmm160) REVERT: B 175 ILE cc_start: 0.9004 (tp) cc_final: 0.8657 (tp) REVERT: B 254 LEU cc_start: 0.8508 (tp) cc_final: 0.8155 (tp) REVERT: B 283 ARG cc_start: 0.7356 (OUTLIER) cc_final: 0.6499 (tpp-160) REVERT: B 464 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7637 (mm) REVERT: C 200 LEU cc_start: 0.9022 (tp) cc_final: 0.8707 (tp) REVERT: C 519 MET cc_start: 0.8345 (tpt) cc_final: 0.7877 (tpt) REVERT: C 580 SER cc_start: 0.8217 (OUTLIER) cc_final: 0.7908 (p) REVERT: D 210 ILE cc_start: 0.8635 (mm) cc_final: 0.8402 (mm) REVERT: D 248 ASP cc_start: 0.5464 (t0) cc_final: 0.5121 (t0) outliers start: 25 outliers final: 18 residues processed: 243 average time/residue: 0.1166 time to fit residues: 42.2750 Evaluate side-chains 237 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 216 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 581 LYS Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 283 ARG Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 462 ASP Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 580 SER Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 506 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 85 optimal weight: 8.9990 chunk 113 optimal weight: 0.9980 chunk 119 optimal weight: 7.9990 chunk 54 optimal weight: 0.6980 chunk 86 optimal weight: 0.0170 chunk 102 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 31 optimal weight: 0.2980 chunk 19 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 chunk 10 optimal weight: 0.0470 overall best weight: 0.3516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 523 ASN ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 GLN ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 288 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.178741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.142413 restraints weight = 22183.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.144913 restraints weight = 33757.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.145659 restraints weight = 25067.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.146353 restraints weight = 16532.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.150557 restraints weight = 14927.326| |-----------------------------------------------------------------------------| r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3747 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3747 r_free = 0.3747 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3747 r_free = 0.3747 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3747 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14949 Z= 0.116 Angle : 0.574 11.594 20297 Z= 0.296 Chirality : 0.040 0.170 2307 Planarity : 0.004 0.053 2493 Dihedral : 10.113 172.633 2147 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.44 % Allowed : 17.78 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.21), residues: 1756 helix: 1.58 (0.15), residues: 1156 sheet: -1.64 (0.61), residues: 69 loop : -1.26 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 327 TYR 0.024 0.001 TYR C 573 PHE 0.027 0.001 PHE C 226 TRP 0.016 0.001 TRP B 203 HIS 0.002 0.000 HIS C 315 Details of bonding type rmsd covalent geometry : bond 0.00249 (14946) covalent geometry : angle 0.57261 (20288) hydrogen bonds : bond 0.03826 ( 918) hydrogen bonds : angle 3.95604 ( 2668) link_NAG-ASN : bond 0.00064 ( 3) link_NAG-ASN : angle 1.73054 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 226 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 ASN cc_start: 0.7208 (OUTLIER) cc_final: 0.6474 (t0) REVERT: A 424 MET cc_start: 0.7445 (ttp) cc_final: 0.7071 (ppp) REVERT: A 473 HIS cc_start: 0.6199 (OUTLIER) cc_final: 0.5312 (t-90) REVERT: A 577 PHE cc_start: 0.6983 (m-10) cc_final: 0.6690 (m-10) REVERT: B 254 LEU cc_start: 0.8497 (tp) cc_final: 0.8109 (tp) REVERT: B 283 ARG cc_start: 0.7371 (OUTLIER) cc_final: 0.6584 (tpp-160) REVERT: B 410 ARG cc_start: 0.7855 (tpm170) cc_final: 0.7367 (tpm170) REVERT: B 464 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7702 (mm) REVERT: C 200 LEU cc_start: 0.9007 (tp) cc_final: 0.8716 (tp) REVERT: C 519 MET cc_start: 0.8456 (tpt) cc_final: 0.8035 (tpt) REVERT: C 580 SER cc_start: 0.8185 (OUTLIER) cc_final: 0.7825 (p) outliers start: 23 outliers final: 16 residues processed: 240 average time/residue: 0.1103 time to fit residues: 39.0905 Evaluate side-chains 232 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 211 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 473 HIS Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 581 LYS Chi-restraints excluded: chain B residue 283 ARG Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 580 SER Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 506 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 146 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 chunk 83 optimal weight: 9.9990 chunk 75 optimal weight: 6.9990 chunk 61 optimal weight: 0.0770 chunk 92 optimal weight: 0.5980 chunk 88 optimal weight: 8.9990 chunk 69 optimal weight: 0.7980 chunk 132 optimal weight: 10.0000 chunk 60 optimal weight: 0.5980 chunk 46 optimal weight: 0.5980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.178442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.144809 restraints weight = 30006.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.140741 restraints weight = 35478.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.137686 restraints weight = 29707.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.139063 restraints weight = 28470.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.139696 restraints weight = 21095.638| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3637 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3637 r_free = 0.3637 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3637 r_free = 0.3637 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3637 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.182 14949 Z= 0.202 Angle : 0.809 59.196 20297 Z= 0.465 Chirality : 0.041 0.224 2307 Planarity : 0.004 0.059 2493 Dihedral : 10.113 172.629 2147 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.44 % Allowed : 17.65 % Favored : 80.90 % Cbeta Deviations : 0.06 % 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: 1756 helix: 1.57 (0.15), residues: 1156 sheet: -1.62 (0.61), residues: 69 loop : -1.24 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 410 TYR 0.048 0.002 TYR D 294 PHE 0.023 0.001 PHE C 226 TRP 0.013 0.001 TRP D 253 HIS 0.006 0.001 HIS C 242 Details of bonding type rmsd covalent geometry : bond 0.00434 (14946) covalent geometry : angle 0.80844 (20288) hydrogen bonds : bond 0.03831 ( 918) hydrogen bonds : angle 3.97508 ( 2668) link_NAG-ASN : bond 0.00061 ( 3) link_NAG-ASN : angle 1.73024 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 213 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 ASN cc_start: 0.7217 (OUTLIER) cc_final: 0.6698 (t0) REVERT: A 424 MET cc_start: 0.7397 (ttp) cc_final: 0.7101 (ppp) REVERT: A 473 HIS cc_start: 0.5978 (OUTLIER) cc_final: 0.5151 (t-90) REVERT: A 577 PHE cc_start: 0.6906 (m-10) cc_final: 0.6650 (m-10) REVERT: B 254 LEU cc_start: 0.8428 (tp) cc_final: 0.8040 (tp) REVERT: B 283 ARG cc_start: 0.7321 (OUTLIER) cc_final: 0.6522 (tpp-160) REVERT: B 464 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7550 (mm) REVERT: C 200 LEU cc_start: 0.9019 (tp) cc_final: 0.8692 (tp) REVERT: C 519 MET cc_start: 0.8378 (tpt) cc_final: 0.8036 (tpt) REVERT: C 580 SER cc_start: 0.8193 (OUTLIER) cc_final: 0.7876 (p) outliers start: 23 outliers final: 17 residues processed: 227 average time/residue: 0.1085 time to fit residues: 36.7860 Evaluate side-chains 234 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 212 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 473 HIS Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 581 LYS Chi-restraints excluded: chain B residue 283 ARG Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 462 ASP Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 580 SER Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 506 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 167 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 chunk 172 optimal weight: 3.9990 chunk 108 optimal weight: 0.0020 chunk 93 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 156 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 61 optimal weight: 0.0670 chunk 47 optimal weight: 0.0060 overall best weight: 0.3742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 288 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.178309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.151233 restraints weight = 25706.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.151897 restraints weight = 48346.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.150382 restraints weight = 21576.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.151060 restraints weight = 17151.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.151416 restraints weight = 12994.430| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3757 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3757 r_free = 0.3757 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3757 r_free = 0.3757 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3757 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.182 14949 Z= 0.211 Angle : 0.693 24.363 20297 Z= 0.405 Chirality : 0.041 0.224 2307 Planarity : 0.004 0.059 2493 Dihedral : 10.113 172.629 2147 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.32 % Allowed : 17.71 % Favored : 80.97 % Cbeta Deviations : 0.06 % 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: 1756 helix: 1.57 (0.15), residues: 1156 sheet: -1.62 (0.61), residues: 69 loop : -1.24 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 410 TYR 0.048 0.002 TYR D 294 PHE 0.023 0.001 PHE C 226 TRP 0.013 0.001 TRP D 253 HIS 0.006 0.001 HIS C 242 Details of bonding type rmsd covalent geometry : bond 0.00447 (14946) covalent geometry : angle 0.69173 (20288) hydrogen bonds : bond 0.03831 ( 918) hydrogen bonds : angle 3.97508 ( 2668) link_NAG-ASN : bond 0.00061 ( 3) link_NAG-ASN : angle 1.73024 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2296.63 seconds wall clock time: 40 minutes 31.03 seconds (2431.03 seconds total)