Starting phenix.real_space_refine on Wed Mar 4 15:29:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eva_28624/03_2026/8eva_28624_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eva_28624/03_2026/8eva_28624.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8eva_28624/03_2026/8eva_28624.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eva_28624/03_2026/8eva_28624.map" model { file = "/net/cci-nas-00/data/ceres_data/8eva_28624/03_2026/8eva_28624_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eva_28624/03_2026/8eva_28624_neut.cif" } resolution = 3.33 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 66 5.16 5 C 9514 2.51 5 N 2373 2.21 5 O 2634 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 194 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14591 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3634 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: 3692 Chain: "B" Number of atoms: 3563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3563 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 14, 'TRANS': 420} Chain breaks: 2 Chain: "C" Number of atoms: 3681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3681 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 14, 'TRANS': 437} Chain: "D" Number of atoms: 3579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3579 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 12, 'TRANS': 424} Chain breaks: 1 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} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N APHE A 392 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 392 " occ=0.50 Time building chain proxies: 4.10, per 1000 atoms: 0.28 Number of scatterers: 14591 At special positions: 0 Unit cell: (110.39, 107.07, 126.16, 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 2634 8.00 N 2373 7.00 C 9514 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: 1.41 Conformation dependent library (CDL) restraints added in 674.3 milliseconds 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 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: 74 helices and 13 sheets defined 66.9% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 166 through 193 Proline residue: A 178 - end of helix removed outlier: 3.845A pdb=" N ASP A 193 " --> pdb=" O ARG A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 199 removed outlier: 3.705A 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 247 through 255 Processing helix chain 'A' and resid 271 through 279 removed outlier: 3.948A pdb=" N PHE A 275 " --> pdb=" O GLU A 272 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N ASN A 276 " --> pdb=" O VAL A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 295 removed outlier: 4.210A 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 407 Processing helix chain 'A' and resid 407 through 427 Processing helix chain 'A' and resid 430 through 448 Processing helix chain 'A' and resid 452 through 457 Processing helix chain 'A' and resid 461 through 473 Processing helix chain 'A' and resid 473 through 478 Processing helix chain 'A' and resid 487 through 498 Processing helix chain 'A' and resid 549 through 554 Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 592 through 608 Processing helix chain 'B' and resid 166 through 193 Proline residue: B 178 - end of helix removed outlier: 4.074A pdb=" N TYR B 184 " --> pdb=" O PHE B 180 " (cutoff:3.500A) 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 255 removed outlier: 3.990A pdb=" N LYS B 250 " --> pdb=" O THR B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 279 Processing helix chain 'B' and resid 280 through 295 removed outlier: 4.321A 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 407 Processing helix chain 'B' and resid 407 through 428 Processing helix chain 'B' and resid 430 through 447 Processing helix chain 'B' and resid 452 through 457 Processing helix chain 'B' and resid 461 through 478 removed outlier: 3.750A pdb=" N ILE B 468 " --> pdb=" O LEU B 464 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA B 469 " --> pdb=" O LYS B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 498 Processing helix chain 'B' and resid 580 through 590 removed outlier: 3.902A pdb=" N LEU B 584 " --> pdb=" O SER B 580 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU B 590 " --> pdb=" O GLU B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 611 removed outlier: 4.355A pdb=" N LYS B 595 " --> pdb=" O TYR B 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 193 Proline residue: C 178 - end of helix removed outlier: 3.926A pdb=" N ASP C 193 " --> pdb=" O ARG C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 199 removed outlier: 3.691A pdb=" N TYR C 199 " --> pdb=" O LEU C 195 " (cutoff:3.500A) 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 255 Processing helix chain 'C' and resid 259 through 267 removed outlier: 3.518A pdb=" N GLY C 267 " --> pdb=" O TYR C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 279 removed outlier: 4.063A pdb=" N VAL C 273 " --> pdb=" O TYR C 270 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ASN C 276 " --> pdb=" O VAL C 273 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU C 278 " --> pdb=" O PHE C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 293 removed outlier: 3.917A 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: 3.612A pdb=" N ASN C 407 " --> pdb=" O ILE C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 427 Processing helix chain 'C' and resid 430 through 447 Processing helix chain 'C' and resid 452 through 457 Processing helix chain 'C' and resid 458 through 460 No H-bonds generated for 'chain 'C' and resid 458 through 460' Processing helix chain 'C' and resid 461 through 478 removed outlier: 5.754A pdb=" N ASP C 475 " --> pdb=" O ASN C 471 " (cutoff:3.500A) removed outlier: 4.787A 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 549 through 554 removed outlier: 4.149A pdb=" N LEU C 553 " --> pdb=" O GLU C 549 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ASN C 554 " --> pdb=" O ILE C 550 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 549 through 554' Processing helix chain 'C' and resid 581 through 588 Processing helix chain 'C' and resid 592 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 271 removed outlier: 3.866A pdb=" N ILE D 271 " --> pdb=" O ASP D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 275 removed outlier: 3.810A pdb=" N LEU D 275 " --> pdb=" O GLN D 272 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 272 through 275' Processing helix chain 'D' and resid 286 through 296 Processing helix chain 'D' and resid 298 through 307 removed outlier: 3.973A pdb=" N LEU D 302 " --> pdb=" O THR D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 314 Processing helix chain 'D' and resid 324 through 329 Processing helix chain 'D' and resid 330 through 345 removed outlier: 4.293A pdb=" N PHE D 334 " --> pdb=" O LYS D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 379 removed outlier: 4.057A 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 removed outlier: 3.594A pdb=" N PHE D 432 " --> pdb=" O PHE D 428 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 469 Processing helix chain 'D' and resid 472 through 491 Processing helix chain 'D' and resid 494 through 500 removed outlier: 3.964A pdb=" N LEU D 498 " --> pdb=" O ASP D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 521 removed outlier: 3.938A pdb=" N VAL D 514 " --> pdb=" O LEU D 510 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N SER D 517 " --> pdb=" O ASP D 513 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N ILE D 518 " --> pdb=" O VAL D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 526 removed outlier: 3.958A pdb=" N LYS D 526 " --> pdb=" O ASP D 523 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 539 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 227 through 228 Processing sheet with id=AA2, first strand: chain 'A' and resid 499 through 503 removed outlier: 3.598A pdb=" N ASP A 575 " --> pdb=" O ASN A 523 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 508 through 510 removed outlier: 6.311A pdb=" N ILE A 568 " --> pdb=" O ILE A 509 " (cutoff:3.500A) removed outlier: 3.836A 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 removed outlier: 3.510A pdb=" N PHE B 547 " --> pdb=" O TYR B 520 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 508 through 510 removed outlier: 7.109A pdb=" N ILE B 568 " --> pdb=" O ILE B 509 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN B 567 " --> pdb=" O VAL B 530 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 227 through 228 Processing sheet with id=AA8, first strand: chain 'C' and resid 499 through 502 Processing sheet with id=AA9, first strand: chain 'C' and resid 508 through 510 removed outlier: 7.010A pdb=" N ILE C 568 " --> pdb=" O ILE C 509 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASN C 567 " --> pdb=" O VAL C 530 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 514 through 515 removed outlier: 3.725A pdb=" N ASP C 514 " --> pdb=" O ARG C 564 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 277 through 279 removed outlier: 4.090A pdb=" N PHE D 277 " --> pdb=" O ILE D 284 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP D 282 " --> pdb=" O ARG D 279 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 541 through 542 Processing sheet with id=AB4, first strand: chain 'D' and resid 550 through 552 removed outlier: 6.652A pdb=" N PHE D 550 " --> pdb=" O ALA D 610 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ALA D 610 " --> pdb=" O PHE D 550 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N CYS D 552 " --> pdb=" O VAL D 608 " (cutoff:3.500A) 925 hydrogen bonds defined for protein. 2683 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: 2.35 Time building geometry restraints manager: 1.85 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: 4442 1.34 - 1.46: 3247 1.46 - 1.58: 7147 1.58 - 1.70: 0 1.70 - 1.81: 105 Bond restraints: 14941 Sorted by residual: bond pdb=" O5' PCG D 901 " pdb=" PA PCG D 901 " ideal model delta sigma weight residual 1.606 1.489 0.117 2.00e-02 2.50e+03 3.41e+01 bond pdb=" O5' PCG B 802 " pdb=" PA PCG B 802 " ideal model delta sigma weight residual 1.606 1.490 0.116 2.00e-02 2.50e+03 3.38e+01 bond pdb=" O5' PCG C 802 " pdb=" PA PCG C 802 " ideal model delta sigma weight residual 1.606 1.490 0.116 2.00e-02 2.50e+03 3.37e+01 bond pdb=" O5' PCG A 802 " pdb=" PA PCG A 802 " ideal model delta sigma weight residual 1.606 1.490 0.116 2.00e-02 2.50e+03 3.37e+01 bond pdb=" O3' PCG A 802 " pdb=" PA PCG A 802 " ideal model delta sigma weight residual 1.617 1.513 0.104 2.00e-02 2.50e+03 2.71e+01 ... (remaining 14936 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.67: 20075 3.67 - 7.33: 150 7.33 - 11.00: 43 11.00 - 14.67: 4 14.67 - 18.34: 12 Bond angle restraints: 20284 Sorted by residual: angle pdb=" C3' PCG B 802 " pdb=" C4' PCG B 802 " pdb=" C5' PCG B 802 " ideal model delta sigma weight residual 109.85 128.19 -18.34 3.00e+00 1.11e-01 3.74e+01 angle pdb=" C3' PCG C 802 " pdb=" C4' PCG C 802 " pdb=" C5' PCG C 802 " ideal model delta sigma weight residual 109.85 128.11 -18.26 3.00e+00 1.11e-01 3.71e+01 angle pdb=" C3' PCG A 802 " pdb=" C4' PCG A 802 " pdb=" C5' PCG A 802 " ideal model delta sigma weight residual 109.85 128.09 -18.24 3.00e+00 1.11e-01 3.70e+01 angle pdb=" C3' PCG D 901 " pdb=" C4' PCG D 901 " pdb=" C5' PCG D 901 " ideal model delta sigma weight residual 109.85 128.09 -18.24 3.00e+00 1.11e-01 3.70e+01 angle pdb=" O1A PCG B 802 " pdb=" PA PCG B 802 " pdb=" O5' PCG B 802 " ideal model delta sigma weight residual 102.28 117.96 -15.68 3.00e+00 1.11e-01 2.73e+01 ... (remaining 20279 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.94: 8289 25.94 - 51.87: 579 51.87 - 77.80: 51 77.80 - 103.74: 12 103.74 - 129.67: 16 Dihedral angle restraints: 8947 sinusoidal: 3725 harmonic: 5222 Sorted by residual: dihedral pdb=" C3' PCG C 802 " pdb=" O3' PCG C 802 " pdb=" PA PCG C 802 " pdb=" O2A PCG C 802 " ideal model delta sinusoidal sigma weight residual 279.09 149.42 129.67 1 3.00e+01 1.11e-03 1.75e+01 dihedral pdb=" C3' PCG B 802 " pdb=" O3' PCG B 802 " pdb=" PA PCG B 802 " pdb=" O2A PCG B 802 " ideal model delta sinusoidal sigma weight residual 279.09 149.44 129.65 1 3.00e+01 1.11e-03 1.75e+01 dihedral pdb=" C3' PCG D 901 " pdb=" O3' PCG D 901 " pdb=" PA PCG D 901 " pdb=" O2A PCG D 901 " ideal model delta sinusoidal sigma weight residual 279.09 149.46 129.63 1 3.00e+01 1.11e-03 1.75e+01 ... (remaining 8944 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.356: 2305 0.356 - 0.712: 0 0.712 - 1.067: 0 1.067 - 1.423: 0 1.423 - 1.779: 4 Chirality restraints: 2309 Sorted by residual: chirality pdb=" C4' PCG B 802 " pdb=" C3' PCG B 802 " pdb=" C5' PCG B 802 " pdb=" O4' PCG B 802 " both_signs ideal model delta sigma weight residual False -2.50 -0.72 -1.78 2.00e-01 2.50e+01 7.91e+01 chirality pdb=" C4' PCG D 901 " pdb=" C3' PCG D 901 " pdb=" C5' PCG D 901 " pdb=" O4' PCG D 901 " both_signs ideal model delta sigma weight residual False -2.50 -0.72 -1.78 2.00e-01 2.50e+01 7.91e+01 chirality pdb=" C4' PCG C 802 " pdb=" C3' PCG C 802 " pdb=" C5' PCG C 802 " pdb=" O4' PCG C 802 " both_signs ideal model delta sigma weight residual False -2.50 -0.72 -1.78 2.00e-01 2.50e+01 7.91e+01 ... (remaining 2306 not shown) Planarity restraints: 2494 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN D 272 " 0.053 5.00e-02 4.00e+02 8.00e-02 1.02e+01 pdb=" N PRO D 273 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO D 273 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO D 273 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 369 " 0.047 5.00e-02 4.00e+02 7.04e-02 7.93e+00 pdb=" N PRO A 370 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO A 370 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 370 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 502 " 0.045 5.00e-02 4.00e+02 6.77e-02 7.34e+00 pdb=" N PRO D 503 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO D 503 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO D 503 " 0.037 5.00e-02 4.00e+02 ... (remaining 2491 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2650 2.77 - 3.30: 13362 3.30 - 3.83: 25074 3.83 - 4.37: 28114 4.37 - 4.90: 49075 Nonbonded interactions: 118275 Sorted by model distance: nonbonded pdb=" O MET C 585 " pdb=" OG1 THR C 589 " model vdw 2.234 3.040 nonbonded pdb=" OD1 ASP D 529 " pdb=" OG SER D 634 " model vdw 2.300 3.040 nonbonded pdb=" OG1 THR A 259 " pdb=" O VAL A 273 " model vdw 2.315 3.040 nonbonded pdb=" ND2 ASN A 317 " pdb=" OD1 ASP A 384 " model vdw 2.334 3.120 nonbonded pdb=" OE1 GLN A 604 " pdb=" NZ LYS A 608 " model vdw 2.334 3.120 ... (remaining 118270 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 258 or resid 270 through 391 or resid 393 thro \ ugh 554 or resid 562 through 802)) selection = (chain 'B' and (resid 159 through 391 or resid 393 through 609 or resid 801 thro \ ugh 802)) selection = (chain 'C' and (resid 159 through 258 or resid 270 through 391 or resid 393 thro \ ugh 554 or resid 562 through 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.870 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 15.310 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 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 0.117 14944 Z= 0.313 Angle : 1.025 18.336 20293 Z= 0.506 Chirality : 0.091 1.779 2309 Planarity : 0.008 0.080 2491 Dihedral : 17.842 129.674 5589 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.82 % Allowed : 16.03 % Favored : 83.16 % 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: -3.78 (0.15), residues: 1755 helix: -2.32 (0.11), residues: 1153 sheet: -2.33 (0.63), residues: 60 loop : -2.49 (0.22), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 481 TYR 0.022 0.002 TYR B 354 PHE 0.019 0.002 PHE C 192 TRP 0.023 0.002 TRP A 171 HIS 0.005 0.001 HIS D 251 Details of bonding type rmsd covalent geometry : bond 0.00677 (14941) covalent geometry : angle 1.02411 (20284) hydrogen bonds : bond 0.11641 ( 925) hydrogen bonds : angle 5.54726 ( 2683) link_NAG-ASN : bond 0.00240 ( 3) link_NAG-ASN : angle 2.28980 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 202 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 448 LYS cc_start: 0.8306 (mtpp) cc_final: 0.8059 (mtmt) REVERT: A 599 GLU cc_start: 0.7332 (tt0) cc_final: 0.6836 (tm-30) REVERT: B 392 PHE cc_start: 0.7506 (t80) cc_final: 0.7254 (t80) REVERT: B 463 LYS cc_start: 0.8043 (OUTLIER) cc_final: 0.7622 (pptt) REVERT: C 193 ASP cc_start: 0.8303 (t70) cc_final: 0.7983 (t0) REVERT: C 439 ARG cc_start: 0.7737 (mtm180) cc_final: 0.7375 (mtp85) REVERT: C 524 GLU cc_start: 0.7288 (tp30) cc_final: 0.7053 (tp30) REVERT: C 563 ARG cc_start: 0.5732 (OUTLIER) cc_final: 0.5491 (mtp85) REVERT: D 352 ARG cc_start: 0.7437 (OUTLIER) cc_final: 0.7201 (mtt90) REVERT: D 443 ASP cc_start: 0.8451 (t0) cc_final: 0.8240 (t0) REVERT: D 453 ASN cc_start: 0.8425 (m-40) cc_final: 0.8011 (m110) REVERT: D 497 ASP cc_start: 0.7679 (t0) cc_final: 0.7419 (t0) outliers start: 13 outliers final: 7 residues processed: 212 average time/residue: 0.1407 time to fit residues: 42.5700 Evaluate side-chains 172 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 162 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain A residue 427 ARG Chi-restraints excluded: chain B residue 297 TYR Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain B residue 546 TYR Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain C residue 563 ARG Chi-restraints excluded: chain D residue 352 ARG Chi-restraints excluded: chain D residue 456 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.2980 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.5980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN A 276 ASN A 405 ASN A 523 ASN B 196 GLN B 237 ASN B 317 ASN B 345 HIS B 422 GLN B 447 ASN B 484 GLN C 248 GLN C 299 ASN C 317 ASN C 567 ASN C 604 GLN D 230 ASN D 232 ASN D 276 GLN D 326 ASN D 340 HIS D 365 HIS D 367 ASN D 426 ASN D 453 ASN D 531 GLN D 630 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.195723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.133821 restraints weight = 24867.024| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.37 r_work: 0.3363 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3223 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3223 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 14944 Z= 0.143 Angle : 0.556 7.631 20293 Z= 0.295 Chirality : 0.041 0.157 2309 Planarity : 0.005 0.062 2491 Dihedral : 13.277 151.927 2173 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.26 % Allowed : 18.92 % Favored : 78.82 % 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: -1.31 (0.18), residues: 1755 helix: -0.23 (0.14), residues: 1158 sheet: -2.00 (0.62), residues: 58 loop : -1.95 (0.25), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 569 TYR 0.016 0.001 TYR B 352 PHE 0.019 0.001 PHE C 413 TRP 0.023 0.001 TRP B 445 HIS 0.003 0.001 HIS B 473 Details of bonding type rmsd covalent geometry : bond 0.00324 (14941) covalent geometry : angle 0.55388 (20284) hydrogen bonds : bond 0.04403 ( 925) hydrogen bonds : angle 4.48865 ( 2683) link_NAG-ASN : bond 0.00120 ( 3) link_NAG-ASN : angle 2.19770 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 188 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 TYR cc_start: 0.5735 (OUTLIER) cc_final: 0.3713 (t80) REVERT: A 344 GLU cc_start: 0.7273 (tp30) cc_final: 0.6725 (tt0) REVERT: A 391 ILE cc_start: 0.6907 (OUTLIER) cc_final: 0.5563 (mp) REVERT: A 418 ASP cc_start: 0.6861 (m-30) cc_final: 0.6280 (p0) REVERT: A 448 LYS cc_start: 0.8711 (mtpp) cc_final: 0.8377 (mtmt) REVERT: A 599 GLU cc_start: 0.8156 (tt0) cc_final: 0.7206 (tm-30) REVERT: B 270 TYR cc_start: 0.4757 (OUTLIER) cc_final: 0.3866 (p90) REVERT: B 392 PHE cc_start: 0.7791 (t80) cc_final: 0.7539 (t80) REVERT: B 508 TYR cc_start: 0.8069 (m-80) cc_final: 0.7853 (m-80) REVERT: B 514 ASP cc_start: 0.8666 (t0) cc_final: 0.7966 (m-30) REVERT: C 193 ASP cc_start: 0.8740 (t70) cc_final: 0.8397 (t0) REVERT: C 223 ARG cc_start: 0.8006 (mtt-85) cc_final: 0.7556 (mtm-85) REVERT: C 426 PHE cc_start: 0.5275 (OUTLIER) cc_final: 0.4568 (t80) REVERT: C 439 ARG cc_start: 0.7991 (mtm180) cc_final: 0.7545 (mtp180) REVERT: C 524 GLU cc_start: 0.7638 (tp30) cc_final: 0.7421 (tp30) REVERT: C 549 GLU cc_start: 0.7688 (pt0) cc_final: 0.6922 (pt0) REVERT: D 443 ASP cc_start: 0.8638 (t0) cc_final: 0.8199 (t0) REVERT: D 497 ASP cc_start: 0.8442 (t0) cc_final: 0.8027 (t0) outliers start: 36 outliers final: 14 residues processed: 213 average time/residue: 0.1215 time to fit residues: 38.7515 Evaluate side-chains 191 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 173 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain B residue 270 TYR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 398 ASN Chi-restraints excluded: chain B residue 422 GLN Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 297 TYR Chi-restraints excluded: chain C residue 426 PHE Chi-restraints excluded: chain D residue 276 GLN Chi-restraints excluded: chain D residue 352 ARG Chi-restraints excluded: chain D residue 492 MET Chi-restraints excluded: chain D residue 531 GLN Chi-restraints excluded: chain D residue 582 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 77 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 8 optimal weight: 6.9990 chunk 106 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 10 optimal weight: 0.1980 chunk 128 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 chunk 168 optimal weight: 10.0000 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 ** C 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 407 ASN D 531 GLN D 570 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.196825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.133350 restraints weight = 20472.838| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.82 r_work: 0.3309 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3311 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3311 r_free = 0.3311 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3311 r_free = 0.3311 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3311 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 14944 Z= 0.125 Angle : 0.523 7.978 20293 Z= 0.274 Chirality : 0.040 0.151 2309 Planarity : 0.004 0.057 2491 Dihedral : 12.912 150.332 2152 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.70 % Allowed : 20.68 % Favored : 77.62 % 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: -0.18 (0.20), residues: 1755 helix: 0.71 (0.15), residues: 1161 sheet: -1.81 (0.63), residues: 58 loop : -1.67 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 302 TYR 0.014 0.001 TYR C 546 PHE 0.025 0.001 PHE D 516 TRP 0.016 0.001 TRP B 445 HIS 0.004 0.001 HIS B 473 Details of bonding type rmsd covalent geometry : bond 0.00279 (14941) covalent geometry : angle 0.52112 (20284) hydrogen bonds : bond 0.04102 ( 925) hydrogen bonds : angle 4.21007 ( 2683) link_NAG-ASN : bond 0.00052 ( 3) link_NAG-ASN : angle 2.13591 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 183 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 TYR cc_start: 0.5907 (OUTLIER) cc_final: 0.4187 (t80) REVERT: A 344 GLU cc_start: 0.7088 (tp30) cc_final: 0.6682 (tt0) REVERT: A 418 ASP cc_start: 0.6808 (m-30) cc_final: 0.6263 (p0) REVERT: A 448 LYS cc_start: 0.8705 (mtpp) cc_final: 0.8357 (mtmt) REVERT: A 596 LYS cc_start: 0.8488 (pptt) cc_final: 0.8021 (tptt) REVERT: A 599 GLU cc_start: 0.8243 (tt0) cc_final: 0.7039 (tm-30) REVERT: B 270 TYR cc_start: 0.4850 (OUTLIER) cc_final: 0.3942 (p90) REVERT: B 392 PHE cc_start: 0.7770 (t80) cc_final: 0.7490 (t80) REVERT: B 425 GLN cc_start: 0.6645 (mp10) cc_final: 0.6333 (mp10) REVERT: B 514 ASP cc_start: 0.8634 (t0) cc_final: 0.8000 (m-30) REVERT: B 570 SER cc_start: 0.8933 (m) cc_final: 0.8018 (p) REVERT: C 193 ASP cc_start: 0.8552 (t70) cc_final: 0.8216 (t0) REVERT: C 223 ARG cc_start: 0.7942 (mtt-85) cc_final: 0.7583 (mtm-85) REVERT: C 426 PHE cc_start: 0.5250 (OUTLIER) cc_final: 0.4409 (t80) REVERT: C 439 ARG cc_start: 0.7916 (mtm180) cc_final: 0.7510 (mtp180) REVERT: D 261 ASP cc_start: 0.8144 (m-30) cc_final: 0.7925 (m-30) REVERT: D 352 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7637 (mtt90) REVERT: D 443 ASP cc_start: 0.8645 (t0) cc_final: 0.8271 (t0) REVERT: D 497 ASP cc_start: 0.8377 (t0) cc_final: 0.7920 (t0) REVERT: D 556 GLU cc_start: 0.8785 (tp30) cc_final: 0.7915 (tt0) REVERT: D 608 VAL cc_start: 0.8789 (t) cc_final: 0.8551 (p) outliers start: 27 outliers final: 10 residues processed: 199 average time/residue: 0.1229 time to fit residues: 36.0457 Evaluate side-chains 184 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 170 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain B residue 270 TYR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 422 GLN Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 426 PHE Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 352 ARG Chi-restraints excluded: chain D residue 531 GLN Chi-restraints excluded: chain D residue 582 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 25 optimal weight: 5.9990 chunk 134 optimal weight: 0.9980 chunk 76 optimal weight: 9.9990 chunk 149 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 78 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 chunk 145 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 GLN ** C 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 407 ASN D 531 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.195217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 109)---------------| | r_work = 0.3499 r_free = 0.3499 target = 0.130651 restraints weight = 22257.671| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 3.11 r_work: 0.3269 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3269 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3269 r_free = 0.3269 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3269 r_free = 0.3269 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3269 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 14944 Z= 0.157 Angle : 0.530 8.220 20293 Z= 0.278 Chirality : 0.041 0.154 2309 Planarity : 0.004 0.046 2491 Dihedral : 12.775 151.572 2152 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.45 % Allowed : 21.31 % Favored : 76.24 % 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: 0.17 (0.20), residues: 1755 helix: 1.00 (0.15), residues: 1160 sheet: -1.76 (0.64), residues: 58 loop : -1.59 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 569 TYR 0.015 0.001 TYR B 352 PHE 0.024 0.001 PHE C 413 TRP 0.015 0.001 TRP B 445 HIS 0.003 0.001 HIS B 473 Details of bonding type rmsd covalent geometry : bond 0.00369 (14941) covalent geometry : angle 0.52869 (20284) hydrogen bonds : bond 0.04212 ( 925) hydrogen bonds : angle 4.16474 ( 2683) link_NAG-ASN : bond 0.00086 ( 3) link_NAG-ASN : angle 2.14237 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 182 time to evaluate : 0.511 Fit side-chains revert: symmetry clash REVERT: A 270 TYR cc_start: 0.5924 (OUTLIER) cc_final: 0.4371 (t80) REVERT: A 391 ILE cc_start: 0.6985 (OUTLIER) cc_final: 0.5640 (mp) REVERT: A 418 ASP cc_start: 0.6705 (m-30) cc_final: 0.6282 (p0) REVERT: A 448 LYS cc_start: 0.8681 (mtpp) cc_final: 0.8166 (ptpp) REVERT: A 596 LYS cc_start: 0.8491 (pptt) cc_final: 0.8003 (tptt) REVERT: A 599 GLU cc_start: 0.8140 (tt0) cc_final: 0.7008 (tm-30) REVERT: B 238 ARG cc_start: 0.7723 (mmm-85) cc_final: 0.7364 (ttp80) REVERT: B 270 TYR cc_start: 0.4783 (OUTLIER) cc_final: 0.3811 (p90) REVERT: B 392 PHE cc_start: 0.7841 (t80) cc_final: 0.7494 (t80) REVERT: B 425 GLN cc_start: 0.6592 (mp10) cc_final: 0.6293 (mp10) REVERT: B 514 ASP cc_start: 0.8738 (t0) cc_final: 0.8009 (m-30) REVERT: B 570 SER cc_start: 0.8968 (m) cc_final: 0.8136 (p) REVERT: C 193 ASP cc_start: 0.8547 (t70) cc_final: 0.8190 (t0) REVERT: C 223 ARG cc_start: 0.7964 (mtt-85) cc_final: 0.7567 (mtm-85) REVERT: C 426 PHE cc_start: 0.5371 (OUTLIER) cc_final: 0.4563 (t80) REVERT: C 439 ARG cc_start: 0.7893 (mtm180) cc_final: 0.7449 (mtp180) REVERT: D 352 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.7821 (mtm-85) REVERT: D 443 ASP cc_start: 0.8673 (t0) cc_final: 0.8222 (t0) REVERT: D 497 ASP cc_start: 0.8510 (t0) cc_final: 0.8047 (t0) REVERT: D 531 GLN cc_start: 0.6809 (OUTLIER) cc_final: 0.6499 (mm110) REVERT: D 556 GLU cc_start: 0.8791 (tp30) cc_final: 0.7814 (tt0) REVERT: D 608 VAL cc_start: 0.8819 (t) cc_final: 0.8555 (p) REVERT: D 639 MET cc_start: 0.6342 (mmm) cc_final: 0.6139 (mmm) outliers start: 39 outliers final: 17 residues processed: 209 average time/residue: 0.1238 time to fit residues: 37.7836 Evaluate side-chains 193 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 170 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 TYR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain B residue 270 TYR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 398 ASN Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 426 PHE Chi-restraints excluded: chain C residue 510 CYS Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 352 ARG Chi-restraints excluded: chain D residue 531 GLN Chi-restraints excluded: chain D residue 561 MET Chi-restraints excluded: chain D residue 569 VAL Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 582 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 12 optimal weight: 0.7980 chunk 39 optimal weight: 20.0000 chunk 5 optimal weight: 1.9990 chunk 162 optimal weight: 0.7980 chunk 145 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 97 optimal weight: 8.9990 chunk 115 optimal weight: 1.9990 chunk 37 optimal weight: 10.0000 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 407 ASN D 531 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.196911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.126865 restraints weight = 28576.385| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 3.14 r_work: 0.3256 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3262 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3262 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 14944 Z= 0.142 Angle : 0.523 8.288 20293 Z= 0.273 Chirality : 0.041 0.151 2309 Planarity : 0.004 0.040 2491 Dihedral : 12.653 151.930 2152 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.64 % Allowed : 22.00 % Favored : 75.36 % 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: 0.46 (0.20), residues: 1755 helix: 1.21 (0.15), residues: 1160 sheet: -1.21 (0.64), residues: 63 loop : -1.49 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 569 TYR 0.014 0.001 TYR B 352 PHE 0.026 0.001 PHE D 516 TRP 0.015 0.001 TRP B 445 HIS 0.003 0.001 HIS B 473 Details of bonding type rmsd covalent geometry : bond 0.00330 (14941) covalent geometry : angle 0.52156 (20284) hydrogen bonds : bond 0.04113 ( 925) hydrogen bonds : angle 4.10040 ( 2683) link_NAG-ASN : bond 0.00071 ( 3) link_NAG-ASN : angle 2.10229 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 176 time to evaluate : 0.523 Fit side-chains revert: symmetry clash REVERT: A 270 TYR cc_start: 0.5903 (OUTLIER) cc_final: 0.4537 (t80) REVERT: A 391 ILE cc_start: 0.6953 (OUTLIER) cc_final: 0.5696 (mp) REVERT: A 418 ASP cc_start: 0.6753 (m-30) cc_final: 0.6365 (p0) REVERT: A 448 LYS cc_start: 0.8643 (mtpp) cc_final: 0.8152 (ptpp) REVERT: A 599 GLU cc_start: 0.8200 (tt0) cc_final: 0.7077 (tm-30) REVERT: B 238 ARG cc_start: 0.7710 (mmm-85) cc_final: 0.7337 (ttp80) REVERT: B 270 TYR cc_start: 0.4792 (OUTLIER) cc_final: 0.3839 (p90) REVERT: B 392 PHE cc_start: 0.7842 (t80) cc_final: 0.7509 (t80) REVERT: B 425 GLN cc_start: 0.6618 (mp10) cc_final: 0.6267 (mp10) REVERT: B 514 ASP cc_start: 0.8699 (t0) cc_final: 0.8035 (m-30) REVERT: B 570 SER cc_start: 0.9002 (m) cc_final: 0.8205 (p) REVERT: C 193 ASP cc_start: 0.8471 (t70) cc_final: 0.8136 (t0) REVERT: C 223 ARG cc_start: 0.7972 (mtt-85) cc_final: 0.7578 (mtm-85) REVERT: C 426 PHE cc_start: 0.5450 (OUTLIER) cc_final: 0.4613 (t80) REVERT: C 439 ARG cc_start: 0.7933 (mtm180) cc_final: 0.7517 (mtp180) REVERT: C 455 GLU cc_start: 0.8173 (mp0) cc_final: 0.7862 (mp0) REVERT: D 261 ASP cc_start: 0.8266 (m-30) cc_final: 0.8020 (m-30) REVERT: D 279 ARG cc_start: 0.8378 (tmm-80) cc_final: 0.8031 (ttp-170) REVERT: D 352 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.7760 (mtm-85) REVERT: D 443 ASP cc_start: 0.8656 (t0) cc_final: 0.8218 (t0) REVERT: D 497 ASP cc_start: 0.8529 (t0) cc_final: 0.8077 (t0) REVERT: D 531 GLN cc_start: 0.6814 (OUTLIER) cc_final: 0.6366 (mm110) REVERT: D 556 GLU cc_start: 0.8785 (tp30) cc_final: 0.7791 (tt0) REVERT: D 608 VAL cc_start: 0.8849 (t) cc_final: 0.8596 (p) outliers start: 42 outliers final: 22 residues processed: 206 average time/residue: 0.1171 time to fit residues: 36.3434 Evaluate side-chains 196 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 168 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 TYR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 270 TYR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 398 ASN Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 426 PHE Chi-restraints excluded: chain C residue 510 CYS Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 591 TYR Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 352 ARG Chi-restraints excluded: chain D residue 492 MET Chi-restraints excluded: chain D residue 531 GLN Chi-restraints excluded: chain D residue 561 MET Chi-restraints excluded: chain D residue 569 VAL Chi-restraints excluded: chain D residue 580 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 132 optimal weight: 4.9990 chunk 167 optimal weight: 6.9990 chunk 173 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 27 optimal weight: 8.9990 chunk 64 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 152 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 164 optimal weight: 6.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 276 GLN D 531 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.189722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.125177 restraints weight = 23501.607| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.73 r_work: 0.3226 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3224 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3224 r_free = 0.3224 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3224 r_free = 0.3224 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3224 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 14944 Z= 0.262 Angle : 0.629 9.328 20293 Z= 0.328 Chirality : 0.045 0.166 2309 Planarity : 0.004 0.039 2491 Dihedral : 12.734 152.247 2152 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.02 % Allowed : 22.25 % Favored : 74.73 % 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: 0.14 (0.20), residues: 1755 helix: 0.95 (0.15), residues: 1153 sheet: -1.33 (0.65), residues: 63 loop : -1.53 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 324 TYR 0.018 0.002 TYR B 352 PHE 0.022 0.002 PHE D 516 TRP 0.016 0.002 TRP B 445 HIS 0.003 0.001 HIS C 242 Details of bonding type rmsd covalent geometry : bond 0.00634 (14941) covalent geometry : angle 0.62770 (20284) hydrogen bonds : bond 0.04855 ( 925) hydrogen bonds : angle 4.36723 ( 2683) link_NAG-ASN : bond 0.00218 ( 3) link_NAG-ASN : angle 2.32282 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 174 time to evaluate : 0.552 Fit side-chains revert: symmetry clash REVERT: A 270 TYR cc_start: 0.5901 (OUTLIER) cc_final: 0.4366 (t80) REVERT: A 391 ILE cc_start: 0.7095 (OUTLIER) cc_final: 0.5853 (mp) REVERT: A 418 ASP cc_start: 0.6778 (m-30) cc_final: 0.6416 (p0) REVERT: A 448 LYS cc_start: 0.8645 (mtpp) cc_final: 0.8230 (ptpp) REVERT: B 184 TYR cc_start: 0.7164 (OUTLIER) cc_final: 0.6951 (m-80) REVERT: B 238 ARG cc_start: 0.7783 (mmm-85) cc_final: 0.7475 (ttp80) REVERT: B 270 TYR cc_start: 0.4808 (OUTLIER) cc_final: 0.3849 (p90) REVERT: B 392 PHE cc_start: 0.7982 (t80) cc_final: 0.7516 (t80) REVERT: B 425 GLN cc_start: 0.6544 (mp10) cc_final: 0.6197 (mp10) REVERT: B 514 ASP cc_start: 0.8742 (t0) cc_final: 0.8122 (m-30) REVERT: B 519 MET cc_start: 0.7769 (OUTLIER) cc_final: 0.7323 (ttp) REVERT: B 570 SER cc_start: 0.9064 (m) cc_final: 0.8351 (p) REVERT: C 211 ASP cc_start: 0.8357 (m-30) cc_final: 0.7810 (m-30) REVERT: C 223 ARG cc_start: 0.7984 (mtt-85) cc_final: 0.7600 (mtm-85) REVERT: C 426 PHE cc_start: 0.5485 (OUTLIER) cc_final: 0.4735 (t80) REVERT: C 439 ARG cc_start: 0.8005 (mtm180) cc_final: 0.7504 (mtp85) REVERT: D 443 ASP cc_start: 0.8703 (t0) cc_final: 0.8286 (t0) REVERT: D 497 ASP cc_start: 0.8525 (t0) cc_final: 0.8105 (t0) REVERT: D 556 GLU cc_start: 0.8786 (tp30) cc_final: 0.7903 (tt0) REVERT: D 608 VAL cc_start: 0.8916 (t) cc_final: 0.8635 (p) outliers start: 48 outliers final: 29 residues processed: 208 average time/residue: 0.1148 time to fit residues: 36.2813 Evaluate side-chains 202 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 167 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain B residue 184 TYR Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 270 TYR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 398 ASN Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 519 MET Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 426 PHE Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 510 CYS Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 276 GLN Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 471 ILE Chi-restraints excluded: chain D residue 492 MET Chi-restraints excluded: chain D residue 561 MET Chi-restraints excluded: chain D residue 569 VAL Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 605 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 11 optimal weight: 0.9990 chunk 78 optimal weight: 6.9990 chunk 134 optimal weight: 0.8980 chunk 101 optimal weight: 0.2980 chunk 71 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 72 optimal weight: 6.9990 chunk 70 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 10 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 HIS ** C 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 453 ASN D 531 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.195142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.127623 restraints weight = 27117.173| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.78 r_work: 0.3270 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3278 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3278 r_free = 0.3278 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3278 r_free = 0.3278 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3278 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 14944 Z= 0.122 Angle : 0.513 8.256 20293 Z= 0.268 Chirality : 0.040 0.145 2309 Planarity : 0.004 0.037 2491 Dihedral : 12.469 153.332 2148 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.83 % Allowed : 22.56 % Favored : 74.61 % 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: 0.69 (0.20), residues: 1755 helix: 1.41 (0.15), residues: 1152 sheet: -1.38 (0.64), residues: 63 loop : -1.38 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 279 TYR 0.013 0.001 TYR D 377 PHE 0.017 0.001 PHE D 516 TRP 0.017 0.001 TRP B 445 HIS 0.004 0.001 HIS B 473 Details of bonding type rmsd covalent geometry : bond 0.00276 (14941) covalent geometry : angle 0.51132 (20284) hydrogen bonds : bond 0.04018 ( 925) hydrogen bonds : angle 4.06464 ( 2683) link_NAG-ASN : bond 0.00043 ( 3) link_NAG-ASN : angle 2.05708 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 175 time to evaluate : 0.543 Fit side-chains revert: symmetry clash REVERT: A 270 TYR cc_start: 0.5917 (OUTLIER) cc_final: 0.4641 (t80) REVERT: A 391 ILE cc_start: 0.6918 (OUTLIER) cc_final: 0.5722 (mp) REVERT: A 418 ASP cc_start: 0.6638 (m-30) cc_final: 0.6331 (p0) REVERT: A 425 GLN cc_start: 0.6796 (OUTLIER) cc_final: 0.6363 (mm110) REVERT: A 448 LYS cc_start: 0.8627 (mtpp) cc_final: 0.8159 (ptpp) REVERT: B 238 ARG cc_start: 0.7715 (mmm-85) cc_final: 0.7507 (mtm110) REVERT: B 270 TYR cc_start: 0.4899 (OUTLIER) cc_final: 0.3905 (p90) REVERT: B 392 PHE cc_start: 0.7830 (t80) cc_final: 0.7451 (t80) REVERT: B 425 GLN cc_start: 0.6356 (mp10) cc_final: 0.6030 (mp10) REVERT: B 511 LYS cc_start: 0.8212 (mmmt) cc_final: 0.7439 (mttt) REVERT: B 519 MET cc_start: 0.7716 (OUTLIER) cc_final: 0.7255 (ttp) REVERT: B 570 SER cc_start: 0.8984 (m) cc_final: 0.8175 (p) REVERT: C 193 ASP cc_start: 0.8486 (t70) cc_final: 0.8162 (t0) REVERT: C 223 ARG cc_start: 0.7928 (mtt-85) cc_final: 0.7551 (mtm-85) REVERT: C 426 PHE cc_start: 0.5429 (OUTLIER) cc_final: 0.4566 (t80) REVERT: C 439 ARG cc_start: 0.7905 (mtm180) cc_final: 0.7392 (mtp180) REVERT: C 455 GLU cc_start: 0.8136 (mp0) cc_final: 0.7815 (mp0) REVERT: D 279 ARG cc_start: 0.8440 (tmm-80) cc_final: 0.8097 (ttp-170) REVERT: D 443 ASP cc_start: 0.8600 (t0) cc_final: 0.8141 (t0) REVERT: D 497 ASP cc_start: 0.8557 (t0) cc_final: 0.8131 (t0) REVERT: D 608 VAL cc_start: 0.8901 (t) cc_final: 0.8630 (p) outliers start: 45 outliers final: 25 residues processed: 209 average time/residue: 0.1203 time to fit residues: 37.6196 Evaluate side-chains 197 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 166 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 270 TYR Chi-restraints excluded: chain B residue 398 ASN Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 519 MET Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 546 TYR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 426 PHE Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 510 CYS Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 591 TYR Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 521 LYS Chi-restraints excluded: chain D residue 561 MET Chi-restraints excluded: chain D residue 569 VAL Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 627 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 69 optimal weight: 0.2980 chunk 53 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 120 optimal weight: 7.9990 chunk 56 optimal weight: 0.8980 chunk 78 optimal weight: 10.0000 chunk 139 optimal weight: 6.9990 chunk 132 optimal weight: 0.2980 chunk 79 optimal weight: 5.9990 chunk 47 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 537 GLN C 299 ASN ** C 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 531 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.196354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.146391 restraints weight = 18316.719| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 4.02 r_work: 0.3209 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3210 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3210 r_free = 0.3210 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3210 r_free = 0.3210 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3210 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 14944 Z= 0.141 Angle : 0.535 9.413 20293 Z= 0.277 Chirality : 0.041 0.173 2309 Planarity : 0.004 0.036 2491 Dihedral : 12.444 153.352 2148 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.45 % Allowed : 23.26 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.20), residues: 1755 helix: 1.47 (0.15), residues: 1153 sheet: -1.36 (0.63), residues: 63 loop : -1.32 (0.27), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 427 TYR 0.014 0.001 TYR B 352 PHE 0.018 0.001 PHE B 426 TRP 0.016 0.001 TRP B 445 HIS 0.003 0.001 HIS B 473 Details of bonding type rmsd covalent geometry : bond 0.00329 (14941) covalent geometry : angle 0.53306 (20284) hydrogen bonds : bond 0.04101 ( 925) hydrogen bonds : angle 4.07161 ( 2683) link_NAG-ASN : bond 0.00073 ( 3) link_NAG-ASN : angle 1.99414 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 174 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 TYR cc_start: 0.5837 (OUTLIER) cc_final: 0.4697 (t80) REVERT: A 391 ILE cc_start: 0.7028 (OUTLIER) cc_final: 0.5749 (mp) REVERT: A 418 ASP cc_start: 0.6618 (m-30) cc_final: 0.6322 (p0) REVERT: A 425 GLN cc_start: 0.6829 (OUTLIER) cc_final: 0.6418 (mm110) REVERT: A 448 LYS cc_start: 0.8610 (mtpp) cc_final: 0.8141 (ptpp) REVERT: B 229 GLN cc_start: 0.8025 (mt0) cc_final: 0.7806 (mt0) REVERT: B 238 ARG cc_start: 0.7722 (mmm-85) cc_final: 0.7478 (ttp80) REVERT: B 270 TYR cc_start: 0.4944 (OUTLIER) cc_final: 0.3951 (p90) REVERT: B 392 PHE cc_start: 0.7899 (t80) cc_final: 0.7533 (t80) REVERT: B 425 GLN cc_start: 0.6325 (mp10) cc_final: 0.6065 (mp10) REVERT: B 511 LYS cc_start: 0.8075 (mmmt) cc_final: 0.7421 (mttt) REVERT: B 519 MET cc_start: 0.7740 (OUTLIER) cc_final: 0.7195 (ttp) REVERT: B 570 SER cc_start: 0.8990 (m) cc_final: 0.8260 (p) REVERT: C 211 ASP cc_start: 0.8190 (m-30) cc_final: 0.7939 (m-30) REVERT: C 223 ARG cc_start: 0.8057 (mtt-85) cc_final: 0.7651 (mtm-85) REVERT: C 426 PHE cc_start: 0.5495 (OUTLIER) cc_final: 0.4763 (t80) REVERT: C 439 ARG cc_start: 0.7971 (mtm180) cc_final: 0.7560 (mtp180) REVERT: D 279 ARG cc_start: 0.8485 (tmm-80) cc_final: 0.8125 (ttp-170) REVERT: D 443 ASP cc_start: 0.8659 (t0) cc_final: 0.8224 (t0) REVERT: D 497 ASP cc_start: 0.8589 (t0) cc_final: 0.8164 (t0) REVERT: D 608 VAL cc_start: 0.8902 (t) cc_final: 0.8635 (p) outliers start: 39 outliers final: 28 residues processed: 201 average time/residue: 0.1214 time to fit residues: 36.4756 Evaluate side-chains 203 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 169 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 270 TYR Chi-restraints excluded: chain B residue 398 ASN Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 519 MET Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain C residue 406 MET Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 426 PHE Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 510 CYS Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 591 TYR Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 521 LYS Chi-restraints excluded: chain D residue 561 MET Chi-restraints excluded: chain D residue 569 VAL Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 605 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 171 optimal weight: 20.0000 chunk 36 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 67 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN A 414 GLN ** C 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 276 GLN D 452 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.192792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 103)---------------| | r_work = 0.3446 r_free = 0.3446 target = 0.126168 restraints weight = 24451.493| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 3.03 r_work: 0.3229 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3233 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3233 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 14944 Z= 0.189 Angle : 0.565 9.024 20293 Z= 0.295 Chirality : 0.043 0.155 2309 Planarity : 0.004 0.036 2491 Dihedral : 12.476 154.137 2148 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.89 % Allowed : 22.88 % Favored : 74.23 % 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: 0.65 (0.20), residues: 1755 helix: 1.34 (0.15), residues: 1151 sheet: -1.30 (0.62), residues: 63 loop : -1.33 (0.27), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 279 TYR 0.016 0.001 TYR B 352 PHE 0.021 0.001 PHE C 413 TRP 0.016 0.001 TRP B 445 HIS 0.003 0.001 HIS B 473 Details of bonding type rmsd covalent geometry : bond 0.00453 (14941) covalent geometry : angle 0.56389 (20284) hydrogen bonds : bond 0.04367 ( 925) hydrogen bonds : angle 4.17736 ( 2683) link_NAG-ASN : bond 0.00144 ( 3) link_NAG-ASN : angle 2.07040 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 175 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 TYR cc_start: 0.5847 (OUTLIER) cc_final: 0.4634 (t80) REVERT: A 391 ILE cc_start: 0.7021 (OUTLIER) cc_final: 0.5768 (mp) REVERT: A 448 LYS cc_start: 0.8634 (mtpp) cc_final: 0.8243 (ptpp) REVERT: A 604 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.8069 (pp30) REVERT: B 238 ARG cc_start: 0.7772 (mmm-85) cc_final: 0.7494 (ttp80) REVERT: B 270 TYR cc_start: 0.4939 (OUTLIER) cc_final: 0.3942 (p90) REVERT: B 392 PHE cc_start: 0.7916 (t80) cc_final: 0.7512 (t80) REVERT: B 425 GLN cc_start: 0.6189 (mp10) cc_final: 0.5915 (mp10) REVERT: B 511 LYS cc_start: 0.7985 (mmmt) cc_final: 0.7341 (mttt) REVERT: B 519 MET cc_start: 0.7649 (OUTLIER) cc_final: 0.7114 (ttp) REVERT: B 569 ARG cc_start: 0.7902 (mmm-85) cc_final: 0.7612 (mmm-85) REVERT: B 570 SER cc_start: 0.9021 (m) cc_final: 0.8301 (p) REVERT: C 211 ASP cc_start: 0.8192 (m-30) cc_final: 0.7968 (m-30) REVERT: C 223 ARG cc_start: 0.7955 (mtt-85) cc_final: 0.7554 (mtm-85) REVERT: C 426 PHE cc_start: 0.5492 (OUTLIER) cc_final: 0.4760 (t80) REVERT: C 439 ARG cc_start: 0.7947 (mtm180) cc_final: 0.7518 (mtp180) REVERT: D 279 ARG cc_start: 0.8467 (tmm-80) cc_final: 0.8101 (ttp-170) REVERT: D 443 ASP cc_start: 0.8693 (t0) cc_final: 0.8260 (t0) REVERT: D 497 ASP cc_start: 0.8585 (t0) cc_final: 0.8168 (t0) REVERT: D 608 VAL cc_start: 0.8902 (t) cc_final: 0.8620 (p) outliers start: 46 outliers final: 35 residues processed: 209 average time/residue: 0.1216 time to fit residues: 37.7450 Evaluate side-chains 211 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 170 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 TYR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 604 GLN Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 270 TYR Chi-restraints excluded: chain B residue 398 ASN Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 519 MET Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain C residue 406 MET Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 426 PHE Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 510 CYS Chi-restraints excluded: chain C residue 591 TYR Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 245 GLN Chi-restraints excluded: chain D residue 276 GLN Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 471 ILE Chi-restraints excluded: chain D residue 521 LYS Chi-restraints excluded: chain D residue 561 MET Chi-restraints excluded: chain D residue 569 VAL Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 605 THR Chi-restraints excluded: chain D residue 627 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 135 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 25 optimal weight: 6.9990 chunk 98 optimal weight: 0.9990 chunk 121 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 161 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 398 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.195258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 103)---------------| | r_work = 0.3514 r_free = 0.3514 target = 0.130622 restraints weight = 26170.483| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 3.08 r_work: 0.3287 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3286 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3286 r_free = 0.3286 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3286 r_free = 0.3286 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3286 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 14944 Z= 0.128 Angle : 0.546 12.004 20293 Z= 0.281 Chirality : 0.042 0.388 2309 Planarity : 0.003 0.036 2491 Dihedral : 12.404 153.807 2148 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.26 % Allowed : 23.57 % Favored : 74.17 % 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: 0.86 (0.20), residues: 1755 helix: 1.50 (0.15), residues: 1152 sheet: -1.21 (0.62), residues: 63 loop : -1.23 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 279 TYR 0.014 0.001 TYR D 377 PHE 0.028 0.001 PHE C 413 TRP 0.017 0.001 TRP B 445 HIS 0.004 0.001 HIS B 473 Details of bonding type rmsd covalent geometry : bond 0.00292 (14941) covalent geometry : angle 0.54470 (20284) hydrogen bonds : bond 0.04024 ( 925) hydrogen bonds : angle 4.08177 ( 2683) link_NAG-ASN : bond 0.00060 ( 3) link_NAG-ASN : angle 1.96986 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 172 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 TYR cc_start: 0.5911 (OUTLIER) cc_final: 0.4797 (t80) REVERT: A 448 LYS cc_start: 0.8622 (mtpp) cc_final: 0.8170 (ptpp) REVERT: A 604 GLN cc_start: 0.8356 (OUTLIER) cc_final: 0.8051 (pp30) REVERT: B 229 GLN cc_start: 0.7937 (mt0) cc_final: 0.7726 (mt0) REVERT: B 238 ARG cc_start: 0.7709 (mmm-85) cc_final: 0.7489 (ttp80) REVERT: B 270 TYR cc_start: 0.4975 (OUTLIER) cc_final: 0.3995 (p90) REVERT: B 392 PHE cc_start: 0.7820 (t80) cc_final: 0.7435 (t80) REVERT: B 412 GLU cc_start: 0.7309 (tp30) cc_final: 0.6826 (pt0) REVERT: B 425 GLN cc_start: 0.6112 (mp10) cc_final: 0.5872 (mp10) REVERT: B 511 LYS cc_start: 0.7999 (mmmt) cc_final: 0.7464 (mmtp) REVERT: B 519 MET cc_start: 0.7648 (OUTLIER) cc_final: 0.7091 (ttp) REVERT: B 570 SER cc_start: 0.8971 (m) cc_final: 0.8193 (p) REVERT: C 223 ARG cc_start: 0.7930 (mtt-85) cc_final: 0.7577 (mtm-85) REVERT: C 426 PHE cc_start: 0.5517 (OUTLIER) cc_final: 0.4786 (t80) REVERT: C 439 ARG cc_start: 0.7907 (mtm180) cc_final: 0.7427 (mtp180) REVERT: D 279 ARG cc_start: 0.8426 (tmm-80) cc_final: 0.8058 (ttp-170) REVERT: D 443 ASP cc_start: 0.8652 (t0) cc_final: 0.8216 (t0) REVERT: D 497 ASP cc_start: 0.8545 (t0) cc_final: 0.8130 (t0) REVERT: D 608 VAL cc_start: 0.8877 (t) cc_final: 0.8611 (p) outliers start: 36 outliers final: 29 residues processed: 201 average time/residue: 0.1189 time to fit residues: 35.7794 Evaluate side-chains 203 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 169 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 604 GLN Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 270 TYR Chi-restraints excluded: chain B residue 398 ASN Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 519 MET Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain C residue 398 ASN Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 426 PHE Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 510 CYS Chi-restraints excluded: chain C residue 591 TYR Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 245 GLN Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 521 LYS Chi-restraints excluded: chain D residue 561 MET Chi-restraints excluded: chain D residue 569 VAL Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 627 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 52 optimal weight: 1.9990 chunk 78 optimal weight: 10.0000 chunk 149 optimal weight: 0.4980 chunk 161 optimal weight: 0.6980 chunk 99 optimal weight: 0.8980 chunk 170 optimal weight: 8.9990 chunk 113 optimal weight: 0.7980 chunk 107 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 chunk 151 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.197014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.129400 restraints weight = 20826.516| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.68 r_work: 0.3280 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3282 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3282 r_free = 0.3282 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3282 r_free = 0.3282 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3282 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.155 14944 Z= 0.183 Angle : 0.765 59.184 20293 Z= 0.442 Chirality : 0.047 1.135 2309 Planarity : 0.004 0.084 2491 Dihedral : 12.411 153.811 2148 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.07 % Allowed : 23.63 % Favored : 74.29 % 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: 0.85 (0.20), residues: 1755 helix: 1.48 (0.15), residues: 1152 sheet: -1.20 (0.62), residues: 63 loop : -1.22 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 324 TYR 0.014 0.001 TYR B 352 PHE 0.026 0.001 PHE C 413 TRP 0.015 0.001 TRP B 445 HIS 0.003 0.001 HIS B 473 Details of bonding type rmsd covalent geometry : bond 0.00357 (14941) covalent geometry : angle 0.76397 (20284) hydrogen bonds : bond 0.04041 ( 925) hydrogen bonds : angle 4.09676 ( 2683) link_NAG-ASN : bond 0.00063 ( 3) link_NAG-ASN : angle 1.97040 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4059.24 seconds wall clock time: 70 minutes 12.77 seconds (4212.77 seconds total)