Starting phenix.real_space_refine on Fri Sep 11 22:19:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6p25_20236/09_2026/6p25_20236_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6p25_20236/09_2026/6p25_20236.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6p25_20236/09_2026/6p25_20236.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6p25_20236/09_2026/6p25_20236.map" model { file = "/net/cci-nas-00/data/ceres_data/6p25_20236/09_2026/6p25_20236_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6p25_20236/09_2026/6p25_20236_neut.cif" } resolution = 3.2 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= 0.007 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 62 5.16 5 C 7739 2.51 5 N 1891 2.21 5 O 2043 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11739 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 731, 5879 Classifications: {'peptide': 731} Link IDs: {'PTRANS': 31, 'TRANS': 699} Chain breaks: 1 Chain: "B" Number of atoms: 5605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5605 Classifications: {'peptide': 690} Link IDs: {'PTRANS': 31, 'TRANS': 658} Chain breaks: 1 Chain: "D" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 26 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Chain: "A" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 111 Unusual residues: {'CPL': 1, 'NAG': 1, 'NNM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 118 Unusual residues: {'CPL': 2, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.37, per 1000 atoms: 0.20 Number of scatterers: 11739 At special positions: 0 Unit cell: (109.074, 107.016, 108.045, 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 62 16.00 P 4 15.00 O 2043 8.00 N 1891 7.00 C 7739 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 490 " - pdb=" SG CYS B 511 " distance=2.04 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 A1001 " - " ASN A 390 " " NAG B1001 " - " ASN B 131 " Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 457.0 milliseconds 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2660 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 11 sheets defined 52.3% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 35 through 42 removed outlier: 3.510A pdb=" N ALA A 39 " --> pdb=" O SER A 35 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG A 42 " --> pdb=" O LEU A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 64 removed outlier: 3.901A pdb=" N LYS A 50 " --> pdb=" O THR A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 91 removed outlier: 3.903A pdb=" N PHE A 81 " --> pdb=" O ASP A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 113 removed outlier: 4.838A pdb=" N TYR A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 159 removed outlier: 4.430A pdb=" N VAL A 149 " --> pdb=" O GLY A 145 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ILE A 150 " --> pdb=" O ALA A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 175 Processing helix chain 'A' and resid 176 through 185 removed outlier: 3.922A pdb=" N TYR A 185 " --> pdb=" O THR A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 208 removed outlier: 3.625A pdb=" N MET A 208 " --> pdb=" O LYS A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 232 removed outlier: 3.567A pdb=" N TYR A 217 " --> pdb=" O SER A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 258 Processing helix chain 'A' and resid 262 through 296 removed outlier: 4.324A pdb=" N VAL A 280 " --> pdb=" O PHE A 276 " (cutoff:3.500A) Proline residue: A 281 - end of helix Processing helix chain 'A' and resid 310 through 314 Processing helix chain 'A' and resid 368 through 371 removed outlier: 3.694A pdb=" N ASN A 371 " --> pdb=" O ASP A 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 368 through 371' Processing helix chain 'A' and resid 438 through 441 removed outlier: 3.637A pdb=" N ASP A 441 " --> pdb=" O ASP A 438 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 438 through 441' Processing helix chain 'A' and resid 455 through 460 removed outlier: 3.830A pdb=" N GLU A 459 " --> pdb=" O GLY A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 507 removed outlier: 3.520A pdb=" N THR A 507 " --> pdb=" O HIS A 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 504 through 507' Processing helix chain 'A' and resid 532 through 550 Processing helix chain 'A' and resid 560 through 567 removed outlier: 3.526A pdb=" N TRP A 564 " --> pdb=" O PRO A 561 " (cutoff:3.500A) Proline residue: A 565 - end of helix Processing helix chain 'A' and resid 586 through 614 removed outlier: 4.167A pdb=" N ALA A 592 " --> pdb=" O ILE A 588 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY A 614 " --> pdb=" O SER A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 640 Processing helix chain 'A' and resid 641 through 645 Processing helix chain 'A' and resid 652 through 655 Processing helix chain 'A' and resid 656 through 677 removed outlier: 3.780A pdb=" N PHE A 662 " --> pdb=" O PRO A 658 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR A 677 " --> pdb=" O ILE A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 704 removed outlier: 3.740A pdb=" N GLY A 686 " --> pdb=" O LYS A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 708 Processing helix chain 'A' and resid 714 through 722 removed outlier: 3.930A pdb=" N LYS A 720 " --> pdb=" O GLU A 716 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLN A 722 " --> pdb=" O CYS A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 743 removed outlier: 4.026A pdb=" N LYS A 742 " --> pdb=" O LEU A 738 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASN A 743 " --> pdb=" O GLU A 739 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 738 through 743' Processing helix chain 'B' and resid 58 through 80 Proline residue: B 68 - end of helix Processing helix chain 'B' and resid 82 through 86 removed outlier: 3.973A pdb=" N ILE B 85 " --> pdb=" O LYS B 82 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ASN B 86 " --> pdb=" O ILE B 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 82 through 86' Processing helix chain 'B' and resid 92 through 105 removed outlier: 3.667A pdb=" N LYS B 98 " --> pdb=" O ALA B 94 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TYR B 103 " --> pdb=" O PHE B 99 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU B 104 " --> pdb=" O GLY B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 127 Processing helix chain 'B' and resid 147 through 173 removed outlier: 4.085A pdb=" N MET B 151 " --> pdb=" O ASP B 147 " (cutoff:3.500A) Proline residue: B 164 - end of helix Processing helix chain 'B' and resid 177 through 189 Processing helix chain 'B' and resid 190 through 197 Processing helix chain 'B' and resid 202 through 222 Processing helix chain 'B' and resid 229 through 250 removed outlier: 3.696A pdb=" N LYS B 250 " --> pdb=" O THR B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 272 removed outlier: 4.079A pdb=" N ILE B 257 " --> pdb=" O GLY B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 294 Processing helix chain 'B' and resid 294 through 312 removed outlier: 3.700A pdb=" N PHE B 301 " --> pdb=" O PRO B 297 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU B 312 " --> pdb=" O HIS B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 322 removed outlier: 3.790A pdb=" N ASN B 321 " --> pdb=" O GLY B 318 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N MET B 322 " --> pdb=" O ASP B 319 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 318 through 322' Processing helix chain 'B' and resid 323 through 330 removed outlier: 3.639A pdb=" N LEU B 330 " --> pdb=" O PHE B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 387 Processing helix chain 'B' and resid 453 through 456 removed outlier: 3.917A pdb=" N ASP B 456 " --> pdb=" O ASP B 453 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 453 through 456' Processing helix chain 'B' and resid 500 through 504 removed outlier: 3.674A pdb=" N PHE B 504 " --> pdb=" O GLU B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 565 Processing helix chain 'B' and resid 579 through 583 Processing helix chain 'B' and resid 609 through 634 removed outlier: 3.724A pdb=" N ALA B 613 " --> pdb=" O ALA B 609 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA B 623 " --> pdb=" O LEU B 619 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N THR B 624 " --> pdb=" O ALA B 620 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL B 626 " --> pdb=" O MET B 622 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ILE B 627 " --> pdb=" O ALA B 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 652 Processing helix chain 'B' and resid 652 through 669 Proline residue: B 665 - end of helix Processing helix chain 'B' and resid 674 through 676 No H-bonds generated for 'chain 'B' and resid 674 through 676' Processing helix chain 'B' and resid 677 through 695 removed outlier: 4.752A pdb=" N ALA B 681 " --> pdb=" O HIS B 677 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR B 683 " --> pdb=" O LEU B 679 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE B 684 " --> pdb=" O PRO B 680 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA B 685 " --> pdb=" O ALA B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 698 through 702 removed outlier: 3.848A pdb=" N ARG B 702 " --> pdb=" O LYS B 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 728 Processing helix chain 'B' and resid 729 through 734 Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 23 Processing sheet with id=AA2, first strand: chain 'A' and resid 323 through 324 Processing sheet with id=AA3, first strand: chain 'A' and resid 332 through 337 removed outlier: 3.750A pdb=" N THR A 395 " --> pdb=" O VAL A 445 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ASN A 514 " --> pdb=" O ILE A 332 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ILE A 332 " --> pdb=" O ASN A 514 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 345 through 351 removed outlier: 3.964A pdb=" N HIS A 348 " --> pdb=" O GLN A 360 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLN A 360 " --> pdb=" O HIS A 348 " (cutoff:3.500A) removed outlier: 16.566A pdb=" N GLN A 359 " --> pdb=" O CYS A 498 " (cutoff:3.500A) removed outlier: 12.055A pdb=" N CYS A 498 " --> pdb=" O GLN A 359 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N SER A 361 " --> pdb=" O VAL A 496 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 345 through 351 removed outlier: 3.964A pdb=" N HIS A 348 " --> pdb=" O GLN A 360 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLN A 360 " --> pdb=" O HIS A 348 " (cutoff:3.500A) removed outlier: 16.566A pdb=" N GLN A 359 " --> pdb=" O CYS A 498 " (cutoff:3.500A) removed outlier: 12.055A pdb=" N CYS A 498 " --> pdb=" O GLN A 359 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N SER A 361 " --> pdb=" O VAL A 496 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N GLN A 493 " --> pdb=" O VAL A 484 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N VAL A 484 " --> pdb=" O GLN A 493 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N GLU A 495 " --> pdb=" O HIS A 482 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N HIS A 482 " --> pdb=" O GLU A 495 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 571 through 576 removed outlier: 6.405A pdb=" N VAL A 581 " --> pdb=" O TYR A 573 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N GLY A 575 " --> pdb=" O ARG A 579 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ARG A 579 " --> pdb=" O GLY A 575 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 348 through 353 removed outlier: 6.583A pdb=" N VAL B 348 " --> pdb=" O HIS B 529 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N HIS B 529 " --> pdb=" O VAL B 348 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N SER B 350 " --> pdb=" O GLU B 527 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 360 through 367 removed outlier: 3.766A pdb=" N HIS B 364 " --> pdb=" O GLN B 376 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLN B 376 " --> pdb=" O HIS B 364 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N VAL B 377 " --> pdb=" O VAL B 443 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N VAL B 443 " --> pdb=" O VAL B 377 " (cutoff:3.500A) removed outlier: 13.099A pdb=" N CYS B 379 " --> pdb=" O TRP B 441 " (cutoff:3.500A) removed outlier: 17.844A pdb=" N TRP B 441 " --> pdb=" O CYS B 379 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLU B 442 " --> pdb=" O HIS B 430 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 389 through 392 removed outlier: 3.643A pdb=" N LYS B 484 " --> pdb=" O VAL B 459 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N SER B 480 " --> pdb=" O MET B 463 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 491 through 498 removed outlier: 3.709A pdb=" N THR B 495 " --> pdb=" O GLU B 508 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N GLU B 508 " --> pdb=" O THR B 495 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 590 through 591 550 hydrogen bonds defined for protein. 1572 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: 2.12 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1750 1.30 - 1.43: 3607 1.43 - 1.56: 6625 1.56 - 1.68: 19 1.68 - 1.81: 105 Bond restraints: 12106 Sorted by residual: bond pdb=" C18 NNM A1003 " pdb=" C19 NNM A1003 " ideal model delta sigma weight residual 1.332 1.561 -0.229 2.00e-02 2.50e+03 1.31e+02 bond pdb=" C38 NNM A1003 " pdb=" C39 NNM A1003 " ideal model delta sigma weight residual 1.332 1.544 -0.212 2.00e-02 2.50e+03 1.12e+02 bond pdb=" C28 NNM A1003 " pdb=" C29 NNM A1003 " ideal model delta sigma weight residual 1.332 1.541 -0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" C13 NNM A1003 " pdb=" C14 NNM A1003 " ideal model delta sigma weight residual 1.332 1.541 -0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" C23 NNM A1003 " pdb=" C24 NNM A1003 " ideal model delta sigma weight residual 1.332 1.538 -0.206 2.00e-02 2.50e+03 1.06e+02 ... (remaining 12101 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.41: 16073 3.41 - 6.82: 290 6.82 - 10.23: 58 10.23 - 13.64: 6 13.64 - 17.04: 5 Bond angle restraints: 16432 Sorted by residual: angle pdb=" N ALA A 531 " pdb=" CA ALA A 531 " pdb=" C ALA A 531 " ideal model delta sigma weight residual 111.24 122.55 -11.31 1.38e+00 5.25e-01 6.71e+01 angle pdb=" C16 NNM A1003 " pdb=" C17 NNM A1003 " pdb=" C18 NNM A1003 " ideal model delta sigma weight residual 112.52 129.56 -17.04 3.00e+00 1.11e-01 3.23e+01 angle pdb=" N LYS A 529 " pdb=" CA LYS A 529 " pdb=" C LYS A 529 " ideal model delta sigma weight residual 109.83 102.66 7.17 1.27e+00 6.20e-01 3.19e+01 angle pdb=" O3P CPL A1002 " pdb=" P CPL A1002 " pdb=" O4P CPL A1002 " ideal model delta sigma weight residual 93.29 109.93 -16.64 3.00e+00 1.11e-01 3.08e+01 angle pdb=" O3P CPL B1002 " pdb=" P CPL B1002 " pdb=" O4P CPL B1002 " ideal model delta sigma weight residual 93.29 109.79 -16.50 3.00e+00 1.11e-01 3.02e+01 ... (remaining 16427 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.84: 6896 35.84 - 71.68: 90 71.68 - 107.52: 16 107.52 - 143.36: 1 143.36 - 179.20: 1 Dihedral angle restraints: 7004 sinusoidal: 2853 harmonic: 4151 Sorted by residual: dihedral pdb=" CA PRO A 712 " pdb=" C PRO A 712 " pdb=" N TRP A 713 " pdb=" CA TRP A 713 " ideal model delta harmonic sigma weight residual 180.00 152.69 27.31 0 5.00e+00 4.00e-02 2.98e+01 dihedral pdb=" CA TRP B 583 " pdb=" C TRP B 583 " pdb=" N PRO B 584 " pdb=" CA PRO B 584 " ideal model delta harmonic sigma weight residual 180.00 154.79 25.21 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA GLY A 160 " pdb=" C GLY A 160 " pdb=" N VAL A 161 " pdb=" CA VAL A 161 " ideal model delta harmonic sigma weight residual -180.00 -154.97 -25.03 0 5.00e+00 4.00e-02 2.51e+01 ... (remaining 7001 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1480 0.077 - 0.154: 239 0.154 - 0.230: 26 0.230 - 0.307: 3 0.307 - 0.384: 2 Chirality restraints: 1750 Sorted by residual: chirality pdb=" CA ALA A 531 " pdb=" N ALA A 531 " pdb=" C ALA A 531 " pdb=" CB ALA A 531 " both_signs ideal model delta sigma weight residual False 2.48 2.10 0.38 2.00e-01 2.50e+01 3.68e+00 chirality pdb=" CA PRO A 530 " pdb=" N PRO A 530 " pdb=" C PRO A 530 " pdb=" CB PRO A 530 " both_signs ideal model delta sigma weight residual False 2.72 2.39 0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" CA LEU A 584 " pdb=" N LEU A 584 " pdb=" C LEU A 584 " pdb=" CB LEU A 584 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 1747 not shown) Planarity restraints: 2032 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 654 " -0.053 5.00e-02 4.00e+02 7.94e-02 1.01e+01 pdb=" N PRO B 655 " 0.137 5.00e-02 4.00e+02 pdb=" CA PRO B 655 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 655 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 729 " -0.015 2.00e-02 2.50e+03 3.11e-02 9.69e+00 pdb=" C TYR A 729 " 0.054 2.00e-02 2.50e+03 pdb=" O TYR A 729 " -0.021 2.00e-02 2.50e+03 pdb=" N ASN A 730 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 268 " 0.014 2.00e-02 2.50e+03 2.89e-02 8.36e+00 pdb=" C LEU B 268 " -0.050 2.00e-02 2.50e+03 pdb=" O LEU B 268 " 0.019 2.00e-02 2.50e+03 pdb=" N TRP B 269 " 0.017 2.00e-02 2.50e+03 ... (remaining 2029 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1568 2.76 - 3.29: 11261 3.29 - 3.83: 20331 3.83 - 4.36: 24306 4.36 - 4.90: 41479 Nonbonded interactions: 98945 Sorted by model distance: nonbonded pdb=" O LEU A 151 " pdb=" OG1 THR A 155 " model vdw 2.221 3.040 nonbonded pdb=" OE2 GLU B 93 " pdb=" OH TYR B 142 " model vdw 2.225 3.040 nonbonded pdb=" O PRO B 68 " pdb=" OG1 THR B 72 " model vdw 2.254 3.040 nonbonded pdb=" OG1 THR B 378 " pdb=" OE1 GLN B 506 " model vdw 2.260 3.040 nonbonded pdb=" OD1 ASN A 580 " pdb=" OH TYR A 734 " model vdw 2.275 3.040 ... (remaining 98940 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.110 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 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 : 0.009 0.229 12109 Z= 0.443 Angle : 1.154 17.045 16440 Z= 0.562 Chirality : 0.058 0.384 1750 Planarity : 0.008 0.079 2030 Dihedral : 12.911 179.205 4341 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 0.40 % Allowed : 5.16 % Favored : 94.44 % 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: -4.48 (0.16), residues: 1414 helix: -3.20 (0.13), residues: 652 sheet: -2.90 (0.48), residues: 85 loop : -2.67 (0.19), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 27 TYR 0.044 0.003 TYR A 573 PHE 0.042 0.003 PHE B 301 TRP 0.049 0.003 TRP A 727 HIS 0.018 0.002 HIS A 632 Details of bonding type rmsd/Z covalent geometry : bond 0.00927 / 0.44 (12106) covalent geometry : angle 1.15356 / 0.56 (16432) SS BOND : bond 0.00718 / 0.48 ( 1) SS BOND : angle 1.34052 / 0.72 ( 2) hydrogen bonds : bond 0.12963 / 8.91 ( 545) hydrogen bonds : angle 10.80251 / 7.53 ( 1572) link_NAG-ASN : bond 0.00120 / 0.08 ( 2) link_NAG-ASN : angle 2.60556 / 1.41 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 256 time to evaluate : 0.416 Fit side-chains revert: symmetry clash REVERT: A 21 ILE cc_start: 0.8388 (pt) cc_final: 0.8060 (mt) REVERT: A 315 LYS cc_start: 0.8390 (mtpm) cc_final: 0.8150 (mtmt) REVERT: A 334 SER cc_start: 0.7783 (m) cc_final: 0.7425 (p) REVERT: A 340 THR cc_start: 0.8539 (m) cc_final: 0.8098 (p) REVERT: A 396 LYS cc_start: 0.8313 (ptpt) cc_final: 0.7575 (pttm) REVERT: A 398 ARG cc_start: 0.6870 (mtt180) cc_final: 0.6080 (ttm-80) REVERT: A 465 ASP cc_start: 0.7828 (t0) cc_final: 0.7612 (m-30) REVERT: A 471 ARG cc_start: 0.8016 (ttp80) cc_final: 0.7756 (ttp-170) REVERT: A 529 LYS cc_start: 0.7733 (OUTLIER) cc_final: 0.7095 (tptp) REVERT: A 538 ILE cc_start: 0.8784 (mm) cc_final: 0.8549 (mm) REVERT: A 546 HIS cc_start: 0.7705 (t70) cc_final: 0.7399 (t70) REVERT: A 610 SER cc_start: 0.8911 (t) cc_final: 0.8602 (p) REVERT: A 615 LYS cc_start: 0.7040 (mmtt) cc_final: 0.6827 (mttt) REVERT: B 70 ILE cc_start: 0.8557 (mm) cc_final: 0.8338 (mt) REVERT: B 181 TRP cc_start: 0.8002 (m-10) cc_final: 0.7765 (m-10) REVERT: B 388 GLU cc_start: 0.5196 (mt-10) cc_final: 0.4726 (pm20) REVERT: B 559 MET cc_start: 0.7373 (mtt) cc_final: 0.6889 (mtp) REVERT: B 560 MET cc_start: 0.7399 (mtp) cc_final: 0.6838 (mtp) REVERT: B 709 MET cc_start: 0.6910 (tpt) cc_final: 0.6519 (tpp) REVERT: B 738 PRO cc_start: 0.8218 (Cg_exo) cc_final: 0.7388 (Cg_endo) REVERT: B 753 ILE cc_start: 0.8556 (tt) cc_final: 0.7620 (tt) outliers start: 5 outliers final: 2 residues processed: 260 average time/residue: 0.1009 time to fit residues: 38.0771 Evaluate side-chains 164 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 161 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 713 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 50.0000 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 50.0000 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 HIS A 316 ASN ** A 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 482 HIS A 546 HIS ** A 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 106 HIS B 110 HIS B 221 HIS B 308 HIS B 354 GLN B 465 GLN B 635 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.172181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.118445 restraints weight = 13045.405| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.01 r_work: 0.2985 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12109 Z= 0.159 Angle : 0.642 6.995 16440 Z= 0.329 Chirality : 0.042 0.144 1750 Planarity : 0.005 0.060 2030 Dihedral : 12.804 173.579 1751 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.74 % Allowed : 9.43 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.43 (0.19), residues: 1414 helix: -0.86 (0.18), residues: 661 sheet: -2.47 (0.49), residues: 90 loop : -2.26 (0.20), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 407 TYR 0.014 0.002 TYR A 88 PHE 0.025 0.002 PHE B 301 TRP 0.027 0.002 TRP A 727 HIS 0.010 0.001 HIS A 632 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (12106) covalent geometry : angle 0.64064 / 0.33 (16432) SS BOND : bond 0.00044 / 0.03 ( 1) SS BOND : angle 0.61035 / 0.33 ( 2) hydrogen bonds : bond 0.04248 / 2.79 ( 545) hydrogen bonds : angle 5.88060 / 3.99 ( 1572) link_NAG-ASN : bond 0.00097 / 0.07 ( 2) link_NAG-ASN : angle 1.92149 / 1.08 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 175 time to evaluate : 0.423 Fit side-chains revert: symmetry clash REVERT: A 21 ILE cc_start: 0.8500 (pt) cc_final: 0.8244 (mt) REVERT: A 214 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8116 (tm) REVERT: A 315 LYS cc_start: 0.8579 (mtpm) cc_final: 0.8300 (mtmt) REVERT: A 340 THR cc_start: 0.8721 (m) cc_final: 0.8120 (p) REVERT: A 389 GLN cc_start: 0.7708 (OUTLIER) cc_final: 0.7116 (tt0) REVERT: A 396 LYS cc_start: 0.8472 (ptpt) cc_final: 0.7743 (pttm) REVERT: A 398 ARG cc_start: 0.7222 (mtt180) cc_final: 0.6835 (mtt90) REVERT: A 465 ASP cc_start: 0.8296 (t0) cc_final: 0.8048 (m-30) REVERT: A 529 LYS cc_start: 0.8118 (OUTLIER) cc_final: 0.7170 (tptp) REVERT: A 615 LYS cc_start: 0.7230 (mmtt) cc_final: 0.6898 (mttt) REVERT: A 739 GLU cc_start: 0.7991 (mp0) cc_final: 0.7749 (mp0) REVERT: B 116 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8362 (tp) REVERT: B 277 MET cc_start: 0.9095 (ttm) cc_final: 0.8887 (ttm) REVERT: B 550 LYS cc_start: 0.7326 (mmtm) cc_final: 0.6925 (mmtt) REVERT: B 559 MET cc_start: 0.7791 (mtt) cc_final: 0.7340 (mtp) REVERT: B 560 MET cc_start: 0.7986 (mtp) cc_final: 0.7686 (mtm) REVERT: B 597 ASP cc_start: 0.7655 (m-30) cc_final: 0.7423 (m-30) REVERT: B 650 MET cc_start: 0.8999 (mmm) cc_final: 0.8478 (mmt) REVERT: B 709 MET cc_start: 0.7283 (tpt) cc_final: 0.6915 (tpt) REVERT: B 753 ILE cc_start: 0.8832 (tt) cc_final: 0.8485 (tt) outliers start: 34 outliers final: 12 residues processed: 197 average time/residue: 0.0923 time to fit residues: 27.1999 Evaluate side-chains 162 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 289 PHE Chi-restraints excluded: chain A residue 389 GLN Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 651 MET Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 672 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 72 optimal weight: 8.9990 chunk 48 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 110 optimal weight: 30.0000 chunk 140 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 chunk 101 optimal weight: 20.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 316 ASN ** A 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 GLN ** A 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 627 HIS B 321 ASN B 354 GLN B 564 ASN ** B 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.160049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.104401 restraints weight = 13259.991| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 1.98 r_work: 0.2764 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.070 12109 Z= 0.316 Angle : 0.754 8.781 16440 Z= 0.381 Chirality : 0.048 0.158 1750 Planarity : 0.005 0.057 2030 Dihedral : 12.328 175.631 1747 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 4.27 % Allowed : 10.23 % Favored : 85.50 % 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: -1.63 (0.21), residues: 1414 helix: -0.06 (0.19), residues: 661 sheet: -2.23 (0.48), residues: 101 loop : -1.95 (0.22), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 469 TYR 0.018 0.002 TYR A 510 PHE 0.026 0.003 PHE A 121 TRP 0.034 0.002 TRP A 727 HIS 0.013 0.002 HIS A 632 Details of bonding type rmsd/Z covalent geometry : bond 0.00763 / 0.32 (12106) covalent geometry : angle 0.75352 / 0.38 (16432) SS BOND : bond 0.00181 / 0.12 ( 1) SS BOND : angle 0.25384 / 0.18 ( 2) hydrogen bonds : bond 0.04691 / 3.02 ( 545) hydrogen bonds : angle 5.50032 / 3.70 ( 1572) link_NAG-ASN : bond 0.00168 / 0.12 ( 2) link_NAG-ASN : angle 2.05979 / 1.28 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 149 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 111 SER cc_start: 0.8696 (t) cc_final: 0.8470 (p) REVERT: A 172 CYS cc_start: 0.8954 (t) cc_final: 0.8614 (m) REVERT: A 214 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8173 (tm) REVERT: A 277 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8905 (mp) REVERT: A 315 LYS cc_start: 0.8441 (mtpm) cc_final: 0.8218 (mtmt) REVERT: A 389 GLN cc_start: 0.7735 (OUTLIER) cc_final: 0.7170 (tt0) REVERT: A 398 ARG cc_start: 0.7248 (mtt180) cc_final: 0.6543 (mtt90) REVERT: A 400 PHE cc_start: 0.7925 (t80) cc_final: 0.7539 (t80) REVERT: A 529 LYS cc_start: 0.7957 (OUTLIER) cc_final: 0.7155 (tptp) REVERT: A 615 LYS cc_start: 0.7454 (mmtt) cc_final: 0.7095 (mttt) REVERT: A 634 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.8065 (mm) REVERT: A 739 GLU cc_start: 0.8196 (mp0) cc_final: 0.7949 (mp0) REVERT: A 748 LYS cc_start: 0.8094 (mttp) cc_final: 0.7373 (mtpt) REVERT: B 95 HIS cc_start: 0.8450 (m170) cc_final: 0.8066 (m170) REVERT: B 116 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8305 (tp) REVERT: B 218 VAL cc_start: 0.8849 (OUTLIER) cc_final: 0.8563 (m) REVERT: B 550 LYS cc_start: 0.7268 (mmtm) cc_final: 0.6935 (mmtt) REVERT: B 559 MET cc_start: 0.7946 (mtt) cc_final: 0.7107 (mtp) REVERT: B 560 MET cc_start: 0.7953 (mtp) cc_final: 0.7637 (mtm) REVERT: B 656 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8579 (tp) REVERT: B 709 MET cc_start: 0.7494 (tpt) cc_final: 0.7221 (tpt) REVERT: B 752 ASP cc_start: 0.8449 (p0) cc_final: 0.8100 (m-30) REVERT: B 753 ILE cc_start: 0.9035 (tt) cc_final: 0.8711 (tt) outliers start: 53 outliers final: 26 residues processed: 191 average time/residue: 0.0887 time to fit residues: 25.2011 Evaluate side-chains 164 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 130 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 389 GLN Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 505 ASP Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 651 MET Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 672 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 25 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 28 optimal weight: 0.0970 chunk 82 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 118 optimal weight: 50.0000 chunk 110 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 10 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 HIS ** A 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 GLN ** B 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 587 ASN ** B 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.164656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.108269 restraints weight = 13076.852| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 1.79 r_work: 0.2872 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12109 Z= 0.149 Angle : 0.602 7.017 16440 Z= 0.306 Chirality : 0.042 0.172 1750 Planarity : 0.004 0.052 2030 Dihedral : 11.693 172.641 1747 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 4.27 % Allowed : 10.80 % Favored : 84.93 % 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: -1.07 (0.21), residues: 1414 helix: 0.51 (0.20), residues: 673 sheet: -2.18 (0.53), residues: 89 loop : -1.83 (0.22), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 569 TYR 0.014 0.001 TYR A 641 PHE 0.016 0.001 PHE B 301 TRP 0.024 0.001 TRP A 727 HIS 0.008 0.001 HIS A 632 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (12106) covalent geometry : angle 0.60131 / 0.31 (16432) SS BOND : bond 0.00046 / 0.03 ( 1) SS BOND : angle 0.12347 / 0.07 ( 2) hydrogen bonds : bond 0.04002 / 2.59 ( 545) hydrogen bonds : angle 4.90802 / 3.30 ( 1572) link_NAG-ASN : bond 0.00146 / 0.10 ( 2) link_NAG-ASN : angle 1.91424 / 1.17 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 149 time to evaluate : 0.245 Fit side-chains revert: symmetry clash REVERT: A 214 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8147 (tm) REVERT: A 315 LYS cc_start: 0.8425 (mtpm) cc_final: 0.8087 (mtmt) REVERT: A 329 ILE cc_start: 0.9296 (mt) cc_final: 0.9015 (tt) REVERT: A 398 ARG cc_start: 0.7147 (mtt180) cc_final: 0.6423 (mtt90) REVERT: A 400 PHE cc_start: 0.8064 (t80) cc_final: 0.7753 (t80) REVERT: A 409 HIS cc_start: 0.6672 (t70) cc_final: 0.6275 (t-90) REVERT: A 465 ASP cc_start: 0.8298 (OUTLIER) cc_final: 0.7895 (m-30) REVERT: A 529 LYS cc_start: 0.7991 (ttmt) cc_final: 0.7251 (tptp) REVERT: A 549 LYS cc_start: 0.7271 (ttpt) cc_final: 0.5875 (tppt) REVERT: A 588 ILE cc_start: 0.8507 (tt) cc_final: 0.8221 (mt) REVERT: A 615 LYS cc_start: 0.7458 (mmtt) cc_final: 0.7132 (mttt) REVERT: A 694 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.8037 (tp) REVERT: A 730 ASN cc_start: 0.8557 (t0) cc_final: 0.8074 (t0) REVERT: A 739 GLU cc_start: 0.8201 (mp0) cc_final: 0.7934 (mp0) REVERT: A 748 LYS cc_start: 0.8016 (mttp) cc_final: 0.7363 (mtpt) REVERT: B 116 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8288 (tm) REVERT: B 254 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8201 (mt) REVERT: B 388 GLU cc_start: 0.4960 (mt-10) cc_final: 0.4617 (pm20) REVERT: B 550 LYS cc_start: 0.7255 (mmtm) cc_final: 0.6883 (mmtt) REVERT: B 559 MET cc_start: 0.7893 (mtt) cc_final: 0.7538 (mtt) REVERT: B 560 MET cc_start: 0.7900 (mtp) cc_final: 0.7597 (mtm) REVERT: B 605 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8454 (pt) REVERT: B 709 MET cc_start: 0.7569 (tpt) cc_final: 0.7124 (tpt) REVERT: B 748 PHE cc_start: 0.8613 (m-10) cc_final: 0.8256 (m-10) REVERT: B 753 ILE cc_start: 0.8860 (tt) cc_final: 0.8555 (tt) outliers start: 53 outliers final: 23 residues processed: 190 average time/residue: 0.0906 time to fit residues: 25.7688 Evaluate side-chains 161 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 132 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 289 PHE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 465 ASP Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 651 MET Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 597 ASP Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 624 THR Chi-restraints excluded: chain B residue 672 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 118 optimal weight: 30.0000 chunk 90 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 3 optimal weight: 0.0050 chunk 112 optimal weight: 0.0270 chunk 49 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 26 optimal weight: 0.0770 chunk 46 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 overall best weight: 0.3410 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 612 GLN A 632 HIS B 354 GLN ** B 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.169243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.113060 restraints weight = 12962.702| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 1.73 r_work: 0.2955 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 12109 Z= 0.113 Angle : 0.553 6.516 16440 Z= 0.282 Chirality : 0.040 0.143 1750 Planarity : 0.004 0.049 2030 Dihedral : 11.030 172.401 1743 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 3.22 % Allowed : 12.65 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.22), residues: 1414 helix: 1.06 (0.20), residues: 670 sheet: -2.19 (0.49), residues: 106 loop : -1.61 (0.23), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 680 TYR 0.014 0.001 TYR A 641 PHE 0.015 0.001 PHE A 537 TRP 0.016 0.001 TRP A 727 HIS 0.005 0.001 HIS A 472 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (12106) covalent geometry : angle 0.55254 / 0.28 (16432) SS BOND : bond 0.00024 / 0.02 ( 1) SS BOND : angle 0.22141 / 0.13 ( 2) hydrogen bonds : bond 0.03611 / 2.35 ( 545) hydrogen bonds : angle 4.47410 / 3.01 ( 1572) link_NAG-ASN : bond 0.00206 / 0.14 ( 2) link_NAG-ASN : angle 1.57240 / 0.97 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 157 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 214 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8154 (tm) REVERT: A 258 ASP cc_start: 0.9191 (t0) cc_final: 0.8956 (t0) REVERT: A 315 LYS cc_start: 0.8527 (mtpm) cc_final: 0.8199 (mtmt) REVERT: A 329 ILE cc_start: 0.9278 (mt) cc_final: 0.9028 (tt) REVERT: A 344 TYR cc_start: 0.8003 (m-80) cc_final: 0.7705 (m-80) REVERT: A 396 LYS cc_start: 0.8190 (ptpp) cc_final: 0.7202 (pttm) REVERT: A 398 ARG cc_start: 0.6921 (mtt180) cc_final: 0.6257 (mtt90) REVERT: A 400 PHE cc_start: 0.8118 (t80) cc_final: 0.7820 (t80) REVERT: A 409 HIS cc_start: 0.6471 (t70) cc_final: 0.6177 (t-90) REVERT: A 465 ASP cc_start: 0.8000 (t0) cc_final: 0.7606 (m-30) REVERT: A 529 LYS cc_start: 0.7992 (ttmt) cc_final: 0.7195 (tptp) REVERT: A 534 ILE cc_start: 0.8321 (mm) cc_final: 0.8005 (mp) REVERT: A 549 LYS cc_start: 0.7050 (ttpt) cc_final: 0.5841 (mmtt) REVERT: A 588 ILE cc_start: 0.8253 (tt) cc_final: 0.7986 (mt) REVERT: A 615 LYS cc_start: 0.7303 (mmtt) cc_final: 0.6962 (mttt) REVERT: A 739 GLU cc_start: 0.8159 (mp0) cc_final: 0.7912 (mp0) REVERT: B 280 LYS cc_start: 0.7729 (tppp) cc_final: 0.7515 (ttpt) REVERT: B 388 GLU cc_start: 0.5004 (mt-10) cc_final: 0.4651 (pm20) REVERT: B 550 LYS cc_start: 0.7305 (mmtm) cc_final: 0.6913 (mmtt) REVERT: B 559 MET cc_start: 0.7866 (mtt) cc_final: 0.7522 (mtt) REVERT: B 560 MET cc_start: 0.7943 (mtp) cc_final: 0.7655 (mtm) REVERT: B 605 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8445 (pt) REVERT: B 671 ARG cc_start: 0.8125 (ttp-170) cc_final: 0.7577 (ttp80) REVERT: B 709 MET cc_start: 0.7456 (tpt) cc_final: 0.6966 (tpt) REVERT: B 748 PHE cc_start: 0.8395 (m-10) cc_final: 0.8081 (m-10) REVERT: B 753 ILE cc_start: 0.8819 (tt) cc_final: 0.8566 (tt) outliers start: 40 outliers final: 23 residues processed: 187 average time/residue: 0.1004 time to fit residues: 27.7444 Evaluate side-chains 161 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 136 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 289 PHE Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 651 MET Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 708 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 111 optimal weight: 30.0000 chunk 27 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 67 optimal weight: 0.5980 chunk 119 optimal weight: 0.0970 chunk 2 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 14 optimal weight: 0.5980 chunk 127 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 317 ASN ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.167962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.111741 restraints weight = 13105.541| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.76 r_work: 0.2926 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12109 Z= 0.124 Angle : 0.550 6.375 16440 Z= 0.280 Chirality : 0.041 0.145 1750 Planarity : 0.004 0.048 2030 Dihedral : 10.822 173.781 1743 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 3.06 % Allowed : 13.30 % Favored : 83.64 % 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: -0.27 (0.22), residues: 1414 helix: 1.31 (0.20), residues: 669 sheet: -2.09 (0.49), residues: 106 loop : -1.47 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 224 TYR 0.014 0.001 TYR A 641 PHE 0.013 0.001 PHE A 537 TRP 0.018 0.001 TRP A 727 HIS 0.005 0.001 HIS A 472 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (12106) covalent geometry : angle 0.54975 / 0.28 (16432) SS BOND : bond 0.00071 / 0.05 ( 1) SS BOND : angle 0.17290 / 0.12 ( 2) hydrogen bonds : bond 0.03616 / 2.35 ( 545) hydrogen bonds : angle 4.34606 / 2.92 ( 1572) link_NAG-ASN : bond 0.00164 / 0.11 ( 2) link_NAG-ASN : angle 1.56362 / 0.95 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 146 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 214 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8135 (tm) REVERT: A 255 MET cc_start: 0.9107 (mtt) cc_final: 0.8879 (mtp) REVERT: A 315 LYS cc_start: 0.8507 (mtpm) cc_final: 0.8163 (mtmt) REVERT: A 329 ILE cc_start: 0.9274 (mt) cc_final: 0.9019 (tt) REVERT: A 344 TYR cc_start: 0.8167 (m-80) cc_final: 0.7826 (m-80) REVERT: A 396 LYS cc_start: 0.8219 (ptpp) cc_final: 0.7253 (pttm) REVERT: A 398 ARG cc_start: 0.7083 (mtt180) cc_final: 0.6397 (mtt90) REVERT: A 400 PHE cc_start: 0.8120 (t80) cc_final: 0.7799 (t80) REVERT: A 465 ASP cc_start: 0.8053 (t0) cc_final: 0.7636 (m-30) REVERT: A 529 LYS cc_start: 0.7992 (ttmt) cc_final: 0.7190 (tptp) REVERT: A 534 ILE cc_start: 0.8310 (mm) cc_final: 0.8010 (mp) REVERT: A 549 LYS cc_start: 0.6934 (ttpt) cc_final: 0.5854 (mmtt) REVERT: A 615 LYS cc_start: 0.7269 (mmtt) cc_final: 0.6931 (mttt) REVERT: A 716 GLU cc_start: 0.7694 (pt0) cc_final: 0.7387 (tp30) REVERT: A 739 GLU cc_start: 0.8157 (mp0) cc_final: 0.7906 (mp0) REVERT: B 119 MET cc_start: 0.9405 (OUTLIER) cc_final: 0.9099 (mtp) REVERT: B 218 VAL cc_start: 0.8737 (OUTLIER) cc_final: 0.8500 (t) REVERT: B 388 GLU cc_start: 0.4967 (mt-10) cc_final: 0.4640 (pm20) REVERT: B 550 LYS cc_start: 0.7290 (mmtm) cc_final: 0.6897 (mmtt) REVERT: B 560 MET cc_start: 0.7990 (mtp) cc_final: 0.7692 (mtm) REVERT: B 605 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8420 (pt) REVERT: B 709 MET cc_start: 0.7502 (tpt) cc_final: 0.7003 (tpt) REVERT: B 753 ILE cc_start: 0.8846 (tt) cc_final: 0.8548 (tt) outliers start: 38 outliers final: 28 residues processed: 175 average time/residue: 0.0900 time to fit residues: 23.7565 Evaluate side-chains 166 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 134 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 289 PHE Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 524 LYS Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 651 MET Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 597 ASP Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 624 THR Chi-restraints excluded: chain B residue 672 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 58 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 99 optimal weight: 9.9990 chunk 132 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 116 optimal weight: 20.0000 chunk 131 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 53 optimal weight: 8.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 317 ASN ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 ASN ** A 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 612 GLN B 191 ASN ** B 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.162184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.105590 restraints weight = 13103.835| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 1.99 r_work: 0.2796 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.3656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 12109 Z= 0.210 Angle : 0.619 7.264 16440 Z= 0.314 Chirality : 0.044 0.184 1750 Planarity : 0.004 0.051 2030 Dihedral : 11.082 175.307 1743 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 3.71 % Allowed : 13.30 % Favored : 83.00 % 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: -0.32 (0.22), residues: 1414 helix: 1.21 (0.20), residues: 664 sheet: -2.12 (0.48), residues: 108 loop : -1.41 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 680 TYR 0.013 0.001 TYR A 641 PHE 0.017 0.002 PHE A 121 TRP 0.028 0.002 TRP A 727 HIS 0.009 0.001 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.21 (12106) covalent geometry : angle 0.61845 / 0.31 (16432) SS BOND : bond 0.00003 / 0.00 ( 1) SS BOND : angle 0.21301 / 0.15 ( 2) hydrogen bonds : bond 0.04061 / 2.62 ( 545) hydrogen bonds : angle 4.53679 / 3.05 ( 1572) link_NAG-ASN : bond 0.00086 / 0.06 ( 2) link_NAG-ASN : angle 1.89954 / 1.17 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 137 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 214 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8251 (tm) REVERT: A 255 MET cc_start: 0.9179 (mtt) cc_final: 0.8928 (mtp) REVERT: A 271 PHE cc_start: 0.7747 (m-10) cc_final: 0.6365 (t80) REVERT: A 315 LYS cc_start: 0.8417 (mtpm) cc_final: 0.8089 (mtmt) REVERT: A 344 TYR cc_start: 0.8351 (m-80) cc_final: 0.8026 (m-80) REVERT: A 398 ARG cc_start: 0.7258 (mtt180) cc_final: 0.6893 (mtt90) REVERT: A 400 PHE cc_start: 0.8195 (t80) cc_final: 0.7852 (t80) REVERT: A 465 ASP cc_start: 0.8446 (t0) cc_final: 0.8043 (m-30) REVERT: A 529 LYS cc_start: 0.8006 (ttmt) cc_final: 0.7236 (tptp) REVERT: A 549 LYS cc_start: 0.7180 (ttpt) cc_final: 0.5884 (mmtt) REVERT: A 615 LYS cc_start: 0.7354 (mmtt) cc_final: 0.6993 (mttt) REVERT: A 748 LYS cc_start: 0.8002 (mttp) cc_final: 0.7391 (mtpt) REVERT: B 119 MET cc_start: 0.9451 (OUTLIER) cc_final: 0.9195 (mtp) REVERT: B 218 VAL cc_start: 0.8815 (OUTLIER) cc_final: 0.8516 (m) REVERT: B 388 GLU cc_start: 0.4838 (mt-10) cc_final: 0.4482 (pm20) REVERT: B 550 LYS cc_start: 0.7314 (mmtm) cc_final: 0.6934 (mmtt) REVERT: B 560 MET cc_start: 0.8154 (mtp) cc_final: 0.7841 (mtm) REVERT: B 699 LYS cc_start: 0.7910 (mttt) cc_final: 0.7377 (pttm) REVERT: B 709 MET cc_start: 0.7822 (tpt) cc_final: 0.7249 (tpt) REVERT: B 748 PHE cc_start: 0.8738 (m-10) cc_final: 0.8420 (m-10) REVERT: B 753 ILE cc_start: 0.9015 (tt) cc_final: 0.8764 (tt) outliers start: 46 outliers final: 36 residues processed: 169 average time/residue: 0.0993 time to fit residues: 25.2128 Evaluate side-chains 171 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 132 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 348 HIS Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 524 LYS Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 651 MET Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 463 MET Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 597 ASP Chi-restraints excluded: chain B residue 624 THR Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 672 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 18 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 71 optimal weight: 5.9990 chunk 112 optimal weight: 0.6980 chunk 43 optimal weight: 5.9990 chunk 83 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 317 ASN ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 428 HIS ** B 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.165254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.109628 restraints weight = 13029.096| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.96 r_work: 0.2855 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12109 Z= 0.133 Angle : 0.565 8.077 16440 Z= 0.287 Chirality : 0.041 0.159 1750 Planarity : 0.004 0.050 2030 Dihedral : 10.789 174.560 1743 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 3.22 % Allowed : 14.02 % Favored : 82.76 % 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 (0.23), residues: 1414 helix: 1.27 (0.20), residues: 676 sheet: -2.08 (0.51), residues: 98 loop : -1.34 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 680 TYR 0.013 0.001 TYR A 641 PHE 0.014 0.001 PHE A 537 TRP 0.021 0.001 TRP A 727 HIS 0.007 0.001 HIS A 472 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 (12106) covalent geometry : angle 0.56449 / 0.29 (16432) SS BOND : bond 0.00038 / 0.03 ( 1) SS BOND : angle 0.26491 / 0.18 ( 2) hydrogen bonds : bond 0.03758 / 2.44 ( 545) hydrogen bonds : angle 4.38299 / 2.95 ( 1572) link_NAG-ASN : bond 0.00130 / 0.09 ( 2) link_NAG-ASN : angle 1.82432 / 1.11 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 135 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 214 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8254 (tm) REVERT: A 255 MET cc_start: 0.9119 (mtt) cc_final: 0.8908 (mtp) REVERT: A 315 LYS cc_start: 0.8495 (mtpm) cc_final: 0.8227 (mtmt) REVERT: A 329 ILE cc_start: 0.9310 (mt) cc_final: 0.9108 (tt) REVERT: A 398 ARG cc_start: 0.7166 (mtt180) cc_final: 0.6788 (mtt90) REVERT: A 400 PHE cc_start: 0.8194 (t80) cc_final: 0.7900 (t80) REVERT: A 465 ASP cc_start: 0.8359 (t0) cc_final: 0.7943 (m-30) REVERT: A 529 LYS cc_start: 0.8014 (ttmt) cc_final: 0.7226 (tptp) REVERT: A 549 LYS cc_start: 0.7082 (ttpt) cc_final: 0.5918 (mmtt) REVERT: A 615 LYS cc_start: 0.7317 (mmtt) cc_final: 0.6976 (mttt) REVERT: B 119 MET cc_start: 0.9427 (OUTLIER) cc_final: 0.9167 (mtp) REVERT: B 218 VAL cc_start: 0.8788 (OUTLIER) cc_final: 0.8485 (t) REVERT: B 388 GLU cc_start: 0.4868 (mt-10) cc_final: 0.4481 (pm20) REVERT: B 550 LYS cc_start: 0.7309 (mmtm) cc_final: 0.6923 (mmtt) REVERT: B 560 MET cc_start: 0.8127 (mtp) cc_final: 0.7806 (mtm) REVERT: B 657 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8837 (tp) REVERT: B 699 LYS cc_start: 0.7864 (mttt) cc_final: 0.7345 (pttm) REVERT: B 709 MET cc_start: 0.7772 (tpt) cc_final: 0.7195 (tpt) REVERT: B 748 PHE cc_start: 0.8691 (m-10) cc_final: 0.8341 (m-10) REVERT: B 753 ILE cc_start: 0.8916 (tt) cc_final: 0.8649 (tt) outliers start: 40 outliers final: 30 residues processed: 165 average time/residue: 0.0990 time to fit residues: 24.6958 Evaluate side-chains 167 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 133 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 289 PHE Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 524 LYS Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 651 MET Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 597 ASP Chi-restraints excluded: chain B residue 624 THR Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 672 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 140 optimal weight: 0.4980 chunk 77 optimal weight: 0.9980 chunk 111 optimal weight: 10.0000 chunk 88 optimal weight: 1.9990 chunk 47 optimal weight: 7.9990 chunk 24 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 55 optimal weight: 0.4980 chunk 46 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 317 ASN ** A 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.166341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.111082 restraints weight = 12875.575| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.83 r_work: 0.2998 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12109 Z= 0.128 Angle : 0.552 7.749 16440 Z= 0.281 Chirality : 0.041 0.158 1750 Planarity : 0.004 0.050 2030 Dihedral : 10.584 174.664 1743 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 3.22 % Allowed : 13.70 % Favored : 83.08 % 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: -0.04 (0.23), residues: 1414 helix: 1.40 (0.20), residues: 676 sheet: -1.89 (0.54), residues: 86 loop : -1.32 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 680 TYR 0.015 0.001 TYR A 344 PHE 0.014 0.001 PHE A 537 TRP 0.019 0.001 TRP A 727 HIS 0.007 0.001 HIS A 472 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (12106) covalent geometry : angle 0.55071 / 0.28 (16432) SS BOND : bond 0.00074 / 0.05 ( 1) SS BOND : angle 0.30791 / 0.21 ( 2) hydrogen bonds : bond 0.03647 / 2.36 ( 545) hydrogen bonds : angle 4.29917 / 2.89 ( 1572) link_NAG-ASN : bond 0.00124 / 0.08 ( 2) link_NAG-ASN : angle 1.69487 / 1.02 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 136 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 214 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8490 (tm) REVERT: A 271 PHE cc_start: 0.7902 (m-80) cc_final: 0.6615 (t80) REVERT: A 344 TYR cc_start: 0.8112 (m-80) cc_final: 0.7739 (m-80) REVERT: A 398 ARG cc_start: 0.7440 (mtt180) cc_final: 0.6785 (ttm170) REVERT: A 400 PHE cc_start: 0.8418 (t80) cc_final: 0.8141 (t80) REVERT: A 465 ASP cc_start: 0.8399 (t0) cc_final: 0.8016 (m-30) REVERT: A 529 LYS cc_start: 0.8070 (ttmt) cc_final: 0.7339 (tptp) REVERT: A 534 ILE cc_start: 0.8521 (mm) cc_final: 0.8290 (mp) REVERT: A 549 LYS cc_start: 0.7185 (ttpt) cc_final: 0.6178 (mmtt) REVERT: A 615 LYS cc_start: 0.7356 (mmtt) cc_final: 0.7069 (mttt) REVERT: B 119 MET cc_start: 0.9415 (OUTLIER) cc_final: 0.9176 (mtp) REVERT: B 218 VAL cc_start: 0.8849 (OUTLIER) cc_final: 0.8552 (t) REVERT: B 388 GLU cc_start: 0.5005 (mt-10) cc_final: 0.4705 (pm20) REVERT: B 550 LYS cc_start: 0.7593 (mmtm) cc_final: 0.7232 (mmtt) REVERT: B 560 MET cc_start: 0.8420 (mtp) cc_final: 0.8097 (mtm) REVERT: B 657 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8870 (tp) REVERT: B 699 LYS cc_start: 0.7831 (mttt) cc_final: 0.7491 (pttm) REVERT: B 709 MET cc_start: 0.8051 (tpt) cc_final: 0.7485 (tpt) REVERT: B 748 PHE cc_start: 0.8710 (m-10) cc_final: 0.8431 (m-10) REVERT: B 753 ILE cc_start: 0.9056 (tt) cc_final: 0.8766 (tt) outliers start: 40 outliers final: 32 residues processed: 166 average time/residue: 0.0963 time to fit residues: 24.1678 Evaluate side-chains 170 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 134 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 289 PHE Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 505 ASP Chi-restraints excluded: chain A residue 524 LYS Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 651 MET Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 597 ASP Chi-restraints excluded: chain B residue 624 THR Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 672 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 97 optimal weight: 2.9990 chunk 116 optimal weight: 20.0000 chunk 6 optimal weight: 0.9980 chunk 46 optimal weight: 0.0870 chunk 33 optimal weight: 0.8980 chunk 85 optimal weight: 0.4980 chunk 18 optimal weight: 0.6980 chunk 44 optimal weight: 8.9990 chunk 30 optimal weight: 7.9990 chunk 103 optimal weight: 40.0000 chunk 74 optimal weight: 0.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 ASN ** 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 = 0.3794 r_free = 0.3794 target = 0.167011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.111358 restraints weight = 13106.055| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.89 r_work: 0.2979 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12109 Z= 0.122 Angle : 0.548 7.671 16440 Z= 0.279 Chirality : 0.041 0.155 1750 Planarity : 0.004 0.049 2030 Dihedral : 10.402 174.572 1743 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.98 % Allowed : 14.10 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.23), residues: 1414 helix: 1.49 (0.20), residues: 676 sheet: -1.72 (0.50), residues: 99 loop : -1.33 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 680 TYR 0.014 0.001 TYR A 344 PHE 0.014 0.001 PHE A 537 TRP 0.017 0.001 TRP A 727 HIS 0.007 0.001 HIS A 472 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (12106) covalent geometry : angle 0.54684 / 0.28 (16432) SS BOND : bond 0.00072 / 0.05 ( 1) SS BOND : angle 0.32673 / 0.23 ( 2) hydrogen bonds : bond 0.03592 / 2.33 ( 545) hydrogen bonds : angle 4.24348 / 2.85 ( 1572) link_NAG-ASN : bond 0.00098 / 0.07 ( 2) link_NAG-ASN : angle 1.70097 / 0.99 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 136 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 214 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8411 (tm) REVERT: A 255 MET cc_start: 0.9147 (mtt) cc_final: 0.8869 (mtp) REVERT: A 344 TYR cc_start: 0.8059 (m-80) cc_final: 0.7652 (m-80) REVERT: A 398 ARG cc_start: 0.7353 (mtt180) cc_final: 0.6684 (ttm170) REVERT: A 400 PHE cc_start: 0.8348 (t80) cc_final: 0.7981 (t80) REVERT: A 429 CYS cc_start: 0.8641 (m) cc_final: 0.7770 (t) REVERT: A 465 ASP cc_start: 0.8342 (t0) cc_final: 0.7909 (m-30) REVERT: A 529 LYS cc_start: 0.8031 (ttmt) cc_final: 0.7274 (tptp) REVERT: A 534 ILE cc_start: 0.8435 (mm) cc_final: 0.8192 (mp) REVERT: A 549 LYS cc_start: 0.7036 (ttpt) cc_final: 0.6034 (mmtt) REVERT: A 615 LYS cc_start: 0.7259 (mmtt) cc_final: 0.6956 (mttt) REVERT: B 119 MET cc_start: 0.9429 (OUTLIER) cc_final: 0.9169 (mtp) REVERT: B 218 VAL cc_start: 0.8829 (OUTLIER) cc_final: 0.8552 (t) REVERT: B 388 GLU cc_start: 0.4984 (mt-10) cc_final: 0.4687 (pm20) REVERT: B 550 LYS cc_start: 0.7540 (mmtm) cc_final: 0.7167 (mmtt) REVERT: B 560 MET cc_start: 0.8303 (mtp) cc_final: 0.7978 (mtm) REVERT: B 657 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8868 (tp) REVERT: B 699 LYS cc_start: 0.7811 (mttt) cc_final: 0.7415 (pttm) REVERT: B 709 MET cc_start: 0.7977 (tpt) cc_final: 0.7387 (tpt) REVERT: B 753 ILE cc_start: 0.8950 (tt) cc_final: 0.8720 (tt) outliers start: 37 outliers final: 31 residues processed: 163 average time/residue: 0.1043 time to fit residues: 25.3977 Evaluate side-chains 168 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 133 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 289 PHE Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 505 ASP Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 651 MET Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 597 ASP Chi-restraints excluded: chain B residue 624 THR Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 672 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 110 optimal weight: 10.0000 chunk 73 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 132 optimal weight: 0.5980 chunk 114 optimal weight: 20.0000 chunk 112 optimal weight: 0.9980 chunk 86 optimal weight: 0.6980 chunk 102 optimal weight: 20.0000 chunk 75 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 ASN ** 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 = 0.3783 r_free = 0.3783 target = 0.165963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.110164 restraints weight = 13058.279| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 1.89 r_work: 0.2864 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12109 Z= 0.136 Angle : 0.556 7.753 16440 Z= 0.283 Chirality : 0.041 0.150 1750 Planarity : 0.004 0.050 2030 Dihedral : 10.378 174.188 1743 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 3.14 % Allowed : 13.78 % Favored : 83.08 % 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: 0.04 (0.23), residues: 1414 helix: 1.49 (0.20), residues: 676 sheet: -1.70 (0.50), residues: 99 loop : -1.33 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 680 TYR 0.013 0.001 TYR A 344 PHE 0.013 0.001 PHE A 537 TRP 0.020 0.001 TRP A 727 HIS 0.007 0.001 HIS A 472 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (12106) covalent geometry : angle 0.55542 / 0.28 (16432) SS BOND : bond 0.00068 / 0.05 ( 1) SS BOND : angle 0.29643 / 0.20 ( 2) hydrogen bonds : bond 0.03633 / 2.35 ( 545) hydrogen bonds : angle 4.26863 / 2.87 ( 1572) link_NAG-ASN : bond 0.00093 / 0.06 ( 2) link_NAG-ASN : angle 1.67183 / 1.00 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3025.09 seconds wall clock time: 53 minutes 1.75 seconds (3181.75 seconds total)