Starting phenix.real_space_refine on Thu Jul 2 23:01:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8omq_16974/07_2026/8omq_16974.cif Found real_map, /net/cci-nas-00/data/ceres_data/8omq_16974/07_2026/8omq_16974.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8omq_16974/07_2026/8omq_16974.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8omq_16974/07_2026/8omq_16974.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8omq_16974/07_2026/8omq_16974.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8omq_16974/07_2026/8omq_16974.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8omq_16974/07_2026/8omq_16974.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8omq_16974/07_2026/8omq_16974.cif" } resolution = 3.11 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= 0.020 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 54 5.16 5 C 6707 2.51 5 N 1811 2.21 5 O 2004 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10584 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 4634 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 577, 4631 Classifications: {'peptide': 577} Link IDs: {'PTRANS': 17, 'TRANS': 559} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 577, 4631 Classifications: {'peptide': 577} Link IDs: {'PTRANS': 17, 'TRANS': 559} Chain breaks: 1 bond proxies already assigned to first conformer: 4716 Chain: "A" Number of atoms: 5886 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 745, 5883 Classifications: {'peptide': 745} Link IDs: {'PTRANS': 22, 'TRANS': 722} Chain breaks: 6 Conformer: "B" Number of residues, atoms: 745, 5883 Classifications: {'peptide': 745} Link IDs: {'PTRANS': 22, 'TRANS': 722} Chain breaks: 6 bond proxies already assigned to first conformer: 5960 Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.55, per 1000 atoms: 0.34 Number of scatterers: 10584 At special positions: 0 Unit cell: (85.0206, 108.79, 171.87, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 54 16.00 P 6 15.00 Mg 2 11.99 O 2004 8.00 N 1811 7.00 C 6707 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 783.0 milliseconds 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2514 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 7 sheets defined 58.9% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'B' and resid 538 through 545 Processing helix chain 'B' and resid 559 through 565 Processing helix chain 'B' and resid 569 through 582 removed outlier: 3.641A pdb=" N ARG B 573 " --> pdb=" O THR B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 603 removed outlier: 3.604A pdb=" N ILE B 590 " --> pdb=" O LYS B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 606 through 617 removed outlier: 4.709A pdb=" N LYS B 617 " --> pdb=" O ASN B 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 630 Processing helix chain 'B' and resid 634 through 654 Processing helix chain 'B' and resid 655 through 663 Processing helix chain 'B' and resid 665 through 673 Processing helix chain 'B' and resid 674 through 679 removed outlier: 3.510A pdb=" N LEU B 678 " --> pdb=" O GLU B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 682 No H-bonds generated for 'chain 'B' and resid 680 through 682' Processing helix chain 'B' and resid 683 through 688 Processing helix chain 'B' and resid 690 through 697 removed outlier: 3.941A pdb=" N VAL B 696 " --> pdb=" O GLN B 692 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY B 697 " --> pdb=" O ALA B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 708 Processing helix chain 'B' and resid 709 through 729 removed outlier: 3.965A pdb=" N LYS B 713 " --> pdb=" O PHE B 709 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N HIS B 729 " --> pdb=" O GLU B 725 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 738 Processing helix chain 'B' and resid 782 through 815 Processing helix chain 'B' and resid 817 through 843 Processing helix chain 'B' and resid 864 through 871 Processing helix chain 'B' and resid 901 through 919 Processing helix chain 'B' and resid 944 through 948 removed outlier: 3.844A pdb=" N GLY B 948 " --> pdb=" O ILE B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 950 through 965 Processing helix chain 'B' and resid 982 through 1000 Processing helix chain 'B' and resid 1011 through 1016 Processing helix chain 'B' and resid 1017 through 1021 Processing helix chain 'B' and resid 1068 through 1076 removed outlier: 3.681A pdb=" N VAL B1072 " --> pdb=" O TYR B1068 " (cutoff:3.500A) Processing helix chain 'B' and resid 1079 through 1111 Processing helix chain 'B' and resid 1115 through 1121 removed outlier: 3.539A pdb=" N LYS B1121 " --> pdb=" O GLN B1117 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 195 Processing helix chain 'A' and resid 210 through 219 Processing helix chain 'A' and resid 228 through 232 Processing helix chain 'A' and resid 236 through 244 removed outlier: 3.686A pdb=" N ARG A 243 " --> pdb=" O GLN A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 262 removed outlier: 3.568A pdb=" N GLU A 262 " --> pdb=" O PRO A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 275 Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 303 through 311 Processing helix chain 'A' and resid 326 through 331 Processing helix chain 'A' and resid 335 through 348 removed outlier: 3.603A pdb=" N ARG A 340 " --> pdb=" O PRO A 336 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU A 341 " --> pdb=" O GLN A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 369 removed outlier: 3.574A pdb=" N ILE A 356 " --> pdb=" O ASP A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 378 Processing helix chain 'A' and resid 380 through 384 Processing helix chain 'A' and resid 388 through 396 Processing helix chain 'A' and resid 400 through 413 removed outlier: 3.540A pdb=" N GLN A 413 " --> pdb=" O GLN A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 424 Processing helix chain 'A' and resid 429 through 456 Proline residue: A 439 - end of helix removed outlier: 4.666A pdb=" N LYS A 449 " --> pdb=" O SER A 445 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N PHE A 450 " --> pdb=" O ASP A 446 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N MET A 453 " --> pdb=" O LYS A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 504 removed outlier: 3.551A pdb=" N ARG A 482 " --> pdb=" O LEU A 478 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU A 483 " --> pdb=" O SER A 479 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE A 484 " --> pdb=" O GLU A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 532 removed outlier: 3.927A pdb=" N GLU A 530 " --> pdb=" O CYS A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 586 removed outlier: 3.653A pdb=" N ILE A 577 " --> pdb=" O ALA A 573 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS A 579 " --> pdb=" O ASP A 575 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N GLU A 580 " --> pdb=" O ALA A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 613 removed outlier: 3.873A pdb=" N VAL A 598 " --> pdb=" O THR A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 645 removed outlier: 3.598A pdb=" N VAL A 644 " --> pdb=" O CYS A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 692 removed outlier: 3.852A pdb=" N GLY A 683 " --> pdb=" O ILE A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 736 Processing helix chain 'A' and resid 755 through 774 removed outlier: 3.535A pdb=" N ILE A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 788 removed outlier: 3.779A pdb=" N THR A 788 " --> pdb=" O HIS A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 794 removed outlier: 3.663A pdb=" N GLN A 793 " --> pdb=" O ALA A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 834 removed outlier: 3.702A pdb=" N VAL A 830 " --> pdb=" O PHE A 826 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 850 Processing helix chain 'A' and resid 871 through 893 removed outlier: 3.769A pdb=" N ILE A 884 " --> pdb=" O GLY A 880 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLN A 885 " --> pdb=" O GLU A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 919 removed outlier: 3.720A pdb=" N ILE A 904 " --> pdb=" O SER A 900 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N THR A 905 " --> pdb=" O GLU A 901 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLU A 914 " --> pdb=" O GLN A 910 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N VAL A 915 " --> pdb=" O LEU A 911 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE A 916 " --> pdb=" O LYS A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 930 Processing sheet with id=AA1, first strand: chain 'B' and resid 754 through 757 Processing sheet with id=AA2, first strand: chain 'B' and resid 880 through 884 removed outlier: 5.042A pdb=" N ASN B 880 " --> pdb=" O ASN B 861 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASN B 861 " --> pdb=" O ASN B 880 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU B 926 " --> pdb=" O LYS B 860 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 935 through 938 removed outlier: 6.383A pdb=" N PHE B 936 " --> pdb=" O ILE B 973 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ASP B 975 " --> pdb=" O PHE B 936 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ARG B 938 " --> pdb=" O ASP B 975 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N TYR B1028 " --> pdb=" O VAL B 891 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N ILE B 893 " --> pdb=" O TYR B1028 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N MET B1030 " --> pdb=" O ILE B 893 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N THR B 895 " --> pdb=" O MET B1030 " (cutoff:3.500A) removed outlier: 8.604A pdb=" N PHE B1032 " --> pdb=" O THR B 895 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ASN B1027 " --> pdb=" O THR B1060 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N THR B1060 " --> pdb=" O ASN B1027 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N HIS B1029 " --> pdb=" O GLN B1058 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N GLN B1058 " --> pdb=" O HIS B1029 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY B1031 " --> pdb=" O LEU B1056 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU B1056 " --> pdb=" O GLY B1031 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 147 through 153 removed outlier: 6.308A pdb=" N LEU A 173 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 301 through 302 removed outlier: 6.822A pdb=" N LYS A 301 " --> pdb=" O ILE A 708 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N ALA A 710 " --> pdb=" O LYS A 301 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N CYS A 707 " --> pdb=" O LEU A 744 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N ILE A 746 " --> pdb=" O CYS A 707 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU A 709 " --> pdb=" O ILE A 746 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N SER A 743 " --> pdb=" O PHE A 777 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N MET A 779 " --> pdb=" O SER A 743 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ILE A 745 " --> pdb=" O MET A 779 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ALA A 781 " --> pdb=" O ILE A 745 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ILE A 747 " --> pdb=" O ALA A 781 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ASN A 799 " --> pdb=" O LYS A 818 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LYS A 818 " --> pdb=" O ASN A 799 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N HIS A 801 " --> pdb=" O GLN A 816 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N GLN A 816 " --> pdb=" O HIS A 801 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N THR A 803 " --> pdb=" O LEU A 814 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A 814 " --> pdb=" O THR A 803 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 540 through 543 removed outlier: 4.538A pdb=" N VAL A 542 " --> pdb=" O LYS A 550 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N LYS A 550 " --> pdb=" O VAL A 542 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 653 through 657 removed outlier: 5.059A pdb=" N ASN A 653 " --> pdb=" O ALA A 636 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA A 636 " --> pdb=" O ASN A 653 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N SER A 699 " --> pdb=" O LYS A 635 " (cutoff:3.500A) 553 hydrogen bonds defined for protein. 1589 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: 1.49 Time building geometry restraints manager: 1.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2908 1.34 - 1.46: 2840 1.46 - 1.58: 4915 1.58 - 1.70: 9 1.70 - 1.82: 86 Bond restraints: 10758 Sorted by residual: bond pdb=" CA SER B 904 " pdb=" CB SER B 904 " ideal model delta sigma weight residual 1.528 1.491 0.038 1.56e-02 4.11e+03 5.89e+00 bond pdb=" CA SER A 607 " pdb=" CB SER A 607 " ideal model delta sigma weight residual 1.529 1.491 0.038 1.58e-02 4.01e+03 5.89e+00 bond pdb=" CA SER A 825 " pdb=" CB SER A 825 " ideal model delta sigma weight residual 1.530 1.489 0.041 1.68e-02 3.54e+03 5.85e+00 bond pdb=" CA SER B 559 " pdb=" CB SER B 559 " ideal model delta sigma weight residual 1.535 1.495 0.040 1.71e-02 3.42e+03 5.58e+00 bond pdb=" CE1 HIS A 665 " pdb=" NE2 HIS A 665 " ideal model delta sigma weight residual 1.321 1.344 -0.023 1.00e-02 1.00e+04 5.27e+00 ... (remaining 10753 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.14: 14458 4.14 - 8.28: 60 8.28 - 12.42: 2 12.42 - 16.56: 1 16.56 - 20.70: 3 Bond angle restraints: 14524 Sorted by residual: angle pdb=" PA ATP A2000 " pdb=" O3A ATP A2000 " pdb=" PB ATP A2000 " ideal model delta sigma weight residual 136.83 116.13 20.70 1.00e+00 1.00e+00 4.29e+02 angle pdb=" PA ATP B2000 " pdb=" O3A ATP B2000 " pdb=" PB ATP B2000 " ideal model delta sigma weight residual 136.83 117.40 19.43 1.00e+00 1.00e+00 3.77e+02 angle pdb=" PB ATP A2000 " pdb=" O3B ATP A2000 " pdb=" PG ATP A2000 " ideal model delta sigma weight residual 139.87 122.47 17.40 1.00e+00 1.00e+00 3.03e+02 angle pdb=" PB ATP B2000 " pdb=" O3B ATP B2000 " pdb=" PG ATP B2000 " ideal model delta sigma weight residual 139.87 123.91 15.96 1.00e+00 1.00e+00 2.55e+02 angle pdb=" C5' ATP B2000 " pdb=" O5' ATP B2000 " pdb=" PA ATP B2000 " ideal model delta sigma weight residual 121.27 110.88 10.39 1.00e+00 1.00e+00 1.08e+02 ... (remaining 14519 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 5718 17.34 - 34.68: 629 34.68 - 52.02: 159 52.02 - 69.36: 43 69.36 - 86.70: 18 Dihedral angle restraints: 6567 sinusoidal: 2701 harmonic: 3866 Sorted by residual: dihedral pdb=" CA THR A 438 " pdb=" C THR A 438 " pdb=" N PRO A 439 " pdb=" CA PRO A 439 " ideal model delta harmonic sigma weight residual 180.00 155.65 24.35 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA GLY B 900 " pdb=" C GLY B 900 " pdb=" N GLY B 901 " pdb=" CA GLY B 901 " ideal model delta harmonic sigma weight residual -180.00 -157.06 -22.94 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" C LYS B 738 " pdb=" N LYS B 738 " pdb=" CA LYS B 738 " pdb=" CB LYS B 738 " ideal model delta harmonic sigma weight residual -122.60 -131.89 9.29 0 2.50e+00 1.60e-01 1.38e+01 ... (remaining 6564 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 872 0.064 - 0.129: 599 0.129 - 0.193: 172 0.193 - 0.258: 26 0.258 - 0.322: 2 Chirality restraints: 1671 Sorted by residual: chirality pdb=" CA LYS B 738 " pdb=" N LYS B 738 " pdb=" C LYS B 738 " pdb=" CB LYS B 738 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CA THR A 438 " pdb=" N THR A 438 " pdb=" C THR A 438 " pdb=" CB THR A 438 " both_signs ideal model delta sigma weight residual False 2.53 2.24 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CA GLU A 878 " pdb=" N GLU A 878 " pdb=" C GLU A 878 " pdb=" CB GLU A 878 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 1668 not shown) Planarity restraints: 1844 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' ATP A2000 " -0.026 2.00e-02 2.50e+03 1.36e-02 5.06e+00 pdb=" C2 ATP A2000 " 0.013 2.00e-02 2.50e+03 pdb=" C4 ATP A2000 " 0.002 2.00e-02 2.50e+03 pdb=" C5 ATP A2000 " 0.004 2.00e-02 2.50e+03 pdb=" C6 ATP A2000 " 0.008 2.00e-02 2.50e+03 pdb=" C8 ATP A2000 " 0.017 2.00e-02 2.50e+03 pdb=" N1 ATP A2000 " 0.002 2.00e-02 2.50e+03 pdb=" N3 ATP A2000 " -0.003 2.00e-02 2.50e+03 pdb=" N6 ATP A2000 " -0.027 2.00e-02 2.50e+03 pdb=" N7 ATP A2000 " 0.006 2.00e-02 2.50e+03 pdb=" N9 ATP A2000 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 438 " 0.008 2.00e-02 2.50e+03 1.52e-02 2.32e+00 pdb=" C THR A 438 " -0.026 2.00e-02 2.50e+03 pdb=" O THR A 438 " 0.010 2.00e-02 2.50e+03 pdb=" N PRO A 439 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 579 " -0.017 2.00e-02 2.50e+03 8.69e-03 1.89e+00 pdb=" CG TRP B 579 " 0.017 2.00e-02 2.50e+03 pdb=" CD1 TRP B 579 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP B 579 " 0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP B 579 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP B 579 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP B 579 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 579 " -0.011 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 579 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 579 " 0.001 2.00e-02 2.50e+03 ... (remaining 1841 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 48 2.46 - 3.07: 7271 3.07 - 3.68: 17292 3.68 - 4.29: 25097 4.29 - 4.90: 40668 Nonbonded interactions: 90376 Sorted by model distance: nonbonded pdb=" O2G ATP B2000 " pdb="MG MG B2001 " model vdw 1.847 2.170 nonbonded pdb=" OG SER A 676 " pdb="MG MG A2001 " model vdw 1.944 2.170 nonbonded pdb=" O2B ATP A2000 " pdb="MG MG A2001 " model vdw 1.946 2.170 nonbonded pdb=" OG SER B 903 " pdb="MG MG B2001 " model vdw 2.087 2.170 nonbonded pdb=" O2G ATP A2000 " pdb="MG MG A2001 " model vdw 2.109 2.170 ... (remaining 90371 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.630 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: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 11.370 Find NCS groups from input model: 0.040 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:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 10758 Z= 0.452 Angle : 1.226 20.705 14524 Z= 0.856 Chirality : 0.084 0.322 1671 Planarity : 0.004 0.034 1844 Dihedral : 16.485 86.699 4053 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 2.99 % Allowed : 13.48 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.30 (0.20), residues: 1306 helix: -1.56 (0.17), residues: 704 sheet: -3.24 (0.39), residues: 120 loop : -2.66 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 680 TYR 0.018 0.003 TYR A 405 PHE 0.014 0.003 PHE A 836 TRP 0.017 0.004 TRP B 579 HIS 0.013 0.002 HIS A 610 Details of bonding type rmsd/Z covalent geometry : bond 0.00673 / 0.45 (10758) covalent geometry : angle 1.22638 / 0.86 (14524) hydrogen bonds : bond 0.14411 / 9.81 ( 553) hydrogen bonds : angle 6.39527 / 4.61 ( 1589) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 315 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 532 MET cc_start: 0.7284 (ttt) cc_final: 0.6885 (ttt) REVERT: B 534 PHE cc_start: 0.8237 (m-80) cc_final: 0.7665 (m-80) REVERT: B 554 MET cc_start: 0.8315 (mmt) cc_final: 0.7982 (mmm) REVERT: B 573 ARG cc_start: 0.7730 (ttt-90) cc_final: 0.7513 (ttt-90) REVERT: B 785 ILE cc_start: 0.7399 (mt) cc_final: 0.7172 (mt) REVERT: B 809 ASP cc_start: 0.7531 (t0) cc_final: 0.7185 (t0) REVERT: B 852 GLN cc_start: 0.8695 (mt0) cc_final: 0.8404 (mt0) REVERT: B 856 LYS cc_start: 0.8500 (tttt) cc_final: 0.8168 (tttp) REVERT: B 863 ARG cc_start: 0.7842 (mtm-85) cc_final: 0.7499 (ptp-110) REVERT: B 953 MET cc_start: 0.7906 (tpt) cc_final: 0.7360 (tpt) REVERT: B 1077 ASP cc_start: 0.7865 (t0) cc_final: 0.7524 (t0) REVERT: B 1084 LYS cc_start: 0.8295 (tptp) cc_final: 0.7989 (tptp) REVERT: A 172 LYS cc_start: 0.7389 (tttp) cc_final: 0.6874 (mmmt) REVERT: A 188 GLU cc_start: 0.7390 (tm-30) cc_final: 0.7181 (tm-30) REVERT: A 244 LEU cc_start: 0.7483 (tp) cc_final: 0.6731 (tp) REVERT: A 253 MET cc_start: 0.7023 (tpt) cc_final: 0.6002 (tpt) REVERT: A 350 LEU cc_start: 0.8175 (mt) cc_final: 0.7969 (mt) REVERT: A 351 MET cc_start: 0.8008 (mmm) cc_final: 0.7693 (tpp) REVERT: A 358 GLU cc_start: 0.8077 (tt0) cc_final: 0.7480 (pt0) REVERT: A 419 GLN cc_start: 0.8458 (tt0) cc_final: 0.8223 (tt0) REVERT: A 422 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7904 (mt-10) REVERT: A 605 VAL cc_start: 0.8207 (t) cc_final: 0.7938 (m) REVERT: A 619 TYR cc_start: 0.8686 (m-10) cc_final: 0.8471 (m-10) REVERT: A 620 VAL cc_start: 0.8699 (t) cc_final: 0.8457 (m) REVERT: A 635 LYS cc_start: 0.8464 (mptt) cc_final: 0.8262 (mptt) REVERT: A 638 ARG cc_start: 0.7884 (mtt180) cc_final: 0.7606 (mtm-85) REVERT: A 720 LYS cc_start: 0.8235 (mttt) cc_final: 0.7986 (mttm) REVERT: A 726 MET cc_start: 0.8256 (tpp) cc_final: 0.7904 (tpp) REVERT: A 793 GLN cc_start: 0.8215 (mt0) cc_final: 0.7967 (mp10) REVERT: A 845 LYS cc_start: 0.8448 (mtpt) cc_final: 0.8228 (mtmm) outliers start: 35 outliers final: 22 residues processed: 341 average time/residue: 0.1077 time to fit residues: 49.1797 Evaluate side-chains 300 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 278 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 671 VAL Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 744 TYR Chi-restraints excluded: chain B residue 777 VAL Chi-restraints excluded: chain B residue 781 HIS Chi-restraints excluded: chain B residue 799 LEU Chi-restraints excluded: chain B residue 817 HIS Chi-restraints excluded: chain B residue 939 MET Chi-restraints excluded: chain B residue 1025 VAL Chi-restraints excluded: chain B residue 1060 THR Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 296 PHE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 539 PHE Chi-restraints excluded: chain A residue 677 THR Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 851 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.3980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.4980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.4980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 538 ASN B 549 GLN B 582 GLN B 613 ASN B 684 HIS ** B 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1098 ASN A 239 GLN A 311 ASN A 343 ASN A 409 GLN ** A 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 462 GLN ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 538 ASN A 596 ASN A 639 HIS A 681 GLN A 690 GLN A 718 GLN A 793 GLN ** A 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 879 GLN A 924 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.179510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.145116 restraints weight = 34140.057| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 3.93 r_work: 0.3660 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3667 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3667 r_free = 0.3667 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3666 r_free = 0.3666 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 8 (10 function evaluations) r_final: 0.3666 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10758 Z= 0.183 Angle : 0.668 9.239 14524 Z= 0.349 Chirality : 0.044 0.267 1671 Planarity : 0.005 0.041 1844 Dihedral : 6.858 56.200 1449 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.58 % Allowed : 20.22 % Favored : 76.19 % 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: -1.80 (0.22), residues: 1306 helix: -0.24 (0.19), residues: 718 sheet: -2.78 (0.42), residues: 118 loop : -2.14 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 406 TYR 0.028 0.002 TYR A 815 PHE 0.037 0.002 PHE A 286 TRP 0.012 0.002 TRP B 562 HIS 0.016 0.002 HIS B 614 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.18 (10758) covalent geometry : angle 0.66755 / 0.35 (14524) hydrogen bonds : bond 0.04603 / 2.99 ( 553) hydrogen bonds : angle 4.93119 / 3.55 ( 1589) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 284 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 534 PHE cc_start: 0.8229 (m-80) cc_final: 0.7665 (m-80) REVERT: B 554 MET cc_start: 0.8209 (mmt) cc_final: 0.7958 (mmm) REVERT: B 565 ASP cc_start: 0.7223 (OUTLIER) cc_final: 0.6965 (t0) REVERT: B 779 ARG cc_start: 0.6260 (mtm-85) cc_final: 0.5752 (mtm180) REVERT: B 785 ILE cc_start: 0.7486 (mt) cc_final: 0.7244 (mt) REVERT: B 809 ASP cc_start: 0.7367 (t0) cc_final: 0.7060 (t0) REVERT: B 852 GLN cc_start: 0.8457 (mt0) cc_final: 0.8224 (mt0) REVERT: B 858 VAL cc_start: 0.8634 (t) cc_final: 0.8362 (m) REVERT: B 949 ARG cc_start: 0.7602 (mtm-85) cc_final: 0.7141 (mtm110) REVERT: B 953 MET cc_start: 0.8061 (tpt) cc_final: 0.7810 (tpt) REVERT: B 975 ASP cc_start: 0.8260 (t0) cc_final: 0.6944 (m-30) REVERT: B 999 ARG cc_start: 0.8129 (ttp-170) cc_final: 0.7915 (ttp-170) REVERT: B 1077 ASP cc_start: 0.7798 (t0) cc_final: 0.7382 (t0) REVERT: B 1084 LYS cc_start: 0.8023 (tptp) cc_final: 0.7606 (tptp) REVERT: B 1103 ARG cc_start: 0.7615 (mtt180) cc_final: 0.6954 (mtt-85) REVERT: A 172 LYS cc_start: 0.7419 (tttp) cc_final: 0.7101 (mmmt) REVERT: A 188 GLU cc_start: 0.6510 (tm-30) cc_final: 0.6263 (tm-30) REVERT: A 244 LEU cc_start: 0.7127 (tp) cc_final: 0.6736 (tp) REVERT: A 253 MET cc_start: 0.6766 (tpt) cc_final: 0.5644 (tpt) REVERT: A 351 MET cc_start: 0.7693 (mmm) cc_final: 0.7323 (mmm) REVERT: A 358 GLU cc_start: 0.7926 (tt0) cc_final: 0.7405 (pt0) REVERT: A 359 ARG cc_start: 0.8202 (ttm170) cc_final: 0.7837 (mtt180) REVERT: A 369 ASP cc_start: 0.7611 (m-30) cc_final: 0.7410 (m-30) REVERT: A 414 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7946 (mp) REVERT: A 442 ASP cc_start: 0.8013 (t70) cc_final: 0.7757 (t0) REVERT: A 620 VAL cc_start: 0.8633 (t) cc_final: 0.8392 (m) REVERT: A 666 ILE cc_start: 0.8174 (mt) cc_final: 0.7068 (tp) REVERT: A 720 LYS cc_start: 0.7747 (mttt) cc_final: 0.7544 (mttm) REVERT: A 726 MET cc_start: 0.8165 (tpp) cc_final: 0.7777 (tpp) REVERT: A 819 LYS cc_start: 0.8155 (tttm) cc_final: 0.7895 (tptt) REVERT: A 845 LYS cc_start: 0.8089 (mtpt) cc_final: 0.7782 (mtmm) outliers start: 42 outliers final: 27 residues processed: 311 average time/residue: 0.1067 time to fit residues: 44.9958 Evaluate side-chains 298 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 269 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 565 ASP Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 671 VAL Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 744 TYR Chi-restraints excluded: chain B residue 781 HIS Chi-restraints excluded: chain B residue 799 LEU Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 1000 ASP Chi-restraints excluded: chain B residue 1025 VAL Chi-restraints excluded: chain B residue 1072 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 677 THR Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 810 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 77 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 chunk 54 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 117 optimal weight: 0.5980 chunk 75 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 65 optimal weight: 0.3980 chunk 57 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 544 ASN ** B 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 684 HIS ** B 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 917 GLN ** B 944 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1098 ASN A 239 GLN A 311 ASN ** A 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 653 ASN A 681 GLN A 690 GLN A 718 GLN ** A 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.179276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.144493 restraints weight = 31804.508| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 3.91 r_work: 0.3690 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3694 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3694 r_free = 0.3694 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3693 r_free = 0.3693 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.3693 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10758 Z= 0.181 Angle : 0.635 8.014 14524 Z= 0.332 Chirality : 0.043 0.314 1671 Planarity : 0.004 0.037 1844 Dihedral : 6.107 53.788 1433 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.41 % Allowed : 21.08 % Favored : 75.51 % 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: -1.36 (0.23), residues: 1306 helix: 0.13 (0.19), residues: 719 sheet: -2.49 (0.43), residues: 118 loop : -2.02 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 638 TYR 0.022 0.002 TYR A 815 PHE 0.018 0.002 PHE A 436 TRP 0.008 0.001 TRP B 807 HIS 0.014 0.001 HIS B 614 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.18 (10758) covalent geometry : angle 0.63495 / 0.33 (14524) hydrogen bonds : bond 0.04406 / 2.85 ( 553) hydrogen bonds : angle 4.71189 / 3.39 ( 1589) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 274 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 534 PHE cc_start: 0.8188 (m-80) cc_final: 0.7986 (m-80) REVERT: B 565 ASP cc_start: 0.7178 (OUTLIER) cc_final: 0.6949 (t0) REVERT: B 779 ARG cc_start: 0.6299 (mtm-85) cc_final: 0.5925 (mtm180) REVERT: B 809 ASP cc_start: 0.7313 (t0) cc_final: 0.6994 (t0) REVERT: B 852 GLN cc_start: 0.8419 (mt0) cc_final: 0.8183 (mt0) REVERT: B 856 LYS cc_start: 0.8436 (tttt) cc_final: 0.8149 (tttp) REVERT: B 949 ARG cc_start: 0.7662 (mtm-85) cc_final: 0.7335 (mtm110) REVERT: B 953 MET cc_start: 0.8010 (tpt) cc_final: 0.7726 (tpt) REVERT: B 975 ASP cc_start: 0.8280 (t0) cc_final: 0.6857 (m-30) REVERT: B 1077 ASP cc_start: 0.7695 (t0) cc_final: 0.7249 (t0) REVERT: B 1084 LYS cc_start: 0.7967 (tptp) cc_final: 0.7511 (tptp) REVERT: B 1092 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7657 (mt-10) REVERT: B 1103 ARG cc_start: 0.7603 (mtt180) cc_final: 0.6920 (mtt-85) REVERT: A 172 LYS cc_start: 0.7406 (tttp) cc_final: 0.7085 (mmmt) REVERT: A 188 GLU cc_start: 0.6495 (tm-30) cc_final: 0.6213 (tm-30) REVERT: A 253 MET cc_start: 0.6529 (tpt) cc_final: 0.5462 (tpt) REVERT: A 351 MET cc_start: 0.7824 (mmm) cc_final: 0.7461 (mmm) REVERT: A 414 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7904 (mp) REVERT: A 442 ASP cc_start: 0.8017 (t70) cc_final: 0.7675 (t0) REVERT: A 492 MET cc_start: 0.5025 (tmm) cc_final: 0.3537 (ttp) REVERT: A 666 ILE cc_start: 0.8099 (mt) cc_final: 0.6991 (tp) REVERT: A 677 THR cc_start: 0.7522 (OUTLIER) cc_final: 0.6280 (m) REVERT: A 726 MET cc_start: 0.8170 (tpp) cc_final: 0.7791 (tpp) REVERT: A 793 GLN cc_start: 0.7898 (mt0) cc_final: 0.7616 (tt0) REVERT: A 845 LYS cc_start: 0.8044 (mtpt) cc_final: 0.7728 (mtmm) REVERT: A 846 GLN cc_start: 0.7712 (OUTLIER) cc_final: 0.7458 (mp10) outliers start: 40 outliers final: 28 residues processed: 297 average time/residue: 0.1023 time to fit residues: 41.1707 Evaluate side-chains 290 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 258 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 565 ASP Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain B residue 671 VAL Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 744 TYR Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 885 SER Chi-restraints excluded: chain B residue 965 LYS Chi-restraints excluded: chain B residue 1000 ASP Chi-restraints excluded: chain B residue 1025 VAL Chi-restraints excluded: chain B residue 1072 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 677 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 846 GLN Chi-restraints excluded: chain A residue 851 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 11 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 99 optimal weight: 0.9980 chunk 45 optimal weight: 0.3980 chunk 5 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 104 optimal weight: 0.0770 chunk 86 optimal weight: 0.7980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 684 HIS ** B 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 781 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN ** A 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 653 ASN ** A 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 681 GLN ** A 798 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 = 0.4331 r_free = 0.4331 target = 0.180714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.146839 restraints weight = 35466.066| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 4.19 r_work: 0.3692 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3699 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3699 r_free = 0.3699 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3699 r_free = 0.3699 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3699 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10758 Z= 0.168 Angle : 0.616 6.888 14524 Z= 0.321 Chirality : 0.043 0.264 1671 Planarity : 0.004 0.044 1844 Dihedral : 5.662 52.420 1428 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.41 % Allowed : 21.84 % Favored : 74.74 % 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: -1.11 (0.23), residues: 1306 helix: 0.33 (0.19), residues: 719 sheet: -2.37 (0.44), residues: 118 loop : -1.89 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 737 TYR 0.018 0.002 TYR A 619 PHE 0.022 0.002 PHE A 436 TRP 0.009 0.001 TRP B 807 HIS 0.015 0.001 HIS B 614 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 (10758) covalent geometry : angle 0.61556 / 0.32 (14524) hydrogen bonds : bond 0.04222 / 2.73 ( 553) hydrogen bonds : angle 4.60883 / 3.31 ( 1589) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 262 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 565 ASP cc_start: 0.7117 (OUTLIER) cc_final: 0.6885 (t0) REVERT: B 779 ARG cc_start: 0.6327 (mtm-85) cc_final: 0.6037 (mtm180) REVERT: B 809 ASP cc_start: 0.7339 (t0) cc_final: 0.7012 (t0) REVERT: B 852 GLN cc_start: 0.8423 (mt0) cc_final: 0.8214 (mt0) REVERT: B 856 LYS cc_start: 0.8372 (tttt) cc_final: 0.8120 (tttp) REVERT: B 944 ASN cc_start: 0.7367 (t0) cc_final: 0.7050 (t0) REVERT: B 949 ARG cc_start: 0.7733 (mtm-85) cc_final: 0.7417 (mtm110) REVERT: B 953 MET cc_start: 0.7945 (tpt) cc_final: 0.7660 (tpt) REVERT: B 1077 ASP cc_start: 0.7678 (t0) cc_final: 0.7160 (t0) REVERT: B 1084 LYS cc_start: 0.7924 (tptp) cc_final: 0.7468 (tptp) REVERT: B 1092 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7676 (mt-10) REVERT: B 1103 ARG cc_start: 0.7640 (mtt180) cc_final: 0.6956 (mtt-85) REVERT: A 172 LYS cc_start: 0.7430 (tttp) cc_final: 0.7116 (mmmt) REVERT: A 188 GLU cc_start: 0.6546 (tm-30) cc_final: 0.6257 (tm-30) REVERT: A 253 MET cc_start: 0.6464 (tpt) cc_final: 0.5476 (tpt) REVERT: A 358 GLU cc_start: 0.7822 (tt0) cc_final: 0.7348 (pt0) REVERT: A 414 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7929 (mp) REVERT: A 442 ASP cc_start: 0.7998 (t70) cc_final: 0.7617 (t0) REVERT: A 702 VAL cc_start: 0.8840 (t) cc_final: 0.8630 (m) REVERT: A 726 MET cc_start: 0.8155 (tpp) cc_final: 0.7811 (tpp) REVERT: A 779 MET cc_start: 0.7109 (mmt) cc_final: 0.6906 (tpp) REVERT: A 793 GLN cc_start: 0.8005 (mt0) cc_final: 0.7711 (tt0) REVERT: A 845 LYS cc_start: 0.8045 (mtpt) cc_final: 0.7704 (mtmm) REVERT: A 846 GLN cc_start: 0.7752 (OUTLIER) cc_final: 0.7504 (mp10) outliers start: 40 outliers final: 30 residues processed: 284 average time/residue: 0.1106 time to fit residues: 42.5334 Evaluate side-chains 292 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 259 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 565 ASP Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain B residue 671 VAL Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 692 GLN Chi-restraints excluded: chain B residue 744 TYR Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 885 SER Chi-restraints excluded: chain B residue 925 GLU Chi-restraints excluded: chain B residue 965 LYS Chi-restraints excluded: chain B residue 1000 ASP Chi-restraints excluded: chain B residue 1025 VAL Chi-restraints excluded: chain B residue 1072 VAL Chi-restraints excluded: chain B residue 1094 GLU Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 846 GLN Chi-restraints excluded: chain A residue 851 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 54 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 78 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 684 HIS ** B 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 944 ASN ** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS B1098 ASN ** A 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 ASN A 653 ASN ** A 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 681 GLN ** A 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.179577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.147979 restraints weight = 19701.139| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 2.43 r_work: 0.3782 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3791 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3791 r_free = 0.3791 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3791 r_free = 0.3791 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3791 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 10758 Z= 0.241 Angle : 0.643 7.513 14524 Z= 0.336 Chirality : 0.045 0.237 1671 Planarity : 0.004 0.041 1844 Dihedral : 5.672 51.308 1426 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 4.27 % Allowed : 20.99 % Favored : 74.74 % 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: -1.14 (0.23), residues: 1306 helix: 0.26 (0.19), residues: 722 sheet: -2.30 (0.45), residues: 120 loop : -1.86 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 737 TYR 0.020 0.002 TYR A 619 PHE 0.028 0.002 PHE A 436 TRP 0.007 0.001 TRP A 764 HIS 0.014 0.001 HIS B 614 Details of bonding type rmsd/Z covalent geometry : bond 0.00540 / 0.24 (10758) covalent geometry : angle 0.64270 / 0.34 (14524) hydrogen bonds : bond 0.04353 / 2.81 ( 553) hydrogen bonds : angle 4.63437 / 3.33 ( 1589) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 264 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 779 ARG cc_start: 0.6185 (mtm-85) cc_final: 0.5918 (mtm180) REVERT: B 809 ASP cc_start: 0.7178 (t0) cc_final: 0.6917 (t0) REVERT: B 877 TYR cc_start: 0.8314 (t80) cc_final: 0.8060 (t80) REVERT: B 902 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7932 (mtmm) REVERT: B 917 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7964 (mp10) REVERT: B 949 ARG cc_start: 0.7674 (mtm-85) cc_final: 0.7410 (mtm110) REVERT: B 1077 ASP cc_start: 0.7479 (t0) cc_final: 0.7095 (t0) REVERT: B 1084 LYS cc_start: 0.7811 (tptp) cc_final: 0.7384 (tptp) REVERT: B 1092 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7399 (mt-10) REVERT: A 188 GLU cc_start: 0.6416 (tm-30) cc_final: 0.6203 (tm-30) REVERT: A 253 MET cc_start: 0.6284 (tpt) cc_final: 0.5283 (tpt) REVERT: A 280 LEU cc_start: 0.6144 (OUTLIER) cc_final: 0.5929 (mt) REVERT: A 442 ASP cc_start: 0.7860 (t70) cc_final: 0.7502 (t0) REVERT: A 666 ILE cc_start: 0.8062 (mm) cc_final: 0.7555 (mt) REVERT: A 768 GLU cc_start: 0.7096 (OUTLIER) cc_final: 0.6809 (pp20) REVERT: A 793 GLN cc_start: 0.7795 (mt0) cc_final: 0.7526 (tt0) REVERT: A 838 LYS cc_start: 0.8194 (ptpp) cc_final: 0.7974 (mtmm) REVERT: A 845 LYS cc_start: 0.8003 (mtpt) cc_final: 0.7700 (mtmm) REVERT: A 846 GLN cc_start: 0.7627 (OUTLIER) cc_final: 0.7358 (mp10) outliers start: 50 outliers final: 35 residues processed: 292 average time/residue: 0.1240 time to fit residues: 49.1984 Evaluate side-chains 303 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 263 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 565 ASP Chi-restraints excluded: chain B residue 577 LYS Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain B residue 671 VAL Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 692 GLN Chi-restraints excluded: chain B residue 744 TYR Chi-restraints excluded: chain B residue 799 LEU Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 885 SER Chi-restraints excluded: chain B residue 902 LYS Chi-restraints excluded: chain B residue 917 GLN Chi-restraints excluded: chain B residue 925 GLU Chi-restraints excluded: chain B residue 965 LYS Chi-restraints excluded: chain B residue 1000 ASP Chi-restraints excluded: chain B residue 1025 VAL Chi-restraints excluded: chain B residue 1072 VAL Chi-restraints excluded: chain B residue 1094 GLU Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 539 PHE Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 768 GLU Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 846 GLN Chi-restraints excluded: chain A residue 851 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 67 optimal weight: 0.9990 chunk 108 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 65 optimal weight: 0.3980 chunk 4 optimal weight: 0.6980 chunk 97 optimal weight: 0.9980 chunk 112 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 chunk 111 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 861 ASN ** B 880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 681 GLN ** A 798 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 = 0.4334 r_free = 0.4334 target = 0.180889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.147287 restraints weight = 32171.751| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 3.81 r_work: 0.3716 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3720 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3720 r_free = 0.3720 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3720 r_free = 0.3720 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3720 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10758 Z= 0.178 Angle : 0.613 6.998 14524 Z= 0.318 Chirality : 0.044 0.357 1671 Planarity : 0.004 0.040 1844 Dihedral : 5.501 50.073 1425 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 4.27 % Allowed : 21.08 % Favored : 74.66 % 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: -0.95 (0.23), residues: 1306 helix: 0.41 (0.19), residues: 724 sheet: -2.27 (0.45), residues: 118 loop : -1.77 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 444 TYR 0.020 0.002 TYR A 678 PHE 0.025 0.002 PHE A 436 TRP 0.007 0.001 TRP B1122 HIS 0.012 0.001 HIS B 614 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.18 (10758) covalent geometry : angle 0.61300 / 0.32 (14524) hydrogen bonds : bond 0.04102 / 2.64 ( 553) hydrogen bonds : angle 4.51739 / 3.25 ( 1589) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 265 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 809 ASP cc_start: 0.7414 (t0) cc_final: 0.7051 (t0) REVERT: B 856 LYS cc_start: 0.8384 (tttt) cc_final: 0.7983 (tmtt) REVERT: B 877 TYR cc_start: 0.8380 (t80) cc_final: 0.7711 (t80) REVERT: B 902 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7977 (mtmm) REVERT: B 928 THR cc_start: 0.7673 (p) cc_final: 0.7467 (p) REVERT: B 944 ASN cc_start: 0.7501 (t0) cc_final: 0.7228 (t0) REVERT: B 1077 ASP cc_start: 0.7576 (t0) cc_final: 0.7230 (t0) REVERT: B 1084 LYS cc_start: 0.7889 (tptp) cc_final: 0.7448 (tptp) REVERT: A 172 LYS cc_start: 0.7682 (mmtt) cc_final: 0.7364 (mttm) REVERT: A 188 GLU cc_start: 0.6670 (tm-30) cc_final: 0.6406 (tm-30) REVERT: A 190 LEU cc_start: 0.6455 (tp) cc_final: 0.6244 (tp) REVERT: A 253 MET cc_start: 0.6377 (tpt) cc_final: 0.5452 (tpt) REVERT: A 414 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7877 (mp) REVERT: A 442 ASP cc_start: 0.8034 (t70) cc_final: 0.7666 (t0) REVERT: A 726 MET cc_start: 0.7901 (tpp) cc_final: 0.7602 (tpp) REVERT: A 768 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.7011 (pp20) REVERT: A 779 MET cc_start: 0.7106 (mmt) cc_final: 0.6863 (tpp) REVERT: A 793 GLN cc_start: 0.8055 (mt0) cc_final: 0.7716 (tt0) REVERT: A 845 LYS cc_start: 0.8029 (mtpt) cc_final: 0.7673 (mtmm) REVERT: A 846 GLN cc_start: 0.7731 (OUTLIER) cc_final: 0.7437 (mp10) outliers start: 50 outliers final: 36 residues processed: 293 average time/residue: 0.1243 time to fit residues: 49.7704 Evaluate side-chains 295 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 255 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 565 ASP Chi-restraints excluded: chain B residue 577 LYS Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain B residue 671 VAL Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 692 GLN Chi-restraints excluded: chain B residue 744 TYR Chi-restraints excluded: chain B residue 794 GLN Chi-restraints excluded: chain B residue 799 LEU Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 885 SER Chi-restraints excluded: chain B residue 902 LYS Chi-restraints excluded: chain B residue 917 GLN Chi-restraints excluded: chain B residue 925 GLU Chi-restraints excluded: chain B residue 958 ASP Chi-restraints excluded: chain B residue 965 LYS Chi-restraints excluded: chain B residue 1025 VAL Chi-restraints excluded: chain B residue 1072 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 539 PHE Chi-restraints excluded: chain A residue 596 ASN Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 741 LYS Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 768 GLU Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 846 GLN Chi-restraints excluded: chain A residue 851 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 6 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 56 optimal weight: 9.9990 chunk 35 optimal weight: 0.0870 chunk 31 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 123 optimal weight: 0.3980 chunk 49 optimal weight: 0.7980 chunk 126 optimal weight: 5.9990 chunk 32 optimal weight: 0.5980 chunk 62 optimal weight: 0.0980 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 684 HIS ** B 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1098 ASN ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 GLN ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 798 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.180699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.147814 restraints weight = 23437.062| |-----------------------------------------------------------------------------| r_work (start): 0.3952 rms_B_bonded: 2.85 r_work: 0.3802 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3808 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3808 r_free = 0.3808 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3808 r_free = 0.3808 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3808 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10758 Z= 0.138 Angle : 0.592 7.763 14524 Z= 0.306 Chirality : 0.042 0.312 1671 Planarity : 0.004 0.040 1844 Dihedral : 5.152 34.951 1423 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.67 % Allowed : 22.70 % Favored : 73.63 % 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: -0.83 (0.23), residues: 1306 helix: 0.58 (0.19), residues: 727 sheet: -2.61 (0.39), residues: 148 loop : -1.60 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 444 TYR 0.025 0.002 TYR A 815 PHE 0.020 0.002 PHE A 436 TRP 0.006 0.001 TRP B 768 HIS 0.006 0.001 HIS A 424 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (10758) covalent geometry : angle 0.59225 / 0.31 (14524) hydrogen bonds : bond 0.03883 / 2.50 ( 553) hydrogen bonds : angle 4.37106 / 3.14 ( 1589) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 261 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 692 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.8330 (mp10) REVERT: B 779 ARG cc_start: 0.6183 (mtm-85) cc_final: 0.5965 (mtm180) REVERT: B 809 ASP cc_start: 0.7292 (t0) cc_final: 0.6957 (t0) REVERT: B 856 LYS cc_start: 0.8258 (tttt) cc_final: 0.7800 (tmtt) REVERT: B 858 VAL cc_start: 0.8474 (t) cc_final: 0.8056 (m) REVERT: B 877 TYR cc_start: 0.8304 (t80) cc_final: 0.7646 (t80) REVERT: B 902 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7963 (mtmm) REVERT: B 917 GLN cc_start: 0.8190 (OUTLIER) cc_final: 0.7176 (mt0) REVERT: B 944 ASN cc_start: 0.7403 (t0) cc_final: 0.7122 (t0) REVERT: B 953 MET cc_start: 0.7795 (tpt) cc_final: 0.6998 (tpt) REVERT: B 975 ASP cc_start: 0.8242 (t0) cc_final: 0.6695 (m-30) REVERT: B 1084 LYS cc_start: 0.7800 (tptp) cc_final: 0.7359 (tptp) REVERT: A 172 LYS cc_start: 0.7672 (mmtt) cc_final: 0.7300 (mttm) REVERT: A 188 GLU cc_start: 0.6598 (tm-30) cc_final: 0.6327 (tm-30) REVERT: A 253 MET cc_start: 0.5982 (tpt) cc_final: 0.5276 (tpt) REVERT: A 383 ARG cc_start: 0.6955 (mtt180) cc_final: 0.6681 (mtt90) REVERT: A 414 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7772 (mp) REVERT: A 442 ASP cc_start: 0.7937 (t70) cc_final: 0.7583 (t0) REVERT: A 453 MET cc_start: 0.7643 (mtt) cc_final: 0.7418 (mmt) REVERT: A 726 MET cc_start: 0.7764 (tpp) cc_final: 0.7471 (tpp) REVERT: A 768 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6587 (pp20) REVERT: A 793 GLN cc_start: 0.7869 (mt0) cc_final: 0.7538 (tt0) REVERT: A 845 LYS cc_start: 0.7970 (mtpt) cc_final: 0.7584 (mtmm) REVERT: A 846 GLN cc_start: 0.7623 (OUTLIER) cc_final: 0.7318 (mp10) outliers start: 43 outliers final: 29 residues processed: 283 average time/residue: 0.1206 time to fit residues: 46.6207 Evaluate side-chains 289 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 254 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 565 ASP Chi-restraints excluded: chain B residue 577 LYS Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain B residue 671 VAL Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 692 GLN Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain B residue 744 TYR Chi-restraints excluded: chain B residue 794 GLN Chi-restraints excluded: chain B residue 799 LEU Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 885 SER Chi-restraints excluded: chain B residue 902 LYS Chi-restraints excluded: chain B residue 917 GLN Chi-restraints excluded: chain B residue 965 LYS Chi-restraints excluded: chain B residue 1017 LEU Chi-restraints excluded: chain B residue 1025 VAL Chi-restraints excluded: chain B residue 1072 VAL Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 596 ASN Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 741 LYS Chi-restraints excluded: chain A residue 768 GLU Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 846 GLN Chi-restraints excluded: chain A residue 851 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 51 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 110 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 95 optimal weight: 9.9990 chunk 112 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 781 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 880 ASN ** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1098 ASN ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 288 GLN ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 402 GLN ** A 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.179461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.146672 restraints weight = 26570.177| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 3.15 r_work: 0.3737 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3738 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3738 r_free = 0.3738 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3738 r_free = 0.3738 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3738 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 10758 Z= 0.222 Angle : 0.647 7.984 14524 Z= 0.334 Chirality : 0.045 0.304 1671 Planarity : 0.004 0.041 1844 Dihedral : 5.318 36.292 1421 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.41 % Allowed : 23.04 % Favored : 73.55 % 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: -0.94 (0.23), residues: 1306 helix: 0.43 (0.19), residues: 726 sheet: -2.62 (0.39), residues: 148 loop : -1.55 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 444 TYR 0.034 0.002 TYR A 815 PHE 0.033 0.002 PHE A 760 TRP 0.007 0.001 TRP B 807 HIS 0.007 0.001 HIS B 781 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.22 (10758) covalent geometry : angle 0.64744 / 0.33 (14524) hydrogen bonds : bond 0.04076 / 2.63 ( 553) hydrogen bonds : angle 4.51744 / 3.26 ( 1589) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 267 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 809 ASP cc_start: 0.7393 (t0) cc_final: 0.7107 (t0) REVERT: B 856 LYS cc_start: 0.8406 (tttt) cc_final: 0.8034 (tttm) REVERT: B 877 TYR cc_start: 0.8303 (t80) cc_final: 0.7640 (t80) REVERT: B 917 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.7237 (mt0) REVERT: B 944 ASN cc_start: 0.7397 (t0) cc_final: 0.7112 (t0) REVERT: B 949 ARG cc_start: 0.7690 (mtm-85) cc_final: 0.7435 (mtm110) REVERT: B 1084 LYS cc_start: 0.7887 (tptp) cc_final: 0.7424 (tptp) REVERT: A 188 GLU cc_start: 0.6591 (tm-30) cc_final: 0.6348 (tm-30) REVERT: A 253 MET cc_start: 0.6094 (tpt) cc_final: 0.5329 (tpt) REVERT: A 332 LYS cc_start: 0.8255 (mmmm) cc_final: 0.8054 (mmmm) REVERT: A 355 ARG cc_start: 0.7600 (mtm180) cc_final: 0.7309 (ttp-110) REVERT: A 383 ARG cc_start: 0.7188 (mtt180) cc_final: 0.6880 (mtt90) REVERT: A 414 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7841 (mp) REVERT: A 442 ASP cc_start: 0.7994 (t70) cc_final: 0.7645 (t0) REVERT: A 768 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.6994 (pp20) REVERT: A 793 GLN cc_start: 0.8005 (mt0) cc_final: 0.7660 (tt0) REVERT: A 845 LYS cc_start: 0.8032 (mtpt) cc_final: 0.7631 (mtmm) REVERT: A 846 GLN cc_start: 0.7694 (OUTLIER) cc_final: 0.7404 (mp10) outliers start: 40 outliers final: 32 residues processed: 290 average time/residue: 0.1227 time to fit residues: 48.5032 Evaluate side-chains 303 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 267 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 565 ASP Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain B residue 671 VAL Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 692 GLN Chi-restraints excluded: chain B residue 744 TYR Chi-restraints excluded: chain B residue 794 GLN Chi-restraints excluded: chain B residue 799 LEU Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 885 SER Chi-restraints excluded: chain B residue 917 GLN Chi-restraints excluded: chain B residue 925 GLU Chi-restraints excluded: chain B residue 965 LYS Chi-restraints excluded: chain B residue 1017 LEU Chi-restraints excluded: chain B residue 1025 VAL Chi-restraints excluded: chain B residue 1072 VAL Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 539 PHE Chi-restraints excluded: chain A residue 596 ASN Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 741 LYS Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 768 GLU Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 815 TYR Chi-restraints excluded: chain A residue 846 GLN Chi-restraints excluded: chain A residue 851 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 78 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 89 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 123 optimal weight: 0.4980 chunk 95 optimal weight: 7.9990 chunk 1 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 549 GLN ** B 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 781 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 852 GLN ** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1098 ASN ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 402 GLN ** A 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.180451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.147672 restraints weight = 30639.764| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 3.65 r_work: 0.3718 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3720 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3720 r_free = 0.3720 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3720 r_free = 0.3720 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3720 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 10758 Z= 0.180 Angle : 0.635 7.926 14524 Z= 0.329 Chirality : 0.044 0.297 1671 Planarity : 0.004 0.040 1844 Dihedral : 5.216 37.279 1421 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.50 % Allowed : 23.12 % Favored : 73.38 % 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: -0.81 (0.23), residues: 1306 helix: 0.50 (0.19), residues: 728 sheet: -2.45 (0.41), residues: 141 loop : -1.52 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 444 TYR 0.029 0.002 TYR A 815 PHE 0.038 0.002 PHE A 760 TRP 0.007 0.001 TRP A 764 HIS 0.007 0.001 HIS B 781 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.18 (10758) covalent geometry : angle 0.63537 / 0.33 (14524) hydrogen bonds : bond 0.03960 / 2.55 ( 553) hydrogen bonds : angle 4.45942 / 3.21 ( 1589) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 264 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 692 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.8365 (mp10) REVERT: B 779 ARG cc_start: 0.6311 (mtm-85) cc_final: 0.6070 (mtm180) REVERT: B 809 ASP cc_start: 0.7410 (t0) cc_final: 0.7110 (t0) REVERT: B 856 LYS cc_start: 0.8390 (tttt) cc_final: 0.8081 (tttm) REVERT: B 877 TYR cc_start: 0.8337 (t80) cc_final: 0.7676 (t80) REVERT: B 944 ASN cc_start: 0.7455 (t0) cc_final: 0.7192 (t0) REVERT: B 949 ARG cc_start: 0.7702 (mtm-85) cc_final: 0.7469 (mtm110) REVERT: B 1084 LYS cc_start: 0.7897 (tptp) cc_final: 0.7447 (tptp) REVERT: B 1091 LYS cc_start: 0.7899 (mttt) cc_final: 0.7664 (mttm) REVERT: A 188 GLU cc_start: 0.6635 (tm-30) cc_final: 0.6380 (tm-30) REVERT: A 253 MET cc_start: 0.5959 (tpt) cc_final: 0.5320 (tpt) REVERT: A 402 GLN cc_start: 0.7741 (tp-100) cc_final: 0.7465 (mm-40) REVERT: A 442 ASP cc_start: 0.8038 (t70) cc_final: 0.7685 (t0) REVERT: A 758 ASP cc_start: 0.7781 (t0) cc_final: 0.7550 (t0) REVERT: A 768 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.7013 (pp20) REVERT: A 793 GLN cc_start: 0.8092 (mt0) cc_final: 0.7753 (tt0) REVERT: A 845 LYS cc_start: 0.8034 (mtpt) cc_final: 0.7639 (mtmm) REVERT: A 846 GLN cc_start: 0.7725 (OUTLIER) cc_final: 0.7436 (mp10) outliers start: 41 outliers final: 33 residues processed: 288 average time/residue: 0.1231 time to fit residues: 48.1737 Evaluate side-chains 297 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 261 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 565 ASP Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain B residue 671 VAL Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 692 GLN Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain B residue 744 TYR Chi-restraints excluded: chain B residue 794 GLN Chi-restraints excluded: chain B residue 799 LEU Chi-restraints excluded: chain B residue 852 GLN Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 885 SER Chi-restraints excluded: chain B residue 925 GLU Chi-restraints excluded: chain B residue 965 LYS Chi-restraints excluded: chain B residue 1017 LEU Chi-restraints excluded: chain B residue 1025 VAL Chi-restraints excluded: chain B residue 1072 VAL Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 539 PHE Chi-restraints excluded: chain A residue 596 ASN Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 741 LYS Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 768 GLU Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 846 GLN Chi-restraints excluded: chain A residue 851 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 124 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 82 optimal weight: 0.3980 chunk 14 optimal weight: 0.0040 chunk 111 optimal weight: 0.1980 chunk 10 optimal weight: 2.9990 chunk 30 optimal weight: 0.4980 chunk 24 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 81 optimal weight: 0.5980 overall best weight: 0.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 781 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1098 ASN ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.178657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.148181 restraints weight = 19699.717| |-----------------------------------------------------------------------------| r_work (start): 0.3938 rms_B_bonded: 2.66 r_work: 0.3790 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3794 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3794 r_free = 0.3794 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3794 r_free = 0.3794 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3794 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.166 10758 Z= 0.226 Angle : 0.935 59.131 14524 Z= 0.523 Chirality : 0.046 0.535 1671 Planarity : 0.004 0.040 1844 Dihedral : 5.214 37.221 1421 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.41 % Allowed : 23.21 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.23), residues: 1306 helix: 0.51 (0.19), residues: 728 sheet: -2.45 (0.41), residues: 141 loop : -1.51 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 444 TYR 0.027 0.002 TYR A 815 PHE 0.035 0.002 PHE A 760 TRP 0.010 0.002 TRP B 562 HIS 0.006 0.001 HIS B 781 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.23 (10758) covalent geometry : angle 0.93501 / 0.52 (14524) hydrogen bonds : bond 0.03953 / 2.54 ( 553) hydrogen bonds : angle 4.46131 / 3.21 ( 1589) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 262 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 692 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.8286 (mp10) REVERT: B 779 ARG cc_start: 0.6237 (mtm-85) cc_final: 0.6008 (mtm180) REVERT: B 809 ASP cc_start: 0.7280 (t0) cc_final: 0.6998 (t0) REVERT: B 856 LYS cc_start: 0.8272 (tttt) cc_final: 0.7962 (tttm) REVERT: B 858 VAL cc_start: 0.8461 (t) cc_final: 0.8045 (m) REVERT: B 877 TYR cc_start: 0.8272 (t80) cc_final: 0.7623 (t80) REVERT: B 944 ASN cc_start: 0.7368 (t0) cc_final: 0.7100 (t0) REVERT: B 949 ARG cc_start: 0.7672 (mtm-85) cc_final: 0.7438 (mtm110) REVERT: B 1084 LYS cc_start: 0.7795 (tptp) cc_final: 0.7349 (tptp) REVERT: B 1091 LYS cc_start: 0.7819 (mttt) cc_final: 0.7592 (mttm) REVERT: A 188 GLU cc_start: 0.6500 (tm-30) cc_final: 0.6266 (tm-30) REVERT: A 402 GLN cc_start: 0.7671 (tp-100) cc_final: 0.7393 (mm-40) REVERT: A 442 ASP cc_start: 0.7939 (t70) cc_final: 0.7581 (t0) REVERT: A 758 ASP cc_start: 0.7648 (t0) cc_final: 0.7410 (t0) REVERT: A 768 GLU cc_start: 0.7157 (OUTLIER) cc_final: 0.6885 (pp20) REVERT: A 793 GLN cc_start: 0.7948 (mt0) cc_final: 0.7611 (tt0) REVERT: A 845 LYS cc_start: 0.7983 (mtpt) cc_final: 0.7588 (mtmm) REVERT: A 846 GLN cc_start: 0.7594 (OUTLIER) cc_final: 0.7305 (mp10) outliers start: 40 outliers final: 33 residues processed: 284 average time/residue: 0.1018 time to fit residues: 39.3404 Evaluate side-chains 297 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 261 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 565 ASP Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain B residue 671 VAL Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 692 GLN Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain B residue 744 TYR Chi-restraints excluded: chain B residue 794 GLN Chi-restraints excluded: chain B residue 799 LEU Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 885 SER Chi-restraints excluded: chain B residue 925 GLU Chi-restraints excluded: chain B residue 965 LYS Chi-restraints excluded: chain B residue 1017 LEU Chi-restraints excluded: chain B residue 1025 VAL Chi-restraints excluded: chain B residue 1072 VAL Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 539 PHE Chi-restraints excluded: chain A residue 596 ASN Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 741 LYS Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 768 GLU Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 846 GLN Chi-restraints excluded: chain A residue 851 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 125 optimal weight: 0.6980 chunk 30 optimal weight: 0.3980 chunk 62 optimal weight: 0.5980 chunk 100 optimal weight: 0.9980 chunk 48 optimal weight: 0.4980 chunk 18 optimal weight: 4.9990 chunk 0 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 116 optimal weight: 0.3980 chunk 9 optimal weight: 0.9980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 781 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1098 ASN ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.180244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.148207 restraints weight = 28049.370| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 3.40 r_work: 0.3729 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3732 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3732 r_free = 0.3732 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3732 r_free = 0.3732 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3732 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.165 10758 Z= 0.223 Angle : 0.930 58.456 14524 Z= 0.521 Chirality : 0.046 0.497 1671 Planarity : 0.004 0.040 1844 Dihedral : 5.213 37.221 1421 Min Nonbonded Distance : 1.722 Molprobity Statistics. All-atom Clashscore : 18.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.07 % Allowed : 23.63 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.23), residues: 1306 helix: 0.51 (0.19), residues: 728 sheet: -2.45 (0.41), residues: 141 loop : -1.51 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 444 TYR 0.026 0.002 TYR A 815 PHE 0.034 0.002 PHE A 760 TRP 0.010 0.002 TRP B 562 HIS 0.006 0.001 HIS B 781 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.22 (10758) covalent geometry : angle 0.92957 / 0.52 (14524) hydrogen bonds : bond 0.03953 / 2.54 ( 553) hydrogen bonds : angle 4.46134 / 3.21 ( 1589) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3109.93 seconds wall clock time: 54 minutes 12.87 seconds (3252.87 seconds total)